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Nabet BY, Hamidi H, Lee MC, Banchereau R, Morris S, Adler L, Gayevskiy V, Elhossiny AM, Srivastava MK, Patil NS, Smith KA, Jesudason R, Chan C, Chang PS, Fernandez M, Rost S, McGinnis LM, Koeppen H, Gay CM, Minna JD, Heymach JV, Chan JM, Rudin CM, Byers LA, Liu SV, Reck M, Shames DS. Immune heterogeneity in small-cell lung cancer and vulnerability to immune checkpoint blockade. Cancer Cell 2024; 42:429-443.e4. [PMID: 38366589 DOI: 10.1016/j.ccell.2024.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 12/02/2023] [Accepted: 01/23/2024] [Indexed: 02/18/2024]
Abstract
Atezolizumab (anti-PD-L1), combined with carboplatin and etoposide (CE), is now a standard of care for extensive-stage small-cell lung cancer (ES-SCLC). A clearer understanding of therapeutically relevant SCLC subsets could identify rational combination strategies and improve outcomes. We conduct transcriptomic analyses and non-negative matrix factorization on 271 pre-treatment patient tumor samples from IMpower133 and identify four subsets with general concordance to previously reported SCLC subtypes (SCLC-A, -N, -P, and -I). Deeper investigation into the immune heterogeneity uncovers two subsets with differing neuroendocrine (NE) versus non-neuroendocrine (non-NE) phenotypes, demonstrating immune cell infiltration hallmarks. The NE tumors with low tumor-associated macrophage (TAM) but high T-effector signals demonstrate longer overall survival with PD-L1 blockade and CE versus CE alone than non-NE tumors with high TAM and high T-effector signal. Our study offers a clinically relevant approach to discriminate SCLC patients likely benefitting most from immunotherapies and highlights the complex mechanisms underlying immunotherapy responses.
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Affiliation(s)
| | | | | | | | | | - Leah Adler
- F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Velimir Gayevskiy
- Genentech Inc., South San Francisco CA, USA; Rancho Biosciences, San Diego, CA, USA
| | | | | | | | | | | | - Caleb Chan
- Genentech Inc., South San Francisco CA, USA
| | | | | | | | | | | | - Carl M Gay
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John D Minna
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX 75390-8593, USA; Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390, USA; Departments of Internal Medicine and Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - John V Heymach
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joseph M Chan
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10016, USA
| | - Charles M Rudin
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10016, USA; Weill Cornell Medical College, New York, NY 10065, USA
| | - Lauren A Byers
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stephen V Liu
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Martin Reck
- Lung Clinic Grosshansdorf, Airway Research Center North, German Center of Lung Research, Grosshansdorf, Germany
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Konopleva MY, Dail M, Daver NG, Garcia JS, Jonas BA, Yee KWL, Kelly KR, Vey N, Assouline S, Roboz GJ, Paolini S, Pollyea DA, Tafuri A, Brandwein JM, Pigneux A, Powell BL, Fenaux P, Olin RL, Visani G, Martinelli G, Onishi M, Wang J, Huang W, Dunshee D, Hamidi H, Ott MG, Hong WJ, Andreeff M. Venetoclax and Cobimetinib in Relapsed/Refractory AML: A Phase 1b Trial. Clin Lymphoma Myeloma Leuk 2024:S2152-2650(24)00036-3. [PMID: 38378362 DOI: 10.1016/j.clml.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/15/2024] [Accepted: 01/15/2024] [Indexed: 02/22/2024]
Abstract
BACKGROUND Therapies for relapsed/refractory acute myeloid leukemia remain limited and outcomes poor, especially amongst patients who are ineligible for cytotoxic chemotherapy or targeted therapies. PATIENTS AND METHODS This phase 1b trial evaluated venetoclax, a B-cell lymphoma-2 (BCL-2) inhibitor, plus cobimetinib, a MEK1/2 inhibitor, in patients with relapsed/refractory acute myeloid leukemia, ineligible for cytotoxic chemotherapy. Two-dimensional dose-escalation was performed for venetoclax dosed daily, and for cobimetinib dosed on days 1-21 of each 28-day cycle. RESULTS Thirty patients (median [range] age: 71.5 years [60-84]) received venetoclax-cobimetinib. The most common adverse events (AEs; in ≥40.0% of patients) were diarrhea (80.0%), nausea (60.0%), vomiting (40.0%), febrile neutropenia (40.0%), and fatigue (40.0%). Overall, 66.7% and 23.3% of patients experienced AEs leading to dose modification/interruption or treatment withdrawal, respectively. The composite complete remission (CRc) rate (complete remission [CR] + CR with incomplete blood count recovery + CR with incomplete platelet recovery) was 15.6%; antileukemic response rate (CRc + morphologic leukemia-free state/partial remission) was 18.8%. For the recommended phase 2 dose (venetoclax: 600 mg; cobimetinib: 40 mg), CRc and antileukemic response rates were both 12.5%. Failure to achieve an antileukemic response was associated with elevated baseline phosphorylated ERK and MCL-1 levels, but not BCL-xL. Baseline mutations in ≥1 signaling gene or TP53 were noted in nonresponders and emerged on treatment. Pharmacodynamic biomarkers revealed inconsistent, transient inhibition of the mitogen-activated protein kinase (MAPK) pathway. CONCLUSION Venetoclax-cobimetinib showed limited preliminary efficacy similar to single-agent venetoclax, but with added toxicity. Our findings will inform future trials of BCL-2/MAPK pathway inhibitor combinations.
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Affiliation(s)
| | | | - Naval G Daver
- University of Texas, MD Anderson Cancer Center, Houston, TX
| | | | - Brian A Jonas
- University of California Davis Comprehensive Cancer Center, Sacramento, CA
| | - Karen W L Yee
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | | | - Norbert Vey
- Hematologie Clinique, Institut Paoli Calmettes, Marseille, France
| | | | - Gail J Roboz
- Weill-Cornell Medical College, New York Presbyterian, New York, NY
| | - Stefania Paolini
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli", Bologna, Italy
| | | | - Agostino Tafuri
- Department of Clinical and Molecular Medicine, University Hospital Sant'Andrea-Sapienza, Rome, Italy
| | | | - Arnaud Pigneux
- Bordeaux Haut-Leveque University Hospital, Pessac, France
| | - Bayard L Powell
- Atrium Health Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC
| | - Pierre Fenaux
- Hôpital Saint-Louis, Université Paris Diderot, Paris, France
| | - Rebecca L Olin
- University of California San Francisco, San Francisco, CA
| | | | - Giovanni Martinelli
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | | | - Jue Wang
- Genentech, Inc., South San Francisco, CA
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Verstovsek S, Foltz L, Gupta V, Hasserjian R, Manshouri T, Mascarenhas J, Mesa R, Pozdnyakova O, Ritchie E, Veletic I, Gamel K, Hamidi H, Han L, Higgins B, Trunzer K, Uguen M, Wang D, El-Galaly TC, Todorov B, Gotlib J. Safety and efficacy of zinpentraxin alfa as monotherapy or in combination with ruxolitinib in myelofibrosis: stage I of a phase II trial. Haematologica 2023; 108:2730-2742. [PMID: 37165840 PMCID: PMC10543197 DOI: 10.3324/haematol.2022.282411] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 05/03/2023] [Indexed: 05/12/2023] Open
Abstract
Pentraxin 2 (PTX-2; serum amyloid P component), a circulating endogenous regulator of the inflammatory response to tissue injury and fibrosis, is reduced in patients with myelofibrosis (MF). Zinpentraxin alfa (RO7490677, PRM-151) is a recombinant form of PTX-2 that has shown preclinical antifibrotic activity and no dose-limiting toxicities in phase I trials. We report results from stage 1 of a phase II trial of zinpentraxin alfa in patients with intermediate-1/2 or high-risk MF. Patients (n=27) received intravenous zinpentraxin α weekly (QW) or every 4 weeks (Q4W), as monotherapy or an additional therapy for patients on stable-dose ruxolitinib. The primary endpoint was overall response rate (ORR; investigatorassessed) adapted from International Working Group-Myeloproliferative Neoplasms Research and Treatment criteria. Secondary endpoints included modified Myeloproliferative Neoplasm-Symptom Assessment Form Total Symptom Score (MPN-SAF TSS) change, bone marrow (BM) MF grade reduction, pharmacokinetics, and safety. ORR at week 24 was 33% (n=9/27) and varied across individual cohorts (QW: 38% [3/8]; Q4W: 14% [1/7]; QW+ruxolitinib: 33% [2/6]; Q4W+ruxolitinib: 50% [3/6]). Five of 18 evaluable patients (28%) experienced a ≥50% reduction in MPN-SAF TSS, and six of 17 evaluable patients (35%) had a ≥1 grade improvement from baseline in BM fibrosis at week 24. Most treatment-emergent adverse events (AE) were grade 1-2, most commonly fatigue. Among others, anemia and thrombocytopenia were infrequent (n=3 and n=1, respectively). Treatment-related serious AE occurred in four patients (15%). Overall, zinpentraxin alfa showed evidence of clinical activity and tolerable safety as monotherapy and in combination with ruxolitinib in this open-label, non-randomized trial (clinicaltrials gov. Identifier: NCT01981850).
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Affiliation(s)
- Srdan Verstovsek
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX.
| | - Lynda Foltz
- St Paul's Hospital, University of British Columbia, Vancouver
| | - Vikas Gupta
- Princess Margaret Cancer Centre, University of Toronto, Toronto
| | | | - Taghi Manshouri
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - John Mascarenhas
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Ruben Mesa
- Mays Cancer Center at UT Health San Antonio MD Anderson, San Antonio, TX
| | - Olga Pozdnyakova
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | | | - Ivo Veletic
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | | | | | - Dao Wang
- F. Hoffmann-La Roche, Ltd., Basel
| | - Tarec Christoffer El-Galaly
- F. Hoffmann-La Roche, Ltd., Basel, Switzerland; Current affiliation: Department of Hematology, Aalborg University Hospital, Aalborg
| | | | - Jason Gotlib
- Stanford Cancer Institute/Stanford University School of Medicine, Stanford, CA
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Wong S, Hamidi H, Costa LJ, Bekri S, Neparidze N, Vij R, Nielsen TG, Raval A, Sareen R, Wassner-Fritsch E, Cho HJ. Multi-omic analysis of the tumor microenvironment shows clinical correlations in Ph1 study of atezolizumab +/- SoC in MM. Front Immunol 2023; 14:1085893. [PMID: 37559718 PMCID: PMC10408441 DOI: 10.3389/fimmu.2023.1085893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 05/23/2023] [Indexed: 08/11/2023] Open
Abstract
Multiple myeloma (MM) remains incurable, and treatment of relapsed/refractory (R/R) disease is challenging. There is an unmet need for more targeted therapies in this setting; deep cellular and molecular phenotyping of the tumor and microenvironment in MM could help guide such therapies. This phase 1b study (NCT02431208) evaluated the safety and efficacy of the anti-programmed death-ligand 1 monoclonal antibody atezolizumab (Atezo) alone or in combination with the standard of care (SoC) treatments lenalidomide (Len) or pomalidomide (Pom) and/or daratumumab (Dara) in patients with R/R MM. Study endpoints included incidence of adverse events (AEs) and overall response rate (ORR). A novel unsupervised integrative multi-omic analysis was performed using RNA sequencing, mass cytometry immunophenotyping, and proteomic profiling of baseline and on-treatment bone marrow samples from patients receiving Atezo monotherapy or Atezo+Dara. A similarity network fusion (SNF) algorithm was applied to preprocessed data. Eighty-five patients were enrolled. Treatment-emergent deaths occurred in 2 patients; both deaths were considered unrelated to study treatment. ORRs ranged from 11.1% (Atezo+Len cohorts, n=18) to 83.3% (Atezo+Dara+Pom cohort, n=6). High-dimensional multi-omic profiling of the tumor microenvironment and integrative SNF analysis revealed novel correlations between cellular and molecular features of the tumor and immune microenvironment, patient selection criteria, and clinical outcome. Atezo monotherapy and SoC combinations were safe in this patient population and demonstrated some evidence of clinical efficacy. Integrative analysis of high dimensional genomics and immune data identified novel clinical correlations that may inform patient selection criteria and outcome assessment in future immunotherapy studies for myeloma.
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Affiliation(s)
- Sandy Wong
- University of California San Francisco (UCSF) Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, United States
| | - Habib Hamidi
- Genentech Inc., South San Francisco, CA, United States
| | - Luciano J. Costa
- O’Neal Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Selma Bekri
- Tisch Cancer Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, United States
| | | | - Ravi Vij
- Division of Oncology, Washington University, St. Louis, MO, United States
| | | | - Aparna Raval
- Genentech Inc., South San Francisco, CA, United States
| | - Rajan Sareen
- Genentech Inc., South San Francisco, CA, United States
| | | | - Hearn J. Cho
- Tisch Cancer Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, United States
- The Multiple Myeloma Research Foundation (MMRF), Norwalk, CT, United States
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5
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Landen CN, Molinero L, Hamidi H, Sehouli J, Miller A, Moore KN, Taskiran C, Bookman M, Lindemann K, Anderson C, Berger R, Myers T, Beiner M, Reid T, Van Nieuwenhuysen E, Green A, Okamoto A, Aghajanian C, Thaker PH, Blank SV, Khor VK, Chang CW, Lin YG, Pignata S. Influence of Genomic Landscape on Cancer Immunotherapy for Newly Diagnosed Ovarian Cancer: Biomarker Analyses from the IMagyn050 Randomized Clinical Trial. Clin Cancer Res 2023; 29:1698-1707. [PMID: 36595569 PMCID: PMC10150250 DOI: 10.1158/1078-0432.ccr-22-2032] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/30/2022] [Accepted: 12/27/2022] [Indexed: 01/04/2023]
Abstract
PURPOSE To explore whether patients with BRCA1/2-mutated or homologous recombination deficient (HRD) ovarian cancers benefitted from atezolizumab in the phase III IMagyn050 (NCT03038100) trial. PATIENTS AND METHODS Patients with newly diagnosed ovarian cancer were randomized to either atezolizumab or placebo with standard chemotherapy and bevacizumab. Programmed death-ligand 1 (PD-L1) status of tumor-infiltrating immune cells (IC) was determined centrally (VENTANA SP142 assay). Genomic alterations, including deleterious BRCA1/2 alterations, genomic loss of heterozygosity (gLOH), tumor mutation burden (TMB), and microsatellite instability (MSI), were evaluated using the FoundationOne assay. HRD was defined as gLOH ≥ 16%, regardless of BRCA1/2 mutation status. Potential associations between progression-free survival (PFS) and genomic biomarkers were evaluated using standard correlation analyses and log-rank of Kaplan-Meier estimates. RESULTS Among biomarker-evaluable samples, 22% (234/1,050) harbored BRCA1/2 mutations and 46% (446/980) were HRD. Median TMB was low irrespective of BRCA1/2 or HRD. Only 3% (29/1,024) had TMB ≥10 mut/Mb, and 0.3% (3/1,022) were MSI-high. PFS was better in BRCA2-mutated versus BRCA2-non-mutated tumors and in HRD versus proficient tumors. PD-L1 positivity (≥1% expression on ICs) was associated with HRD but not BRCA1/2 mutations. PFS was not improved by adding atezolizumab in BRCA2-mutated or HRD tumors; there was a trend toward enhanced PFS with atezolizumab in BRCA1-mutated tumors. CONCLUSIONS Most ovarian tumors have low TMB despite BRCA1/2 mutations or HRD. Neither BRCA1/2 mutation nor HRD predicted enhanced benefit from atezolizumab. This is the first randomized double-blind trial in ovarian cancer demonstrating that genomic instability triggered by BRCA1/2 mutation or HRD is not associated with improved sensitivity to immune checkpoint inhibitors. See related commentary by Al-Rawi et al., p. 1645.
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Affiliation(s)
- Charles N. Landen
- Gynecologic Oncology Group Foundation (GOG-F) and Department of Obstetrics and Gynecology, University of Virginia, Charlottesville, Virginia
| | - Luciana Molinero
- Oncology Biomarker Development, Genentech, Inc., South San Francisco, California
| | - Habib Hamidi
- Oncology Biomarker Development, Genentech, Inc., South San Francisco, California
| | - Jalid Sehouli
- Arbeitsgemeinschaft Gynaekologische Onkologie (AGO)/Nord-Ostdeutsche Gesellschaft für Gynäkologische Onkologie (North-Eastern German Society of Gynaecologic Oncology; NOGGO) and Charité-Medical University of Berlin (Campus Virchow Klinikum), Berlin, Germany
| | - Austin Miller
- GOG-F and Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Kathleen N. Moore
- GOG-F and Stephenson Cancer Center at the University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, and Sarah Cannon Research Institute, Nashville, Tennessee
| | - Cagatay Taskiran
- Turkish Society of Gynecologic Oncology (TRSGO) and Koc University School of Medicine and VKV American Hospital, Istanbul, Turkey
| | - Michael Bookman
- GOG-F and Kaiser Permanente Northern California, San Francisco, California
| | - Kristina Lindemann
- Nordic Society of Gynaecological Oncology (NSGO) and Department of Gynecological Oncology, Division of Cancer Medicine, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | - Regina Berger
- AGO-Austria and Department for Gynecology and Obstetrics, Innsbruck Medical University, Innsbruck, Austria
| | - Tashanna Myers
- GOG-F and Baystate Medical Center, Springfield, Massachusetts
| | - Mario Beiner
- Israeli Society of Gynecologic Oncology (ISGO) and Gynecologic Oncology Division, Meir Medical Center, Tel Aviv University, Kfar Saba, Israel
| | - Thomas Reid
- GOG-F and Kettering Medical Center, Kettering, Ohio
| | - Els Van Nieuwenhuysen
- Belgium and Luxembourg Gynaecological Oncology Group (BGOG) and UZ Leuven Gasthuisberg, Leuven, Belgium
| | - Andrew Green
- GOG-F and Northeast Georgia Medical Center, Gainesville, Georgia
| | - Aikou Okamoto
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Tokyo, Japan
| | - Carol Aghajanian
- GOG-F and Memorial Sloan Kettering Cancer Center, New York, New York
| | - Premal H. Thaker
- GOG-F and Washington University School of Medicine, St. Louis, Missouri
| | | | - Victor K. Khor
- Product Development Oncology, Genentech, Inc., South San Francisco, California
| | - Ching-Wei Chang
- Personalized Healthcare and Early Development Oncology Biostatistics, Genentech, Inc., South San Francisco, California
| | - Yvonne G. Lin
- Product Development Oncology, Genentech, Inc., South San Francisco, California
| | - Sandro Pignata
- Multicentre Italian Trials in Ovarian Cancer and Gynecologic Malignancies (MITO) and Istituto Nazionale Tumori IRCCS Fondazione G Pascale, Napoli, Italy
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Krishnan V, Chang CW, Hamidi H, Bookman MA, Landen C, Myers T, Kajiyama H, Hietanen S, Willmott L, Thaker P, Taskiran C, Sehouli J, Khor V, Liu YL, Pignata S, Moore K, Molinero L. Abstract 5702: Ovarian cancer tumor microenvironment and atezolizumab (atezo) clinical activity: IMagyn050 sub-study. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-5702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Background: Tumor biomarkers such as CD8 density and location (i.e., immune inflamed phenotype) and immune rich molecular subtype have been linked to immune checkpoint blockade (ICB) overall survival (OS) in different cancers. The IMagyn050 trial (NCT03038100), which evaluated the efficacy of Atezo vs placebo (Pla) with carboplatin, paclitaxel and bevacizumab (CPB) in front line ovarian cancer patient (pts), did not meet its co-primary endpoints of PFS in ITT or PD-L1+ (Moore et al. JCO 2021). In the current IMagyn050 substudy we assessed potential predictive tumor immune biomarkers for Atezo clinical benefit.
Methods: FFPE tumors from the biomarker evaluable population were tested for PD-L1 IHC, CD8/PanCK IHC (total CD8 T cells and immune location phenotypes [inflamed, excluded, desert]) and RNA-seq (to derive molecular subtypes, biological pathways and cellular components [xCELL]) in tissue from baseline (n=860), on-treatment (OT, 9 weeks, n=233), intra- (n=8) and inter-lesion (n=12) matched samples. Hazard ratio (HR) interaction test from multivariate adjusted Cox-regression analysis for PFS and OS was performed to test predictive biomarkers.
Results: While tumors with CD8 T cells, immunoreactive molecular subtypes or immune inflamed phenotype were enriched for PD-L1+, only pts with immune inflamed tumors showed improved OS Atezo benefit (HR 0.67). Improved Atezo PFS/OS benefit was also observed in pts with whose tumors had high oxidative phosphorylation (OXPHOS, HR: 0.72/0.65) and UV Response (UV, HR: 0.64/0.58) but not IFNγ response. Plasma B cells were linked to improved OS Atezo benefit vs Pla (HR 0.53). We leveraged OT samples from pts in the neoadjuvant cohort to assess treatment effect on the tumor microenvironment. Analyses showed that CPB reduced tumor proliferation and increased tumor immune inflammation (CD8 T cells, PD-L1 and IFNα/IFNγ response), further increased by Atezo. Immune inflammation is challenging in ovarian cancer due to extensive tumor heterogeneity. Prevalence of tumor biomarkers varied by anatomic locations: total CD8, CD8 localization and molecular subtypes. Inter- and intra-lesion biomarker status within the same pt showed PD-L1 and plasma B cells as most consistent. Molecular subtypes and immune phenotypes had moderate intra-lesion agreement but discordant between lesions. PD-L1 and OXPHOS were the only biomarkers linked to Atezo benefit regardless of anatomical location.
Conclusion: This comprehensive exploratory study suggests that DNA damage, OXPHOS, plasma B cells and immune inflamed tumors, but not molecular subtypes or total CD8 T cells, may predict Atezo + CPB OS. This treatment promotes immune inflammation in OC tumors. Notably, we found that several biomarkers are highly heterogeneous. Our findings highlight the challenges of achieving durable clinical benefit from targeted immunotherapy in ovarian cancer pts.
Citation Format: Venkatesh Krishnan, Ching-Wei Chang, Habib Hamidi, Michael A. Bookman, Charles Landen, Tashanna Myers, Hiroaki Kajiyama, Sakari Hietanen, Lyndsay Willmott, Premal Thaker, Cagatay Taskiran, Jalid Sehouli, Victor Khor, Yvonne Lin Liu, Sandro Pignata, Kathleen Moore, Luciana Molinero. Ovarian cancer tumor microenvironment and atezolizumab (atezo) clinical activity: IMagyn050 sub-study. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5702.
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Affiliation(s)
- Venkatesh Krishnan
- 1Oncology Biomarker Development, Genentech, Inc., South San Francisco, CA
| | - Ching-Wei Chang
- 2Personalized Healthcare and Early Development Oncology Biostatistics, Genentech, Inc., South San Francisco, CA
| | - Habib Hamidi
- 1Oncology Biomarker Development, Genentech, Inc., South San Francisco, CA
| | - Michael A. Bookman
- 3Gynecologic Oncology Group Foundation (GOG-F) and Kaiser Permanente Northern California, San Francisco, CA
| | - Charles Landen
- 4Gynecologic Oncology Group Foundation (GOG-F) and University of Virginia, Charlottesville, VA
| | - Tashanna Myers
- 5Gynecologic Oncology Group Foundation (GOG-F) and Baystate Medical Center, Springfield, MA
| | | | | | | | - Premal Thaker
- 9Gynecologic Oncology Group Foundation (GOG-F) and Washington University School of Medicine, St Louis, MO
| | - Cagatay Taskiran
- 10Turkish Society of Gynecologic Oncology (TRSGO) and Koc University School of Medicine and VKV American Hospital, Istanbul, Turkey
| | - Jalid Sehouli
- 11Arbeitsgemeinschaft Gynaekologische Onkologie (AGO)/Nord-Ostdeutsche Gesellschaft für Gynäkologische Onkologie (North-Eastern German Society of Gynaecologic Oncology; NOGGO) and Charité-Medical University of Berlin (Campus Virchow Klinikum), Berlin, Germany
| | - Victor Khor
- 12Product Development Oncology, Genentech, Inc., South San Francisco, CA
| | - Yvonne Lin Liu
- 12Product Development Oncology, Genentech, Inc., South San Francisco, CA
| | - Sandro Pignata
- 13Multicentre Italian Trials in Ovarian Cancer and Gynecologic Malignancies (MITO) and Istituto Nazionale Tumori IRCCS Fondazione G Pascale, Napoli, Italy
| | - Kathleen Moore
- 14Gynecologic Oncology Group Foundation (GOG-F) and Stephenson Cancer Center at the University of Oklahoma Health Sciences Center, Oklahoma City, OK and Sarah Cannon Research Institute, Nashville, TN
| | - Luciana Molinero
- 1Oncology Biomarker Development, Genentech, Inc., South San Francisco, CA
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Huseni MA, Wang L, Klementowicz JE, Yuen K, Breart B, Orr C, Liu LF, Li Y, Gupta V, Li C, Rishipathak D, Peng J, Şenbabaoǧlu Y, Modrusan Z, Keerthivasan S, Madireddi S, Chen YJ, Fraser EJ, Leng N, Hamidi H, Koeppen H, Ziai J, Hashimoto K, Fassò M, Williams P, McDermott DF, Rosenberg JE, Powles T, Emens LA, Hegde PS, Mellman I, Turley SJ, Wilson MS, Mariathasan S, Molinero L, Merchant M, West NR. CD8 + T cell-intrinsic IL-6 signaling promotes resistance to anti-PD-L1 immunotherapy. Cell Rep Med 2023; 4:100878. [PMID: 36599350 PMCID: PMC9873827 DOI: 10.1016/j.xcrm.2022.100878] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 10/14/2022] [Accepted: 12/08/2022] [Indexed: 01/05/2023]
Abstract
Although immune checkpoint inhibitors (ICIs) are established as effective cancer therapies, overcoming therapeutic resistance remains a critical challenge. Here we identify interleukin 6 (IL-6) as a correlate of poor response to atezolizumab (anti-PD-L1) in large clinical trials of advanced kidney, breast, and bladder cancers. In pre-clinical models, combined blockade of PD-L1 and the IL-6 receptor (IL6R) causes synergistic regression of large established tumors and substantially improves anti-tumor CD8+ cytotoxic T lymphocyte (CTL) responses compared with anti-PD-L1 alone. Circulating CTLs from cancer patients with high plasma IL-6 display a repressed functional profile based on single-cell RNA sequencing, and IL-6-STAT3 signaling inhibits classical cytotoxic differentiation of CTLs in vitro. In tumor-bearing mice, CTL-specific IL6R deficiency is sufficient to improve anti-PD-L1 activity. Thus, based on both clinical and experimental evidence, agents targeting IL-6 signaling are plausible partners for combination with ICIs in cancer patients.
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Affiliation(s)
| | - Lifen Wang
- Genentech, South San Francisco, CA 94080, USA
| | | | - Kobe Yuen
- Genentech, South San Francisco, CA 94080, USA
| | | | | | - Li-Fen Liu
- Genentech, South San Francisco, CA 94080, USA
| | - Yijin Li
- Genentech, South San Francisco, CA 94080, USA
| | | | - Congfen Li
- Genentech, South San Francisco, CA 94080, USA
| | | | - Jing Peng
- Genentech, South San Francisco, CA 94080, USA
| | | | | | | | | | | | | | - Ning Leng
- Genentech, South San Francisco, CA 94080, USA
| | | | | | - James Ziai
- Genentech, South San Francisco, CA 94080, USA
| | | | | | | | | | - Jonathan E Rosenberg
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Thomas Powles
- Barts Experimental Cancer Medicine Centre, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Leisha A Emens
- University of Pittsburgh Medical Center, Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | | | - Ira Mellman
- Genentech, South San Francisco, CA 94080, USA
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8
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Rajasekaran K, Guan X, Tafazzol A, Hamidi H, Darwish M, Yadav M. Tetramer-aided sorting and single-cell RNA sequencing facilitate transcriptional profiling of antigen-specific CD8+ T cells. Transl Oncol 2022; 27:101559. [PMID: 36279715 PMCID: PMC9594627 DOI: 10.1016/j.tranon.2022.101559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recent advances in single-cell technologies and an improved understanding of tumor antigens have empowered researchers to investigate tumor antigen-specific CD8+ T cells at the single-cell level. Peptide-MHC I tetramers are often utilized to enrich antigen-specific CD8+ T cells, which however, introduces the undesired risk of altering their clonal distribution or their transcriptional state. This study addresses the feasibility of utilizing tetramers to enrich antigen-specific CD8+ T cells for single-cell analysis. METHODS HLA-A*02:01-restricted human cytomegalovirus (CMV) pp65 peptide-specific CD8+ T cells were used as a model for analyzing antigen-specific CD8+ T cells. Single-cell RNA sequencing and TCR sequencing were performed to compare the frequency and gene expression profile of pp65-specific TCR clones between tetramer-sorted, unstimulated- and tetramer-stimulated total CD8+ T cells. RESULTS The relative frequency of pp65-specific TCR clones and their transcriptional profile remained largely unchanged following tetramer-based sorting. In contrast, tetramer-mediated stimulation of CD8+ T cells resulted in significant gene expression changes in pp65-specific CD8+ T cells. An Antigen-Specific Response (ASR) gene signature was derived from tetramer-stimulated pp65-specific CD8+ T cells. The ASR signature had a predictive value and was significantly associated with progression free survival in lung cancer patients treated with anti-PD-L1, anti-VEGF, chemotherapy combination (NCT02366143). The predictive power of the ASR signature was independent of the conventional CD8 effector signature. CONCLUSIONS Our findings validate the approach of enriching antigen-specific CD8+ T cells through tetramer-aided Fluorescence-Activated Cell Sorting (FACS) sorting for single-cell analysis and also identifies an ASR gene signature that has value in predicting response to cancer immunotherapy.
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9
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Wang J, Hu Y, Hamidi H, Dos Santos C, Zhang J, Punnoose E, Li W. Immune microenvironment characteristics in multiple myeloma progression from transcriptome profiling. Front Oncol 2022; 12:948548. [PMID: 36033464 PMCID: PMC9413314 DOI: 10.3389/fonc.2022.948548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/14/2022] [Indexed: 11/30/2022] Open
Abstract
Multiple myeloma (MM) is characterized by clonal expansion of malignant plasma cells in the bone marrow (BM). Despite the significant advances in treatment, relapsed and refractory MM has not yet been completely cured due to the immune dysfunction in the tumor microenvironment (TME). In this study, we analyzed the transcriptome data from patients with newly diagnosed (ND) and relapsed/refractory (R/R) MM to characterize differences in the TME and further decipher the mechanism of tumor progression in MM. We observed highly expressed cancer testis antigens and immune suppressive cell infiltration, such as Th2 and M2 cells, are associated with MM progression. Furthermore, the TGF-β signature contributes to the worse outcome of patients with R/R MM. Moreover, patients with ND MM could be classified into immune-low and immune-high phenotypes. Immune-high patients with higher IFN-g signatures are associated with MHC-II–mediated CD4+ T-cell response through CIITA stimulation. The baseline TME status could potentially inform new therapeutic choices for the ND MM who are ineligible for autologous stem cell transplantation and may help predict the response to CAR-T for patients with R/R MM. Our study demonstrates how integrating tumor transcriptome and clinical information to characterize MM immune microenvironment and elucidate potential mechanisms of tumor progression and immune evasion, which will provide insights into MM treatment selection.
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Affiliation(s)
- Jin Wang
- Oncology Biomarker Development, Roche (China) Holding Ltd., Shanghai, China
| | - Yi Hu
- Oncology Biomarker Development, Roche (China) Holding Ltd., Shanghai, China
| | - Habib Hamidi
- Oncology Biomarker Development, Genentech, Ltd., South San Francisco, CA, United States
| | - Cedric Dos Santos
- Oncology Biomarker Development, Genentech, Ltd., South San Francisco, CA, United States
| | - Jingyu Zhang
- Oncology Biomarker Development, Roche (China) Holding Ltd., Shanghai, China
| | - Elizabeth Punnoose
- Oncology Biomarker Development, Genentech, Ltd., South San Francisco, CA, United States
| | - Wenjin Li
- Oncology Biomarker Development, Roche (China) Holding Ltd., Shanghai, China
- *Correspondence: Wenjin Li,
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10
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Yuen KC, Tran B, Anton A, Hamidi H, Costello AJ, Corcoran NM, Lawrentschuk N, Rainey N, Semira MCG, Gibbs P, Mariathasan S, Sandhu S, Kadel EE. Molecular classification of hormone-sensitive and castration-resistant prostate cancer, using nonnegative matrix factorization molecular subtyping of primary and metastatic specimens. Prostate 2022; 82:993-1002. [PMID: 35435276 PMCID: PMC9321082 DOI: 10.1002/pros.24346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 02/12/2022] [Accepted: 03/14/2022] [Indexed: 11/12/2022]
Abstract
BACKGROUND Despite the rapidly evolving therapeutic landscape, immunotherapy has demonstrated limited activity in prostate cancer. A greater understanding of the molecular landscape, particularly the expression of immune-related pathways, will inform future immunotherapeutic strategies. Consensus nonnegative matrix factorization (cNMF) is a novel model of molecular classification analyzing gene expression data, focusing on biological interpretation of metagenes and selecting meaningful clusters. OBJECTIVE We aimed to identify molecular subtypes of prostate cancer using cNMF and correlate these with existing biomarkers to inform future immunotherapeutic strategies. METHODS A cohort of archival tumor specimens from hormone-sensitive and castration-resistant disease was studied. Whole transcriptomic profiles were generated using TruSeq RNA Access technology and subjected to cNMF. Comprehensive genomic profiling was performed with the FoundationOne assay. NMF subtypes were characterized by gene expression pathways, genomic alterations and correlated with clinical data, then applied to The Cancer Genome Atlas data set. RESULTS We studied 164 specimens, including 52 castration-resistant and 13 paired primary/metastatic specimens. cNMF identified four distinct subtypes. NMF1 (19%) is enriched for immune-related and stromal-related pathways with transforming growth factor β (TGFβ) signature. NMF2 (36%) is associated with FOXO-mediated transcription signature and AKT signaling, NMF3 (26%) is enriched for ribosomal RNA processing, while NMF4 (19%) is enriched for cell cycle and DNA-repair pathways. The most common gene alterations included TMPRSS22 (42%), TP53 (23%), and DNA-repair genes (19%), occurring across all subtypes. NMF4 is significantly enriched for MYC and Wnt-signaling gene alterations. TMB, CD8 density, and PD-L1 expression were low overall. NMF1 and NMF4 were NMF2 was associated with superior overall survival. CONCLUSIONS Using cNMF, we identified four molecularly distinct subtypes which may inform treatment selection. NMF1 demonstrates the most inflammatory signature with asuppressive TGFβ signature, suggesting potential benefit with immunotherapy combination strategies targeting TGFβ and PD-(L)1. Prospective studies are required to evaluate the use of this novel model to molecularly stratify patients for optimal treatment selection.
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Affiliation(s)
- Kobe C. Yuen
- Department of Oncology Biomarker DevelopmentGenentech, Inc.South San FranciscoCaliforniaUSA
| | - Ben Tran
- Sir Peter MacCallum Department of OncologyThe University of MelbourneMelbourneVictoriaAustralia
- Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
| | - Angelyn Anton
- Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Eastern HealthMelbourneVictoriaAustralia
| | - Habib Hamidi
- Department of Oncology Biomarker DevelopmentGenentech, Inc.South San FranciscoCaliforniaUSA
| | - Anthony J. Costello
- Royal Melbourne HospitalMelbourneVictoriaAustralia
- Department of SurgeryThe University of MelbourneMelbourneVictoriaAustralia
- Australian Prostate CentreNorth MelbourneVictoriaAustralia
| | - Niall M. Corcoran
- Royal Melbourne HospitalMelbourneVictoriaAustralia
- Department of SurgeryThe University of MelbourneMelbourneVictoriaAustralia
| | - Nathan Lawrentschuk
- Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Royal Melbourne HospitalMelbourneVictoriaAustralia
- Department of SurgeryThe University of MelbourneMelbourneVictoriaAustralia
| | - Natalie Rainey
- Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
| | - Marie C. G. Semira
- Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
| | - Peter Gibbs
- Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
| | - Sanjeev Mariathasan
- Department of Oncology Biomarker DevelopmentGenentech, Inc.South San FranciscoCaliforniaUSA
| | - Shahneen Sandhu
- Sir Peter MacCallum Department of OncologyThe University of MelbourneMelbourneVictoriaAustralia
| | - Edward E. Kadel
- Department of Oncology Biomarker DevelopmentGenentech, Inc.South San FranciscoCaliforniaUSA
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11
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Hodgin JB, Mariani LH, Zee J, Liu Q, Smith AR, Eddy S, Hartman J, Hamidi H, Gaut JP, Palmer MB, Nast CC, Chang A, Hewitt S, Gillespie BW, Kretzler M, Holzman LB, Barisoni L. Quantification of Glomerular Structural Lesions: Associations With Clinical Outcomes and Transcriptomic Profiles in Nephrotic Syndrome. Am J Kidney Dis 2022; 79:807-819.e1. [PMID: 34864148 DOI: 10.1053/j.ajkd.2021.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 10/20/2021] [Indexed: 12/18/2022]
Abstract
RATIONALE & OBJECTIVE The current classification system for focal segmental glomerulosclerosis (FSGS) and minimal change disease (MCD) does not fully capture the complex structural changes in kidney biopsies nor the clinical and molecular heterogeneity of these diseases. STUDY DESIGN Prospective observational cohort study. SETTING & PARTICIPANTS 221 MCD and FSGS patients enrolled in the Nephrotic Syndrome Study Network (NEPTUNE). EXPOSURE The NEPTUNE Digital Pathology Scoring System (NDPSS) was applied to generate scores for 37 glomerular descriptors. OUTCOME Time from biopsy to complete proteinuria remission, time from biopsy to kidney disease progression (40% estimated glomerular filtration rate [eGFR] decline or kidney failure), and eGFR over time. ANALYTICAL APPROACH Cluster analysis was used to group patients with similar morphologic characteristics. Glomerular descriptors and patient clusters were assessed for associations with outcomes using adjusted Cox models and linear mixed models. Messenger RNA from glomerular tissue was used to assess differentially expressed genes between clusters and identify genes associated with individual descriptors driving cluster membership. RESULTS Three clusters were identified: X (n = 56), Y (n = 68), and Z (n = 97). Clusters Y and Z had higher probabilities of proteinuria remission (HRs of 1.95 [95% CI, 0.99-3.85] and 3.29 [95% CI, 1.52-7.13], respectively), lower hazards of disease progression (HRs of 0.22 [95% CI, 0.08-0.57] and 0.11 [95% CI, 0.03-0.45], respectively), and lower loss of eGFR over time compared with X. Cluster X had 1,920 genes that were differentially expressed compared with Y+Z; these reflected activation of pathways of immune response and inflammation. Six descriptors driving the clusters individually correlated with clinical outcomes and gene expression. LIMITATIONS Low prevalence of some descriptors and biopsy at a single time point. CONCLUSIONS The NDPSS allows for categorization of FSGS/MCD patients into clinically and biologically relevant subgroups, and uncovers histologic parameters associated with clinical outcomes and molecular signatures not included in current classification systems.
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Affiliation(s)
- Jeffrey B Hodgin
- Renal Pathology, Department of Pathology, University of Michigan, Ann Arbor, Michigan.
| | - Laura H Mariani
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Jarcy Zee
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania; Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Qian Liu
- Arbor Research Collaborative for Health, Ann Arbor, Michigan, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Abigail R Smith
- Arbor Research Collaborative for Health, Ann Arbor, Michigan, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sean Eddy
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - John Hartman
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Habib Hamidi
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Joseph P Gaut
- Department of Pathology and Immunology, and Internal Medicine, Washington University, St. Louis, Missouri
| | - Matthew B Palmer
- Department of Pathology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Cynthia C Nast
- Department of Pathology, Cedars-Sinai Medical Center, Los Angeles, California
| | - Anthony Chang
- Department of Pathology, University of Chicago Medicine, Chicago, Illinois
| | - Stephen Hewitt
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Brenda W Gillespie
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan
| | - Matthias Kretzler
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Lawrence B Holzman
- Renal-Electrolyte and Hypertension Division, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Laura Barisoni
- Department of Pathology, Division of AI & Computational Pathology, Duke University, Durham, North Carolina; Department of Medicine, Division of Nephrology, Duke University, Durham, North Carolina.
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12
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Motzer RJ, Powles T, Atkins MB, Escudier B, McDermott DF, Alekseev BY, Lee JL, Suarez C, Stroyakovskiy D, De Giorgi U, Donskov F, Mellado B, Banchereau R, Hamidi H, Khan O, Craine V, Huseni M, Flinn N, Dubey S, Rini BI. Final Overall Survival and Molecular Analysis in IMmotion151, a Phase 3 Trial Comparing Atezolizumab Plus Bevacizumab vs Sunitinib in Patients With Previously Untreated Metastatic Renal Cell Carcinoma. JAMA Oncol 2022; 8:275-280. [PMID: 34940781 PMCID: PMC8855230 DOI: 10.1001/jamaoncol.2021.5981] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
IMPORTANCE Interim analyses of the IMmotion151 trial (A Study of Atezolizumab in Combination With Bevacizumab Versus Sunitinib in Participants With Untreated Advanced Renal Cell Carcinoma) reported improved progression-free survival (PFS) for patients with programmed death ligand 1-positive (PD-L1+) metastatic renal cell carcinoma (mRCC) receiving the PD-L1 inhibitor atezolizumab plus the vascular endothelial growth factor (VEGF) inhibitor bevacizumab vs the receptor tyrosine kinase inhibitor sunitinib. Overall survival (OS) results were immature at interim analyses. OBJECTIVE To report the final OS results, safety, and exploratory biomarker analyses of the association of transcriptomic subgroups with OS in the IMmotion151 trial. DESIGN, SETTING, AND PARTICIPANTS IMmotion151 was a multicenter, open-label, phase 3 randomized clinical trial that compared the efficacy and safety of atezolizumab plus bevacizumab vs sunitinib in patients with untreated mRCC. IMmotion151 included patients from 152 academic medical centers and community oncology practices in 21 countries. Adult patients with mRCC with components of clear cell or sarcomatoid histologic features, measurable disease (according to Response Evaluation Criteria in Solid Tumors, version 1.1), adequate performance status, hematologic and end organ function, and tumor tissue available for PD-L1 testing were included. IMmotion151 was initiated on May 20, 2015, and the study is ongoing. This final analysis was performed from May 20, 2015, to February 14, 2020. INTERVENTIONS Receipt of 1200 mg of intravenous (IV) atezolizumab every 3 weeks and 15 mg/kg of IV bevacizumab every 3 weeks or 50 mg orally once daily of sunitinib (4 weeks on and 2 weeks off). MAIN OUTCOMES AND MEASURES The coprimary end points were PFS (previously reported) in patients with PD-L1+ disease and OS in the intention-to-treat population. Additional exploratory outcomes included OS in the PD-L1+ population, association with transcriptomic subgroups, and safety. RESULTS The IMmotion151 trial assessed 915 patients with metastatic renal cell carcinoma. Mean (IQR) age was 62 (56-69) years for patients receiving atezolizumab plus bevacizumab and 60 (54-66) years for patients receiving sunitinib; 669 (73.1%) were male and 246 (26.9%) were female. The final analysis showed similar median OS in patients receiving atezolizumab plus bevacizumab vs sunitinib in the intention-to-treat (36.1 vs 35.3 months) and PD-L1+ (38.7 vs 31.6 months) populations. No new safety signals were reported. The additional exploratory outcome of atezolizumab plus bevacizumab vs sunitinib showed improved median OS trends in patients whose tumors were characterized by T-effector/proliferative, proliferative, or small nucleolar RNA transcriptomic profiles (35.4 vs 21.2 months; hazard ratio, 0.70; 95% CI, 0.50-0.98). CONCLUSIONS AND RELEVANCE The primary end point of PFS was met at interim analyses, although no improvement in OS was observed with atezolizumab plus bevacizumab at the final analysis. Biomarker analyses provided insight into which patients with mRCC may benefit from combined anti-PD-L1 and anti-VEGF therapy. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT02420821.
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Affiliation(s)
| | - Thomas Powles
- Barts Cancer Institute and the Royal Free Hospital, Queen Mary University of London, London, UK
| | | | - Bernard Escudier
- Department of Medical Oncology, Vall d’Hebron Institute of Oncology, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - David F. McDermott
- Biologic Therapy and Cutaneous Oncology Programs, Hematology/Oncology, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | | | - Jae-Lyun Lee
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Cristina Suarez
- Vall d’Hebron University Hospital and Institute of Oncology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Ugo De Giorgi
- IRCCS Istituto Romagnolo per lo Studio dei Tumori Dino Amadori, Meldola, Italy
| | - Frede Donskov
- Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Begoña Mellado
- Hospital Clínic of Barcelona, Medical Oncology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
| | | | | | - Omara Khan
- F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | | | | | - Nick Flinn
- F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | | | - Brian I. Rini
- Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
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13
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Panayiotidis P, Tumyan G, Thieblemont C, Ptushkin VV, Marin-Niebla A, García-Sanz R, Le Gouill S, Stathis A, Bottos A, Hamidi H, Katz P, Perretti T, Willis JC, Buske C. A phase-II study of atezolizumab in combination with obinutuzumab or rituximab for relapsed or refractory mantle cell or marginal zone lymphoma or Waldenström's macroglobulinemia. Leuk Lymphoma 2022; 63:1058-1069. [PMID: 35045765 DOI: 10.1080/10428194.2021.2015765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
We report efficacy, safety and biomarker data from a phase-II study evaluating atezolizumab (eight 21-day cycle as induction therapy) in combination with obinutuzumab in patients with relapsed/refractory mantle cell lymphoma (MCL, n = 30) or Waldenström's macroglobulinemia (WM, n = 4), and in combination with rituximab in patients with marginal zone lymphoma (MZL, n = 21). All patients received atezolizumab monotherapy as maintenance for ≤10 cycles. Objective response rates at end of induction were 16.7% (MCL) and 42.9% (MZL), with no responses in WM. Median duration of response was 6.8 months (range 5.7-not estimable) for MCL and not reached for MZL. Treatment-emergent adverse events (TEAEs) occurred in 93.3%, 95.2% and 100% of MCL, MZL and WM patients, respectively. One fatal TEAE (pneumonia) occurred in each of the MCL and MZL groups. Biomarker analysis highlighted the importance of characterizing the immune environment to optimize efficacy of immunotherapy regimens.Trial registration details: EudraCT: 2016-003579-22.
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Affiliation(s)
| | - Gayane Tumyan
- N.N. Blokhin Russian Cancer Research Centre, Moscow, Russian Federation
| | | | - Vadim V Ptushkin
- City Clinical Hospital Named After S.P. Botkin, Moscow, Russian Federation
| | | | - Ramon García-Sanz
- Hospital Universitario de Salamanca (HUSA/IBSAL/CIBERONC), Salamanca, Spain
| | - Steven Le Gouill
- Service d'Hématologie Clinique du CHU de Nantes, INSERM CRCINA Nantes-Angers, NeXT Université de Nantes, Nantes, France
| | - Anastasios Stathis
- Oncology Institute of Southern Switzerland, EOC, Bellinzona, Switzerland, and Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
| | | | | | - Pablo Katz
- F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | | | | | - Christian Buske
- CCC Ulm, Institute of Experimental Cancer Research, University Hospital Ulm, Ulm, Germany
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14
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Rini BI, Atkins MB, Escudier B, Powles T, McDermott DF, Alekseev BY, Lee JL, Stroyakovskiy D, Rodriguez CS, De Giorgi U, Donskov F, Mellado B, Banchereau R, Hamidi H, Khan O, Craine V, Huseni M, Flinn N, Dubey S, Motzer R. Abstract CT188: IMmotion151: updated overall survival (OS) and exploratory analysis of the association of gene expression and clinical outcomes with atezolizumab plus bevacizumab vs sunitinib in patients with locally advanced or metastatic renal cell carcinoma (mRCC). Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-ct188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: In IMmotion151 (NCT02420821), atezo (anti-PD-L1) + bev (anti-VEGF) improved PFS vs sun as 1L treatment in patients (pts) with mRCC (Rini, Lancet 2019). Gene expression analyses of baseline tumor tissue revealed 7 distinct transcriptomic clusters associated with objective response rate and PFS (Motzer, Cancer Cell 2020). Final OS, safety and association of transcriptome subsets with OS are presented.
Methods: Treatment-naive pts across prognostic risk groups were randomized 1:1 to receive atezo 1200 mg IV + bev 15 mg/kg IV q3w or sun 50 mg PO QD 4 wk on/2 wk off. Co-primary endpoints were PFS by investigator per RECIST 1.1 in PD-L1+ (≥ 1% IC) pts and OS in ITT pts. Secondary endpoints included OS in PD-L1+ pts and safety. Exploratory endpoints included biomarker analyses.
Results: In the final analysis (minimum follow-up 40 mo) with a 55% (504/915) OS event rate, atezo + bev did not show an OS benefit vs sun (Table). Treatment-related AEs (TRAEs) were observed in 92% (415/451) and 96% (430/446) of ITT pts in the atezo + bev and sun arms, and Grade 3-4 TRAEs were observed in 46% (205/451) and 56% (250/446), respectively. In exploratory biomarker analyses, sun showed an improved OS trend in tumors characterized by an angiogenic transcription profile, and atezo + bev showed improved OS trend in tumors characterized by T-effector/proliferative, proliferative or small nucleolar RNA transcription profiles (Table). When the latter 3 groups were combined, atezo + bev resulted in better OS than sun (HR, 0.70; 95% CI: 0.50, 0.98).
Conclusions: Overall, in this final analysis, no OS improvement with atezo + bev vs sun was seen. The safety of atezo + bev was consistent with the known safety profile of each component. Biomarker studies generated hypotheses for which pt subgroups are most likely to benefit from combined anti-VEGF + anti-PD-L1 therapy.
PopulationCluster transcription profileHR (95% CI)P valueMedian OS (atezo + bev)Median OS (sun)ITT (n=915)NA0.91 (0.76, 1.08)a0.27b36.135.3PD-L1+ (n=362)NA0.85 (0.64, 1.13)a0.2638.731.6Cluster 1 (n=98)Angiogenic/stromal0.94 (0.52, 1.72)_NR48.2Cluster 2 (n=245)Angiogenic1.32 (0.91, 1.91)_46.2NRCluster 3 (n=156)Complement/Ω-oxidative0.99 (0.64, 1.54)_35.036.6Cluster 4 (n=116)T-effector/proliferative0.66 (0.41, 1.06)_38.723.3Cluster 5 (n=74)Proliferative0.66 (0.39, 1.12)_21.715.5Cluster 6 (n=106)Stromal/proliferative0.90 (0.57, 1.40)_15.912.7Cluster 7 (n=28)snoRNANC_NR42.1Gene expression clusters 4 (T-effector/proliferative) + 5 (proliferative) + 7 (snoRNA) (n=218)_0.70 (0.50, 0.98)_35.421.2aPts were stratified by MSKCC Risk Score (good vs intermediate vs poor), liver metastases (yes vs no) and PD-L1 IHC status (< 1% vs ≥ 1% PD-L1 expression on IC; SP142 IHC assay).bThe pre-specified α boundary was 0.0203.atezo, atezolizumab; bev, bevacizumab; HR, hazard ratio; IC, tumor-infiltrating immune cells; IHC, immunohistochemistry; ITT, intention to treat; MSKCC, Memorial Sloan Kettering Cancer Center; NA, not applicable; NC, not calculated; NR, not reported; OS, overall survival; PD-L1, programmed death-ligand 1; PFS, progression free survival; snoRNA, small nucleolar RNA; sun, sunitinib.
Citation Format: Brian I. Rini, Michael B. Atkins, Bernard Escudier, Thomas Powles, David F. McDermott, Boris Y. Alekseev, Jae-Lyun Lee, Daniil Stroyakovskiy, Cristina Suarez Rodriguez, Ugo De Giorgi, Frede Donskov, Begoña Mellado, Romain Banchereau, Habib Hamidi, Omara Khan, Veronica Craine, Mahrukh Huseni, Nick Flinn, Sarita Dubey, Robert Motzer. IMmotion151: updated overall survival (OS) and exploratory analysis of the association of gene expression and clinical outcomes with atezolizumab plus bevacizumab vs sunitinib in patients with locally advanced or metastatic renal cell carcinoma (mRCC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr CT188.
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Affiliation(s)
| | | | | | - Thomas Powles
- 4Barts Cancer Institute and the Royal Free Hospital, Queen Mary University of London, London, United Kingdom
| | | | | | - Jae-Lyun Lee
- 7Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | | | - Cristina Suarez Rodriguez
- 9Vall d'Hebron University Hospital and Institute of Oncology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ugo De Giorgi
- 10Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST), IRCCS, Meldola, Italy
| | - Frede Donskov
- 11Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Begoña Mellado
- 12Hospital Clínic of Barcelona, Medical Oncology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
| | | | | | - Omara Khan
- 14F. Hoffmann-La Roche, Ltd, Basel, Switzerland
| | | | | | - Nick Flinn
- 14F. Hoffmann-La Roche, Ltd, Basel, Switzerland
| | | | - Robert Motzer
- 15Memorial Sloan Kettering Cancer Center, New York, NY
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15
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El-Achkar TM, Eadon MT, Menon R, Lake BB, Sigdel TK, Alexandrov T, Parikh S, Zhang G, Dobi D, Dunn KW, Otto EA, Anderton CR, Carson JM, Luo J, Park C, Hamidi H, Zhou J, Hoover P, Schroeder A, Joanes M, Azeloglu EU, Sealfon R, Winfree S, Steck B, He Y, D’Agati V, Iyengar R, Troyanskaya OG, Barisoni L, Gaut J, Zhang K, Laszik Z, Rovin BH, Dagher PC, Sharma K, Sarwal MM, Hodgin JB, Alpers CE, Kretzler M, Jain S. A multimodal and integrated approach to interrogate human kidney biopsies with rigor and reproducibility: guidelines from the Kidney Precision Medicine Project. Physiol Genomics 2021; 53:1-11. [PMID: 33197228 PMCID: PMC7847045 DOI: 10.1152/physiolgenomics.00104.2020] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Comprehensive and spatially mapped molecular atlases of organs at a cellular level are a critical resource to gain insights into pathogenic mechanisms and personalized therapies for diseases. The Kidney Precision Medicine Project (KPMP) is an endeavor to generate three-dimensional (3-D) molecular atlases of healthy and diseased kidney biopsies by using multiple state-of-the-art omics and imaging technologies across several institutions. Obtaining rigorous and reproducible results from disparate methods and at different sites to interrogate biomolecules at a single-cell level or in 3-D space is a significant challenge that can be a futile exercise if not well controlled. We describe a "follow the tissue" pipeline for generating a reliable and authentic single-cell/region 3-D molecular atlas of human adult kidney. Our approach emphasizes quality assurance, quality control, validation, and harmonization across different omics and imaging technologies from sample procurement, processing, storage, shipping to data generation, analysis, and sharing. We established benchmarks for quality control, rigor, reproducibility, and feasibility across multiple technologies through a pilot experiment using common source tissue that was processed and analyzed at different institutions and different technologies. A peer review system was established to critically review quality control measures and the reproducibility of data generated by each technology before their being approved to interrogate clinical biopsy specimens. The process established economizes the use of valuable biopsy tissue for multiomics and imaging analysis with stringent quality control to ensure rigor and reproducibility of results and serves as a model for precision medicine projects across laboratories, institutions and consortia.
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Affiliation(s)
| | | | - Rajasree Menon
- 2University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Blue B. Lake
- 3Jacobs School of Engineering, University of California, San Diego, California
| | - Tara K. Sigdel
- 4University of California San Francisco School of Medicine, San Francisco, California
| | | | - Samir Parikh
- 6Ohio State University College of Medicine, Columbus, Ohio
| | - Guanshi Zhang
- 7UT-Health San Antonio School of Medicine, San Antonio, Texas
| | - Dejan Dobi
- 4University of California San Francisco School of Medicine, San Francisco, California
| | - Kenneth W. Dunn
- 1Indiana University School of Medicine, Indianapolis, Indiana
| | - Edgar A. Otto
- 2University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Christopher R. Anderton
- 7UT-Health San Antonio School of Medicine, San Antonio, Texas,8Pacific Northwest National Laboratory, Richland, Washington
| | - Jonas M. Carson
- 9Schools of Medicine and Public Health, University of Washington, Seattle, Washington
| | - Jinghui Luo
- 2University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Chris Park
- 9Schools of Medicine and Public Health, University of Washington, Seattle, Washington
| | - Habib Hamidi
- 2University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Jian Zhou
- 12Princeton University, Princeton, New Jersey,14Columbia University School of Medicine, New York City, New York
| | - Paul Hoover
- 10Harvard University School of Medicine, Boston Massachusetts
| | - Andrew Schroeder
- 4University of California San Francisco School of Medicine, San Francisco, California
| | - Marianinha Joanes
- 4University of California San Francisco School of Medicine, San Francisco, California
| | | | - Rachel Sealfon
- 12Princeton University, Princeton, New Jersey,14Columbia University School of Medicine, New York City, New York
| | - Seth Winfree
- 1Indiana University School of Medicine, Indianapolis, Indiana
| | - Becky Steck
- 2University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Yongqun He
- 2University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Vivette D’Agati
- 14Columbia University School of Medicine, New York City, New York
| | - Ravi Iyengar
- 11Icahn School of Medicine at Mount Sinai, New York City, New York
| | - Olga G. Troyanskaya
- 12Princeton University, Princeton, New Jersey,14Columbia University School of Medicine, New York City, New York
| | - Laura Barisoni
- 15Duke University School of Medicine, Durham, North Carolina
| | - Joseph Gaut
- 16Washington University in Saint Louis School of Medicine, St. Louis, Missouri
| | - Kun Zhang
- 3Jacobs School of Engineering, University of California, San Diego, California
| | - Zoltan Laszik
- 4University of California San Francisco School of Medicine, San Francisco, California
| | - Brad H. Rovin
- 6Ohio State University College of Medicine, Columbus, Ohio
| | | | - Kumar Sharma
- 7UT-Health San Antonio School of Medicine, San Antonio, Texas
| | - Minnie M. Sarwal
- 4University of California San Francisco School of Medicine, San Francisco, California
| | | | - Charles E. Alpers
- 9Schools of Medicine and Public Health, University of Washington, Seattle, Washington
| | | | - Sanjay Jain
- 16Washington University in Saint Louis School of Medicine, St. Louis, Missouri
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16
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Motzer RJ, Banchereau R, Hamidi H, Powles T, McDermott D, Atkins MB, Escudier B, Liu LF, Leng N, Abbas AR, Fan J, Koeppen H, Lin J, Carroll S, Hashimoto K, Mariathasan S, Green M, Tayama D, Hegde PS, Schiff C, Huseni MA, Rini B. Molecular Subsets in Renal Cancer Determine Outcome to Checkpoint and Angiogenesis Blockade. Cancer Cell 2020; 38:803-817.e4. [PMID: 33157048 PMCID: PMC8436590 DOI: 10.1016/j.ccell.2020.10.011] [Citation(s) in RCA: 230] [Impact Index Per Article: 57.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 08/21/2020] [Accepted: 10/07/2020] [Indexed: 12/28/2022]
Abstract
Integrated multi-omics evaluation of 823 tumors from advanced renal cell carcinoma (RCC) patients identifies molecular subsets associated with differential clinical outcomes to angiogenesis blockade alone or with a checkpoint inhibitor. Unsupervised transcriptomic analysis reveals seven molecular subsets with distinct angiogenesis, immune, cell-cycle, metabolism, and stromal programs. While sunitinib and atezolizumab + bevacizumab are effective in subsets with high angiogenesis, atezolizumab + bevacizumab improves clinical benefit in tumors with high T-effector and/or cell-cycle transcription. Somatic mutations in PBRM1 and KDM5C associate with high angiogenesis and AMPK/fatty acid oxidation gene expression, while CDKN2A/B and TP53 alterations associate with increased cell-cycle and anabolic metabolism. Sarcomatoid tumors exhibit lower prevalence of PBRM1 mutations and angiogenesis markers, frequent CDKN2A/B alterations, and increased PD-L1 expression. These findings can be applied to molecularly stratify patients, explain improved outcomes of sarcomatoid tumors to checkpoint blockade versus antiangiogenics alone, and develop personalized therapies in RCC and other indications.
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MESH Headings
- Angiogenesis Inhibitors/pharmacology
- Angiogenesis Inhibitors/therapeutic use
- Antibodies, Monoclonal, Humanized/pharmacology
- Antibodies, Monoclonal, Humanized/therapeutic use
- Antineoplastic Combined Chemotherapy Protocols/pharmacology
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Bevacizumab/pharmacology
- Bevacizumab/therapeutic use
- Biomarkers, Tumor/genetics
- Carcinoma, Renal Cell/drug therapy
- Carcinoma, Renal Cell/genetics
- Clinical Trials, Phase III as Topic
- Computational Biology/methods
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic/drug effects
- Humans
- Immune Checkpoint Inhibitors/pharmacology
- Immune Checkpoint Inhibitors/therapeutic use
- Kidney Neoplasms/drug therapy
- Kidney Neoplasms/genetics
- Prognosis
- Randomized Controlled Trials as Topic
- Sequence Analysis, RNA
- Sunitinib/pharmacology
- Sunitinib/therapeutic use
- Treatment Outcome
- Unsupervised Machine Learning
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Affiliation(s)
- Robert J Motzer
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Romain Banchereau
- Oncology Biomarker Development, Genentech, Inc, South San Francisco, CA 94080, USA
| | - Habib Hamidi
- Oncology Biomarker Development, Genentech, Inc, South San Francisco, CA 94080, USA
| | - Thomas Powles
- Barts Cancer Institute and the Royal Free Hospital, Queen Mary University of London, London, UK
| | | | - Michael B Atkins
- Georgetown Lombardi Comprehensive Cancer Center, Washington, DC, USA
| | | | - Li-Fen Liu
- Oncology Biomarker Development, Genentech, Inc, South San Francisco, CA 94080, USA
| | - Ning Leng
- Oncology Biomarker Development, Genentech, Inc, South San Francisco, CA 94080, USA
| | - Alexander R Abbas
- Oncology Biomarker Development, Genentech, Inc, South San Francisco, CA 94080, USA
| | - Jinzhen Fan
- Oncology Biomarker Development, Genentech, Inc, South San Francisco, CA 94080, USA
| | - Hartmut Koeppen
- Oncology Biomarker Development, Genentech, Inc, South San Francisco, CA 94080, USA
| | - Jennifer Lin
- Oncology Biomarker Development, Genentech, Inc, South San Francisco, CA 94080, USA
| | | | | | - Sanjeev Mariathasan
- Oncology Biomarker Development, Genentech, Inc, South San Francisco, CA 94080, USA
| | - Marjorie Green
- Oncology Biomarker Development, Genentech, Inc, South San Francisco, CA 94080, USA
| | - Darren Tayama
- Oncology Biomarker Development, Genentech, Inc, South San Francisco, CA 94080, USA
| | | | - Christina Schiff
- Oncology Biomarker Development, Genentech, Inc, South San Francisco, CA 94080, USA
| | - Mahrukh A Huseni
- Oncology Biomarker Development, Genentech, Inc, South San Francisco, CA 94080, USA.
| | - Brian Rini
- Vanderbilt University Medical Center, Nashville, TN, USA
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17
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Abstract
The kidney is a complex organ responsible for maintaining multiple aspects of homeostasis in the human body. The combination of distinct, yet interrelated, molecular functions across different cell types make the delineation of factors associated with loss or decline in kidney function challenging. Consequently, there has been a paucity of new diagnostic markers and treatment options becoming available to clinicians and patients in managing kidney diseases. A systems biology approach to understanding the kidney leverages recent advances in computational technology and methods to integrate diverse sets of data. It has the potential to unravel the interplay of multiple genes, proteins, and molecular mechanisms that drive key functions in kidney health and disease. The emergence of large, detailed, multilevel biologic and clinical data from national databases, cohort studies, and trials now provide the critical pieces needed for meaningful application of systems biology approaches in nephrology. The purpose of this review is to provide an overview of the current state in the evolution of the field. Recent successes of systems biology to identify targeted therapies linked to mechanistic biomarkers in the kidney are described to emphasize the relevance to clinical care and the outlook for improving outcomes for patients with kidney diseases.
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Affiliation(s)
- Jennifer A Schaub
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Habib Hamidi
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Lalita Subramanian
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Matthias Kretzler
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
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18
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Mulder S, Hamidi H, Kretzler M, Ju W. An integrative systems biology approach for precision medicine in diabetic kidney disease. Diabetes Obes Metab 2018; 20 Suppl 3:6-13. [PMID: 30294956 PMCID: PMC6541014 DOI: 10.1111/dom.13416] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 06/08/2018] [Indexed: 12/12/2022]
Abstract
Current therapeutic approaches are ineffective in many patients with established diabetic kidney disease (DKD), an epidemic affecting one in three patients with diabetes. Early identification of patients at high risk for progression and individualizing therapies have the potential to mitigate kidney complications due to diabetes. To achieve this, a better understanding of the complex pathophysiology of DKD is needed. A system biology approach integrating large-scale omic data is well suited to unravel the molecular mechanisms driving DKD and may offer new perspectives how to personalize therapy. Recent studies indeed show that integrating genome scale data sets generated from prospectively designed clinical cohort studies with model systems using innovative bioinformatics analysis revealed critical molecular pathways in DKD and led to the development of candidate prognostic molecular biomarkers. This review seeks to provide an overview of the recent progress in the application of the integrative systems biology approaches specifically in the field of molecular biomarkers for DKD. We will mainly focus the discussion on how to use integrative system biology approach to first identify patients at high risk of progression, and second to identify patients who may or may not respond to treatment. Challenges and opportunities in applying precision medicine in DKD will also be discussed.
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Affiliation(s)
- Skander Mulder
- University Medical Center Groningen, Groningen, Netherlands
| | - Habib Hamidi
- University of Michigan, Ann Arbor, MI, United States
| | | | - Wenjun Ju
- University of Michigan, Ann Arbor, MI, United States
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19
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Winterhoff B, Hamidi H, Wang C, Kalli KR, Fridley BL, Dering J, Chen HW, Cliby WA, Wang HJ, Dowdy S, Gostout BS, Keeney GL, Goode EL, Konecny GE. Molecular classification of high grade endometrioid and clear cell ovarian cancer using TCGA gene expression signatures. Gynecol Oncol 2016; 141:95-100. [PMID: 27016234 PMCID: PMC5616158 DOI: 10.1016/j.ygyno.2016.02.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 01/15/2016] [Accepted: 02/21/2016] [Indexed: 01/01/2023]
Abstract
BACKGROUND It is unclear whether the transcriptional subtypes of high grade serous ovarian cancer (HGSOC) apply to high grade clear cell (HGCCOC) or high grade endometrioid ovarian cancer (HGEOC). We aim to delineate transcriptional profiles of HGCCOCs and HGEOCs. METHODS We used Agilent microarrays to determine gene expression profiles of 276 well annotated ovarian cancers (OCs) including 37 HGCCOCs and 66 HGEOCs. We excluded low grade OCs as these are known to be distinct molecular entities. We applied the prespecified TCGA and CLOVAR gene signatures using consensus non-negative matrix factorization (NMF). RESULTS We confirm the presence of four TCGA transcriptional subtypes and their significant prognostic relevance (p<0.001) across all three histological subtypes (HGSOC, HGCCOC and HGEOCs). However, we also demonstrate that 22/37 (59%) HGCCOCs and 30/67 (45%) HGEOCs form 2 additional separate clusters with distinct gene signatures. Importantly, of the HGCCOC and HGEOCs that clustered separately 62% and 65% were early stage (FIGO I/II), respectively. These finding were confirmed using the reduced CLOVAR gene set for classification where most early stage HGCCOCs and HGEOCs formed a distinct cluster of their own. When restricting the analysis to the four TCGA signatures (ssGSEA or NMF with CLOVAR genes) most early stage HGCCOCs and HGEOC were assigned to the differentiated subtype. CONCLUSIONS Using transcriptional profiling the current study suggests that HGCCOCs and HGEOCs of advanced stage group together with HGSOCs. However, HGCCOCs and HGEOCs of early disease stages may have distinct transcriptional signatures similar to those seen in their low grade counterparts.
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Affiliation(s)
- Boris Winterhoff
- Department of Obstetrics/Gynecology & Women's Health, University of Minnesota, Minneapolis, MN, United States
| | - Habib Hamidi
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | - Chen Wang
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, United States
| | - Kimberly R Kalli
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, United States
| | - Brooke L Fridley
- Department of Biostatistics, University of Kansas, Kansas City, KS, United States
| | - Judy Dering
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | - Hsiao-Wang Chen
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | - William A Cliby
- Department of Gynecologic Surgery, Mayo Clinic, Rochester, MN, United States
| | - He-Jing Wang
- Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | - Sean Dowdy
- Department of Gynecologic Surgery, Mayo Clinic, Rochester, MN, United States
| | - Bobbie S Gostout
- Department of Gynecologic Surgery, Mayo Clinic, Rochester, MN, United States
| | - Gary L Keeney
- Department of Gynecologic Surgery, Mayo Clinic, Rochester, MN, United States
| | - Ellen L Goode
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, United States
| | - Gottfried E Konecny
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States.
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20
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He Y, Wu AC, Harrington BS, Davies CM, Wallace SJ, Adams MN, Palmer JS, Roche DK, Hollier BG, Westbrook TF, Hamidi H, Konecny GE, Winterhoff B, Chetty NP, Crandon AJ, Oliveira NB, Shannon CM, Tinker AV, Gilks CB, Coward JI, Lumley JW, Perrin LC, Armes JE, Hooper JD. Elevated CDCP1 predicts poor patient outcome and mediates ovarian clear cell carcinoma by promoting tumor spheroid formation, cell migration and chemoresistance. Oncogene 2015; 35:468-78. [PMID: 25893298 DOI: 10.1038/onc.2015.101] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 01/27/2015] [Accepted: 02/16/2015] [Indexed: 01/25/2023]
Abstract
Hematogenous metastases are rarely present at diagnosis of ovarian clear cell carcinoma (OCC). Instead dissemination of these tumors is characteristically via direct extension of the primary tumor into nearby organs and the spread of exfoliated tumor cells throughout the peritoneum, initially via the peritoneal fluid, and later via ascites that accumulates as a result of disruption of the lymphatic system. The molecular mechanisms orchestrating these processes are uncertain. In particular, the signaling pathways used by malignant cells to survive the stresses of anchorage-free growth in peritoneal fluid and ascites, and to colonize remote sites, are poorly defined. We demonstrate that the transmembrane glycoprotein CUB-domain-containing protein 1 (CDCP1) has important and inhibitable roles in these processes. In vitro assays indicate that CDCP1 mediates formation and survival of OCC spheroids, as well as cell migration and chemoresistance. Disruption of CDCP1 via silencing and antibody-mediated inhibition markedly reduce the ability of TOV21G OCC cells to form intraperitoneal tumors and induce accumulation of ascites in mice. Mechanistically our data suggest that CDCP1 effects are mediated via a novel mechanism of protein kinase B (Akt) activation. Immunohistochemical analysis also suggested that CDCP1 is functionally important in OCC, with its expression elevated in 90% of 198 OCC tumors and increased CDCP1 expression correlating with poor patient disease-free and overall survival. This analysis also showed that CDCP1 is largely restricted to the surface of malignant cells where it is accessible to therapeutic antibodies. Importantly, antibody-mediated blockade of CDCP1 in vivo significantly increased the anti-tumor efficacy of carboplatin, the chemotherapy most commonly used to treat OCC. In summary, our data indicate that CDCP1 is important in the progression of OCC and that targeting pathways mediated by this protein may be useful for the management of OCC, potentially in combination with chemotherapies and agents targeting the Akt pathway.
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Affiliation(s)
- Y He
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - A C Wu
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - B S Harrington
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - C M Davies
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia.,Mater Health Services, South Brisbane, Queensland, Australia
| | - S J Wallace
- Mater Health Services, South Brisbane, Queensland, Australia
| | - M N Adams
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - J S Palmer
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - D K Roche
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - B G Hollier
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Queensland, Australia
| | - T F Westbrook
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - H Hamidi
- University of California, Los Angeles, CA, USA
| | - G E Konecny
- University of California, Los Angeles, CA, USA
| | | | - N P Chetty
- Mater Health Services, South Brisbane, Queensland, Australia
| | - A J Crandon
- Mater Health Services, South Brisbane, Queensland, Australia
| | - N B Oliveira
- Mater Health Services, South Brisbane, Queensland, Australia
| | - C M Shannon
- Mater Health Services, South Brisbane, Queensland, Australia
| | - A V Tinker
- Division of Medical Oncology, Vancouver Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.,Cheryl Brown Ovarian Cancer Outcomes Unit, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - C B Gilks
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - J I Coward
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia.,Mater Health Services, South Brisbane, Queensland, Australia
| | - J W Lumley
- Wesley Hospital, Auchenflower, Queensland, Australia
| | - L C Perrin
- Mater Health Services, South Brisbane, Queensland, Australia
| | - J E Armes
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia.,Mater Health Services, South Brisbane, Queensland, Australia
| | - J D Hooper
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
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21
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Drew BG, Hamidi H, Zhou Z, Villanueva CJ, Krum SA, Calkin AC, Parks BW, Ribas V, Kalajian NY, Phun J, Daraei P, Christofk HR, Hewitt SC, Korach KS, Tontonoz P, Lusis AJ, Slamon DJ, Hurvitz SA, Hevener AL. Estrogen receptor (ER)α-regulated lipocalin 2 expression in adipose tissue links obesity with breast cancer progression. J Biol Chem 2014; 290:5566-81. [PMID: 25468909 DOI: 10.1074/jbc.m114.606459] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Obesity is associated with increased breast cancer (BrCA) incidence. Considering that inactivation of estrogen receptor (ER)α promotes obesity and metabolic dysfunction in women and female mice, understanding the mechanisms and tissue-specific sites of ERα action to combat metabolic-related disease, including BrCA, is of clinical importance. To study the role of ERα in adipose tissue we generated fat-specific ERα knock-out (FERKO) mice. Herein we show that ERα deletion increased adipocyte size, fat pad weight, and tissue expression and circulating levels of the secreted glycoprotein, lipocalin 2 (Lcn2), an adipokine previously associated with BrCA development. Chromatin immunoprecipitation and luciferase reporter studies showed that ERα binds the Lcn2 promoter to repress its expression. Because adipocytes constitute an important cell type of the breast microenvironment, we examined the impact of adipocyte ERα deletion on cancer cell behavior. Conditioned medium from ERα-null adipocytes and medium containing pure Lcn2 increased proliferation and migration of a subset of BrCA cells in culture. The proliferative and promigratory effects of ERα-deficient adipocyte-conditioned medium on BrCA cells was reversed by Lcn2 deletion. BrCA cell responsiveness to exogenous Lcn2 was heightened in cell types where endogenous Lcn2 expression was minimal, but components of the Lcn2 signaling pathway were enriched, i.e. SLC22A17 and 3-hydroxybutyrate dehydrogenase (BDH2). In breast tumor biopsies from women diagnosed with BrCA we found that BDH2 expression was positively associated with adiposity and circulating Lcn2 levels. Collectively these data suggest that reduction of ERα expression in adipose tissue promotes adiposity and is linked with the progression and severity of BrCA via increased adipocyte-specific Lcn2 production and enhanced tumor cell Lcn2 sensitivity.
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Affiliation(s)
- Brian G Drew
- From the David Geffen School of Medicine, Department of Medicine, Division of Endocrinology, Diabetes and Hypertension
| | - Habib Hamidi
- Division of Hematology-Oncology, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, California 90095
| | - Zhenqi Zhou
- From the David Geffen School of Medicine, Department of Medicine, Division of Endocrinology, Diabetes and Hypertension
| | - Claudio J Villanueva
- the Department of Pathology and Laboratory Medicine, Howard Hughes Medical Institute, UCLA, Los Angeles, California 90095
| | - Susan A Krum
- the Orthopaedic Hospital Department of Orthopaedic Surgery and the Orthopaedic Hospital Research Center, UCLA, Los Angeles, California 90095
| | - Anna C Calkin
- the Department of Pathology and Laboratory Medicine, Howard Hughes Medical Institute, UCLA, Los Angeles, California 90095
| | | | - Vicent Ribas
- From the David Geffen School of Medicine, Department of Medicine, Division of Endocrinology, Diabetes and Hypertension
| | - Nareg Y Kalajian
- From the David Geffen School of Medicine, Department of Medicine, Division of Endocrinology, Diabetes and Hypertension
| | - Jennifer Phun
- From the David Geffen School of Medicine, Department of Medicine, Division of Endocrinology, Diabetes and Hypertension
| | - Pedram Daraei
- From the David Geffen School of Medicine, Department of Medicine, Division of Endocrinology, Diabetes and Hypertension
| | - Heather R Christofk
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, California 90095, Molecular and Medical Pharmacology, UCLA, Los Angeles, California 90095
| | - Sylvia C Hewitt
- the Receptor Biology Section, Reproductive and Developmental Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709, and
| | - Kenneth S Korach
- the Receptor Biology Section, Reproductive and Developmental Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709, and
| | - Peter Tontonoz
- the Department of Pathology and Laboratory Medicine, Howard Hughes Medical Institute, UCLA, Los Angeles, California 90095
| | | | - Dennis J Slamon
- Division of Hematology-Oncology, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, California 90095, the Translational Research in Oncology-US
| | - Sara A Hurvitz
- Division of Hematology-Oncology, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, California 90095, the Translational Research in Oncology-US
| | - Andrea L Hevener
- From the David Geffen School of Medicine, Department of Medicine, Division of Endocrinology, Diabetes and Hypertension, Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, California 90095, Iris Cantor-UCLA Women's Health Center, Los Angeles, California 90095
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22
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Konecny GE, Wang C, Hamidi H, Winterhoff B, Kalli KR, Dering J, Ginther C, Chen HW, Dowdy S, Cliby W, Gostout B, Podratz KC, Keeney G, Wang HJ, Hartmann LC, Slamon DJ, Goode EL. Prognostic and therapeutic relevance of molecular subtypes in high-grade serous ovarian cancer. J Natl Cancer Inst 2014. [PMID: 25269487 DOI: 10.1093/jnci/dju249]+[] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Molecular classification of high-grade serous ovarian cancer (HGSOC) using transcriptional profiling has proven to be complex and difficult to validate across studies. We determined gene expression profiles of 174 well-annotated HGSOCs and demonstrate prognostic significance of the prespecified TCGA Network gene signatures. Furthermore, we confirm the presence of four HGSOC transcriptional subtypes using a de novo classification. Survival differed statistically significantly between de novo subtypes (log rank, P = .006) and was the best for the immunoreactive-like subtype, but statistically significantly worse for the proliferative- or mesenchymal-like subtypes (adjusted hazard ratio = 1.89, 95% confidence interval = 1.18 to 3.02, P = .008, and adjusted hazard ratio = 2.45, 95% confidence interval = 1.43 to 4.18, P = .001, respectively). More prognostic information was provided by the de novo than the TCGA classification (Likelihood Ratio tests, P = .003 and P = .04, respectively). All statistical tests were two-sided. These findings were replicated in an external data set of 185 HGSOCs and confirm the presence of four prognostically relevant molecular subtypes that have the potential to guide therapy decisions.
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Affiliation(s)
- Gottfried E Konecny
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Chen Wang
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Habib Hamidi
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Boris Winterhoff
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Kimberly R Kalli
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Judy Dering
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Charles Ginther
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Hsiao-Wang Chen
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Sean Dowdy
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - William Cliby
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Bobbie Gostout
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Karl C Podratz
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Gary Keeney
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - He-Jing Wang
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Lynn C Hartmann
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Dennis J Slamon
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Ellen L Goode
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
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23
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Konecny GE, Wang C, Hamidi H, Winterhoff B, Kalli KR, Dering J, Ginther C, Chen HW, Dowdy S, Cliby W, Gostout B, Podratz KC, Keeney G, Wang HJ, Hartmann LC, Slamon DJ, Goode EL. Prognostic and therapeutic relevance of molecular subtypes in high-grade serous ovarian cancer. J Natl Cancer Inst 2014. [PMID: 25269487 DOI: 10.1093/jnci/dju249.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Molecular classification of high-grade serous ovarian cancer (HGSOC) using transcriptional profiling has proven to be complex and difficult to validate across studies. We determined gene expression profiles of 174 well-annotated HGSOCs and demonstrate prognostic significance of the prespecified TCGA Network gene signatures. Furthermore, we confirm the presence of four HGSOC transcriptional subtypes using a de novo classification. Survival differed statistically significantly between de novo subtypes (log rank, P = .006) and was the best for the immunoreactive-like subtype, but statistically significantly worse for the proliferative- or mesenchymal-like subtypes (adjusted hazard ratio = 1.89, 95% confidence interval = 1.18 to 3.02, P = .008, and adjusted hazard ratio = 2.45, 95% confidence interval = 1.43 to 4.18, P = .001, respectively). More prognostic information was provided by the de novo than the TCGA classification (Likelihood Ratio tests, P = .003 and P = .04, respectively). All statistical tests were two-sided. These findings were replicated in an external data set of 185 HGSOCs and confirm the presence of four prognostically relevant molecular subtypes that have the potential to guide therapy decisions.
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Affiliation(s)
- Gottfried E Konecny
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Chen Wang
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Habib Hamidi
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Boris Winterhoff
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Kimberly R Kalli
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Judy Dering
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Charles Ginther
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Hsiao-Wang Chen
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Sean Dowdy
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - William Cliby
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Bobbie Gostout
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Karl C Podratz
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Gary Keeney
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - He-Jing Wang
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Lynn C Hartmann
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Dennis J Slamon
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Ellen L Goode
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
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24
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Konecny GE, Wang C, Hamidi H, Winterhoff B, Kalli KR, Dering J, Ginther C, Chen HW, Dowdy S, Cliby W, Gostout B, Podratz KC, Keeney G, Wang HJ, Hartmann LC, Slamon DJ, Goode EL. Prognostic and therapeutic relevance of molecular subtypes in high-grade serous ovarian cancer. J Natl Cancer Inst 2014. [PMID: 25269487 DOI: 10.1093/jnci/dju249] [] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Molecular classification of high-grade serous ovarian cancer (HGSOC) using transcriptional profiling has proven to be complex and difficult to validate across studies. We determined gene expression profiles of 174 well-annotated HGSOCs and demonstrate prognostic significance of the prespecified TCGA Network gene signatures. Furthermore, we confirm the presence of four HGSOC transcriptional subtypes using a de novo classification. Survival differed statistically significantly between de novo subtypes (log rank, P = .006) and was the best for the immunoreactive-like subtype, but statistically significantly worse for the proliferative- or mesenchymal-like subtypes (adjusted hazard ratio = 1.89, 95% confidence interval = 1.18 to 3.02, P = .008, and adjusted hazard ratio = 2.45, 95% confidence interval = 1.43 to 4.18, P = .001, respectively). More prognostic information was provided by the de novo than the TCGA classification (Likelihood Ratio tests, P = .003 and P = .04, respectively). All statistical tests were two-sided. These findings were replicated in an external data set of 185 HGSOCs and confirm the presence of four prognostically relevant molecular subtypes that have the potential to guide therapy decisions.
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Affiliation(s)
- Gottfried E Konecny
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Chen Wang
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Habib Hamidi
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Boris Winterhoff
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Kimberly R Kalli
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Judy Dering
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Charles Ginther
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Hsiao-Wang Chen
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Sean Dowdy
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - William Cliby
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Bobbie Gostout
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Karl C Podratz
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Gary Keeney
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - He-Jing Wang
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Lynn C Hartmann
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Dennis J Slamon
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Ellen L Goode
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
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Wong DJ, Garon EB, Silveira DD, Kamranpour N, Pitts S, Chalukya M, Hamidi H, Dubinett S, Linnartz R, Finn RS, Slamon DJ. Abstract 743: Potent anti-tumor activity of the MEK1/2 inhibitor MEK162 in human non-small cell lung cancer (NSCLC) and squamous cell carcinoma of the head and neck (SCCHN) cell lines. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
BACKGROUND: MAPK pathway dysregulation is frequently seen in cancer. For NSCLC, this may be due to driver mutations or gene amplification in EGFR, KRAS, or BRAF, though tumors without such mutations frequently display pathway hyperactivity. Aberrant EGFR signaling in SCCHN may lead to hyperactivity of the MAPK or PI3K pathways. MEK162 (ARRY-438162) is a potent, tight binding, uncompetitive MEK inhibitor currently in clinical development for treatment of solid tumors. MEK162 has an IC50 of 10nM against purified MEK1/2. We evaluated whether MEK162 would inhibit NSCLC and SCCHN cell lines and whether specific molecular alterations predicted anti-tumor activity. We also evaluated the combination of MEK162 in combination with BYL719, a potent PI3K alpha inhibitor.
METHODS: The 50% inhibitory concentration (IC50) of MEK162, alone or in combination with BYL719, was determined in 40 human NSCLC and 30 SCCHN cell lines in vitro. Effects on MAPK and PI3K/AKT pathway signaling were studied by western blot analysis. Effects of MEK162 alone or in combination with BYL719 on cell cycle progression were also determined by flow cytometry.
RESULTS: Using previously published cut-offs for sensitivity in cell lines, among NSCLC cell lines, 20/40 (50%) were sensitive to MEK162 (IC50 ≤ 500nM), 9/40 were intermediately sensitive (IC50 500nM-1µM), and 11/40 were resistant (IC50 ≥ 1µm). Using the same cut-offs, 80% (24/30) of SCCHN cell lines were sensitive, 2/30 were intermediately sensitive, and 4/30 were resistant to MEK162. MEK162 exposure resulted in increased cells in G0/G1 and decreased cells in S-phase. MEK162 decreased phosphorylated ERK (p-ERK) in all cell lines treated and resulted in an increase in phosphorylated AKT (p-AKT), presumably as a compensatory result from MAPK pathway inhibition. Combined treatment with MEK162 and BYL719 resulted in synergistic growth inhibition for all cell lines and decreased levels of both p-ERK and p-AKT levels at 24 hours.
CONCLUSION: MEK162 potently inhibited growth of human NSCLC and SCCHN cell lines in most cell lines tested and led to synergistic inhibition when combined with BYL719. The compensatory increase in pAKT seen with MEK162 was abrogated with dual treatment with MEK162 and BYL719, demonstrating that synergy may be mediated by simultaneous blockade of MAPK and PI3K/AKT pathways. These data provide a preclinical rationale for evaluating MEK162, alone or in combination with BYL719, in metastatic NSCLC and SCCHN.
Supported by 1K23CA149079, P50 CA090440, V Foundation for Cancer Research, Jonsson Comprehensive Cancer Center, Wolfen Family Lung Cancer Research Program, Stiles Program in Oncology, National Lung Cancer Partnership and One Ball Matt Memorial Golf Tournament.
Citation Format: Deborah JL Wong, Edward B. Garon, Danielle D. Silveira, Naeimeh Kamranpour, Sharon Pitts, Meenal Chalukya, Habib Hamidi, Steven Dubinett, Ronald Linnartz, Richard S. Finn, Dennis J. Slamon. Potent anti-tumor activity of the MEK1/2 inhibitor MEK162 in human non-small cell lung cancer (NSCLC) and squamous cell carcinoma of the head and neck (SCCHN) cell lines. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 743. doi:10.1158/1538-7445.AM2014-743
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Affiliation(s)
- Deborah J. Wong
- 1Department of Medicine, Division of Hematology/Oncology, Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Edward B. Garon
- 1Department of Medicine, Division of Hematology/Oncology, Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Danielle D. Silveira
- 1Department of Medicine, Division of Hematology/Oncology, Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Naeimeh Kamranpour
- 1Department of Medicine, Division of Hematology/Oncology, Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Sharon Pitts
- 1Department of Medicine, Division of Hematology/Oncology, Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Meenal Chalukya
- 1Department of Medicine, Division of Hematology/Oncology, Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Habib Hamidi
- 1Department of Medicine, Division of Hematology/Oncology, Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Steven Dubinett
- 2Department of Medicine, Division of Pulmonary and Critical Care, Geffen School of Medicine at UCLA, Los Angeles, CA
| | | | - Richard S. Finn
- 1Department of Medicine, Division of Hematology/Oncology, Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Dennis J. Slamon
- 1Department of Medicine, Division of Hematology/Oncology, Geffen School of Medicine at UCLA, Los Angeles, CA
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Wainberg ZA, Yufa A, Anghel A, Rogers AM, Manivong T, Adhami S, Hamidi H, Conklin D, Finn RS, Slamon DJ. Abstract 4557: Expression of p16 in colon cancer and cyclin D1 in gastric cancer predicts response to CDK4/6 inhibition in vitro. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-4557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Cyclin-dependent kinases (CDKs) play a significant role in regulating cell cycle progression through association with cyclins. CDK4 and CDK6 interact with cyclin D1 to mediate hyperphosphorylation of retinoblastoma (Rb) during early G1 phase. Palbociclib is a highly selective inhibitor of CDK4 and CDK6 which functions by blocking pRb phosphorylation resulting in G1 arrest in sensitive cell lines. We evaluated the effect of palbociclib in gastric and colon cancer cell lines to explore potential biomarkers of response and to guide patient selection in colon and gastric cancer.
Methods: Panels of 17 gastric and 27 colon cancer cell lines were exposed in vitro to palbociclib over various concentrations to generate dose response curves. Analysis of variance (ANOVA) was used to identify differentially expressed genes between sensitive and resistant cell lines. Genes identified by ANOVA and effects of palbociclib on pRB were analyzed via western blot.
Results: Palbociclib was found to have potent anti-proliferative activity in the low nanomolar range (< 150 nM) for 14 of the 44 gastric and colon cancer cell lines tested. In gastric cancer, cyclin D1-amplified cells cells expressed greater sensitivity to the compound when compared to cyclin D1-negative cells. HER2 amplified cell lines were also statistically more sensitive than HER2 negative cells. Combination studies with palbociclib and trastuzumab demonstrated significant synergy in HER2 amplified gastric cancer models. Furthermore, cyclin E emerged as a biomarker for resistance to the compound in gastric cancers. Contrary to observations made in other cancers, expression levels of p16 (CDK4 inhibitor) and p21 (CDK2 inhibitor) in colon cancer indicated that p16 loss and p21 gain predict for resistance rather than sensitivity to CDK4 and CDK6 inhibition.
Conclusions: Palbociclib demonstrates anti-proliferative activity in several gastric and colon cancer cell lines. Molecular markers found to predict for sensitivity to this agent enhance patient selection for future clinical studies of palbociclib.
Citation Format: Zev A. Wainberg, Ann Yufa, Adrian Anghel, Amy M. Rogers, Tin Manivong, Shahriar Adhami, Habib Hamidi, Dylan Conklin, Richard S. Finn, Dennis J. Slamon. Expression of p16 in colon cancer and cyclin D1 in gastric cancer predicts response to CDK4/6 inhibition in vitro. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4557. doi:10.1158/1538-7445.AM2014-4557
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Affiliation(s)
| | - Ann Yufa
- UCLA Medical Center-Santa Monica, Santa Monica, CA
| | | | | | - Tin Manivong
- UCLA Medical Center-Santa Monica, Santa Monica, CA
| | | | - Habib Hamidi
- UCLA Medical Center-Santa Monica, Santa Monica, CA
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27
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Konecny GE, Wang C, Hamidi H, Winterhoff B, Kalli KR, Dering J, Ginther C, Chen HW, Dowdy S, Cliby W, Gostout B, Podratz KC, Keeney G, Wang HJ, Hartmann LC, Slamon DJ, Goode EL. Prognostic and therapeutic relevance of molecular subtypes in high-grade serous ovarian cancer. J Natl Cancer Inst 2014; 106:dju249. [PMID: 25269487 DOI: 10.1093/jnci/dju249] [Citation(s) in RCA: 257] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Molecular classification of high-grade serous ovarian cancer (HGSOC) using transcriptional profiling has proven to be complex and difficult to validate across studies. We determined gene expression profiles of 174 well-annotated HGSOCs and demonstrate prognostic significance of the prespecified TCGA Network gene signatures. Furthermore, we confirm the presence of four HGSOC transcriptional subtypes using a de novo classification. Survival differed statistically significantly between de novo subtypes (log rank, P = .006) and was the best for the immunoreactive-like subtype, but statistically significantly worse for the proliferative- or mesenchymal-like subtypes (adjusted hazard ratio = 1.89, 95% confidence interval = 1.18 to 3.02, P = .008, and adjusted hazard ratio = 2.45, 95% confidence interval = 1.43 to 4.18, P = .001, respectively). More prognostic information was provided by the de novo than the TCGA classification (Likelihood Ratio tests, P = .003 and P = .04, respectively). All statistical tests were two-sided. These findings were replicated in an external data set of 185 HGSOCs and confirm the presence of four prognostically relevant molecular subtypes that have the potential to guide therapy decisions.
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Affiliation(s)
- Gottfried E Konecny
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Chen Wang
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Habib Hamidi
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Boris Winterhoff
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Kimberly R Kalli
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Judy Dering
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Charles Ginther
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Hsiao-Wang Chen
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Sean Dowdy
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - William Cliby
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Bobbie Gostout
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Karl C Podratz
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Gary Keeney
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - He-Jing Wang
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Lynn C Hartmann
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Dennis J Slamon
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Ellen L Goode
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
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28
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Cunningham JM, Cicek MS, Larson NB, Davila J, Wang C, Larson MC, Song H, Dicks EM, Harrington P, Wick M, Winterhoff BJ, Hamidi H, Konecny GE, Chien J, Bibikova M, Fan JB, Kalli KR, Lindor NM, Fridley BL, Pharoah PPD, Goode EL. Clinical characteristics of ovarian cancer classified by BRCA1, BRCA2, and RAD51C status. Sci Rep 2014; 4:4026. [PMID: 24504028 PMCID: PMC4168524 DOI: 10.1038/srep04026] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 01/20/2014] [Indexed: 12/20/2022] Open
Abstract
We evaluated homologous recombination deficient (HRD) phenotypes in epithelial ovarian cancer (EOC) considering BRCA1, BRCA2, and RAD51C in a large well-annotated patient set. We evaluated EOC patients for germline deleterious mutations (n = 899), somatic mutations (n = 279) and epigenetic alterations (n = 482) in these genes using NGS and genome-wide methylation arrays. Deleterious germline mutations were identified in 32 (3.6%) patients for BRCA1, in 28 (3.1%) for BRCA2 and in 26 (2.9%) for RAD51C. Ten somatically sequenced patients had deleterious alterations, six (2.1%) in BRCA1 and four (1.4%) in BRCA2. Fifty two patients (10.8%) had methylated BRCA1 or RAD51C. HRD patients with germline or somatic alterations in any gene were more likely to be high grade serous, have an earlier diagnosis age and have ovarian and/or breast cancer family history. The HRD phenotype was most common in high grade serous EOC. Identification of EOC patients with an HRD phenotype may help tailor specific therapies.
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Affiliation(s)
- J. M. Cunningham
- Department of Laboratory Medicine and Pathology, Division of Experimental Pathology, Mayo Clinic, Rochester, Minnesota
| | - M. S. Cicek
- Department of Health Sciences Research, Division of Epidemiology, Mayo Clinic, Rochester, Minnesota
| | - N. B. Larson
- Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - J. Davila
- Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - C. Wang
- Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - M. C. Larson
- Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - H. Song
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - E. M. Dicks
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - P. Harrington
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - M. Wick
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Minnesota
| | - B. J. Winterhoff
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Minnesota
| | - H. Hamidi
- Department of Medicine, Division of Hematology and Oncology, David Geffen School of Medicine, University of California at Los Angeles and Jonsson Comprehensive Cancer Center, Los Angeles, California
| | - G. E. Konecny
- Department of Medicine, Division of Hematology and Oncology, David Geffen School of Medicine, University of California at Los Angeles and Jonsson Comprehensive Cancer Center, Los Angeles, California
| | - J. Chien
- Department of Translational Genomics, University of Kansas Medical Center, Kansas City, Kansas
| | | | - J.-B. Fan
- Illumina Corporation, San Diego, California
| | - K. R. Kalli
- Department of Medical Oncology, Mayo Clinic, Rochester, Minnesota
| | - N. M. Lindor
- Department of Health Science Research, Medical Genetics, Mayo Clinic, Scottsdale, Arizona
| | - B. L. Fridley
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, Kansas
| | - P. P. D. Pharoah
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - E. L. Goode
- Department of Health Sciences Research, Division of Epidemiology, Mayo Clinic, Rochester, Minnesota
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Logan JE, Mostofizadeh N, Desai AJ, VON Euw E, Conklin D, Konkankit V, Hamidi H, Eckardt M, Anderson L, Chen HW, Ginther C, Taschereau E, Bui PH, Christensen JG, Belldegrun AS, Slamon DJ, Kabbinavar FF. PD-0332991, a potent and selective inhibitor of cyclin-dependent kinase 4/6, demonstrates inhibition of proliferation in renal cell carcinoma at nanomolar concentrations and molecular markers predict for sensitivity. Anticancer Res 2013; 33:2997-3004. [PMID: 23898052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
BACKGROUND PD-0332991 is an inhibitor of cyclin-dependent kinases (CDK) 4 and 6, and was evaluated to determine its anti-proliferative effects in 25 renal cell carcinoma (RCC) cell lines. MATERIALS AND METHODS Half-maximal inhibitory concentrations (IC50) of PD-0332991 were determined with cell line proliferation assays, as were its effects on the cell cycle, apoptosis, and retinoblastoma (RB) phosphorylation. Molecular markers for response prediction, including p16, p15, cyclin D1 (CCND1), cyclin E1 (CCNE1), E2F transcription factor 1 (E2F1), RB, CDK4 and CDK6, were studied using array comparative genomic hybridization (CGH) and gene expression. RESULTS IC50 values for PD-0332991 ranged from 25.0 nM to 700 nM, and the agent demonstrated G0/G1 cell-cycle arrest, induction of late apoptosis, and blockade of RB phosphorylation. Through genotype and expression data p16, p15 and E2F1 were identified as having significant association between loss and sensitivity to PD-0332991: p16 (p=0.021), p15 (p=0.047), and E2F1 (p=0.041). CONCLUSION PD-0332991 has antiproliferative activity in RCC cell lines, and molecular markers predict for sensitivity to this agent.
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Affiliation(s)
- Joshua E Logan
- Institute of Urologic Oncology, Department of Urology, David Geffen School of Medicine, University of California, Los Angeles, 924 Westwood Blvd., Suite 1050, Los Angeles, CA 90095, USA.
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30
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Garon EB, Finn RS, Hamidi H, Dering J, Pitts S, Kamranpour N, Desai AJ, Hosmer W, Ide S, Avsar E, Jensen MR, Quadt C, Liu M, Dubinett SM, Slamon DJ. The HSP90 inhibitor NVP-AUY922 potently inhibits non-small cell lung cancer growth. Mol Cancer Ther 2013; 12:890-900. [PMID: 23493311 PMCID: PMC3681857 DOI: 10.1158/1535-7163.mct-12-0998] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Heat shock protein 90 (HSP90) is involved in protein folding and functions as a chaperone for numerous client proteins, many of which are important in non-small cell lung cancer (NSCLC) pathogenesis. We sought to define preclinical effects of the HSP90 inhibitor NVP-AUY922 and identify predictors of response. We assessed in vitro effects of NVP-AUY922 on proliferation and protein expression in NSCLC cell lines. We evaluated gene expression changes induced by NVP-AUY922 exposure. Xenograft models were evaluated for tumor control and biological effects. NVP-AUY922 potently inhibited in vitro growth in all 41 NSCLC cell lines evaluated with IC50 < 100 nmol/L. IC100 (complete inhibition of proliferation) < 40 nmol/L was seen in 36 of 41 lines. Consistent gene expression changes after NVP-AUY922 exposure involved a wide range of cellular functions, including consistently decreased dihydrofolate reductase after exposure. NVP-AUY922 slowed growth of A549 (KRAS-mutant) xenografts and achieved tumor stability and decreased EGF receptor (EGFR) protein expression in H1975 xenografts, a model harboring a sensitizing and a resistance mutation for EGFR-tyrosine kinase inhibitors in the EGFR gene. These data will help inform the evaluation of correlative data from a recently completed phase II NSCLC trial and a planned phase IB trial of NVP-AUY922 in combination with pemetrexed in NSCLCs.
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Affiliation(s)
- Edward B Garon
- Department of Medicine, Division of Hematology/Oncology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA.
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31
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Konecny GE, Wang C, Winterhoff B, Dering J, Ginther C, Chen HW, Hamidi H, Podratz KC, Cliby W, Dowdy SC, Haluska P, Hartmann LC, Kalli K, Goode EL, Slamon DJ. Prognostic relevance of gene signatures in high-grade serous ovarian carcinoma. J Clin Oncol 2013. [DOI: 10.1200/jco.2013.31.15_suppl.5510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
5510 Background: Transcriptional profiling of ovarian cancers has proven to be complex. As such it has been difficult to validate existing signatures across studies. Cancer Genome Atlas (TCGA) researchers have identified four molecular subtypes of high-grade serous ovarian cancer (HGSOC). However, survival duration did not differ significantly for the TCGA subtypes. Potential limitations of the TCGA data include short clinical follow-up (45% were alive at the time of last follow-up) and the need to unify gene expression measures from multiple platforms. Methods: Clinically annotated stage-II–IV HGSOC samples (n = 175) with >70% tumor cell content were profiled using the Agilent Whole Human Genome 4 x 44K chip. To identify subtypes non-negative matrix factorization (NMF) of mRNA expression was performed using ~2000 genes with the highest variability across patients. In parallel differentially expressed genes were identified using the Rosetta Similarity Search Tool as well as analysis of variance based on genes known to be involved in epithelial to mesenchymal transition. Results: Median follow-up time was 35 months (range, 0–202 months, 12% were alive at the time of last follow-up). NMF clustering confirmed four HGSOC subtypes (immunoreactive, differentiated, proliferative, and mesenchymal) on the basis of gene content in the clusters. Pathway signatures with therapeutic potential were identified for individual or multiple subtypes. Survival differed significantly between the four molecular subgroups in univariate (Hazard Ratio [HR] 2.4, 95% CI 1.5-4.1, p = 0.007) and multivariate (HR 2.3, 95% CI 1.3-4.0, p = 0.003) analyses when accounting for age, stage, grade, and postoperative residual tumor. Using the supervised clustering approach two distinct molecular subtypes of HGSOC based on epithelial and mesenchymal gene expression signatures were identified with significantly different survival outcomes. Conclusions: Here we independently validate and expand upon the molecular TCGA classification of HGSOC. The potential of these two prognostic classifiers may lie in their ability to recognize categories of patients that are more likely to respond to particular therapies.
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Affiliation(s)
- Gottfried E. Konecny
- David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA
| | | | - Boris Winterhoff
- 1. Division of Gynecologic Surgery, Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Rochester, MN
| | - Judy Dering
- University of California, Los Angeles, School of Medicine/Translational Oncology Research Laboratory, Los Angeles, CA
| | - Charles Ginther
- University of California, Los Angeles, Translational Oncology Research Laboratory, Santa Monica, CA
| | - Hsiao-Wang Chen
- University of California, Los Angeles, School of Medicine/Translational Oncology Research Laboratory, Los Angeles, CA
| | - Habib Hamidi
- University of California, Los Angeles, Translational Oncology Research Laboratory, Santa Monica, CA
| | | | | | | | | | | | | | | | - Dennis J. Slamon
- University of California, Los Angeles, School of Medicine/Translational Oncology Research Laboratory, Los Angeles, CA
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Cicek MS, Koestler DC, Fridley BL, Kalli KR, Armasu SM, Larson MC, Wang C, Winham SJ, Vierkant RA, Rider DN, Block MS, Klotzle B, Konecny G, Winterhoff BJ, Hamidi H, Shridhar V, Fan JB, Visscher DW, Olson JE, Hartmann LC, Bibikova M, Chien J, Cunningham JM, Goode EL. Epigenome-wide ovarian cancer analysis identifies a methylation profile differentiating clear-cell histology with epigenetic silencing of the HERG K+ channel. Hum Mol Genet 2013; 22:3038-47. [PMID: 23571109 DOI: 10.1093/hmg/ddt160] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Ovarian cancer remains the leading cause of death in women with gynecologic malignancies, despite surgical advances and the development of more effective chemotherapeutics. As increasing evidence indicates that clear-cell ovarian cancer may have unique pathogenesis, further understanding of molecular features may enable us to begin to understand the underlying biology and histology-specific information for improved outcomes. To study epigenetics in clear-cell ovarian cancer, fresh frozen tumor DNA (n = 485) was assayed on Illumina Infinium HumanMethylation450 BeadChips. We identified a clear-cell ovarian cancer tumor methylation profile (n = 163) which we validated in two independent replication sets (set 1, n = 163; set 2, n = 159), highlighting 22 CpG loci associated with nine genes (VWA1, FOXP1, FGFRL1, LINC00340, KCNH2, ANK1, ATXN2, NDRG21 and SLC16A11). Nearly all of the differentially methylated CpGs showed a propensity toward hypermethylation among clear-cell cases. Several loci methylation inversely correlated with tumor gene expression, most notably KCNH2 (HERG, a potassium channel) (P = 9.5 × 10(-7)), indicating epigenetic silencing. In addition, a predicted methylation class mainly represented by the clear-cell cases (20 clear cell out of 23 cases) had improved survival time. Although these analyses included only 30 clear-cell carcinomas, results suggest that loss of expression of KCNH2 (HERG) by methylation could be a good prognostic marker, given that overexpression of the potassium (K(+)) channel Eag family members promotes increased proliferation and results in poor prognosis. Validation in a bigger cohort of clear-cell tumors of the ovary is warranted.
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Affiliation(s)
- Mine S Cicek
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
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Logan J, Mostofizadeh N, Desai A, von Euw E, Conklin D, Konkankit V, Hamidi H, Eckardt M, Anderson L, Chen HW, Ginther C, Taschereau E, Christensen J, Belldegrun A, Slamon D, Kabbinaar F. 612 PD-0332991, AN INHIBITOR OF CYCLIN-DEPENDENT KINASE 4/6, DEMONSTRATES INHIBITION OF PROLIFERATION IN RENAL CELL CARCINOMA AT NANOMOLAR CONCENTRATIONS AND MOLECULAR MARKERS PREDICT FOR SENSITIVITY. J Urol 2013. [DOI: 10.1016/j.juro.2013.02.163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Logan JE, Mostofizadeh N, Desai AJ, Von Euw EM, Conklin D, Konkatkit V, Hamidi H, Eckardt MA, Anderson L, Cheng HW, Ginther C, Taschereau E, Christensen JG, Belldegrun AS, Slamon DJ, Kabbinavar FF. Effect of PD-0332991, a potent and selective inhibitor of cyclin-dependent kinase 4/6, on proliferation in renal cell carcinoma at nanomolar concentrations and prediction of sensitivity by molecular markers. J Clin Oncol 2013. [DOI: 10.1200/jco.2013.31.6_suppl.413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
413 Background: Cell cycle dysregulation is prevalent in renal cell carcinoma (RCC). PD-0332991 is an orally active, potent, and selective inhibitor of cyclin-dependent kinases (CDK) 4 and 6, blocking retinoblastoma (Rb) phosphorylation at nanomolar concentrations. Methods: 28 RCC and immortalized kidney cell lines were used to examine the effects of PD-0332991 on proliferation to determine the half maximal inhibitory concentration (IC50). Effects of PD-0332991 on cell-cycle, apoptosis, and Rb phosphorylation were assessed with flow cytometry and western blot analysis for five of the cell lines: RCC-HB and SW 156 (sensitive/malignant), R444 and Hs 891.T (resistant/malignant), and CCD 1103 (resistant/immortalized non-malignant). Molecular markers for response prediction were studied using array CGH and gene expression profiling. Results: Concentration-dependent inhibition of proliferation was identified in response to PD-0332991, with IC50values ranging from 25.0nM up to 700nM; five cell lines were identified as completely resistant at 1000nM. PD-0332991 induced G0/G1 cell cycle arrest, as well as induction of late apoptosis in SW 156, and Rb phosphorylation was blocked in a time-dependent fashion in both sensitive cell lines, while resistant lines were unaffected. Genotype and expression data of CDKN2A and CDKN2B were combined and a consensus was made regarding p16 and p15 status; significant association between loss and sensitivity to PD-0332991 was identified for p16 (p = 0.027). For CCND1, CCNE1, E2F1, Rb, CDK4, and CDK6 no amplifications or homozygous deletions were identified by array CGH; cell lines were then classified as having high or low expression for each of these markers. E2F1 had low expression levels significantly associated with response to PD-0332991 (p = 0.041). Conclusions: PD-0332991 shows anti-proliferative activity in RCC through blockade of the cell cycle. The decreased expression of molecular markers p16 and E2F1 predict for sensitivity to PD-0332991 in RCC.
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Affiliation(s)
- Joshua E. Logan
- Institute of Urologic Oncology, Department of Urology, UCLA, Los Angeles, CA
| | - Nikayeh Mostofizadeh
- University of California, Los Angeles School of Medicine/Translational Oncology Research Laboratory, Los Angeles, CA
| | - Amrita J. Desai
- University of California, Los Angeles School of Medicine/Translational Oncology Research Laboratory, Los Angeles, CA
| | - Erika Maria Von Euw
- University of California, Los Angeles School of Medicine/Translational Oncology Research Laboratory, Los Angeles, CA
| | - Dylan Conklin
- University of California, Los Angeles School of Medicine/Translational Oncology Research Laboratory, Los Angeles, CA
| | - Veerauo Konkatkit
- University of California, Los Angeles School of Medicine/Translational Oncology Research Laboratory, Los Angeles, CA
| | - Habib Hamidi
- University of California, Los Angeles School of Medicine/Translational Oncology Research Laboratory, Los Angeles, CA
| | - Mark A. Eckardt
- University of California, Los Angeles Translational Oncology Research Laboratory, Santa Monica, CA
| | - Lee Anderson
- University of California, Los Angeles School of Medicine/Translational Oncology Research Laboratory, Los Angeles, CA
| | - Hsiao-Wang Cheng
- University of California, Los Angeles School of Medicine/Translational Oncology Research Laboratory, Los Angeles, CA
| | - Charles Ginther
- University of California, Los Angeles School of Medicine/Translational Oncology Research Laboratory, Los Angeles, CA
| | - Eileen Taschereau
- University of California, Los Angeles School of Medicine/Translational Oncology Research Laboratory, Los Angeles, CA
| | - James G. Christensen
- Department of Cancer Research, Pfizer Global Research and Development, La Jolla, CA
| | - Arie S. Belldegrun
- Institute of Urologic Oncology, Department of Urology, UCLA, Los Angeles, CA
| | - Dennis J. Slamon
- University of California, Los Angeles School of Medicine/Translational Oncology Research Laboratory, Los Angeles, CA
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35
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Hamidi H, Gustafason D, Pellegrini M, Gasson J. Identification of novel targets of CSL-dependent Notch signaling in hematopoiesis. PLoS One 2011; 6:e20022. [PMID: 21637838 PMCID: PMC3102675 DOI: 10.1371/journal.pone.0020022] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Accepted: 04/08/2011] [Indexed: 12/13/2022] Open
Abstract
Somatic activating mutations in the Notch1 receptor result in the overexpression of activated Notch1, which can be tumorigenic. The goal of this study is to understand the molecular mechanisms underlying the phenotypic changes caused by the overexpression of ligand independent Notch 1 by using a tetracycline inducible promoter in an in vitro embryonic stem (ES) cells/OP9 stromal cells coculture system, recapitulating normal hematopoiesis. First, an in silico analysis of the promoters of Notch regulated genes (previously determined by microarray analysis) revealed that the motifs recognized by regulatory proteins known to mediate hematopoiesis were overrepresented. Notch 1 does not bind DNA but instead binds the CSL transcription factor to regulate gene expression. The in silico analysis also showed that there were putative CSL binding sites observed in the promoters of 28 out of 148 genes. A custom ChIP-chip array was used to assess the occupancy of CSL in the promoter regions of the Notch1 regulated genes in vivo and showed that 61 genes were bound by activated Notch responsive CSL. Then, comprehensive mapping of the CSL binding sites genome-wide using ChIP-seq analysis revealed that over 10,000 genes were bound within 10 kb of the TSS (transcription start site). The majority of the targets discovered by ChIP-seq belong to pathways that have been shown by others to crosstalk with Notch signaling. Finally, 83 miRNAs were significantly differentially expressed by greater than 1.5-fold during the course of in vitro hematopoiesis. Thirty one miRNA were up-regulated and fifty two were down-regulated. Overexpression of Notch1 altered this pattern of expression of microRNA: six miRNAs were up-regulated and four were down regulated as a result of activated Notch1 overexpression during the course of hematopoiesis. Time course analysis of hematopoietic development revealed that cells with Notch 1 overexpression mimic miRNA expression of cells in a less mature stage, which is consistent with our previous biological characterization.
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Affiliation(s)
- Habib Hamidi
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Derek Gustafason
- UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Matteo Pellegrini
- UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Judith Gasson
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- Division of Hematology-Oncology, Department of Medicine, and Department of Biological Chemistry and Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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36
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Eradat HA, Eckardt MA, Dorfman E, Hamidi H, Ginther C, Finn RS, Los G, Christensen JG, De Vos S, Slamon DJ. Cell cycle effects of CDK 4/6 inhibitor PD 0332991 in diffuse large B-cell lymphoma cell lines in vitro. J Clin Oncol 2011. [DOI: 10.1200/jco.2011.29.15_suppl.8061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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37
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Hamidi H, Jahanian R, Pourreza J. Effect of Dietary Betaine on Performance, Immunocompetence and Gut Contents Osmolarity of Broilers Challenged With a Mixed Coccidial Infection. ACTA ACUST UNITED AC 2010. [DOI: 10.3923/ajava.2010.193.201] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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38
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Hamidi H, Pourreza J. Effects of Zinc-methionine and Feed Restriction on Performance, Immunocompetence and Gut Content Osmolarity of Broilers Challenged with a Mixed Coccidial Infection. ACTA ACUST UNITED AC 2009. [DOI: 10.3923/jbs.2009.669.675] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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39
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Vega VB, Woo XY, Hamidi H, Yeo HC, Yeo ZX, Bourque G, Clarke ND. Inferring direct regulatory targets of a transcription factor in the DREAM2 challenge. Ann N Y Acad Sci 2009; 1158:215-23. [PMID: 19348643 DOI: 10.1111/j.1749-6632.2008.03759.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the DREAM2 community-wide experiment on regulatory network inference, one of the challenges was to identify which genes, in a list of 200, are direct regulatory targets of the transcription factor BCL6. The organizers of the challenge defined targets based on gene expression and chromatin immunoprecipitation experiments (ChIP-chip). The expression data were publicly available; the ChIP-chip data were not. In order to assess the likelihood that a gene is a BCL6 target, we used three classes of information: expression-level differences, over-representation of sequence motifs in promoter regions, and gene ontology annotations. A weight was attached to each analysis based on how well it identified BCL6-bound genes as defined by publicly available ChIP-chip data. By the organizers' criteria, our group, GenomeSingapore, performed best. However, our retrospective analysis indicates that this success was dominated by a gene expression analysis that was predicated on a regulatory model known to be favored by the organizers. We also noted that the 200-gene test set was enriched only in genes that are upregulated, while genes bound by BCL6 are enriched in both upregulated and downregulated genes. Together, these observations suggest possible model biases in the selection of the gold-standard gene set and imply that our success was attained in part by adhering to the same assumptions. We argue that model biases of this type are unavoidable in the inference of regulatory networks and, for that reason, we suggest that future community-wide experiments of this type should focus on the prediction of data, rather than models.
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Abstract
The purpose of this research was to investigate effect of dietary betaine on intestinal morphology after an experimental coccidiosis. Hence a total of 189 male and female broiler chicks were randomly assigned to 9 floor cages. Chicks were fed a basal diet supplemented with 0, 0.6 or 1.2 g kg(-1) betaine. All birds were inoculated orally with Eimeria oocysts on day 28. Duodenal morphology parameters and lesions were scored by microscopic observation on intestine samples which were taken at day 42 of age. Adding 1.2 g kg(-1) betaine to diet diminished intestinal lesions (p < 0.05). Dietary supplementation with 0.6 or 1.2 g kg(-1) betaine significantly (p < 0.01) increased intraepithelial lymphocytes as well. Level of additive betaine had no effect on the ratio of villus height/crypt depth or villus surface area. Lamina propria of duodenum became thicker in the intestine of chickens which received more supplemental betaine via their diet. In conclusion, since the number of intraepithelial lymphocytes and thickness of lamina propria represent the condition of gut immune response, it seems that dietary betaine may immunomodulate the gastrointestinal tract of broilers. In addition, betaine effect on villus morphology measured later in life differed from what had been measured already earlier in life of the chicks.
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Affiliation(s)
- H Hamidi
- Department of Animal Science, Faculty of Agriculture, Isfahan University of Technology, Isfahan, Iran
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41
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Hamidi H, Mohammadi K. Modeling Fault Tolerant and Secure Mobile Agent Execution in Distributed Systems. International Journal of Intelligent Information Technologies 2006. [DOI: 10.4018/jiit.2006010102] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- H. Hamidi
- Iran University of Science & Technology, Iran
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42
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Deneen B, Hamidi H, Denny CT. Functional analysis of the EWS/ETS target gene uridine phosphorylase. Cancer Res 2003; 63:4268-74. [PMID: 12874036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
The EWS/ETS fusion proteins associated with Ewings family tumors (EFTs) are thought to promote oncogenesis by acting as aberrant transcription factors. Uridine phosphorylase is a gene that is up-regulated by structurally distinct EWS/ETS fusions. Ectopic expression of uridine phosphorylase was able to support anchorage-independent cell growth, indicating that it plays an active role in the oncogenic process. Transcriptional up-regulation of uridine phosphorylase is shown to be mediated in a DNA binding-dependent manner, and reporter gene assays demonstrated that EWS/FLI1 and RAS mediate activation through a single activator protein 1/ETS site located in the uridine phosphorylase promoter. Chromatin immunoprecipitation assays reveal that EWS/FLI1 directly associates with the uridine phosphorylase promoter in vivo. Up-regulation of uridine phosphorylase by EWS/FLI1 sensitizes cells to growth inhibition by the pyrimidine analogue, 5'-deoxy-5'fluorouridine, both in tissue culture and in vivo model systems.
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Affiliation(s)
- Benjamin Deneen
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California 90024, USA
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Jaboin J, Wild J, Hamidi H, Khanna C, Kim CJ, Robey R, Bates SE, Thiele CJ. MS-27-275, an inhibitor of histone deacetylase, has marked in vitro and in vivo antitumor activity against pediatric solid tumors. Cancer Res 2002; 62:6108-15. [PMID: 12414635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
The antitumor efficacy of the synthetic benzamide derivative MS-27-275 (MS-275), an inhibitor of histone deacetylation [T. Suzuki et al., J. Med. Chem., 42: 3001-3003, 1999], was evaluated in a series of pediatric solid tumor cell lines, including neuroblastoma, rhabdomyosarcoma, Ewing's sarcoma (EWS), retinoblastoma, medulloblastoma, undifferentiated sarcoma (US), osteosarcoma, and malignant rhabdoid tumors. Treatment with MS-275 results in an increase in acetylation of histones within 4 h of drug exposure. The cell lines were treated with various concentrations of MS-275 for 3 days and incubated with [(3)H]thymidine for 20 h before cell harvest. MS-275 inhibited [(3)H]thymidine uptake in a dose-dependent manner in all tumor cell lines examined. The IC(50) ranged from 50 nm in the D283 medulloblastoma cell line to 1.3 micro M in the US. A common feature of MS-275 treatment of pediatric tumor cell lines was induction of p21mRNA. However, the effects on cell cycle were diverse because in some cases MS-275 induced an increase in G(1) or G(2), whereas in others, there was an induction of apoptosis. In EWS, the EWS/fli chimeric transcription factor created by the t(11;22) suppresses transforming growth factor (TGF) betaRII transcription, however, MS-275 was able to induce an increase in TGF-betaRII mRNA and restore TGF-beta signaling. Using xenograft orthotopic models of US, EWS, and neuroblastoma, we find that the growth of established tumors is inhibited in mice treated with MS-275.
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Affiliation(s)
- Jerry Jaboin
- Cell and Molecular Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
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