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Hsu, Shiao-Wen David

Positions:

William Dalton Family Assistant Professor of Medical Oncology, in the School of Medicine

Medicine, Medical Oncology
School of Medicine

Assistant Professor of Medicine

Medicine, Medical Oncology
School of Medicine

Member of the Duke Cancer Institute

Duke Cancer Institute
School of Medicine

Education:

M.D. 2001

M.D. — University of North Carolina at Chapel Hill

Grants:

Selectively targeting apoptosis in PIK3CA mutant colorectal cancers

Administered By
Pharmacology & Cancer Biology
AwardedBy
National Institutes of Health
Role
Collaborator
Start Date
August 12, 2016
End Date
July 31, 2021

Targeting differential apoptosis regulation in triple negative breast cancer

Administered By
Pharmacology & Cancer Biology
AwardedBy
Department of Defense
Role
Collaborator
Start Date
September 30, 2016
End Date
September 29, 2019

Using bacterial CRISPR/Cas endonucleases to selectively eliminate HPV-transformed cells in vivo

Administered By
Molecular Genetics and Microbiology
AwardedBy
National Institutes of Health
Role
Co Investigator
Start Date
September 02, 2015
End Date
August 31, 2017

Targeting Calreticulin in Colorectal Cancer Liver Metastasis

Administered By
Medicine, Medical Oncology
AwardedBy
National Institutes of Health
Role
Principal Investigator
Start Date
July 01, 2015
End Date
June 30, 2017

Development and Validation of Novel Therapeutic Targets in Anal Cancer

Administered By
Medicine, Medical Oncology
AwardedBy
The Farrah Fawcett Foundation
Role
Principal Investigator
Start Date
January 01, 2015
End Date
December 31, 2016

Aptamer Targeted Drug and Toxin Delivery to Prostate Cancer

Administered By
Surgery, Surgical Sciences
AwardedBy
Department of Defense
Role
Collaborator
Start Date
September 30, 2014
End Date
November 29, 2016

A Platform for Real-time Drug Profiling of Patient-Derived Melanomas

Administered By
Surgery
AwardedBy
National Institutes of Health
Role
Collaborator
Start Date
August 01, 2014
End Date
July 31, 2016

In Vivo Selection of Tumor-Specific RNA Binding Motifs

Administered By
Surgery, Advanced Oncologic and Gastrointestinal Surgery
AwardedBy
National Institutes of Health
Role
Collaborator
Start Date
September 01, 2011
End Date
February 28, 2015

Administrative Supplement for Recruitment of New Faculty

Administered By
Duke Cancer Institute
AwardedBy
National Cancer Institute
Role
Project PI
Start Date
September 30, 2009
End Date
September 29, 2011
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Publications:

Development of a Novel c-MET-Based CTC Detection Platform.

Amplification of the MET oncogene is associated with poor prognosis, metastatic dissemination, and drug resistance in many malignancies. We developed a method to capture and characterize circulating tumor cells (CTC) expressing c-MET using a ferromagnetic antibody. Immunofluorescence was used to characterize cells for c-MET, DAPI, and pan-CK, excluding CD45(+) leukocytes. The assay was validated using appropriate cell line controls spiked into peripheral blood collected from healthy volunteers (HV). In addition, peripheral blood was analyzed from patients with metastatic gastric, pancreatic, colorectal, bladder, renal, or prostate cancers. CTCs captured by c-MET were enumerated, and DNA FISH for MET amplification was performed. The approach was highly sensitive (80%) for MET-amplified cells, sensitive (40%-80%) for c-MET-overexpressed cells, and specific (100%) for both c-MET-negative cells and in 20 HVs. Of 52 patients with metastatic carcinomas tested, c-MET CTCs were captured in replicate samples from 3 patients [gastric, colorectal, and renal cell carcinoma (RCC)] with 6% prevalence. CTC FISH demonstrated that MET amplification in both gastric and colorectal cancer patients and trisomy 7 with gain of MET gene copies in the RCC patient. The c-MET CTC assay is a rapid, noninvasive, sensitive, and specific method for detecting MET-amplified tumor cells. CTCs with MET amplification can be detected in patients with gastric, colorectal, and renal cancers.This study developed a novel c-MET CTC assay for detecting c-MET CTCs in patients with MET amplification and warrants further investigation to determine its clinical applicability. Mol Cancer Res; 14(6); 539-47. ©2016 AACR.

Authors
Zhang, T; Boominathan, R; Foulk, B; Rao, C; Kemeny, G; Strickler, JH; Abbruzzese, JL; Harrison, MR; Hsu, DS; Healy, P; Li, J; Pi, C; Prendergast, KM; Hobbs, C; Gemberling, S; George, DJ; Hurwitz, HI; Connelly, M; Garcia-Blanco, MA; Armstrong, AJ
MLA Citation
Zhang, T, Boominathan, R, Foulk, B, Rao, C, Kemeny, G, Strickler, JH, Abbruzzese, JL, Harrison, MR, Hsu, DS, Healy, P, Li, J, Pi, C, Prendergast, KM, Hobbs, C, Gemberling, S, George, DJ, Hurwitz, HI, Connelly, M, Garcia-Blanco, MA, and Armstrong, AJ. "Development of a Novel c-MET-Based CTC Detection Platform." Molecular cancer research : MCR 14.6 (June 2016): 539-547.
Website
http://hdl.handle.net/10161/11944
PMID
26951228
Source
epmc
Published In
Molecular cancer research : MCR
Volume
14
Issue
6
Publish Date
2016
Start Page
539
End Page
547
DOI
10.1158/1541-7786.mcr-16-0011

In Vivo Selection Against Human Colorectal Cancer Xenografts Identifies an Aptamer That Targets RNA Helicase Protein DHX9.

The ability to selectively target disease-related tissues with molecules is critical to the design of effective therapeutic and diagnostic reagents. Recognizing the differences between the in vivo environment and in vitro conditions, we employed an in vivo selection strategy to identify RNA aptamers (targeting motifs) that could localize to tumor in situ. One of the selected molecules is an aptamer that binds to the protein DHX9, an RNA helicase that is known to be upregulated in colorectal cancer. Upon systemic administration, the aptamer preferentially localized to the nucleus of cancer cells in vivo and thus has the potential to be used for targeted delivery.

Authors
Mi, J; Ray, P; Liu, J; Kuan, C-T; Xu, J; Hsu, D; Sullenger, BA; White, RR; Clary, BM
MLA Citation
Mi, J, Ray, P, Liu, J, Kuan, C-T, Xu, J, Hsu, D, Sullenger, BA, White, RR, and Clary, BM. "In Vivo Selection Against Human Colorectal Cancer Xenografts Identifies an Aptamer That Targets RNA Helicase Protein DHX9." Molecular therapy. Nucleic acids 5 (April 26, 2016): e315-.
PMID
27115840
Source
epmc
Published In
Molecular Therapy - Nucleic Acids
Volume
5
Publish Date
2016
Start Page
e315
DOI
10.1038/mtna.2016.27

Cystine Deprivation Triggers Programmed Necrosis in VHL-Deficient Renal Cell Carcinomas.

Oncogenic transformation may reprogram tumor metabolism and render cancer cells addicted to extracellular nutrients. Deprivation of these nutrients may therefore represent a therapeutic opportunity, but predicting which nutrients cancer cells become addicted remains difficult. Here, we performed a nutrigenetic screen to determine the phenotypes of isogenic pairs of clear cell renal cancer cells (ccRCC), with or without VHL, upon the deprivation of individual amino acids. We found that cystine deprivation triggered rapid programmed necrosis in VHL-deficient cell lines and primary ccRCC tumor cells, but not in VHL-restored counterparts. Blocking cystine uptake significantly delayed xenograft growth of ccRCC. Importantly, cystine deprivation triggered similar metabolic changes regardless of VHL status, suggesting that metabolic responses alone are not sufficient to explain the observed distinct fates of VHL-deficient and restored cells. Instead, we found that increased levels of TNFα associated with VHL loss forced VHL-deficient cells to rely on intact RIPK1 to inhibit apoptosis. However, the preexisting elevation in TNFα expression rendered VHL-deficient cells susceptible to necrosis triggered by cystine deprivation. We further determined that reciprocal amplification of the Src-p38 (MAPK14)-Noxa (PMAIP1) signaling and TNFα-RIP1/3 (RIPK1/RIPK3)-MLKL necrosis pathways potentiated cystine-deprived necrosis. Together, our findings reveal that cystine deprivation in VHL-deficient RCCs presents an attractive therapeutic opportunity that may bypass the apoptosis-evading mechanisms characteristic of drug-resistant tumor cells. Cancer Res; 76(7); 1892-903. ©2016 AACR.

Authors
Tang, X; Wu, J; Ding, C-K; Lu, M; Keenan, MM; Lin, C-C; Lin, C-A; Wang, CC; George, D; Hsu, DS; Chi, J-T
MLA Citation
Tang, X, Wu, J, Ding, C-K, Lu, M, Keenan, MM, Lin, C-C, Lin, C-A, Wang, CC, George, D, Hsu, DS, and Chi, J-T. "Cystine Deprivation Triggers Programmed Necrosis in VHL-Deficient Renal Cell Carcinomas." Cancer research 76.7 (April 2016): 1892-1903.
PMID
26833124
Source
epmc
Published In
Cancer Research
Volume
76
Issue
7
Publish Date
2016
Start Page
1892
End Page
1903
DOI
10.1158/0008-5472.can-15-2328

miR-1269 promotes metastasis and forms a positive feedback loop with TGF-β.

As patient survival drops precipitously from early-stage cancers to late-stage and metastatic cancers, microRNAs that promote relapse and metastasis can serve as prognostic and predictive markers as well as therapeutic targets for chemoprevention. Here we show that miR-1269a promotes colorectal cancer (CRC) metastasis and forms a positive feedback loop with TGF-β signalling. miR-1269a is upregulated in late-stage CRCs, and long-term monitoring of 100 stage II CRC patients revealed that miR-1269a expression in their surgically removed primary tumours is strongly associated with risk of CRC relapse and metastasis. Consistent with clinical observations, miR-1269a significantly increases the ability of CRC cells to invade and metastasize in vivo. TGF-β activates miR-1269 via Sox4, while miR-1269a enhances TGF-β signalling by targeting Smad7 and HOXD10, hence forming a positive feedback loop. Our findings suggest that miR-1269a is a potential marker to inform adjuvant chemotherapy decisions for CRC patients and a potential therapeutic target to deter metastasis.

Authors
Bu, P; Wang, L; Chen, K-Y; Rakhilin, N; Sun, J; Closa, A; Tung, K-L; King, S; Kristine Varanko, A; Xu, Y; Huan Chen, J; Zessin, AS; Shealy, J; Cummings, B; Hsu, D; Lipkin, SM; Moreno, V; Gümüş, ZH; Shen, X
MLA Citation
Bu, P, Wang, L, Chen, K-Y, Rakhilin, N, Sun, J, Closa, A, Tung, K-L, King, S, Kristine Varanko, A, Xu, Y, Huan Chen, J, Zessin, AS, Shealy, J, Cummings, B, Hsu, D, Lipkin, SM, Moreno, V, Gümüş, ZH, and Shen, X. "miR-1269 promotes metastasis and forms a positive feedback loop with TGF-β." Nature communications 6 (April 15, 2015): 6879-.
PMID
25872451
Source
epmc
Published In
Nature Communications
Volume
6
Publish Date
2015
Start Page
6879
DOI
10.1038/ncomms7879

Mismatch repair gone awry: Management of Lynch syndrome.

The hallmark of Lynch syndrome involves germline mutations of genes important in DNA mismatch repair. Affected family kindreds will have multiple associated malignancies, the most common of which is colorectal adenocarcinoma. Recently, evidence has shown that clinical diagnostic criteria provided by the Amsterdam Criteria and the Bethesda Guidelines must be linked with microsatellite instability testing to correctly diagnose Lynch syndrome. We present a case of metachronous colorectal adenocarcinomas in a patient less than 50 years of age, followed by a discussion of Lynch syndrome, with an emphasis on surveillance and prevention of malignancies.

Authors
Zhang, T; Boswell, EL; McCall, SJ; Hsu, DS
MLA Citation
Zhang, T, Boswell, EL, McCall, SJ, and Hsu, DS. "Mismatch repair gone awry: Management of Lynch syndrome." Critical reviews in oncology/hematology 93.3 (March 2015): 170-179.
PMID
25459670
Source
epmc
Published In
Critical Reviews in Oncology/Hematology
Volume
93
Issue
3
Publish Date
2015
Start Page
170
End Page
179
DOI
10.1016/j.critrevonc.2014.10.005

Adjuvant chemotherapy for t1 node-positive colon cancers provides significant survival benefit.

Contemporary treatment of node-positive (N+) colon cancer consists of adjuvant chemotherapy; however, randomized data supporting this practice were derived from lesions T2 or greater. Minimal data exist regarding the use and need for adjuvant chemotherapy in T1N+ disease.The aim of this study was to determine treatment trends and the effects of adjuvant chemotherapy on T1N+ colon cancers by using the National Cancer Database.This was a retrospective study. Baseline demographics, tumor, and cancer treatment characteristics were compared. Groups were matched on the propensity to receive chemotherapy. Adjusted long-term survival stratified by chemotherapy use was compared by using the Kaplan-Meier method with the log-rank test. Predictors of not receiving chemotherapy were identified by using a multivariable logistic regression model.Data were collected from the National Cancer Database, which collects cancer data from over 1500 cancer centers.We identified patients from 1998 to 2006 with T1N+ disease, excluding those with metastatic disease or previous cancer. Patients were stratified based on whether or not they received chemotherapy.The primary outcome measure of this study was long-term survival.Three thousand one hundred thirty-seven patients had T1N+ disease; 70.6% (n = 2216) received chemotherapy, and utilization significantly increased from 1998 to 2011 (p < 0.001). Unadjusted analysis revealed that patients treated with chemotherapy were statistically younger and healthier, and had shorter postoperative lengths of stay (all p < 0.001). Unadjusted 5-year survival was higher in patients receiving chemotherapy (87.9% vs 63.0% in patients with no chemotherapy; p < 0.001) and this persisted after propensity matching with (83.4% and 63.0% in patients with or without chemotherapy; p < 0.001). Only age (OR, 0.29; p < 0.001) predicted not receiving chemotherapy.Limitations include potential selection bias as well as the inability to compare disease-free survival/recurrence.Adjuvant chemotherapy appears to significantly improve long-term survival in patients receiving chemotherapy in T1N+ disease. Thus, the use of chemotherapy in T1N+ disease is justified and provides a highly significant survival benefit.

Authors
Ganapathi, AM; Speicher, PJ; Englum, BR; Castleberry, AW; Migaly, J; Hsu, DS; Mantyh, CR
MLA Citation
Ganapathi, AM, Speicher, PJ, Englum, BR, Castleberry, AW, Migaly, J, Hsu, DS, and Mantyh, CR. "Adjuvant chemotherapy for t1 node-positive colon cancers provides significant survival benefit." Diseases of the colon and rectum 57.12 (December 2014): 1341-1348.
PMID
25379998
Source
epmc
Published In
Diseases of the Colon and Rectum
Volume
57
Issue
12
Publish Date
2014
Start Page
1341
End Page
1348
DOI
10.1097/dcr.0000000000000245

The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells.

In this study, we define the genetic landscape of mantle cell lymphoma (MCL) through exome sequencing of 56 cases of MCL. We identified recurrent mutations in ATM, CCND1, MLL2, and TP53. We further identified a number of novel genes recurrently mutated in patients with MCL including RB1, WHSC1, POT1, and SMARCA4. We noted that MCLs have a distinct mutational profile compared with lymphomas from other B-cell stages. The ENCODE project has defined the chromatin structure of many cell types. However, a similar characterization of primary human mature B cells has been lacking. We defined, for the first time, the chromatin structure of primary human naïve, germinal center, and memory B cells through chromatin immunoprecipitation and sequencing for H3K4me1, H3K4me3, H3Ac, H3K36me3, H3K27me3, and PolII. We found that somatic mutations that occur more frequently in either MCLs or Burkitt lymphomas were associated with open chromatin in their respective B cells of origin, naïve B cells, and germinal center B cells. Our work thus elucidates the landscape of gene-coding mutations in MCL and the critical interplay between epigenetic alterations associated with B-cell differentiation and the acquisition of somatic mutations in cancer.

Authors
Zhang, J; Jima, D; Moffitt, AB; Liu, Q; Czader, M; Hsi, ED; Fedoriw, Y; Dunphy, CH; Richards, KL; Gill, JI; Sun, Z; Love, C; Scotland, P; Lock, E; Levy, S; Hsu, DS; Dunson, D; Dave, SS
MLA Citation
Zhang, J, Jima, D, Moffitt, AB, Liu, Q, Czader, M, Hsi, ED, Fedoriw, Y, Dunphy, CH, Richards, KL, Gill, JI, Sun, Z, Love, C, Scotland, P, Lock, E, Levy, S, Hsu, DS, Dunson, D, and Dave, SS. "The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells." Blood 123.19 (May 2014): 2988-2996.
PMID
24682267
Source
epmc
Published In
Blood
Volume
123
Issue
19
Publish Date
2014
Start Page
2988
End Page
2996
DOI
10.1182/blood-2013-07-517177

Phase i study of dasatinib in combination with capecitabine, oxaliplatin and bevacizumab followed by an expanded cohort in previously untreated metastatic colorectal cancer

Purpose Dasatinib inhibits src family kinases and has anti-angiogenic properties. We conducted a phase I study of dasatinib, capecitabine, oxaliplatin, and bevacizumab (CapeOx/bevacizumab), with an expansion cohort in metastatic colorectal cancer (CRC). Methods Patients were enrolled in a dose escalation cohort to establish the maximum tolerated dose (MTD) and the recommended phase II dose (RP2D). Using a "3 + 3" design, twelve patients with advanced solid tumors received dasatinib (50 mg twice daily or 70 mg daily), capecitabine (850 mg/m2 twice daily, days 1-14), oxaliplatin (130 mg/m2 on day 1) and bevacizumab (7.5 mg/kg on day1), every 3 weeks. Ten patients with previously untreated metastatic CRC were then enrolled in an expansion cohort. Activated src (srcact) expression was measured by immunohistochemistry, using an antibody that selectively recognizes the active conformation of src (clone 28). Results Twenty-two patients were enrolled between June 2009 and May 2011. Two DLTs were observed in the 50 mg bid dasatinib cohort, and one DLT was observed in the 70 mg daily dasatinib cohort. The MTD and RP2D for dasatinib was 70 mg daily. The most common treatment-related adverse events were fatigue (20; 91 %) and diarrhea (18; 82 %). Biomarker analysis of srcact expression demonstrated that the overall response rate (ORR) was 75 % (6/8) for patients with high src act expression (IHC ≥ 2), compared to 0 % (0/8) for patients with low srcact expression (IHC 0 or 1); (p = 0.007). Conclusions The RP2D of dasatinib is 70 mg daily in combination with CapeOx/bevacizumab. High levels of srcact expression may predict those patients most likely to benefit from dasatinib. © 2013 Springer Science+Business Media New York.

Authors
Strickler, JH; McCall, S; Nixon, AB; Brady, JC; Pang, H; Rushing, C; Cohn, A; Starodub, A; Arrowood, C; Haley, S; Meadows, KL; Morse, MA; Uronis, HE; Blobe, GC; Hsu, SD; Zafar, SY; Hurwitz, HI
MLA Citation
Strickler, JH, McCall, S, Nixon, AB, Brady, JC, Pang, H, Rushing, C, Cohn, A, Starodub, A, Arrowood, C, Haley, S, Meadows, KL, Morse, MA, Uronis, HE, Blobe, GC, Hsu, SD, Zafar, SY, and Hurwitz, HI. "Phase i study of dasatinib in combination with capecitabine, oxaliplatin and bevacizumab followed by an expanded cohort in previously untreated metastatic colorectal cancer." Investigational New Drugs 32.2 (January 1, 2014): 330-339.
Source
scopus
Published In
Investigational New Drugs
Volume
32
Issue
2
Publish Date
2014
Start Page
330
End Page
339
DOI
10.1007/s10637-013-0042-9

Phase I study of capecitabine, oxaliplatin, bevacizumab, and everolimus in advanced solid tumors

Purpose: To define maximum tolerated dose (MTD), toxicities, and pharmacodynamics of capecitabine, oxaliplatin, bevacizumab, and everolimus in advanced solid tumor patients. Design: This was a standard "3 + 3" dose-escalation trial. All subjects received bevacizumab 7.5 mg/kg on day 1 of each cycle. Doses for capecitabine, oxaliplatin and everolimus were modified per dose limiting toxicity (DLT). Baseline and on-treatment plasma biomarkers were analyzed. Archived tumor mRNA levels were evaluated for NRP1, NRP2 and VEGF-A isoforms. Results: Twenty-nine patients were evaluable for toxicity and 30 for efficacy. Two DLTs were observed in cohort 1 and one DLT each was observed in cohort -1 and -1b. Grade ≥3 toxicities included neutropenia, hypertension, perforation/fistula/hemorrhage, hypertriglyceridemia, diarrhea, and thromboembolism. Twelve subjects experienced partial response (PR); 12 had stable disease as best response. Three of seven chemorefractory metastatic colorectal cancer (mCRC) subjects experienced PR; 8 of 15 chemonaive mCRC subjects experienced PR. Plasma TβRIII and IL-6 increased on treatment but without correlation to outcome. Increased VEGF165 levels significantly correlated with longer progression free survival. Conclusions: Everolimus with full dose capecitabine, oxaliplatin, and bevacizumab had unacceptable toxicity. MTD was: everolimus 5 mg daily; capecitabine 680 mg/m2 BID days 1-14; oxaliplatin 100 mg/m2 and bevacizumab 7.5 mg/kg, day 1. Activity was noted in mCRC. © 2014 Springer Science+Business Media.

Authors
Rangwala, F; Bendell, JC; Kozloff, MF; Arrowood, CC; Dellinger, A; Meadows, J; Tourt-Uhlig, S; Murphy, J; Meadows, KL; Starr, A; Broderick, S; Brady, JC; Cushman, SM; Morse, MA; Uronis, HE; Hsu, SD; Zafar, SY; Wallace, J; Starodub, AN; Strickler, JH; Pang, H; Nixon, AB; Hurwitz, HI
MLA Citation
Rangwala, F, Bendell, JC, Kozloff, MF, Arrowood, CC, Dellinger, A, Meadows, J, Tourt-Uhlig, S, Murphy, J, Meadows, KL, Starr, A, Broderick, S, Brady, JC, Cushman, SM, Morse, MA, Uronis, HE, Hsu, SD, Zafar, SY, Wallace, J, Starodub, AN, Strickler, JH, Pang, H, Nixon, AB, and Hurwitz, HI. "Phase I study of capecitabine, oxaliplatin, bevacizumab, and everolimus in advanced solid tumors." Investigational New Drugs 32.4 (January 1, 2014): 700-709.
Source
scopus
Published In
Investigational New Drugs
Volume
32
Issue
4
Publish Date
2014
Start Page
700
End Page
709
DOI
10.1007/s10637-014-0089-2

A randomized phase II study of immunization with dendritic cells modified with poxvectors encoding CEA and MUC1 compared with the same poxvectors plus GM-CSF for resected metastatic colorectal cancer

OBJECTIVE:: To determine whether 1 of 2 vaccines based on dendritic cells (DCs) and poxvectors encoding CEA (carcinoembryonic antigen) and MUC1 (PANVAC) would lengthen survival in patients with resected metastases of colorectal cancer (CRC). BACKGROUND:: Recurrences after complete resections of metastatic CRC remain frequent. Immune responses to CRC are associated with fewer recurrences, suggesting a role for cancer vaccines as adjuvant therapy. Both DCs and poxvectors are potent stimulators of immune responses against cancer antigens. METHODS:: Patients, disease-free after CRC metastasectomy and perioperative chemotherapy (n = 74), were randomized to injections of autologous DCs modified with PANVAC (DC/PANVAC) or PANVAC with per injection GM-CSF (granulocyte-macrophage colony-stimulating factor). Endpoints were recurrence-free survival overall survival, and rate of CEA-specific immune responses. Clinical outcome was compared with that of an unvaccinated, contemporary group of patients who had undergone CRC metastasectomy, received similar perioperative therapy, and would have otherwise been eligible for the study. RESULTS:: Recurrence-free survival at 2 years was similar (47% and 55% for DC/PANVAC and PANVAC/GM-CSF, respectively) (χ P = 0.48). At a median follow-up of 35.7 months, there were 2 of 37 deaths in the DC/PANVAC arm and 5 of 37 deaths in the PANVAC/GM-CSF arm. The rate and magnitude of T-cell responses against CEA was statistically similar between study arms. As a group, vaccinated patients had superior survival compared with the contemporary unvaccinated group. CONCLUSIONS:: Both DC and poxvector vaccines have similar activity. Survival was longer for vaccinated patients than for a contemporary unvaccinated group, suggesting that a randomized trial of poxvector vaccinations compared with standard follow-up after metastasectomy is warranted. © 2013 Lippincott Williams and Wilkins.

Authors
Morse, MA; Niedzwiecki, D; Marshall, JL; Garrett, C; Chang, DZ; Aklilu, M; Crocenzi, TS; Cole, DJ; Dessureault, S; Hobeika, AC; Osada, T; Onaitis, M; Clary, BM; Hsu, D; Devi, GR; Bulusu, A; Annechiarico, RP; Chadaram, V; Clay, TM; Lyerly, HK
MLA Citation
Morse, MA, Niedzwiecki, D, Marshall, JL, Garrett, C, Chang, DZ, Aklilu, M, Crocenzi, TS, Cole, DJ, Dessureault, S, Hobeika, AC, Osada, T, Onaitis, M, Clary, BM, Hsu, D, Devi, GR, Bulusu, A, Annechiarico, RP, Chadaram, V, Clay, TM, and Lyerly, HK. "A randomized phase II study of immunization with dendritic cells modified with poxvectors encoding CEA and MUC1 compared with the same poxvectors plus GM-CSF for resected metastatic colorectal cancer." Annals of Surgery 258.6 (December 1, 2013): 879-886.
Source
scopus
Published In
Annals of Surgery
Volume
258
Issue
6
Publish Date
2013
Start Page
879
End Page
886
DOI
10.1097/SLA.0b013e318292919e

Novel adenoviral vector induces T-cell responses despite anti-adenoviral neutralizing antibodies in colorectal cancer patients.

First-generation, E1-deleted adenovirus subtype 5 (Ad5)-based vectors, although promising platforms for use as cancer vaccines, are impeded in activity by naturally occurring or induced Ad-specific neutralizing antibodies. Ad5-based vectors with deletions of the E1 and the E2b regions (Ad5 [E1-, E2b-]), the latter encoding the DNA polymerase and the pre-terminal protein, by virtue of diminished late phase viral protein expression, were hypothesized to avoid immunological clearance and induce more potent immune responses against the encoded tumor antigen transgene in Ad-immune hosts. Indeed, multiple homologous immunizations with Ad5 [E1-, E2b-]-CEA(6D), encoding the tumor antigen carcinoembryonic antigen (CEA), induced CEA-specific cell-mediated immune (CMI) responses with antitumor activity in mice despite the presence of preexisting or induced Ad5-neutralizing antibody. In the present phase I/II study, cohorts of patients with advanced colorectal cancer were immunized with escalating doses of Ad5 [E1-, E2b-]-CEA(6D). CEA-specific CMI responses were observed despite the presence of preexisting Ad5 immunity in a majority (61.3 %) of patients. Importantly, there was minimal toxicity, and overall patient survival (48 % at 12 months) was similar regardless of preexisting Ad5 neutralizing antibody titers. The results demonstrate that, in cancer patients, the novel Ad5 [E1-, E2b-] gene delivery platform generates significant CMI responses to the tumor antigen CEA in the setting of both naturally acquired and immunization-induced Ad5-specific immunity.

Authors
Morse, MA; Chaudhry, A; Gabitzsch, ES; Hobeika, AC; Osada, T; Clay, TM; Amalfitano, A; Burnett, BK; Devi, GR; Hsu, DS; Xu, Y; Balcaitis, S; Dua, R; Nguyen, S; Balint, JP; Jones, FR; Lyerly, HK
MLA Citation
Morse, MA, Chaudhry, A, Gabitzsch, ES, Hobeika, AC, Osada, T, Clay, TM, Amalfitano, A, Burnett, BK, Devi, GR, Hsu, DS, Xu, Y, Balcaitis, S, Dua, R, Nguyen, S, Balint, JP, Jones, FR, and Lyerly, HK. "Novel adenoviral vector induces T-cell responses despite anti-adenoviral neutralizing antibodies in colorectal cancer patients." Cancer Immunol Immunother 62.8 (August 2013): 1293-1301.
PMID
23624851
Source
pubmed
Published In
Cancer Immunology, Immunotherapy
Volume
62
Issue
8
Publish Date
2013
Start Page
1293
End Page
1301
DOI
10.1007/s00262-013-1400-3

Modest advances in survival for patients with colorectal-associated peritoneal carcinomatosis in the era of modern chemotherapy.

BACKGROUND: The treatment of metastatic colorectal cancer (CRC) has evolved rapidly over the last decade, with combination chemotherapy and targeted biologic agents leading to significant improvements in survival. Despite these advances, little is known about their effectiveness in CRC-associated peritoneal carcinomatosis. The purpose of this study was to evaluate outcomes in patients with CRC-associated PC treated in the era of modern chemotherapy. METHODS: We retrospectively reviewed an institutional tumor database from 1996 to 2008. Survival data were evaluated for patients treated with PC before and after 2003. No patients before 2003 were treated with combination chemotherapy or biologic therapy. The modern chemotherapy group consisted of patients treated after 2003. Survival curves were estimated. RESULTS: Overall, 173 patients were identified. Median follow-up was 8.6 months. Median survival in the historic group (n = 91) was 8.9 months and 16.3 months in the modern chemotherapy group (n = 82) (P < 0.004). Age was the only significant covariate. The survival difference between the modern chemotherapy cohort and control cohort persisted after adjustment for age. In a subset of patients in the modern chemotherapy era group, for which treatment regimen could be definitively identified, survival was even greater-23.8 months. CONCLUSIONS: Patients with CRC-associated PC treated with modern combination chemotherapy and biologic therapy have a significantly longer median survival compared to our historical cohort. Despite these improvements, outcomes still remain poor. Therapeutic adjuncts such as surgical cytoreduction and hyperthermic intraperitoneal chemotherapy (HIPEC) in appropriately selected patients remain promising options to improve outcomes for patients with peritoneal-based disease.

Authors
Zani, S; Papalezova, K; Stinnett, S; Tyler, D; Hsu, D; Blazer, DG
MLA Citation
Zani, S, Papalezova, K, Stinnett, S, Tyler, D, Hsu, D, and Blazer, DG. "Modest advances in survival for patients with colorectal-associated peritoneal carcinomatosis in the era of modern chemotherapy." J Surg Oncol 107.4 (March 2013): 307-311.
PMID
22811275
Source
pubmed
Published In
Journal of Surgical Oncology
Volume
107
Issue
4
Publish Date
2013
Start Page
307
End Page
311
DOI
10.1002/jso.23222

A phase II study of capecitabine, oxaliplatin, and bevacizumab in the treatment of metastatic esophagogastric adenocarcinomas.

BACKGROUND: Esophageal and gastric cancers often present at an advanced stage. Systemic chemotherapy is the mainstay of treatment, but survival with current regimens remains poor. We evaluated the safety, tolerability, and efficacy of the combination capecitabine, oxaliplatin, and bevacizumab in the treatment of metastatic esophagogastric adenocarcinomas. METHODS: Thirty-seven patients with metastatic or unresectable gastric/gastroesophageal junction tumors were enrolled and treated with capecitabine 850 mg/m(2) BID on days 1-14, and oxaliplatin 130 mg/m(2) with bevacizumab 15 mg/kg on day 1 of a 21-day cycle. The primary endpoint was progression-free survival (PFS). Secondary endpoints included response rate (RR) and overall survival (OS). Neuropilin-1 (NRP1) and -2 (NRP2) mRNA expression was evaluated in archived tumor. RESULTS: Thirty-five patients were evaluable for efficacy. Median PFS was 7.2 months; median OS was 10.8 months. RR was estimated at 51.4%. The regimen was tolerable with expected drug class-related toxicities. NRP2 mRNA levels significantly correlated with PFS (p = 0.042) and showed a trend toward significance with OS (p = 0.051). Nonsignificant trends for NRP1 were noted for higher expression levels and worse outcome. CONCLUSIONS: Bevacizumab can be given safely with chemotherapy in patients with metastatic esophagogastric adenocarcinomas. The combination of capecitabine, oxaliplatin, plus bevacizumab has activity comparable to other bevacizumab-containing regimens in metastatic gastroesophageal cancer.

Authors
Uronis, HE; Bendell, JC; Altomare, I; Blobe, GC; Hsu, SD; Morse, MA; Pang, H; Zafar, SY; Conkling, P; Favaro, J; Arrowood, CC; Cushman, SM; Meadows, KL; Brady, JC; Nixon, AB; Hurwitz, HI
MLA Citation
Uronis, HE, Bendell, JC, Altomare, I, Blobe, GC, Hsu, SD, Morse, MA, Pang, H, Zafar, SY, Conkling, P, Favaro, J, Arrowood, CC, Cushman, SM, Meadows, KL, Brady, JC, Nixon, AB, and Hurwitz, HI. "A phase II study of capecitabine, oxaliplatin, and bevacizumab in the treatment of metastatic esophagogastric adenocarcinomas." Oncologist 18.3 (2013): 271-272.
PMID
23485624
Source
pubmed
Published In
The oncologist
Volume
18
Issue
3
Publish Date
2013
Start Page
271
End Page
272
DOI
10.1634/theoncologist.2012-0404

Modest advances in survival for patients with colorectal-associated peritoneal carcinomatosis in the era of modern chemotherapy

Background The treatment of metastatic colorectal cancer (CRC) has evolved rapidly over the last decade, with combination chemotherapy and targeted biologic agents leading to significant improvements in survival. Despite these advances, little is known about their effectiveness in CRC-associated peritoneal carcinomatosis. The purpose of this study was to evaluate outcomes in patients with CRC-associated PC treated in the era of modern chemotherapy. Methods We retrospectively reviewed an institutional tumor database from 1996 to 2008. Survival data were evaluated for patients treated with PC before and after 2003. No patients before 2003 were treated with combination chemotherapy or biologic therapy. The modern chemotherapy group consisted of patients treated after 2003. Survival curves were estimated. Results Overall, 173 patients were identified. Median follow-up was 8.6 months. Median survival in the historic group (n = 91) was 8.9 months and 16.3 months in the modern chemotherapy group (n = 82) (P < 0.004). Age was the only significant covariate. The survival difference between the modern chemotherapy cohort and control cohort persisted after adjustment for age. In a subset of patients in the modern chemotherapy era group, for which treatment regimen could be definitively identified, survival was even greater - 23.8 months. Conclusions Patients with CRC-associated PC treated with modern combination chemotherapy and biologic therapy have a significantly longer median survival compared to our historical cohort. Despite these improvements, outcomes still remain poor. Therapeutic adjuncts such as surgical cytoreduction and hyperthermic intraperitoneal chemotherapy (HIPEC) in appropriately selected patients remain promising options to improve outcomes for patients with peritoneal-based disease. Copyright © 2012 Wiley Periodicals, Inc.

Authors
Zani, S; Papalezova, K; Stinnett, S; Tyler, D; Hsu, D; III, DGB
MLA Citation
Zani, S, Papalezova, K, Stinnett, S, Tyler, D, Hsu, D, and III, DGB. "Modest advances in survival for patients with colorectal-associated peritoneal carcinomatosis in the era of modern chemotherapy." Journal of Surgical Oncology 107.4 (2013): 307-311.
Source
scival
Published In
Journal of Surgical Oncology
Volume
107
Issue
4
Publish Date
2013
Start Page
307
End Page
311
DOI
10.1002/jso.23222

Novel adenoviral vector induces T-cell responses despite anti-adenoviral neutralizing antibodies in colorectal cancer patients

First-generation, E1-deleted adenovirus subtype 5 (Ad5)-based vectors, although promising platforms for use as cancer vaccines, are impeded in activity by naturally occurring or induced Ad-specific neutralizing antibodies. Ad5-based vectors with deletions of the E1 and the E2b regions (Ad5 [E1-, E2b-]), the latter encoding the DNA polymerase and the pre-terminal protein, by virtue of diminished late phase viral protein expression, were hypothesized to avoid immunological clearance and induce more potent immune responses against the encoded tumor antigen transgene in Ad-immune hosts. Indeed, multiple homologous immunizations with Ad5 [E1-, E2b-]-CEA(6D), encoding the tumor antigen carcinoembryonic antigen (CEA), induced CEA-specific cell-mediated immune (CMI) responses with antitumor activity in mice despite the presence of preexisting or induced Ad5-neutralizing antibody. In the present phase I/II study, cohorts of patients with advanced colorectal cancer were immunized with escalating doses of Ad5 [E1-, E2b-]-CEA(6D). CEA-specific CMI responses were observed despite the presence of preexisting Ad5 immunity in a majority (61.3 %) of patients. Importantly, there was minimal toxicity, and overall patient survival (48 % at 12 months) was similar regardless of preexisting Ad5 neutralizing antibody titers. The results demonstrate that, in cancer patients, the novel Ad5 [E1-, E2b-] gene delivery platform generates significant CMI responses to the tumor antigen CEA in the setting of both naturally acquired and immunization-induced Ad5-specific immunity. © 2013 Springer-Verlag Berlin Heidelberg.

Authors
Morse, MA; Chaudhry, A; Gabitzsch, ES; Hobeika, AC; Osada, T; Clay, TM; Amalfitano, A; Burnett, BK; Devi, GR; Hsu, DS; Xu, Y; Balcaitis, S; Dua, R; Nguyen, S; Jr, JPB; Jones, FR; Lyerly, HK
MLA Citation
Morse, MA, Chaudhry, A, Gabitzsch, ES, Hobeika, AC, Osada, T, Clay, TM, Amalfitano, A, Burnett, BK, Devi, GR, Hsu, DS, Xu, Y, Balcaitis, S, Dua, R, Nguyen, S, Jr, JPB, Jones, FR, and Lyerly, HK. "Novel adenoviral vector induces T-cell responses despite anti-adenoviral neutralizing antibodies in colorectal cancer patients." Cancer Immunology, Immunotherapy 62.8 (2013): 1293-1301.
Source
scival
Published In
Cancer Immunology, Immunotherapy
Volume
62
Issue
8
Publish Date
2013
Start Page
1293
End Page
1301
DOI
10.1007/s00262-013-1400-3

Use of molecular biomarkers to inform adjuvant therapy for colon cancer

The decision about who may derive benefit from adjuvant chemotherapy in colon cancer is often a difficult one for clinicians. While multiple trials have demonstrated that adjuvant chemotherapy reduces the risk of recurrence and improves overall survival in patients with stage III disease, the data supporting the use of adjuvant chemotherapy in patients with stage II disease are not as compelling. Because adjuvant therapy can have significant toxicity, tools to help clinicians determine who may derive a benefit from therapy are of the utmost importance. Recent advances in high throughput technologies have led to the identification of molecular biomarkers-including microsatellite instability (MSI), loss of heterozygosity (LOH), p53, Kirsten rat sarcoma viral oncogene homolog (KRAS), v-raf murine sarcoma viral oncogene homolog B1 (BRAF), thymidylate synthase (TS), and excision repair cross-complementation group 1 (ERCC1)-as well as various multigene assays that are being studied for their ability to offer both prognostic and predictive information to clinicians. Here we review the current knowledge about molecular biomarkers that may aid the clinician in offering personalized cancer therapy based on the genetic landscape of an individual patient's tumor.

Authors
Mettu, NB; Hurwitz, H; Hsu, DS
MLA Citation
Mettu, NB, Hurwitz, H, and Hsu, DS. "Use of molecular biomarkers to inform adjuvant therapy for colon cancer." ONCOLOGY (United States) 27.8 (2013).
Source
scival
Published In
Oncology
Volume
27
Issue
8
Publish Date
2013

Characterization of an oxaliplatin sensitivity predictor in a preclinical murine model of colorectal cancer.

Despite advances in contemporary chemotherapeutic strategies, long-term survival still remains elusive for patients with metastatic colorectal cancer. A better understanding of the molecular markers of drug sensitivity to match therapy with patient is needed to improve clinical outcomes. In this study, we used in vitro drug sensitivity data from the NCI-60 cell lines together with their Affymetrix microarray data to develop a gene expression signature to predict sensitivity to oxaliplatin. To validate our oxaliplatin sensitivity signature, patient-derived colorectal cancer explants (PDCCE) were developed in nonobese diabetic/severe combined immunodeficient (NOD/SCID) mice from resected human colorectal tumors. Analysis of gene expression profiles found similarities between the PDCCEs and their parental human tumors, suggesting their utility to study drug sensitivity in vivo. The oxaliplatin sensitivity signature was then validated in vivo with response data from 14 PDCCEs treated with oxaliplatin and was found to have an accuracy of 92.9% (sensitivity = 87.5%; specificity = 100%). Our findings suggest that PDCCEs can be a novel source to study drug sensitivity in colorectal cancer. Furthermore, genomic-based analysis has the potential to be incorporated into future strategies to optimize individual therapy for patients with metastatic colorectal cancer.

Authors
Kim, MK; Osada, T; Barry, WT; Yang, XY; Freedman, JA; Tsamis, KA; Datto, M; Clary, BM; Clay, T; Morse, MA; Febbo, PG; Lyerly, HK; Hsu, DS
MLA Citation
Kim, MK, Osada, T, Barry, WT, Yang, XY, Freedman, JA, Tsamis, KA, Datto, M, Clary, BM, Clay, T, Morse, MA, Febbo, PG, Lyerly, HK, and Hsu, DS. "Characterization of an oxaliplatin sensitivity predictor in a preclinical murine model of colorectal cancer." Mol Cancer Ther 11.7 (July 2012): 1500-1509.
PMID
22351745
Source
pubmed
Published In
Molecular cancer therapeutics
Volume
11
Issue
7
Publish Date
2012
Start Page
1500
End Page
1509
DOI
10.1158/1535-7163.MCT-11-0937

Retraction in part: A genomic approach to identify molecular pathways associated with chemotherapy resistance.

Authors
Riedel, RF; Porrello, A; Pontzer, E; Chenette, EJ; Hsu, DS; Balakumaran, B; Potti, A; Nevins, J; Febbo, PC
MLA Citation
Riedel, RF, Porrello, A, Pontzer, E, Chenette, EJ, Hsu, DS, Balakumaran, B, Potti, A, Nevins, J, and Febbo, PC. "Retraction in part: A genomic approach to identify molecular pathways associated with chemotherapy resistance." Mol Cancer Ther 11.5 (May 2012): 1214-1215.
PMID
22461660
Source
pubmed
Published In
Molecular cancer therapeutics
Volume
11
Issue
5
Publish Date
2012
Start Page
1214
End Page
1215
DOI
10.1158/1535-7163.MCT-12-0210

Retraction: Acharya CR, et al. Gene expression signatures, clinicopathological features, and individualized therapy in breast cancer. JAMA. 2008;299(13):1574-1587.

Authors
Acharya, CR; Hsu, DS; Anders, CK; Anguiano, A; Salter, KH; Walters, KS; Redman, RC; Tuchman, SA; Moylan, CA; Mukherjee, S; Barry, WT; Dressman, HK; Ginsburg, GS; Marcom, KP; Garman, KS; Lyman, GH; Nevins, JR; Potti, A
MLA Citation
Acharya, CR, Hsu, DS, Anders, CK, Anguiano, A, Salter, KH, Walters, KS, Redman, RC, Tuchman, SA, Moylan, CA, Mukherjee, S, Barry, WT, Dressman, HK, Ginsburg, GS, Marcom, KP, Garman, KS, Lyman, GH, Nevins, JR, and Potti, A. "Retraction: Acharya CR, et al. Gene expression signatures, clinicopathological features, and individualized therapy in breast cancer. JAMA. 2008;299(13):1574-1587." JAMA 307.5 (February 1, 2012): 453-.
PMID
22228686
Source
pubmed
Published In
JAMA : the journal of the American Medical Association
Volume
307
Issue
5
Publish Date
2012
Start Page
453
DOI
10.1001/jama.2012.2

Histological and molecular evaluation of patient-derived colorectal cancer explants.

Mouse models have been developed to investigate colorectal cancer etiology and evaluate new anti-cancer therapies. While genetically engineered and carcinogen-induced mouse models have provided important information with regard to the mechanisms underlying the oncogenic process, tumor xenograft models remain the standard for the evaluation of new chemotherapy and targeted drug treatments for clinical use. However, it remains unclear to what extent explanted colorectal tumor tissues retain inherent pathological features over time. In this study, we have generated a panel of 27 patient-derived colorectal cancer explants (PDCCEs) by direct transplantation of human colorectal cancer tissues into NOD-SCID mice. Using this panel, we performed a comparison of histology, gene expression and mutation status between PDCCEs and the original human tissues from which they were derived. Our findings demonstrate that PDCCEs maintain key histological features, basic gene expression patterns and KRAS/BRAF mutation status through multiple passages. Altogether, these findings suggest that PDCCEs maintain similarity to the patient tumor from which they are derived and may have the potential to serve as a reliable preclinical model that can be incorporated into future strategies to optimize individual therapy for patients with colorectal cancer.

Authors
Uronis, JM; Osada, T; McCall, S; Yang, XY; Mantyh, C; Morse, MA; Lyerly, HK; Clary, BM; Hsu, DS
MLA Citation
Uronis, JM, Osada, T, McCall, S, Yang, XY, Mantyh, C, Morse, MA, Lyerly, HK, Clary, BM, and Hsu, DS. "Histological and molecular evaluation of patient-derived colorectal cancer explants." PLoS One 7.6 (2012): e38422-.
PMID
22675560
Source
pubmed
Published In
PloS one
Volume
7
Issue
6
Publish Date
2012
Start Page
e38422
DOI
10.1371/journal.pone.0038422

Gene expression profiling of peritoneal metastases from appendiceal and colon cancer demonstrates unique biologic signatures and predicts patient outcomes

Background: Treatment of peritoneal metastases from appendiceal and colon cancer with cytoreductive surgery and hyperthermic intraperitoneal chemotherapy (HIPEC) shows great promise. Although long-term disease-free survival is achieved in some cases with this procedure, many patients have recurrence. Oncologists have treated such recurrences of appendiceal cancer similarly to colorectal carcinoma, which has been largely ineffective. This study uses gene expression analysis of peritoneal metastases to better understand these neoplasms. Study Design: From a prospectively maintained database and tissue bank, 41 snap frozen samples of peritoneal metastases (26 appendiceal, 15 colorectal) from patients undergoing HIPEC with complete cytoreduction and more than 3 years of follow-up underwent global gene expression analysis. Distinct phenotypes were identified using unsupervised hierarchical clustering based on differential gene expression. Survival curves restratified by genotype were generated. Results: Three distinct phenotypes were found, 2 consisting of predominantly low grade appendiceal samples (10 of 13 in Cluster 1 and 15 of 20 in Cluster 2) and 1 consisting of predominantly colorectal samples (7 of 8 in Cluster 3). Cluster 1 consisted of patients with good prognosis and Clusters 2 and 3 consisted of patients with poor prognosis (p = 0.006). Signatures predicted survival of low- (Cluster 1) vs high-risk (Cluster 2) appendiceal (p = 0.04) and low-risk appendiceal (Cluster 1) vs colon primary (Cluster 3) (p = 0.0002). Conclusions: This study represents the first use of gene expression profiling for appendiceal cancer, and demonstrates genomic signatures quite distinct from colorectal cancer, confirming their unique biology. Consequently, therapy for appendiceal lesions extrapolated from colonic cancer regimens may be unfounded. These phenotypes may predict outcomes guiding patient management. © 2012 by the American College of Surgeons.

Authors
Levine, EA; III, DGB; Kim, MK; Shen, P; IV, JHS; Guy, C; Hsu, DS
MLA Citation
Levine, EA, III, DGB, Kim, MK, Shen, P, IV, JHS, Guy, C, and Hsu, DS. "Gene expression profiling of peritoneal metastases from appendiceal and colon cancer demonstrates unique biologic signatures and predicts patient outcomes." Journal of the American College of Surgeons 214.4 (2012): 599-606.
PMID
22342786
Source
scival
Published In
Journal of The American College of Surgeons
Volume
214
Issue
4
Publish Date
2012
Start Page
599
End Page
606
DOI
10.1016/j.jamcollsurg.2011.12.028

Retraction for Garman et al: A genomic approach to colon cancer risk stratification yields biologic insights into therapeutic opportunities.

Authors
Garman, KS; Acharya, CR; Edelman, E; Grade, M; Gaedcke, J; Sud, S; Barry, W; Diehl, AM; Provenzale, D; Ginsburg, GS; Ghadimi, BM; Ried, T; Nevins, JR; Mukherjee, S; Hsu, D; Potti, A
MLA Citation
Garman, KS, Acharya, CR, Edelman, E, Grade, M, Gaedcke, J, Sud, S, Barry, W, Diehl, AM, Provenzale, D, Ginsburg, GS, Ghadimi, BM, Ried, T, Nevins, JR, Mukherjee, S, Hsu, D, and Potti, A. "Retraction for Garman et al: A genomic approach to colon cancer risk stratification yields biologic insights into therapeutic opportunities." Proc Natl Acad Sci U S A 108.42 (October 18, 2011): 17569-.
PMID
21969600
Source
pubmed
Published In
Proceedings of the National Academy of Sciences of USA
Volume
108
Issue
42
Publish Date
2011
Start Page
17569
DOI
10.1073/pnas.1115170108

A methodology for utilization of predictive genomic signatures in FFPE samples.

BACKGROUND: Gene expression signatures developed to measure the activity of oncogenic signaling pathways have been used to dissect the heterogeneity of tumor samples and to predict sensitivity to various cancer drugs that target components of the relevant pathways, thus potentially identifying therapeutic options for subgroups of patients. To facilitate broad use, including in a clinical setting, the ability to generate data from formalin-fixed, paraffin-embedded (FFPE) tissues is essential. METHODS: Patterns of pathway activity in matched fresh-frozen and FFPE xenograft tumor samples were generated using the MessageAmp Premier methodology in combination with assays using Affymetrix arrays. Results generated were compared with those obtained from fresh-frozen samples using a standard Affymetrix assay. In addition, gene expression data from patient matched fresh-frozen and FFPE melanomas were also utilized to evaluate the consistency of predictions of oncogenic signaling pathway status. RESULTS: Significant correlation was observed between pathway activity predictions from paired fresh-frozen and FFPE xenograft tumor samples. In addition, significant concordance of pathway activity predictions was also observed between patient matched fresh-frozen and FFPE melanomas. CONCLUSIONS: Reliable and consistent predictions of oncogenic pathway activities can be obtained from FFPE tumor tissue samples. The ability to reliably utilize FFPE patient tumor tissue samples for genomic analyses will lead to a better understanding of the biology of disease progression and, in the clinical setting, will provide tools to guide the choice of therapeutics to those most likely to be effective in treating a patient's disease.

Authors
Freedman, JA; Augustine, CK; Selim, AM; Holshausen, KC; Wei, Z; Tsamis, KA; Hsu, DS; Dressman, HK; Barry, WT; Tyler, DS; Nevins, JR
MLA Citation
Freedman, JA, Augustine, CK, Selim, AM, Holshausen, KC, Wei, Z, Tsamis, KA, Hsu, DS, Dressman, HK, Barry, WT, Tyler, DS, and Nevins, JR. "A methodology for utilization of predictive genomic signatures in FFPE samples. (Published online)" BMC Med Genomics 4 (July 11, 2011): 58-.
PMID
21745407
Source
pubmed
Published In
BMC Medical Genomics
Volume
4
Publish Date
2011
Start Page
58
DOI
10.1186/1755-8794-4-58

Antihelminth compound niclosamide downregulates Wnt signaling and elicits antitumor responses in tumors with activating APC mutations.

Wnt/β-catenin pathway activation caused by adenomatous polyposis coli (APC) mutations occurs in approximately 80% of sporadic colorectal cancers (CRC). The antihelminth compound niclosamide downregulates components of the Wnt pathway, specifically Dishevelled-2 (Dvl2) expression, resulting in diminished downstream β-catenin signaling. In this study, we determined whether niclosamide could inhibit the Wnt/β-catenin pathway in human CRCs and whether its inhibition might elicit antitumor effects in the presence of APC mutations. We found that niclosamide inhibited Wnt/β-catenin pathway activation, downregulated Dvl2, decreased downstream β-catenin signaling, and exerted antiproliferative effects in human colon cancer cell lines and CRC cells isolated by surgical resection of metastatic disease, regardless of mutations in APC. In contrast, inhibition of NF-κB or mTOR did not exert similar antiproliferative effects in these CRC model systems. In mice implanted with human CRC xenografts, orally administered niclosamide was well tolerated, achieved plasma and tumor levels associated with biologic activity, and led to tumor control. Our findings support clinical explorations to reposition niclosamide for the treatment of CRC.

Authors
Osada, T; Chen, M; Yang, XY; Spasojevic, I; Vandeusen, JB; Hsu, D; Clary, BM; Clay, TM; Chen, W; Morse, MA; Lyerly, HK
MLA Citation
Osada, T, Chen, M, Yang, XY, Spasojevic, I, Vandeusen, JB, Hsu, D, Clary, BM, Clay, TM, Chen, W, Morse, MA, and Lyerly, HK. "Antihelminth compound niclosamide downregulates Wnt signaling and elicits antitumor responses in tumors with activating APC mutations." Cancer Res 71.12 (June 15, 2011): 4172-4182.
PMID
21531761
Source
pubmed
Published In
Cancer Research
Volume
71
Issue
12
Publish Date
2011
Start Page
4172
End Page
4182
DOI
10.1158/0008-5472.CAN-10-3978

A phase II trial of bevacizumab plus everolimus for patients with refractory metastatic colorectal cancer.

PURPOSE: For patients with metastatic colorectal cancer (mCRC), no standard therapy exists after progression on 5-fluorouracil, oxaliplatin, irinotecan, bevacizumab, and cetuximab or panitumumab. Preclinical data demonstrated that combined vascular endothelial growth factor and mammalian target of rapamycin inhibition has greater antiangiogenic and antitumor activity than either monotherapy. A phase I study of bevacizumab plus everolimus demonstrated that the combination is safe; activity was seen in several patients with refractory mCRC. METHODS: Fifty patients with refractory mCRC were enrolled and received bevacizumab at 10 mg/kg every 2 weeks and everolimus at 10 mg orally daily. RESULTS: Of the 50 patients enrolled, the median age was 56 years and the median number of prior regimens was four. Forty-seven patients (96%) had prior bevacizumab exposure and 42 patients (84%) had documented progression on prior bevacizumab-based therapy. Forty-nine patients were evaluable for response; eight patients had minor responses (16%) and an additional 15 patients (30%) had stable disease (SD). No complete or partial responses were seen. The median progression-free survival interval was 2.3 months; however, 26% of patients achieved prolonged SD for ≥6 months, and three patients (6%) were on study for >1 year. The median overall survival duration was 8.1 months. The most common grade 1-2 toxicities were mucositis (68%) and hyperlipidemia (64%). Clinically significant grade ≥3 toxicities included hypertension (14%), fistula/abscess/perforation (8%), mucositis (6%), and hemorrhage (2%). CONCLUSIONS: Bevacizumab plus everolimus is generally tolerable but may have risks related to mucosal damage and/or wound healing. Bevacizumab plus everolimus appears to have modest activity in refractory mCRC in patients.

Authors
Altomare, I; Bendell, JC; Bullock, KE; Uronis, HE; Morse, MA; Hsu, SD; Zafar, SY; Blobe, GC; Pang, H; Honeycutt, W; Sutton, L; Hurwitz, HI
MLA Citation
Altomare, I, Bendell, JC, Bullock, KE, Uronis, HE, Morse, MA, Hsu, SD, Zafar, SY, Blobe, GC, Pang, H, Honeycutt, W, Sutton, L, and Hurwitz, HI. "A phase II trial of bevacizumab plus everolimus for patients with refractory metastatic colorectal cancer." Oncologist 16.8 (2011): 1131-1137.
PMID
21795432
Source
pubmed
Published In
The oncologist
Volume
16
Issue
8
Publish Date
2011
Start Page
1131
End Page
1137
DOI
10.1634/theoncologist.2011-0078

A genomic approach to colon cancer risk stratification yields biologic insights into therapeutic opportunities (Proceedings of the National Academy of Sciences of the United States of America (2008) 105, 49, (19432-19437) DOI: 10.1073/pnas.0806674105)

Authors
Garman, KS; Acharya, CR; Edelman, E; Grade, M; Gaedcke, J; Sud, S; Barry, W; Diehl, AM; Provenzale, D; Ginsburg, GS; Ghadimi, BM; Ried, T; Nevins, JR; Mukherjee, S; Hsu, D; Potti, A
MLA Citation
Garman, KS, Acharya, CR, Edelman, E, Grade, M, Gaedcke, J, Sud, S, Barry, W, Diehl, AM, Provenzale, D, Ginsburg, GS, Ghadimi, BM, Ried, T, Nevins, JR, Mukherjee, S, Hsu, D, and Potti, A. "A genomic approach to colon cancer risk stratification yields biologic insights into therapeutic opportunities (Proceedings of the National Academy of Sciences of the United States of America (2008) 105, 49, (19432-19437) DOI: 10.1073/pnas.0806674105)." Proceedings of the National Academy of Sciences of the United States of America 108.42 (2011): 17569--.
Source
scival
Published In
Proceedings of the National Academy of Sciences of USA
Volume
108
Issue
42
Publish Date
2011
Start Page
17569-
DOI
10.1073/pnas.1115170108

Characterizing the developmental pathways TTF-1, NKX2-8, and PAX9 in lung cancer (Proceedings of the National Academy of Sciences of the United States of America (2009) 106, 13 (5312-5317) DOI: 10.1073/pnas.0900827106)

Authors
Hsu, DS; Acharya, CR; Balakumaran, BS; Riedel, RF; Kim, MK; Stevenson, M; Tuchman, S; Mukherjee, S; Barry, W; Dressman, HK; al, E
MLA Citation
Hsu, DS, Acharya, CR, Balakumaran, BS, Riedel, RF, Kim, MK, Stevenson, M, Tuchman, S, Mukherjee, S, Barry, W, Dressman, HK, and al, E. "Characterizing the developmental pathways TTF-1, NKX2-8, and PAX9 in lung cancer (Proceedings of the National Academy of Sciences of the United States of America (2009) 106, 13 (5312-5317) DOI: 10.1073/pnas.0900827106)." Proceedings of the National Academy of Sciences of the United States of America 108.35 (2011): 14705--.
Source
scival
Published In
Proceedings of the National Academy of Sciences of USA
Volume
108
Issue
35
Publish Date
2011
Start Page
14705-
DOI
10.1073/pnas.1111196108

Predictive and prognostic biomarkers in colorectal cancer

Colorectal cancer is the third most common cancer and the second leading cause of cancer-related death in the United States. Three quarters of patients diagnosed with colorectal cancer will have early stage disease and despite surgical resection for curative intent, approximately 20%-25% of patients will recur with their disease within five years. The other 25% will present with advanced or metastatic disease and clinicians are faced with the challenge of choosing the most appropriate therapy for individual patients. Despite multiple treatment options which are now available and concomitant improvements in survival, advanced colorectal cancer remains universally fatal. The challenge for clinicians is to identify prognostic and predictive biomarkers that can assist in tailoring available treatments for an individual patient to improve clinical outcomes. This review will summarize current and future biomarkers in colorectal cancer and discuss their utility in managing patient care. © 2011 Higher Education Press and Springer-Verlag Berlin Heidelberg.

Authors
Deusen, JV; Hsu, DS
MLA Citation
Deusen, JV, and Hsu, DS. "Predictive and prognostic biomarkers in colorectal cancer." Frontiers in Biology 6.6 (2011): 482-489.
Source
scival
Published In
Frontiers in Biology
Volume
6
Issue
6
Publish Date
2011
Start Page
482
End Page
489
DOI
10.1007/s11515-011-1158-y

CSPG4 protein as a new target for the antibody-based immunotherapy of triple-negative breast cancer.

BACKGROUND: The cell surface proteoglycan, chondroitin sulfate proteoglycan 4 (CSPG4), is a potential target for monoclonal antibody (mAb)-based immunotherapy for many types of cancer. The lack of effective therapy for triple-negative breast cancer (TNBC) prompted us to examine whether CSPG4 is expressed in TNBC and can be targeted with CSPG4-specific mAb. METHODS: CSPG4 protein expression was assessed in 44 primary TNBC lesions, in TNBC cell lines HS578T, MDA-MB-231, MDA-MB-435, and SUM149, and in tumor cells in pleural effusions from 12 metastatic breast cancer patients. The effect of CSPG4-specific mAb 225.28 on growth, adhesion, and migration of TNBC cells was tested in vitro. The ability of mAb 225.28 to induce regression of tumor metastases (n = 7 mice) and to inhibit spontaneous metastasis and tumor recurrence (n = 12 mice per group) was tested in breast cancer models in mice. The mechanisms responsible for the antitumor effect of mAb 225.28 were also investigated in the cell lines and in the mouse models. All statistical tests were two-sided. RESULTS: CSPG4 protein was preferentially expressed in 32 of the 44 (72.7%) primary TNBC lesions tested, in TNBC cell lines, and in tumor cells in pleural effusions from 12 metastatic breast cancer patients. CSPG4-specific mAb 225.28 statistically significantly inhibited growth, adhesion, and migration of TNBC cells in vitro. mAb 225.28 induced 73.1% regression of tumor metastasis in a TNBC cell-derived experimental lung metastasis model (mAb 225.28 vs control, mean area of metastatic nodules = 44590.8 vs 165950.8 μm(2); difference of mean = 121360.0 μm(2), 95% confidence interval = 91010.7 to 151709.4 μm(2); P < .001). Additionally, mAb 225.28 statistically significantly reduced spontaneous lung metastases and tumor recurrences in an orthotopic xenograft mouse model. The mechanisms responsible for antitumor effect included increased apoptosis and reduced mitotic activity in tumor cells, decreased blood vessel density in the tumor microenvironment, and reduced activation of signaling pathways involved in cell survival, proliferation and metastasis. CONCLUSIONS: This study identified CSPG4 as a new target for TNBC. The antitumor activity of CSPG4-specific mAb was mediated by multiple mechanisms, including the inhibition of signaling pathways crucial for TNBC cell survival, proliferation, and metastasis.

Authors
Wang, X; Osada, T; Wang, Y; Yu, L; Sakakura, K; Katayama, A; McCarthy, JB; Brufsky, A; Chivukula, M; Khoury, T; Hsu, DS; Barry, WT; Lyerly, HK; Clay, TM; Ferrone, S
MLA Citation
Wang, X, Osada, T, Wang, Y, Yu, L, Sakakura, K, Katayama, A, McCarthy, JB, Brufsky, A, Chivukula, M, Khoury, T, Hsu, DS, Barry, WT, Lyerly, HK, Clay, TM, and Ferrone, S. "CSPG4 protein as a new target for the antibody-based immunotherapy of triple-negative breast cancer." J Natl Cancer Inst 102.19 (October 6, 2010): 1496-1512.
PMID
20852124
Source
pubmed
Published In
Journal of the National Cancer Institute
Volume
102
Issue
19
Publish Date
2010
Start Page
1496
End Page
1512
DOI
10.1093/jnci/djq343

Immune signatures predict prognosis in localized cancer.

The host immune response can impact cancer growth, prognosis, and response to therapy. In colorectal cancer, the presence of cells involved with T-cell-mediated adaptive immunity predicts survival better than the current staging method. We used the expression of genes recently associated with host immune responses (T(H1)-mediated adaptive immunity, inflammation, and immune suppression) to perform hierarchical clustering of multiple large cohorts of cancer specimens to determine if immune-related gene expression resulted in clinical significant groupings of tumors. Microarray data from prostate cancer (n = 79), breast cancer (n = 132), lung cancer (n = 84), glioblastoma multiforme (n = 120), and lymphoma (n = 127) were analyzed. Among adenocarcinomas, the T(H1)-mediated adaptive immunity genes were consistently associated with better prognosis, while genes associated with inflammation and immune suppression were variably associated with outcome. Specifically, increased expression of the T(H1)-mediated adaptive immunity genes was associated with good prognosis in breast cancer patients under 45 years of age (p = .04, hazard ratio [HR] = 0.42) and in prostate cancer patients (p = .03, HR = 0.36) but not in lung cancer patients (p = 0.45, HR = 1.37). In lymphoma, patients with increased expression of inflammation and immune suppression genes had better prognosis than those expressing the T(H1)-mediated adaptive immunity genes (p = .01, HR = 0.43) and in glioblastoma multiforme, the expression of inflammation genes conferred improved prognosis than those expressing immune suppression genes (p = 0.05, HR = 0.62). In aggregate, the gene expression signatures implicating specific components of the immune response hold prognostic import across solid tumors.

Authors
Hsu, DS; Kim, MK; Balakumaran, BS; Acharya, CR; Anders, CK; Clay, T; Lyerly, HK; Drake, CG; Morse, MA; Febbo, PG
MLA Citation
Hsu, DS, Kim, MK, Balakumaran, BS, Acharya, CR, Anders, CK, Clay, T, Lyerly, HK, Drake, CG, Morse, MA, and Febbo, PG. "Immune signatures predict prognosis in localized cancer." Cancer Invest 28.7 (August 2010): 765-773.
PMID
20569070
Source
pubmed
Published In
Cancer Investigation (Informa)
Volume
28
Issue
7
Publish Date
2010
Start Page
765
End Page
773
DOI
10.3109/07357900903095755

Metastatic colorectal cancer cells from patients previously treated with chemotherapy are sensitive to T-cell killing mediated by CEA/CD3-bispecific T-cell-engaging BiTE antibody.

BACKGROUND: Novel technologies to redirect T-cell killing against cancer cells are emerging. We hypothesised that metastatic human colorectal cancer (CRC) previously treated with conventional chemotherapy would be sensitive to T-cell killing mediated by carcinoembryonic antigen (CEA)/CD3-bispecific T-cell-engaging BiTE antibody (MEDI-565). METHODS: We analysed proliferation and lysis of CEA-positive (CEA+) CRC specimens that had survived previous systemic chemotherapy and biologic therapy to determine whether they could be killed by patient T cells engaged by MEDI-565 in vitro. RESULTS: At low concentrations (0.1-1 ng ml(-1)), MEDI-565+ T cells caused reduced proliferation and enhanced apoptosis of CEA+ human CRC specimens. High levels of soluble CEA did not impair killing by redirected T cells and there was no increase in resistance to T-cell killing despite multiple rounds of exposure. CONCLUSIONS: This study shows for the first time that metastatic CRC specimens derived from patients previously treated with conventional chemotherapy can be lysed by patient T cells. Clinical testing of cancer immunotherapies, such as MEDI-565 that result in exposure of tumours to large numbers of T cells, is warranted.

Authors
Osada, T; Hsu, D; Hammond, S; Hobeika, A; Devi, G; Clay, TM; Lyerly, HK; Morse, MA
MLA Citation
Osada, T, Hsu, D, Hammond, S, Hobeika, A, Devi, G, Clay, TM, Lyerly, HK, and Morse, MA. "Metastatic colorectal cancer cells from patients previously treated with chemotherapy are sensitive to T-cell killing mediated by CEA/CD3-bispecific T-cell-engaging BiTE antibody." Br J Cancer 102.1 (January 5, 2010): 124-133.
PMID
19953093
Source
pubmed
Published In
British Journal of Cancer
Volume
102
Issue
1
Publish Date
2010
Start Page
124
End Page
133
DOI
10.1038/sj.bjc.6605364

Pharmacogenomic strategies provide a rational approach to the treatment of cisplatin-resistant patients with advanced cancer (Journal of Clinical Oncology (2007) 25, (4350-4357))

Authors
Hsu, DS; Balakumaran, BS; Acharya, CR; Vlahovic, V; Walters, KS; Garman, K; Anders, C; Riedel, RF; Lancaster, J; Harpole, D; al, E
MLA Citation
Hsu, DS, Balakumaran, BS, Acharya, CR, Vlahovic, V, Walters, KS, Garman, K, Anders, C, Riedel, RF, Lancaster, J, Harpole, D, and al, E. "Pharmacogenomic strategies provide a rational approach to the treatment of cisplatin-resistant patients with advanced cancer (Journal of Clinical Oncology (2007) 25, (4350-4357))." Journal of Clinical Oncology 28.35 (2010): 5229--.
Source
scival
Published In
Journal of Clinical Oncology
Volume
28
Issue
35
Publish Date
2010
Start Page
5229-
DOI
10.1200/JCO.2010.33.7311

MYC activity mitigates response to rapamycin in prostate cancer through eukaryotic initiation factor 4E-binding protein 1-mediated inhibition of autophagy.

Loss of PTEN and activation of phosphoinositide 3-kinase are commonly observed in advanced prostate cancer. Inhibition of mammalian target of rapamycin (mTOR), a downstream target of phosphoinositide 3-kinase signaling, results in cell cycle arrest and apoptosis in multiple in vitro and in vivo models of prostate cancer. However, single-agent use of mTOR inhibition has limited clinical success, and the identification of molecular events mitigating tumor response to mTOR inhibition remains a critical question. Here, using genetically engineered human prostate epithelial cells (PrEC), we show that MYC, a frequent target of genetic gain in prostate cancers, abrogates sensitivity to rapamycin by decreasing rapamycin-induced cytostasis and autophagy. Analysis of MYC and the mTOR pathway in human prostate tumors and PrEC showed selective increased expression of eukaryotic initiation factor 4E-binding protein 1 (4EBP1) with gain in MYC copy number or forced MYC expression, respectively. We have also found that MYC binds to regulatory regions of the 4EBP1 gene. Suppression of 4EBP1 expression resulted in resensitization of MYC-expressing PrEC to rapamycin and increased autophagy. Taken together, our findings suggest that MYC expression abrogates sensitivity to rapamycin through increased expression of 4EBP1 and reduced autophagy.

Authors
Balakumaran, BS; Porrello, A; Hsu, DS; Glover, W; Foye, A; Leung, JY; Sullivan, BA; Hahn, WC; Loda, M; Febbo, PG
MLA Citation
Balakumaran, BS, Porrello, A, Hsu, DS, Glover, W, Foye, A, Leung, JY, Sullivan, BA, Hahn, WC, Loda, M, and Febbo, PG. "MYC activity mitigates response to rapamycin in prostate cancer through eukaryotic initiation factor 4E-binding protein 1-mediated inhibition of autophagy." Cancer Res 69.19 (October 1, 2009): 7803-7810.
Website
http://hdl.handle.net/10161/4170
PMID
19773438
Source
pubmed
Published In
Cancer Research
Volume
69
Issue
19
Publish Date
2009
Start Page
7803
End Page
7810
DOI
10.1158/0008-5472.CAN-09-0910

MYC activity mitigates response to rapamycin in prostate cancer through eukaryotic initiation factor 4E-binding protein 1-mediated inhibition of autophagy

Loss of PTEN and activation of phosphoinositide 3-kinase are commonly observed in advanced prostate cancer. Inhibition of mammalian target of rapamycin (mTOR), a downstream target of phosphoinositide 3-kinase signaling, results in cell cycle arrest and apoptosis in multiple in vitro and in vivo models of prostate cancer. However, single-agent use of mTOR inhibition has limited clinical success, and the identification of molecular events mitigating tumor response to mTOR inhibition remains a critical question. Here, using genetically engineered human prostate epithelial cells (PrEC), we show that MYC, a frequent target of genetic gain in prostate cancers, abrogates sensitivity to rapamycin by decreasing rapamycin-induced cytostasis and autophagy. Analysis of MYC and the mTOR pathway in human prostate tumors and PrEC showed selective increased expression of eukaryotic initiation factor 4E-binding protein 1 (4EBP1) with gain in MYC copy number or forced MYC expression, respectively. We have also found that MYC binds to regulatory regions of the 4EBP1 gene. Suppression of 4EBP1 expression resulted in resensitization of MYC-expressing PrEC to rapamycin and increased autophagy. Taken together, our findings suggest that MYC expression abrogates sensitivity to rapamycin through increased expression of 4EBP1 and reduced autophagy. ©2009 American Association for Cancer Research.

Authors
Balakumaran, BS; Porrello, A; Hsu, DS; Glover, W; Foye, A; Leung, JY; Sullivan, BA; Hahn, WC; Loda, M; Febbo, PG
MLA Citation
Balakumaran, BS, Porrello, A, Hsu, DS, Glover, W, Foye, A, Leung, JY, Sullivan, BA, Hahn, WC, Loda, M, and Febbo, PG. "MYC activity mitigates response to rapamycin in prostate cancer through eukaryotic initiation factor 4E-binding protein 1-mediated inhibition of autophagy." Cancer Research 69.19 (October 1, 2009): 7803-7810.
Source
scopus
Published In
Cancer Research
Volume
69
Issue
19
Publish Date
2009
Start Page
7803
End Page
7810
DOI
10.1158/0008-5472.CAN-09-0910

Characterizing the developmental pathways TTF-1, NKX2-8, and PAX9 in lung cancer.

We investigated the clinical implications of lung developmental transcription factors (TTF-1, NKX2-8, and PAX9) that we recently discovered as cooperating oncogenes activated by way of gene amplification at chromosome 14q13 in lung cancer. Using stable transfectants of human bronchial epithelial cells, RNA expression profiles (signatures) representing activation of the biological pathways defined by each of the 3 genes were determined and used to risk stratify a non-small-cell lung cancer (NSCLC) clinical data set consisting of 91 early stage tumors. Coactivation of the TTF-1 and NKX2-8 pathways identified a cluster of patients with poor survival, representing approximately 20% of patients with early stage NSCLC, whereas activation of individual pathways did not reveal significant prognostic power. Importantly, the poor prognosis associated with coactivation of TTF-1 and NKX2-8 was validated in 2 other independent clinical data sets. Furthermore, lung cancer cell lines showing coactivation of the TTF-1 and NKX2-8 pathways were shown to exhibit resistance to cisplatin, the standard of care for the treatment of NSCLC. This suggests that the cohort of patients with coactivation of TTF-1 and NKX2-8 pathways appears to be resistant to standard cisplatin therapy, suggesting the need for alternative therapies in this cohort of high-risk patients.

Authors
Hsu, DS; Acharya, CR; Balakumaran, BS; Riedel, RF; Kim, MK; Stevenson, M; Tuchman, S; Mukherjee, S; Barry, W; Dressman, HK; Nevins, JR; Powers, S; Mu, D; Potti, A
MLA Citation
Hsu, DS, Acharya, CR, Balakumaran, BS, Riedel, RF, Kim, MK, Stevenson, M, Tuchman, S, Mukherjee, S, Barry, W, Dressman, HK, Nevins, JR, Powers, S, Mu, D, and Potti, A. "Characterizing the developmental pathways TTF-1, NKX2-8, and PAX9 in lung cancer." Proc Natl Acad Sci U S A 106.13 (March 31, 2009): 5312-5317.
PMID
19279207
Source
pubmed
Published In
Proceedings of the National Academy of Sciences of USA
Volume
106
Issue
13
Publish Date
2009
Start Page
5312
End Page
5317
DOI
10.1073/pnas.0900827106

Erratum: A genomic approach to colon cancer risk stratification yields biologic insights into therapeutic opportunities (Proceedings of the National Academy of Sciences of the United States of America (2008) 105:49 (19432-19437) Doi: 10.1073/pnas.0806674105)

Authors
Garman, KS; Acharya, CR; Edelman, E; Grade, M; Gaedcke, J; Sud, S; Barry, W; Diehl, AM; Provenzale, D; Ginsburg, GS; Ghadimi, BM; Ried, T; Nevins, JR; Mukherjee, S; Hsu, D; Potti, A
MLA Citation
Garman, KS, Acharya, CR, Edelman, E, Grade, M, Gaedcke, J, Sud, S, Barry, W, Diehl, AM, Provenzale, D, Ginsburg, GS, Ghadimi, BM, Ried, T, Nevins, JR, Mukherjee, S, Hsu, D, and Potti, A. "Erratum: A genomic approach to colon cancer risk stratification yields biologic insights into therapeutic opportunities (Proceedings of the National Academy of Sciences of the United States of America (2008) 105:49 (19432-19437) Doi: 10.1073/pnas.0806674105)." Proceedings of the National Academy of Sciences of the United States of America 106.16 (2009): 6878--.
Source
scival
Published In
Proceedings of the National Academy of Sciences of USA
Volume
106
Issue
16
Publish Date
2009
Start Page
6878-
DOI
10.1073/pnas.0902004106

Immune Cells and the Tumor Microenvironment

Authors
Hsu, DS; Morse, M; Clay, T; Devi, G; Lyerly, HK
MLA Citation
Hsu, DS, Morse, M, Clay, T, Devi, G, and Lyerly, HK. "Immune Cells and the Tumor Microenvironment." 2009. 818-829.
Source
scival
Publish Date
2009
Start Page
818
End Page
829
DOI
10.1016/B978-0-12-369420-1.00068-8

A genomic approach to colon cancer risk stratification yields biologic insights into therapeutic opportunities.

Gene expression profiles provide an opportunity to dissect the heterogeneity of solid tumors, including colon cancer, to improve prognosis and predict response to therapies. Bayesian binary regression methods were used to generate a signature of disease recurrence in patients with resected early stage colon cancer validated in an independent cohort. A 50-gene signature was developed that effectively distinguished early stage colon cancer patients with a low or high risk of disease recurrence. RT-PCR analysis of the 50-gene signature validated 9 of the top 10 differentially expressed genes. When applied to two independent validation cohorts of 55 and 73 patients, the 50-gene model accurately predicted recurrence. Standard Kaplan-Meier survival analysis confirmed the prognostic accuracy (P < 0.01, log rank), as did multivariate Cox proportional hazard models. We tested potential targeted therapeutic options for patients at high risk for disease recurrence and found a clinically important relationship between sensitivity to celecoxib, LY-294002 (PI3kinase inhibitor), retinol, and sulindac in colon cancer cell lines expressing the poor prognostic phenotype (P < 0.01, t test), which performed better than standard chemotherapy (5-FU and oxaliplatin). We present a genomic strategy in early stage colon cancer to identify patients at highest risk of recurrence. An ability to move beyond current staging by refining the estimation of prognosis in early stage colon cancer also has implications for individualized therapy.

Authors
Garman, KS; Acharya, CR; Edelman, E; Grade, M; Gaedcke, J; Sud, S; Barry, W; Diehl, AM; Provenzale, D; Ginsburg, GS; Ghadimi, BM; Ried, T; Nevins, JR; Mukherjee, S; Hsu, D; Potti, A
MLA Citation
Garman, KS, Acharya, CR, Edelman, E, Grade, M, Gaedcke, J, Sud, S, Barry, W, Diehl, AM, Provenzale, D, Ginsburg, GS, Ghadimi, BM, Ried, T, Nevins, JR, Mukherjee, S, Hsu, D, and Potti, A. "A genomic approach to colon cancer risk stratification yields biologic insights into therapeutic opportunities." Proc Natl Acad Sci U S A 105.49 (December 9, 2008): 19432-19437.
PMID
19050079
Source
pubmed
Published In
Proceedings of the National Academy of Sciences of USA
Volume
105
Issue
49
Publish Date
2008
Start Page
19432
End Page
19437
DOI
10.1073/pnas.0806674105

A genomic approach to identify molecular pathways associated with chemotherapy resistance.

Resistance to chemotherapy in cancer is common. As gene expression profiling has been shown to anticipate chemotherapeutic resistance, we sought to identify cellular pathways associated with resistance to facilitate effective combination therapy. Gene set enrichment analysis was used to associate pathways with resistance in two data sets: the NCI-60 cancer cell lines deemed sensitive and resistant to specific chemotherapeutic agents (Adriamycin, cyclophosphamide, docetaxel, etoposide, 5-fluorouracil, paclitaxel, and topotecan) and a series of 40 lung cancer cell lines for which sensitivity to cisplatin and docetaxel was determined. Candidate pathways were further screened in silico using the Connectivity Map. The lead candidate pathway was functionally validated in vitro. Gene set enrichment analysis associated the matrix metalloproteinase, p53, methionine metabolism, and free pathways with cytotoxic resistance in the NCI-60 cell lines across multiple agents, but no gene set was common to all drugs. Analysis of the lung cancer cell lines identified the bcl-2 pathway to be associated with cisplatin resistance and the AKT pathway enriched in cisplatin- and docetaxel-resistant cell lines. Results from Connectivity Map supported an association between phosphatidylinositol 3-kinase/AKT and docetaxel resistance but did not support the association with cisplatin. Targeted inhibition of the phosphatidylinositol 3-kinase/AKT pathway with LY294002, in combination with docetaxel, resulted in a synergistic effect in previously docetaxel-resistant cell lines but not with cisplatin. These results support the use of a genomic approach to identify drug-specific targets associated with the development of chemotherapy resistance and underscore the importance of disease context in identifying these pathways.

Authors
Riedel, RF; Porrello, A; Pontzer, E; Chenette, EJ; Hsu, DS; Balakumaran, B; Potti, A; Nevins, J; Febbo, PG
MLA Citation
Riedel, RF, Porrello, A, Pontzer, E, Chenette, EJ, Hsu, DS, Balakumaran, B, Potti, A, Nevins, J, and Febbo, PG. "A genomic approach to identify molecular pathways associated with chemotherapy resistance." Mol Cancer Ther 7.10 (October 2008): 3141-3149.
PMID
18852117
Source
pubmed
Published In
Molecular cancer therapeutics
Volume
7
Issue
10
Publish Date
2008
Start Page
3141
End Page
3149
DOI
10.1158/1535-7163.MCT-08-0642

Young age at diagnosis correlates with worse prognosis and defines a subset of breast cancers with shared patterns of gene expression.

PURPOSE: Breast cancer arising in young women is correlated with inferior survival and higher incidence of negative clinicopathologic features. The biology driving this aggressive disease has yet to be defined. PATIENTS AND METHODS: Clinically annotated, microarray data from 784 early-stage breast cancers were identified, and prospectively defined, age-specific cohorts (young: /= 65 years, n = 211) were compared by prognosis, clinicopathologic variables, mRNA expression values, single-gene analysis, and gene set enrichment analysis (GSEA). Univariate and multivariate analyses were performed. RESULTS: Using clinicopathologic variables, young women illustrated lower estrogen receptor (ER) positivity (immunohistochemistry [IHC], P = .027), larger tumors (P = .012), higher human epidermal growth factor receptor 2 (HER-2) overexpression (IHC, P = .075), lymph node positivity (P = .008), higher grade tumors (P < .0001), and trends toward inferior disease-free survival (DFS; hazard ratio = 1.32; P = .094). Using genomic expression analysis, tumors arising in young women had significantly lower ERalpha mRNA (P < .0001), ERbeta (P = .02), and progesterone receptor (PR) expression (P < .0001), but higher HER-2 (P < .0001) and epidermal growth factor receptor (EGFR) expression (P < .0001). Exploratory analysis (GSEA) revealed 367 biologically relevant gene sets significantly distinguishing breast tumors arising in young women. Combining clinicopathologic and genomic variables among tumors arising in young women demonstrated that younger age and lower ERbeta and higher EGFR mRNA expression were significant predictors of inferior DFS. CONCLUSION: This large-scale genomic analysis illustrates that breast cancer arising in young women is a unique biologic entity driven by unifying oncogenic signaling pathways, is characterized by less hormone sensitivity and higher HER-2/EGFR expression, and warrants further study to offer this poor-prognosis group of women better preventative and therapeutic options.

Authors
Anders, CK; Hsu, DS; Broadwater, G; Acharya, CR; Foekens, JA; Zhang, Y; Wang, Y; Marcom, PK; Marks, JR; Febbo, PG; Nevins, JR; Potti, A; Blackwell, KL
MLA Citation
Anders, CK, Hsu, DS, Broadwater, G, Acharya, CR, Foekens, JA, Zhang, Y, Wang, Y, Marcom, PK, Marks, JR, Febbo, PG, Nevins, JR, Potti, A, and Blackwell, KL. "Young age at diagnosis correlates with worse prognosis and defines a subset of breast cancers with shared patterns of gene expression." J Clin Oncol 26.20 (July 10, 2008): 3324-3330.
PMID
18612148
Source
pubmed
Published In
Journal of Clinical Oncology
Volume
26
Issue
20
Publish Date
2008
Start Page
3324
End Page
3330
DOI
10.1200/JCO.2007.14.2471

Gene expression signatures, clinicopathological features, and individualized therapy in breast cancer.

CONTEXT: Gene expression profiling may be useful for prognostic and therapeutic strategies in breast carcinoma. OBJECTIVES: To demonstrate the value in integrating genomic information with clinical and pathological risk factors, to refine prognosis, and to improve therapeutic strategies for early stage breast cancer. DESIGN, SETTING, AND PATIENTS: Retrospective study of patients with early stage breast carcinoma who were candidates for adjuvant chemotherapy; 964 clinically annotated breast tumor samples (573 in the initial discovery set and 391 in the validation cohort) with corresponding microarray data were used. All patients were assigned relapse risk scores based on their respective clinicopathological features. Signatures representing oncogenic pathway activation and tumor biology/microenvironment status were applied to these samples to obtain patterns of deregulation that correspond with relapse risk scores to refine prognosis with the clinicopathological prognostic model alone. Predictors of chemotherapeutic response were also applied to further characterize clinically relevant heterogeneity in early stage breast cancer. MAIN OUTCOME MEASURES: Gene expression signatures and clinicopathological variables in early stage breast cancer to determine a refined estimation of relapse-free survival and sensitivity to chemotherapy. RESULTS: In the initial data set of 573 patients, prognostically significant clusters representing patterns of oncogenic pathway activation and tumor biology/microenvironment states were identified within the low-risk (log-rank P = .004), intermediate-risk (log-rank P = .01), and high-risk (log-rank P = .003) model cohorts, representing clinically important genomic subphenotypes of breast cancer. As an example, in the low-risk cohort, of 6 prognostically significant clusters, patients in cluster 4 had an inferior relapse-free survival vs patients in cluster 1 (log-rank P = .004) and cluster 5 (log-rank P = .03). Median relapse-free survival for patients in cluster 4 was 16 months less than for patients in cluster 1 (95% CI, 7.5-24.5 months) and 19 months less than for patients in cluster 5 (95% CI, 10.5-27.5 months). Multivariate analyses confirmed the independent prognostic value of the genomic clusters (low risk, P = .05; high risk, P = .02). The reproducibility and validity of these patterns of pathway deregulation in predicting relapse risk was established using related but not identical clusters in the independent validation cohort. The prognostic clinicogenomic clusters also have unique sensitivity patterns to commonly used cytotoxic therapies. CONCLUSIONS: These results provide preliminary evidence that incorporation of gene expression signatures into clinical risk stratification can refine prognosis. Prospective studies are needed to determine the value of this approach for individualizing therapeutic strategies.

Authors
Acharya, CR; Hsu, DS; Anders, CK; Anguiano, A; Salter, KH; Walters, KS; Redman, RC; Tuchman, SA; Moylan, CA; Mukherjee, S; Barry, WT; Dressman, HK; Ginsburg, GS; Marcom, KP; Garman, KS; Lyman, GH; Nevins, JR; Potti, A
MLA Citation
Acharya, CR, Hsu, DS, Anders, CK, Anguiano, A, Salter, KH, Walters, KS, Redman, RC, Tuchman, SA, Moylan, CA, Mukherjee, S, Barry, WT, Dressman, HK, Ginsburg, GS, Marcom, KP, Garman, KS, Lyman, GH, Nevins, JR, and Potti, A. "Gene expression signatures, clinicopathological features, and individualized therapy in breast cancer." JAMA 299.13 (April 2, 2008): 1574-1587.
PMID
18387932
Source
pubmed
Published In
JAMA : the journal of the American Medical Association
Volume
299
Issue
13
Publish Date
2008
Start Page
1574
End Page
1587
DOI
10.1001/jama.299.13.1574

Age-specific differences in oncogenic pathway deregulation seen in human breast tumors.

PURPOSE: To define the biology driving the aggressive nature of breast cancer arising in young women. EXPERIMENTAL DESIGN: Among 784 patients with early stage breast cancer, using prospectively-defined, age-specific cohorts (young or=65 years), 411 eligible patients (n = 200or=65 years) with clinically-annotated Affymetrix microarray data were identified. GSEA, signatures of oncogenic pathway deregulation and predictors of chemotherapy sensitivity were evaluated within the two age-defined cohorts. RESULTS: In comparing deregulation of oncogenic pathways between age groups, a higher probability of PI3K (p = 0.006) and Myc (p = 0.03) pathway deregulation was observed in breast tumors arising in younger women. When evaluating unique patterns of pathway deregulation, a low probability of Src and E2F deregulation in tumors of younger women, concurrent with a higher probability of PI3K, Myc, and beta-catenin, conferred a worse prognosis (HR = 4.15). In contrast, a higher probability of Src and E2F pathway activation in tumors of older women, with concurrent low probability of PI3K, Myc and beta-catenin deregulation, was associated with poorer outcome (HR = 2.7). In multivariate analyses, genomic clusters of pathway deregulation illustrate prognostic value. CONCLUSION: Results demonstrate that breast cancer arising in young women represents a distinct biologic entity characterized by unique patterns of deregulated signaling pathways that are prognostic, independent of currently available clinico-pathologic variables. These results should enable refinement of targeted treatment strategies in this clinically challenging situation.

Authors
Anders, CK; Acharya, CR; Hsu, DS; Broadwater, G; Garman, K; Foekens, JA; Zhang, Y; Wang, Y; Marcom, K; Marks, JR; Mukherjee, S; Nevins, JR; Blackwell, KL; Potti, A
MLA Citation
Anders, CK, Acharya, CR, Hsu, DS, Broadwater, G, Garman, K, Foekens, JA, Zhang, Y, Wang, Y, Marcom, K, Marks, JR, Mukherjee, S, Nevins, JR, Blackwell, KL, and Potti, A. "Age-specific differences in oncogenic pathway deregulation seen in human breast tumors. (Published online)" PLoS One 3.1 (January 2, 2008): e1373-.
Website
http://hdl.handle.net/10161/4481
PMID
18167534
Source
pubmed
Published In
PloS one
Volume
3
Issue
1
Publish Date
2008
Start Page
e1373
DOI
10.1371/journal.pone.0001373

Pharmacogenomic strategies provide a rational approach to the treatment of cisplatin-resistant patients with advanced cancer.

PURPOSE: Standard treatment for advanced non-small-cell lung cancer (NSCLC) includes the use of a platinum-based chemotherapy regimen. However, response rates are highly variable. Newer agents, such as pemetrexed, have shown significant activity as second-line therapy and are currently being evaluated in the front-line setting. We utilized a genomic strategy to develop signatures predictive of chemotherapeutic response to both cisplatin and pemetrexed to provide a rational approach to effective individualized medicine. METHODS: Using in vitro drug sensitivity data, coupled with microarray data, we developed gene expression signatures predicting sensitivity to cisplatin and pemetrexed. Signatures were validated with response data from 32 independent ovarian and lung cancer cell lines as well as 59 samples from patients previously treated with cisplatin. RESULTS: Genomic-derived signatures of cisplatin and pemetrexed sensitivity were shown to accurately predict sensitivity in vitro and, in the case of cisplatin, to predict treatment response in patients treated with cisplatin. The accuracy of the cisplatin predictor, based on available clinical data, was 83.1% (sensitivity, 100%; specificity 57%; positive predictive value, 78%; negative predictive value, 100%). Interestingly, an inverse correlation was seen between in vitro cisplatin and pemetrexed sensitivity, and importantly, between the likelihood of cisplatin and pemetrexed response in patients. CONCLUSION: The use of genomic predictors of response to cisplatin and pemetrexed can be incorporated into strategies to optimize therapy for advanced solid tumors.

Authors
Hsu, DS; Balakumaran, BS; Acharya, CR; Vlahovic, V; Walters, KS; Garman, K; Anders, C; Riedel, RF; Lancaster, J; Harpole, D; Dressman, HK; Nevins, JR; Febbo, PG; Potti, A
MLA Citation
Hsu, DS, Balakumaran, BS, Acharya, CR, Vlahovic, V, Walters, KS, Garman, K, Anders, C, Riedel, RF, Lancaster, J, Harpole, D, Dressman, HK, Nevins, JR, Febbo, PG, and Potti, A. "Pharmacogenomic strategies provide a rational approach to the treatment of cisplatin-resistant patients with advanced cancer." J Clin Oncol 25.28 (October 1, 2007): 4350-4357.
PMID
17906199
Source
pubmed
Published In
Journal of Clinical Oncology
Volume
25
Issue
28
Publish Date
2007
Start Page
4350
End Page
4357
DOI
10.1200/JCO.2007.11.0593

Role of mouse cryptochrome blue-light photoreceptor in circadian photoresponses

Cryptochromes are photoactive pigments in the eye that have been proposed to function as circadian photopigments. Mice lacking the cryptochrome 2 blue-light photoreceptor gene (mCry2) were tested for circadian clock-related functions. The mutant mice had a lower sensitivity to acute light induction of mPer1 in the suprachiasmatic nucleus (SCN) but exhibited normal circadian oscillations of mPer1 and mCry1 messenger RNA in the SCN. Behaviorally, the mutants had an intrinsic circadian period about 1 hour longer than normal and exhibited high-amplitude phase shifts in response to light pulses administered at circadian time 17. These data are consistent with the hypothesis that CRY2 protein modulates circadian responses in mice and suggest that cryptochromes have a role in circadian photoreception in mammals.

Authors
Thresher, RJ; Vitaterna, MH; Miyamoto, Y; Kazantsev, A; Hsu, DS; Petit, C; Selby, CP; Dawut, L; Smithies, O; Takahashi, JS; Sancar, A
MLA Citation
Thresher, RJ, Vitaterna, MH, Miyamoto, Y, Kazantsev, A, Hsu, DS, Petit, C, Selby, CP, Dawut, L, Smithies, O, Takahashi, JS, and Sancar, A. "Role of mouse cryptochrome blue-light photoreceptor in circadian photoresponses." Science 282.5393 (1998): 1490-1494.
PMID
9822380
Source
scival
Published In
Science
Volume
282
Issue
5393
Publish Date
1998
Start Page
1490
End Page
1494

Reaction mechanism of (6-4) photolyase

The (6-4) photolyase catalyzes the photoreversal of the (6-4) dipyrimidine photoproducts induced in DNA by ultraviolet light. Using the cloned Drosophila melanogaster (6-4) photolyase gene, we overproduced and purified the recombinant enzyme. The binding and catalytic properties of the enzyme were investigated using natural substrates, T[6-4]T and T[6-4]C, and the Dewar isomer of (6-4) photoproduct and substrate analogs s5T[6- 4]T/thietane, mes5T[6-4]T, and the N-methyl-3'T thietane analog of the oxetane intermediate. The enzyme binds to the natural substrates and to mes5T[6-4]T with high affinity (K(D) ~10-9-10-10 M) and produces a DNase I footprint of about 20 base pairs around the photolesion. Several lines of evidence suggest that upon binding by the enzyme, the photoproduct flips out of the duplex. Of the four substrates that bind with high affinity to the enzyme, T[6-4]T and T[6-4]C are repaired with relatively high quantum yields compared with the Dewar isomer and the mes5T[6-4]T which are repaired with 300-400-fold lower quantum yield than the former two photoproducts. Reduction of the FAD cofactor with dithionite increases the quantum yield of repair. Taken together, the data are consistent with photoinduced electron transfer from reduced FAD to substrate, in a manner analogous to the cyclobutane pyrimidine dimer photolyase.

Authors
Zhao, X; Liu, J; Hsu, DS; Zhao, S; Taylor, J-S; Sancar, A
MLA Citation
Zhao, X, Liu, J, Hsu, DS, Zhao, S, Taylor, J-S, and Sancar, A. "Reaction mechanism of (6-4) photolyase." Journal of Biological Chemistry 272.51 (1997): 32580-32590.
PMID
9405473
Source
scival
Published In
The Journal of biological chemistry
Volume
272
Issue
51
Publish Date
1997
Start Page
32580
End Page
32590
DOI
10.1074/jbc.272.51.32580

Characterization of reaction intermediates of human excision repair nuclease

Nucleotide excision repair in humans is a complex reaction involving 14 polypeptides in six repair factors for dual incisions on either sides of a DNA lesion. To identify the reaction intermediates that form by the human excision repair nuclease, we adopted three approaches: purification of functional DNA · protein complexes, permanganate footprinting, and the employment as substrate of presumptive DNA reaction intermediates containing unwound sequences 5' to, 3' to, or encompassing the DNA lesion. The first detectable reaction intermediate was formed by substrate binding of XPA, RPA, XPC·HHR23B plus TFIIH (preincision complex 1, PIC1). In this complex the DNA was unwound on either side of the lesion by no more than 10 bases. Independent of the XPG nuclease function, the XPG protein stabilized this complex, forming a long lived preincision complex 2 (PIC2). The XPF · ERCC1 complex bound to PIC2, forming PIC3, which led to dual incisions and the release of the excised oligomer. With partially unwound DNAs, thymine cyclobutane dimer was excised at a fast rate independent of XPC · HHR23B, indicating that a major function of this protein is to stabilize the unwound DNA or to aid lesion unwinding in preincision complexes.

Authors
Mu, D; Wakasugi, M; Hsu, DS; Sancar, A
MLA Citation
Mu, D, Wakasugi, M, Hsu, DS, and Sancar, A. "Characterization of reaction intermediates of human excision repair nuclease." Journal of Biological Chemistry 272.46 (1997): 28971-28979.
PMID
9360969
Source
scival
Published In
The Journal of biological chemistry
Volume
272
Issue
46
Publish Date
1997
Start Page
28971
End Page
28979
DOI
10.1074/jbc.272.46.28971

Reaction mechanism of human DNA repair excision nuclease

Nucleotide excision repair consists of removal of the damaged nucleotide(s) from DNA by dual incision of the damaged strand on both sides of the lesion, followed by filling of the resulting gap and ligation. In humans, 14-16 polypeptides are required for the dual incision step. We have purified the required proteins to homogeneity and reconstituted the dual incision activity (excision nuclease) in a defined enzyme/substrate system. The system was highly efficient, removing >30% of the thymine dimers under optimal conditions. All of the six fractions that constitute the excision nuclease were required for dual incision of the thymine dimer substrate. However, when a cholesterol-substituted oligonucleotide was used as substrate, excision occurred in the absence of the XPC-HHR23B complex, reminiscent of transcription-coupled repair in the XP-C mutant cell line. Replication protein A is absolutely required for both incisions. The XPG subunit is essential to the formation of the preincision complex, but the repair complex can assemble and produce normal levels of 3'-incision in the absence of XPF-ERCC1. Kinetic experiments revealed that the 3'-incision precedes the 5'-incision. Consistent with the kinetic data, uncoupled 5'- incision was never observed in the reconstituted system. Two forms of TFIIH were used in the reconstitution reaction, one containing the CDK7-cyclin H pair and one lacking it. Both forms were equally active in excision. The excised oligomer dissociated from the gapped DNA in a nucleoprotein complex. In total, these results provide a detailed account of the reactions occurring during damage removal by human excision nuclease.

Authors
Mu, D; Hsu, DS; Sancar, A
MLA Citation
Mu, D, Hsu, DS, and Sancar, A. "Reaction mechanism of human DNA repair excision nuclease." Journal of Biological Chemistry 271.14 (1996): 8285-8294.
PMID
8626523
Source
scival
Published In
The Journal of biological chemistry
Volume
271
Issue
14
Publish Date
1996
Start Page
8285
End Page
8294
DOI
10.1074/jbc.271.14.8285

Putative human blue-light photoreceptors hCRY1 and hCRY2 are flavoproteins

Recently, a human cDNA clone with high sequence homology to the photolyase/blue-light photoreceptor family was identified. The putative protein encoded by this gene exhibited a strikingly high (48% identity) degree of homology to the Drosophila melanogaster (6-4) photolyase [Todo et al. (1996) Science 272, 109-112]. We have now identified a second human gene whose amino acid sequence displays 73% identity to the first one and have named the two genes CRY1 and CRY2, respectively. The corresponding proteins hCRY1 and hCRY2 were purified and characterized as maltose-binding fusion proteins. Similar to other members of the photolyase/blue-light photoreceptor family, both proteins were found to contain FAD and a pterin cofactor. Like the plant blue-light photoreceptors, both hCRY1 and hCRY2 lacked photolyase activity on the cyclobutane pyrimidine dimer and the (6-4) photoproduct. We conclude that these newly discovered members of the photolyase/photoreceptor family are not photolyases and instead may function as blue-light photoreceptors in humans.

Authors
Hsu, DS; Zhao, X; Zhao, S; Kazantsev, A; Wang, R-P; Todo, T; Wei, Y-F; Sancar, A
MLA Citation
Hsu, DS, Zhao, X, Zhao, S, Kazantsev, A, Wang, R-P, Todo, T, Wei, Y-F, and Sancar, A. "Putative human blue-light photoreceptors hCRY1 and hCRY2 are flavoproteins." Biochemistry 35.44 (1996): 13871-13877.
PMID
8909283
Source
scival
Published In
Biochemistry
Volume
35
Issue
44
Publish Date
1996
Start Page
13871
End Page
13877
DOI
10.1021/bi962209o

Structure and function of the UvrB protein

UvrB plays a central role in (A)BC excinuclease. To identify the regions of UvrB which are involved in interacting with UvrA, UvrC, and DNA, deletion mutants, point mutants, and various fusion forms of UvrB were constructed and characterized. We found that the region encompassing amino acid residues 115- 250 of UvrB binds to UvrA, while the region encompassing amino acid residues 547-673 binds to both UvrA and UvrC. In addition, the region between these two domains, which contains the helicase motifs II-VI, was found to be involved in binding to DNA. Within this DNA-binding region, two point mutants, E265A and E338A, were found to be unable to bind DNA while two residues, Phe-365 and Phe-496, were identified to interact with DNA. Furthermore, fluorescence quenching studies with mutants F365W and F496W and repair of thymine cyclobutane dimers by photoinduced electron transfer by these mutants suggest that residues Phe-365 and Phe-496 interact with DNA most likely through stacking interactions.

Authors
Hsu, DS; Kim, S-T; Sun, Q; Sancar, A
MLA Citation
Hsu, DS, Kim, S-T, Sun, Q, and Sancar, A. "Structure and function of the UvrB protein." Journal of Biological Chemistry 270.14 (1995): 8319-8327.
PMID
7713940
Source
scival
Published In
Journal of Biological Chemistry
Volume
270
Issue
14
Publish Date
1995
Start Page
8319
End Page
8327
DOI
10.1074/jbc.270.14.8319

Reconstitution of human DNA repair excision nuclease in a highly defined system

Xeroderma pigmentosum is a hereditary disease caused by defective DNA repair. Somatic cell genetics and biochemical studies with cell-free extracts indicate that at least 16 polypeptides are required to carry out the repair reaction proper, i.e. the removal of the lesion from the DNA by the dual incisions of the damaged strand. To find out if these proteins are necessary and sufficient for excision repair, they were obtained at a high level of purity in five fractions. The mixture of these five fractions reconstituted the excision nuclease (excinuclease) activity. Using the reconstituted excinuclease, we found that the excised fragment remains associated with the post-incision DNA-protein complex, suggesting that accessory proteins are needed to release the excised oligomer.

Authors
Mu, D; Park, C-H; Matsunaga, T; Hsu, DS; Reardon, JT; Sancar, A
MLA Citation
Mu, D, Park, C-H, Matsunaga, T, Hsu, DS, Reardon, JT, and Sancar, A. "Reconstitution of human DNA repair excision nuclease in a highly defined system." Journal of Biological Chemistry 270.6 (1995): 2415-2418.
PMID
7852297
Source
scival
Published In
Journal of Biological Chemistry
Volume
270
Issue
6
Publish Date
1995
Start Page
2415
End Page
2418
DOI
10.1074/jbc.270.6.2415

The other function of DNA photolyase: Stimulation of excision repair of chemical damage to DNA

DNA photolyase is a light-dependent DNA repair enzyme. It binds to cyclobutane pyrimidine dimers (Pyr<>Pyr) in DNA and upon excitation with a blue light photon splits the cyclobutane ring and restores the pyrimidines to native forms. The enzyme is specific for pyrimidine dimers, and it is not known to catalyze any other reaction either in ground or in excited state. However, when photolyase binds to Pyr<>Pyr but cannot catalyze repair because of lack of photoreactivating light, it still aids DNA repair by stimulating the nucleotide excision repair system. Recently, it was found that yeast photolyase binds to other lesions in DNA. In particular, the binding to cisplatin damaged DNA was highly specific. However, in vivo experiments revealed that this binding, in contrast to Pyr<>Pyr binding, did not stimulate but actually inhibited the removal of cisplatin damage by excision repair and hence photolyase sensitized cells to killing by cisplatin. In the present study, it is demonstrated that Escherichia coli DNA photolyase binds specifically to cisplatin 1,2-d(GpG) intrastrand cross-link and stimulates the removal of the lesion by E. coli excision nuclease in vitro. In agreement with the in vitro data, in vivo experiments revealed that photolyase makes cells more resistant to cisplatin killing.

Authors
Ozer, Z; Reardon, JT; Hsu, DS; Malhotra, K; Sancar, A
MLA Citation
Ozer, Z, Reardon, JT, Hsu, DS, Malhotra, K, and Sancar, A. "The other function of DNA photolyase: Stimulation of excision repair of chemical damage to DNA." Biochemistry 34.49 (1995): 15886-15889.
PMID
8519744
Source
scival
Published In
Biochemistry
Volume
34
Issue
49
Publish Date
1995
Start Page
15886
End Page
15889
DOI
10.1021/bi00049a002

Substrate spectrum of human excinuclease: Repair of abasic sites, methylated bases, mismatches, and bulky adducts

Nucleotide-excision repair is the repair system for removing bulky lesions from DNA. Humans deficient in this repair pathway suffer from xeroderma pigmentosum (XP), a disease characterized by photodermatoses, including skin cancers. At the cellular level, XP patients fail to remove cyclobutane pyrimidine dimers and pyrimidine(6-4)pyrimidone photoproducts induced by UV light, as well as other bulky DNA lesions caused by various genotoxic agents. XP cells are not particularly sensitive to ionizing radiation or to alkylating agents that cause mostly nonbulky DNA lesions. Therefore, it has generally been assumed that the human nucleotide-excision repair enzyme (excinuclease) is specific for bulky adducts. To determine the substrate range of human excinuclease we used the highly sensitive excision assay and tested bulky adducts, synthetic apurinic/apyrimidinic sites, N6- methyladenine, O6-methylguanine, and mismatches as potential substrates. We found that all of these 'lesions' were removed by human excinuclease, although with vastly different efficiencies.

Authors
Huang, J-C; Hsu, DS; Kazantsev, A; Sancar, A
MLA Citation
Huang, J-C, Hsu, DS, Kazantsev, A, and Sancar, A. "Substrate spectrum of human excinuclease: Repair of abasic sites, methylated bases, mismatches, and bulky adducts." Proceedings of the National Academy of Sciences of the United States of America 91.25 (1994): 12213-12217.
PMID
7991608
Source
scival
Published In
Proceedings of the National Academy of Sciences of USA
Volume
91
Issue
25
Publish Date
1994
Start Page
12213
End Page
12217
DOI
10.1073/pnas.91.25.12213

Flow linear dichroism and electron microscopic analysis of protein-DNA complexes of a mutant UvrB protein that binds to but cannot kink DNA

(A)BC excinuclease of Escherichia coli is the enzymatic activity resulting from sequential and partially overlapping actions of UvrA, UvrB, and UvrC protein. UvrA is a molecular matchmaker which promotes the formation of a stable UvrB-damaged DNA complex in which the DNA is kinked by about 130°. The UvrB-DNA complex is then recognized by UvrC and two incisions are made in the DNA by the joint actions of UvrC and UvrB. A mutant of UvrB (D478A) can be loaded onto the DNA but it does not interact with UvrC to cause a nick 3' to the lesion. Based on the lack of a DNase-I-hypersensitive site in the footprint of the mutant, it was proposed that the lack of incision was due to the inability of the mutant UvrB to kink the DNA. In the current study we have investigated the interaction of the mutant UvrB with DNA using two biophysical methods, flow linear dichroism and electron microscopy. Both methods reveal that the mutant UvrB is unable to bend DNA.

Authors
Hsu, DS; Takahashi, M; Delagoutte, E; Bertrand-Burggraf, E; Wang, Y-H; Norden, B; Fuchs, RPP; Griffith, J; Sancar, A
MLA Citation
Hsu, DS, Takahashi, M, Delagoutte, E, Bertrand-Burggraf, E, Wang, Y-H, Norden, B, Fuchs, RPP, Griffith, J, and Sancar, A. "Flow linear dichroism and electron microscopic analysis of protein-DNA complexes of a mutant UvrB protein that binds to but cannot kink DNA." Journal of Molecular Biology 241.5 (1994): 645-650.
PMID
8071991
Source
scival
Published In
Journal of Molecular Biology
Volume
241
Issue
5
Publish Date
1994
Start Page
645
End Page
650
DOI
10.1006/jmbi.1994.1541
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