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Nakazawa MS, Silverman IM, Rimkunas V, Veloso A, Glodzik D, Johnson A, Ohsumi TK, Patel SR, Conley AP, Roland CL, Soliman PT, Beird HC, Wu CC, Ingram DR, Lazcano R, Song D, Wani KM, Lazar AJ, Yap TA, Wang WL, Livingston JA. Loss of the DNA Repair Gene RNase H2 Identifies a Unique Subset of DDR-Deficient Leiomyosarcomas. Mol Cancer Ther 2024:742109. [PMID: 38561019 DOI: 10.1158/1535-7163.mct-23-0761] [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] [Received: 11/18/2023] [Revised: 01/26/2024] [Accepted: 03/29/2024] [Indexed: 04/04/2024]
Abstract
Targeting the DNA damage response (DDR) pathway is an emerging therapeutic approach for leiomyosarcoma (LMS), and loss of RNase H2, a DDR pathway member, is a potentially actionable alteration for DDR targeted treatments. Therefore, we designed a protein and genomic based RNase H2 screening assay to determine its prevalence and prognostic significance. Using a selective RNase H2 antibody on a pan-tumor tissue microarray (TMA), RNase H2 loss was more common in LMS (11.5%, 9/78) than across all tumors (3.8%, 32/843). In a separate LMS cohort, RNase H2 deficiency was confirmed in uterine LMS (U-LMS, 21%, 23/108) and soft-tissue LMS (ST-LMS) (30%, 39/102). In the TCGA database, RNASEH2B homozygous deletions (HomDels) were found in 6% (5/80) of LMS cases, with a higher proportion in U-LMS (15%; 4/27) compared to ST-LMS (2%; 1/53). Using the SNiPDx targeted-NGS sequencing assay to detect biallelic loss of function in select DDR related genes, we found RNASEH2B HomDels in 54% (19/35) of U-LMS cases with RNase H2 loss by IHC, and 7% (3/43) HomDels in RNase H2 intact cases. No RNASEH2B HomDels were detected in ST-LMS. In U-LMS patient cohort (n = 109), no significant overall survival difference was seen in patients with RNase H2 loss versus intact, or RNASEH2B HomDel (n=12) vs Non-HomDel (n=37). The overall diagnostic accuracy, sensitivity, and specificity of RNase H2 IHC for detecting RNASEH2B HomDels in U-LMS was 76%, 93% and 71% respectively, and it is being developed for future predictive biomarker driven clinical trials targeting DDR in U-LMS.
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Affiliation(s)
- Michael S Nakazawa
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ian M Silverman
- Repare Therapeutics, Cambridge, Massachusetts, United States
| | | | | | | | | | | | - Shreyaskumar R Patel
- The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
| | - Anthony P Conley
- The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
| | - Christina L Roland
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Pamela T Soliman
- The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
| | - Hannah C Beird
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Chia-Chin Wu
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Davis R Ingram
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Rossana Lazcano
- The University of Texas MD Anderson Cancer Center, Houston, United States
| | - Dawon Song
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Khalida M Wani
- The University of Texas MD Anderson Cancer Center, Houston, Tx, United States
| | - Alexander J Lazar
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Timothy A Yap
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Wei-Lien Wang
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - J Andrew Livingston
- The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
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2
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Pilie PG, Giuliani V, Wang WL, McGrail DJ, Bristow CA, Ngoi NYL, Kyewalabye K, Wani KM, Le H, Campbell E, Sánchez NS, Yang D, Gheeya JS, Goswamy RV, Holla V, Shaw KR, Meric-Bernstam F, Liu CY, Ma X, Feng N, Machado AA, Bardenhagen JP, Vellano CP, Marszalek JR, Rajendra E, Piscitello D, Johnson TI, Likhatcheva M, Elinati E, Majithiya J, Neves J, Grinkevich V, Ranzani M, Roy-Luzarraga M, Boursier M, Armstrong L, Geo L, Lillo G, Tse WY, Lazar AJ, Kopetz SE, Geck Do MK, Lively S, Johnson MG, Robinson HMR, Smith GCM, Carroll CL, Di Francesco ME, Jones P, Heffernan TP, Yap TA. Ataxia-Telangiectasia Mutated (ATM) loss of function displays variant and tissue-specific differences across tumor types. Clin Cancer Res 2024:734972. [PMID: 38416404 DOI: 10.1158/1078-0432.ccr-23-1763] [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] [Received: 06/15/2023] [Revised: 10/31/2023] [Accepted: 02/21/2024] [Indexed: 02/29/2024]
Abstract
PURPOSE Mutations in the ATM gene are common in multiple cancers, but clinical studies of therapies targeting ATM aberrant cancers have yielded mixed results. Refinement of ATM loss of function (LOF) as a predictive biomarker of response is urgently needed. EXPERIMENTAL DESIGN We present the first disclosure and preclinical development of a novel, selective ATR inhibitor, ART0380, and test its antitumor activity in multiple preclinical cancer models. To refine ATM LOF as a predictive biomarker, we performed a comprehensive pan-cancer analysis of ATM variants in patient tumors, and then assessed the ATM variant-to-protein relationship. Finally, we assessed a novel ATM LOF biomarker approach in retrospective clinical datasets of patients treated with platinum-based chemotherapy or ATR inhibition. RESULTS ART0380 had potent, selective anti-tumor activity in a range of preclinical cancer models with differing degrees of ATM LOF. Pan-cancer analysis identified 10609 ATM variants in 8587 patient tumors. Cancer-lineage specific differences were seen in: the prevalence of deleterious (Tier 1) versus unknown/benign (Tier 2) variants, selective pressure for loss of heterozygosity, and concordance between a deleterious variant and ATM loss of protein (LOP). A novel ATM LOF biomarker approach that accounts for variant classification, relationship to ATM LOP, and tissue-specific penetrance significantly enriched for patients who benefited from platinum-based chemotherapy or ATR inhibition. CONCLUSIONS These data help to better define ATM LOF across tumor types in order to optimize patient selection and improve molecularly targeted therapeutic approaches for patients with ATM LOF cancers.
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Affiliation(s)
- Patrick G Pilie
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Virginia Giuliani
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Wei-Lien Wang
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | | | | | - Natalie Y L Ngoi
- National University Cancer Institute, Singapore, Singapore, Singapore, Singapore
| | - Keith Kyewalabye
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Khalida M Wani
- The University of Texas MD Anderson Cancer Center, Houston, Tx, United States
| | - Hung Le
- The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
| | - Erick Campbell
- The University of Texas MD Anderson Cancer Center, Houston, United States
| | | | - Dong Yang
- Astellas Pharma, Northbrook, IL, United States
| | | | | | | | - Kenna Rael Shaw
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | | | - Chiu-Yi Liu
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | | | - Ningping Feng
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Annette A Machado
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | | | | | - Joseph R Marszalek
- The University of Texas MD Anderson Cancer Center, Houston, United States
| | | | | | | | | | | | | | - Joana Neves
- Artios Pharma Ltd, Cambridge, United Kingdom
| | | | | | | | | | | | - Lerin Geo
- Arios Pharma, Cambridge, United Kingdom
| | - Giorgia Lillo
- Artios Pharma, cambridge, cambridgshire, United Kingdom
| | | | - Alexander J Lazar
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Scott E Kopetz
- University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Mary K Geck Do
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | | | | | | | | | | | | | - Philip Jones
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | | | - Timothy A Yap
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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3
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Hahn AW, Menk AV, Rivadeneira DB, Augustin RC, Xu M, Li J, Wu X, Mishra AK, Gide TN, Quek C, Zang Y, Spencer CN, Menzies AM, Daniel CR, Hudgens CW, Nowicki T, Haydu LE, Khan MAW, Gopalakrishnan V, Burton EM, Malke J, Simon JM, Bernatchez C, Putluri N, Woodman SE, Vashisht Gopal YN, Guerrieri R, Fischer GM, Wang J, Wani KM, Thompson JF, Lee JE, Hwu P, Ajami N, Gershenwald JE, Long GV, Scolyer RA, Tetzlaff MT, Lazar AJ, Schadendorf D, Wargo JA, Kirkwood JM, DeBerardinis RJ, Liang H, Futreal A, Zhang J, Wilmott JS, Peng W, Davies MA, Delgoffe GM, Najjar YG, McQuade JL. Obesity Is Associated with Altered Tumor Metabolism in Metastatic Melanoma. Clin Cancer Res 2023; 29:154-164. [PMID: 36166093 DOI: 10.1158/1078-0432.ccr-22-2661] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/14/2022] [Accepted: 09/22/2022] [Indexed: 02/06/2023]
Abstract
PURPOSE Overweight/obese (OW/OB) patients with metastatic melanoma unexpectedly have improved outcomes with immune checkpoint inhibitors (ICI) and BRAF-targeted therapies. The mechanism(s) underlying this association remain unclear, thus we assessed the integrated molecular, metabolic, and immune profile of tumors, as well as gut microbiome features, for associations with patient body mass index (BMI). EXPERIMENTAL DESIGN Associations between BMI [normal (NL < 25) or OW/OB (BMI ≥ 25)] and tumor or microbiome characteristics were examined in specimens from 782 patients with metastatic melanoma across 7 cohorts. DNA associations were evaluated in The Cancer Genome Atlas cohort. RNA sequencing from 4 cohorts (n = 357) was batch corrected and gene set enrichment analysis (GSEA) by BMI category was performed. Metabolic profiling was conducted in a subset of patients (x = 36) by LC/MS, and in flow-sorted melanoma tumor cells (x = 37) and patient-derived melanoma cell lines (x = 17) using the Seahorse XF assay. Gut microbiome features were examined in an independent cohort (n = 371). RESULTS DNA mutations and copy number variations were not associated with BMI. GSEA demonstrated that tumors from OW/OB patients were metabolically quiescent, with downregulation of oxidative phosphorylation and multiple other metabolic pathways. Direct metabolite analysis and functional metabolic profiling confirmed decreased central carbon metabolism in OW/OB metastatic melanoma tumors and patient-derived cell lines. The overall structure, diversity, and taxonomy of the fecal microbiome did not differ by BMI. CONCLUSIONS These findings suggest that the host metabolic phenotype influences melanoma metabolism and provide insight into the improved outcomes observed in OW/OB patients with metastatic melanoma treated with ICIs and targeted therapies. See related commentary by Smalley, p. 5.
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Affiliation(s)
- Andrew W Hahn
- Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ashley V Menk
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - Ryan C Augustin
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Mingchu Xu
- Department of Genomic Medicine, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jun Li
- Department of Bioinformatics and Computational Biology, Division of Basic Sciences, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xiaogang Wu
- Department of Genomic Medicine, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Aditya K Mishra
- Department of Genomic Medicine, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Tuba N Gide
- Melanoma Institute of Australia, The University of Sydney, Sydney, New South Wales, Australia
| | - Camelia Quek
- Melanoma Institute of Australia, The University of Sydney, Sydney, New South Wales, Australia
| | - Yan Zang
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - Alexander M Menzies
- Melanoma Institute of Australia, The University of Sydney, Sydney, New South Wales, Australia
| | - Carrie R Daniel
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Courtney W Hudgens
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Theodore Nowicki
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, University of California Los Angeles, Los Angeles, California.,Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, California.,Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, California
| | - Lauren E Haydu
- Department of Surgical Oncology, Division of Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - M A Wadud Khan
- Department of Surgical Oncology, Division of Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Vancheswaran Gopalakrishnan
- Department of Surgical Oncology, Division of Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Elizabeth M Burton
- Department of Genomic Medicine, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jared Malke
- Department of Surgical Oncology, Division of Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Julie M Simon
- Department of Surgical Oncology, Division of Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chantale Bernatchez
- Department of Biologics Development, Division of Therapeutics Discovery, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Nagireddy Putluri
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Scott E Woodman
- Department of Genomic Medicine, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Y N Vashisht Gopal
- Department of Melanoma Medical Oncology, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Renato Guerrieri
- Department of Melanoma Medical Oncology, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Grant M Fischer
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Jian Wang
- Department of Biostatistics, Division of Biosciences, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Khalida M Wani
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John F Thompson
- Melanoma Institute of Australia, The University of Sydney, Sydney, New South Wales, Australia
| | - Jeffrey E Lee
- Department of Surgical Oncology, Division of Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Patrick Hwu
- Department of Cutaneous Oncology, Moffitt Cancer Center, Tampa Bay, Florida
| | - Nadim Ajami
- Department of Genomic Medicine, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jeffrey E Gershenwald
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, California
| | - Georgina V Long
- Melanoma Institute of Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Richard A Scolyer
- Melanoma Institute of Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.,Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, New South Wales, Australia
| | - Michael T Tetzlaff
- Division of Dermatopathology, Department of Pathology, University of California San Francisco, San Francisco, California
| | - Alexander J Lazar
- Department of Genomic Medicine, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Dirk Schadendorf
- Department of Dermatology, Venereology, and Allergology, University Hospital Essen and German Cancer Consortium, Partner site Essen, Germany
| | - Jennifer A Wargo
- Department of Genomic Medicine, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Surgical Oncology, Division of Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John M Kirkwood
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Ralph J DeBerardinis
- Children's Medical Research Institute and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Han Liang
- Department of Bioinformatics and Computational Biology, Division of Basic Sciences, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Andrew Futreal
- Department of Genomic Medicine, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianhua Zhang
- Department of Genomic Medicine, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - James S Wilmott
- Melanoma Institute of Australia, The University of Sydney, Sydney, New South Wales, Australia
| | - Weiyi Peng
- Department of Biology and Biochemistry, University of Houston, Houston, Texas
| | - Michael A Davies
- Department of Melanoma Medical Oncology, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Greg M Delgoffe
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Yana G Najjar
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jennifer L McQuade
- Department of Melanoma Medical Oncology, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
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4
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Lazcano R, Barreto CM, Salazar R, Carapeto F, Traweek RS, Leung CH, Gite S, Mehta J, Ingram DR, Wani KM, Vu KAT, Parra ER, Lu W, Zhou J, Witt RG, Cope B, Thirasastr P, Lin HY, Scally CP, Conley AP, Ratan R, Livingston JA, Zarzour AM, Ludwig J, Araujo D, Ravi V, Patel S, Benjamin R, Wargo J, Wistuba II, Somaiah N, Roland CL, Keung EZ, Solis L, Wang WL, Lazar AJ, Nassif EF. The immune landscape of undifferentiated pleomorphic sarcoma. Front Oncol 2022; 12:1008484. [PMID: 36313661 PMCID: PMC9597628 DOI: 10.3389/fonc.2022.1008484] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 07/31/2022] [Accepted: 09/19/2022] [Indexed: 11/25/2022] Open
Abstract
Introduction Undifferentiated pleomorphic sarcoma (UPS) can be associated with a relatively dense immune infiltration. Immune checkpoint inhibitors (anti-PD1, anti-PDL1, and anti-CTLA4) are effective in 20% of UPS patients. We characterize the immune microenvironment of UPS and its association with oncologic outcomes. Material and methods Surgically resected UPS samples were stained by immunohistochemistry (IHC) for the following: tumor-associated immune cells (CD3, CD8, CD163, CD20), immune checkpoints (stimulatory: OX40, ICOS; inhibitory: PD-L1, LAG3, IDO1, PD1), and the adenosine pathway (CD73, CD39). Sections were reviewed for the presence of lymphoid aggregates (LA). Clinical data were retrospectively obtained for all samples. The Wilcoxon rank-sum and Kruskal-Wallis tests were used to compare distributions. Correlations between biomarkers were measured by Spearman correlation. Univariate and multivariate Cox models were used to identify biomarkers associated with overall survival (OS) and disease-free survival (DFS). Unsupervised clustering was performed, and Kaplan-Meier curves and log-rank tests used for comparison of OS and DFS between immune clusters. Results Samples analyzed (n=105) included 46 primary tumors, 34 local recurrences, and 25 metastases. LA were found in 23% (n=10/43), 17% (n=4/24), and 30% (n=7/23) of primary, recurrent, and metastatic samples, respectively. In primary UPS, CD73 expression was significantly higher after preoperative radiation therapy (p=0.009). CD39 expression was significantly correlated with PD1 expression (primary: p=0.002, recurrent: p=0.004, metastatic: p=0.001), PD-L1 expression (primary: p=0.009), and CD3+ cell densities (primary: p=0.016, recurrent: p=0.043, metastatic: p=0.028). In recurrent tumors, there was a strong correlation between CD39 and CD73 (p=0.015), and both were also correlated with CD163+ cell densities (CD39 p=0.013; CD73 p<0.001). In multivariate analyses, higher densities of CD3+ and CD8+ cells (Cox Hazard Ratio [HR]=0.33; p=0.010) were independently associated with OS (CD3+, HR=0.19, p<0.001; CD8+, HR= 0.33, p=0.010) and DFS (CD3+, HR=0.34, p=0.018; CD8+, HR=0.34, p= 0.014). Unsupervised clustering of IHC values revealed three immunologically distinct clusters: immune high, intermediate, and low. In primary tumors, these clusters were significantly associated with OS (log-rank p<0.0001) and DFS (p<0.001). Conclusion We identified three immunologically distinct clusters of UPS Associated with OS and DFS. Our data support further investigations of combination anti-PD-1/PD-L1 and adenosine pathway inhibitors in UPS.
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Affiliation(s)
- Rossana Lazcano
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Carmelia M. Barreto
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ruth Salazar
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Fernando Carapeto
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Raymond S. Traweek
- Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Cheuk H. Leung
- Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Swati Gite
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jay Mehta
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Davis R. Ingram
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Khalida M. Wani
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Kim-Anh T. Vu
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Edwin R. Parra
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Wei Lu
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jianling Zhou
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Russell G. Witt
- Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Brandon Cope
- Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Prapassorn Thirasastr
- Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Heather Y. Lin
- Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Christopher P. Scally
- Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Anthony P. Conley
- Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ravin Ratan
- Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - J. Andrew Livingston
- Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Alexandra M. Zarzour
- Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Joseph Ludwig
- Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Dejka Araujo
- Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Vinod Ravi
- Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Shreyaskumar Patel
- Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Robert Benjamin
- Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jennifer Wargo
- Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ignacio I. Wistuba
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Division of Pathology and Laboratory Medicine, The University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Neeta Somaiah
- Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Christina L. Roland
- Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Emily Z. Keung
- Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Luisa Solis
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Wei-Lien Wang
- Division of Pathology and Laboratory Medicine, The University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Alexander J. Lazar
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Division of Pathology and Laboratory Medicine, The University of Texas, MD Anderson Cancer Center, Houston, TX, United States
- Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Elise F. Nassif
- Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- *Correspondence: Elise F. Nassif,
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5
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Andrews MC, Oba J, Wu CJ, Zhu H, Karpinets T, Creasy CA, Forget MA, Yu X, Song X, Mao X, Robertson AG, Romano G, Li P, Burton EM, Lu Y, Sloane RS, Wani KM, Rai K, Lazar AJ, Haydu LE, Bustos MA, Shen J, Chen Y, Morgan MB, Wargo JA, Kwong LN, Haymaker CL, Grimm EA, Hwu P, Hoon DSB, Zhang J, Gershenwald JE, Davies MA, Futreal PA, Bernatchez C, Woodman SE. Multi-modal molecular programs regulate melanoma cell state. Nat Commun 2022; 13:4000. [PMID: 35810190 PMCID: PMC9271073 DOI: 10.1038/s41467-022-31510-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 03/09/2021] [Accepted: 06/20/2022] [Indexed: 12/12/2022] Open
Abstract
Melanoma cells display distinct intrinsic phenotypic states. Here, we seek to characterize the molecular regulation of these states using multi-omic analyses of whole exome, transcriptome, microRNA, long non-coding RNA and DNA methylation data together with reverse-phase protein array data on a panel of 68 highly annotated early passage melanoma cell lines. We demonstrate that clearly defined cancer cell intrinsic transcriptomic programs are maintained in melanoma cells ex vivo and remain highly conserved within melanoma tumors, are associated with distinct immune features within tumors, and differentially correlate with checkpoint inhibitor and adoptive T cell therapy efficacy. Through integrative analyses we demonstrate highly complex multi-omic regulation of melanoma cell intrinsic programs that provide key insights into the molecular maintenance of phenotypic states. These findings have implications for cancer biology and the identification of new therapeutic strategies. Further, these deeply characterized cell lines will serve as an invaluable resource for future research in the field.
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Affiliation(s)
- Miles C. Andrews
- grid.1002.30000 0004 1936 7857Department of Medicine, Monash University, Melbourne, VIC Australia ,grid.240145.60000 0001 2291 4776Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Junna Oba
- grid.240145.60000 0001 2291 4776Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA ,grid.26091.3c0000 0004 1936 9959Department of Extended Intelligence for Medicine, The Ishii-Ishibashi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Chang-Jiun Wu
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Haifeng Zhu
- grid.240145.60000 0001 2291 4776Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Tatiana Karpinets
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Caitlin A. Creasy
- grid.240145.60000 0001 2291 4776Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Marie-Andrée Forget
- grid.240145.60000 0001 2291 4776Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Xiaoxing Yu
- grid.26091.3c0000 0004 1936 9959Department of Extended Intelligence for Medicine, The Ishii-Ishibashi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Xingzhi Song
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Xizeng Mao
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - A. Gordon Robertson
- grid.434706.20000 0004 0410 5424Canada’s Michael Smith Genome Sciences Center, BC Cancer, Vancouver, BC Canada ,Dxige Research Inc., Courtenay, BC Canada
| | - Gabriele Romano
- grid.240145.60000 0001 2291 4776Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Peng Li
- grid.240145.60000 0001 2291 4776Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Elizabeth M. Burton
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Yiling Lu
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Robert Szczepaniak Sloane
- grid.240145.60000 0001 2291 4776Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Khalida M. Wani
- grid.240145.60000 0001 2291 4776Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Kunal Rai
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Alexander J. Lazar
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA ,grid.240145.60000 0001 2291 4776Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA ,grid.240145.60000 0001 2291 4776Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Lauren E. Haydu
- grid.240145.60000 0001 2291 4776Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Matias A. Bustos
- grid.416507.10000 0004 0450 0360Departments of Translational Molecular Medicine and Genomic Sequencing Center, St John’s Cancer Institute, Providence Saint John’s Health Center, Santa Monica, CA USA
| | - Jianjun Shen
- grid.240145.60000 0001 2291 4776Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX USA
| | - Yueping Chen
- grid.240145.60000 0001 2291 4776Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX USA
| | - Margaret B. Morgan
- grid.240145.60000 0001 2291 4776Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Jennifer A. Wargo
- grid.240145.60000 0001 2291 4776Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA ,grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Lawrence N. Kwong
- grid.240145.60000 0001 2291 4776Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Cara L. Haymaker
- grid.240145.60000 0001 2291 4776Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Elizabeth A. Grimm
- grid.240145.60000 0001 2291 4776Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Patrick Hwu
- grid.240145.60000 0001 2291 4776Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA ,grid.468198.a0000 0000 9891 5233H Lee Moffitt Cancer Center, Tampa, FL USA
| | - Dave S. B. Hoon
- grid.416507.10000 0004 0450 0360Departments of Translational Molecular Medicine and Genomic Sequencing Center, St John’s Cancer Institute, Providence Saint John’s Health Center, Santa Monica, CA USA
| | - Jianhua Zhang
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Jeffrey E. Gershenwald
- grid.240145.60000 0001 2291 4776Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Michael A. Davies
- grid.240145.60000 0001 2291 4776Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - P. Andrew Futreal
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Chantale Bernatchez
- grid.240145.60000 0001 2291 4776Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA ,grid.240145.60000 0001 2291 4776Department of Biologics Development, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Scott E. Woodman
- grid.240145.60000 0001 2291 4776Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA ,grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
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6
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Zhou Y, Medik YB, Patel B, Zamler DB, Chen S, Chapman T, Schneider S, Babcock RL, Chrisikos TT, Kahn LM, Dyevoich AM, Park EM, Cogdill AP, Johnson DH, Johnson SB, Wani KM, Ledesma DA, Hudgens CW, Wang J, Khan MAW, Joon AY, Peng W, Li HS, Arora R, Tang X, Raso MG, Zhang X, Foo WC, Tetzlaff MT, Diehl GE, Clise-Dwyer K, Whitley EM, Gubin MM, Allison JP, Hwu P, Ajami NJ, Diab A, Wargo JA, Watowich SS. Abstract 5545: Intestinal toxicity to CTLA-4 blockade driven by IL-6 and myeloid infiltration. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-5545] [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: 11/16/2022]
Abstract
Abstract
Immunotherapies such as anti-CTLA-4 immune checkpoint blockade (ICB) have revolutionized cancer treatment, yet quality of life and continuation of therapy can be constrained by off-target tissue damage or immune-related adverse events (irAEs). At present, there is limited understanding of irAE mechanisms, hampering development of approaches to mitigate their damage. We addressed this problem by generating animal models of intestinal irAE. Our results show that disruption of homeostatic immunity by genetic predisposition to intestinal inflammation or acute gastrointestinal infection sensitizes mice to anti-CTLA-4-mediated intestinal toxicity. Inflammation-prone mice treated with anti-CTLA-4 showed neutrophil accumulation, systemic interleukin-6 (IL-6) release, and dysbiosis. Significantly, IL-6 blockade combined with antibiotic treatment improved anti-CTLA-4 therapeutic efficacy and reduced intestinal irAEs. Immune signatures were validated in biopsies from patients who developed colitis during ICB, supporting the utility of our models. This study provides new pre-clinical models, mechanistic insight into irAEs, and potential approaches to enhance ICB efficacy while mitigating irAEs.
Citation Format: Yifan Zhou, Yusra B. Medik, Bhakti Patel, Daniel B. Zamler, Sijie Chen, Thomas Chapman, Sarah Schneider, Rachel L. Babcock, Taylor T. Chrisikos, Laura M. Kahn, Allison M. Dyevoich, Elizabeth M. Park, Alexandria P. Cogdill, Daniel H. Johnson, Sarah B. Johnson, Khalida M. Wani, Debora A. Ledesma, Courtney W. Hudgens, Jingjing Wang, Md Abdul Wadud Khan, Aron Y. Joon, Weiyi Peng, Haiyan S. Li, Reetakshi Arora, Ximing Tang, Maria Gabriela Raso, Xuegong Zhang, Wai Chin Foo, Michael T. Tetzlaff, Gretchen E. Diehl, Karen Clise-Dwyer, Elizabeth M. Whitley, Matthew M. Gubin, James P. Allison, Patrick Hwu, Nadim J. Ajami, Adi Diab, Jennifer A. Wargo, Stephanie S. Watowich. Intestinal toxicity to CTLA-4 blockade driven by IL-6 and myeloid infiltration [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5545.
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Affiliation(s)
- Yifan Zhou
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Yusra B. Medik
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Bhakti Patel
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Thomas Chapman
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sarah Schneider
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Laura M. Kahn
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | | | - Khalida M. Wani
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Jingjing Wang
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Aron Y. Joon
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Weiyi Peng
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Haiyan S. Li
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Reetakshi Arora
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ximing Tang
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Wai Chin Foo
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | | | | | - Patrick Hwu
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Nadim J. Ajami
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Adi Diab
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
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7
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Qin Y, Bollin K, de Macedo MP, Carapeto F, Kim KB, Roszik J, Wani KM, Reuben A, Reddy ST, Williams MD, Tetzlaff MT, Wang WL, Gombos DS, Esmaeli B, Lazar AJ, Hwu P, Patel SP. Immune profiling of uveal melanoma identifies a potential signature associated with response to immunotherapy. J Immunother Cancer 2020; 8:jitc-2020-000960. [PMID: 33203661 PMCID: PMC7674090 DOI: 10.1136/jitc-2020-000960] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [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] [Accepted: 10/27/2020] [Indexed: 12/14/2022] Open
Abstract
Background To date, no systemic therapy, including immunotherapy, exists to improve clinical outcomes in metastatic uveal melanoma (UM) patients. To understand the role of immune infiltrates in the genesis, metastasis, and response to treatment for UM, we systematically characterized immune profiles of UM primary and metastatic tumors, as well as samples from UM patients treated with immunotherapies. Methods Relevant immune markers (CD3, CD8, FoxP3, CD68, PD-1, and PD-L1) were analyzed by immunohistochemistry on 27 primary and 31 metastatic tumors from 47 patients with UM. Immune gene expression profiling was conducted by NanoString analysis on pre-treatment and post-treatment tumors from patients (n=6) receiving immune checkpoint blockade or 4-1BB and OX40 dual costimulation. The immune signature of UM tumors responding to immunotherapy was further characterized by Ingenuity Pathways Analysis and validated in The Cancer Genome Atlas data set. Results Both primary and metastatic UM tumors showed detectable infiltrating lymphocytes. Compared with primary tumors, treatment-naïve metastatic UM showed significantly higher levels of CD3+, CD8+, FoxP3+ T cells, and CD68+ macrophages. Notably, levels of PD-1+ infiltrates and PD-L1+ tumor cells were low to absent in primary and metastatic UM tumors. No metastatic organ-specific differences were seen in immune infiltrates. Our NanoString analysis revealed significant differences in a set of immune markers between responders and non-responders. A group of genes relevant to the interferon-γ signature was differentially up-expressed in the pre-treatment tumors of responders. Among these genes, suppressor of cytokine signaling 1 was identified as a marker potentially contributing to the response to immunotherapy. A panel of genes that encoded pro-inflammatory cytokines and molecules were expressed significantly higher in pre-treatment tumors of non-responders compared with responders. Conclusion Our study provides critical insight into immune profiles of UM primary and metastatic tumors, which suggests a baseline tumor immune signature predictive of response and resistance to immunotherapy in UM.
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Affiliation(s)
- Yong Qin
- Pharmaceutical Sciences, School of Pharmacy, The University of Texas at El Paso, El Paso, Texas, USA
| | - Kathryn Bollin
- Medical Oncology, Scripps MD Anderson Cancer Center, San Diego, California, USA
| | | | - Fernando Carapeto
- Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Kevin B Kim
- Center for Melanoma Research and Treatment, California Pacific Medical Center Research Institute, San Francisco, California, USA
| | - Jason Roszik
- Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Khalida M Wani
- Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Alexandre Reuben
- Thoracic/Head & Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sujan T Reddy
- Neurology, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Michelle D Williams
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Michael T Tetzlaff
- Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Wei-Lien Wang
- Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Dan S Gombos
- Department of Head and Neck Surgery, Section of Ophthalmology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Bita Esmaeli
- Orbital Oncology & Ophthalmic Plastic Surgery, Department of Plastic Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Alexander J Lazar
- Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Patrick Hwu
- Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sapna P Patel
- Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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8
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Barreto CM, Solis-Soto LM, Salazar R, Gite S, Parra ER, Mino B, Ingram D, Wani KM, Leung CH, Lin H, Wistuba II, Lazar A, Wang WL. Abstract 3857: Characterization of immune cell biomarkers in undifferentiated pleomorphic sarcoma. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-3857] [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: 11/16/2022]
Abstract
Abstract
Background: Undifferentiated pleomorphic sarcoma (UPS) are genetically complex sarcomas often showing a relatively higher immune infiltration among sarcomas, and a demonstrated benefit for immunotherapy in a subset of patients. This study characterizes the immune microenvironment of UPS including tumor infiltrating lymphocytes (TILs), as well as immune checkpoint (IC) and related biomarkers.
Methods: We used FFPE surgical resected UPS from 90 patients (43 primary, 28 recurrence and 19 metastasis) placed in a tissue microarray and stained with immunohistochemistry for the following biomarkers: IC (stimulatory: OX40 & ICOS; inhibitory: PD-L1, LAG3, IDO1, & PD1), TILs (CD3 & CD8), monocytes-macrophages (CD163), Adenosine Pathway (CD73 & CD39), and pSTAT3. We scored TIL and IC biomarkers as positive cell densities, and PD-L1, pSTAT3, CD73 and CD39 as percentage of expression in malignant cells. Clinicopathological data and clinical outcome were available for all patients. Spearman correlation was used to assess the correlation between two biomarkers. Cox proportional hazard regression models were used to identify the prognostic biomarkers for overall survival (OS), recurrence-free survival (RFS), and metastasis-free survival (MFS).
Results: In our cohort, PD-L1, pSTAT3, CD73 and CD39 positive expression (cut-off ≥1%) was 19, 73 78 and 68% respectively. These biomarkers were positively correlated with immune infiltrates: CD3 (p=0.013, 0.009, 0.009, <.001), CD8 (p=0.004, 0.016, <.001, <.001) and ICOS (p=0.005, 0.222, 0.007, 0.022). CD73 and CD39 were also positively correlated with both CD163 (p=0.001, <.001) and PD-1 (p=0.012, <.001). In recurrent tumors, smaller tumors had higher CD3, CD8, ICOS and PD-1 (p=0.011, 0.045, 0.013, 0.045). In metastatic tumor, CD163 and OX40 were positively correlated with age (p=0.045, 0.019). OX40 was inversely correlated with tumor size (p=0.04). ICOS positively correlated with PD-1, PD-L1 and CD39 (p<.001, 0.002, 0.003) in primary tumors; with IDO1 and PD1 (p=0.012, <.001) in recurrent tumors; and with PD-L1 expression (p=0.031) in metastatic tumors. Low CD3, CD8, CD163 densities (cut-off median) were associated with inferior OS (HR: 3.19 [1.37, 7.42]; p=0.007), RFS (HR: 2.79 [1.21, 6.42], p=0.016), and MFS (HR: 2.42 [1.05, 5.56]; p=0.038) after adjusting for size, respectively. Low CD73 and PD-L1 (cut-off median) were associated with inferior OS (HR 3.03 [HR: 1.21, 7.61], p=0.018), RFS (HR: 2.59 [1.06, 6.36]; p=0.037), and MFS (HR: 2.43 [1.00, 5.89], p=0.049), respectively.
Conclusions: In this study, we characterized the immune cell infiltrates and the expression of PD-L1, pSTAT3, CD73 and CD39 in UPS. These biomarkers differentially correlated with clinicopathological characteristics in primary, recurrent and metastatic tumors. Lower TILs and low CD73/PD-L1 expression were associated with inferior survival outcomes.
Citation Format: Carmelia M. Barreto, Luisa M. Solis-Soto, Ruth Salazar, Swati Gite, Edwin R. Parra, Barbara Mino, Davis Ingram, Khalida M. Wani, Cheuk H. Leung, Heather Lin, Ignacio I. Wistuba, Alexander Lazar, Wei-Lien Wang. Characterization of immune cell biomarkers in undifferentiated pleomorphic sarcoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3857.
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Affiliation(s)
| | | | | | - Swati Gite
- UT MD Anderson Cancer Center, Houston, TX
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9
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Pilie PG, Gheeya JS, Kyewalabye K, Goswamy RV, Wani KM, Le H, Campbell E, Sanchez NS, Yang D, Garmezy B, Ileana Dumbrava EE, Rodon Ahnert J, Heffernan T, Holla V, Shaw KR, Meric-Bernstam F, Lazar AJ, Wang WL, Yap TA. Identifying functional loss of ATM gene in patients with advanced cancer. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.3629] [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
3629 Background: ATM is frequently mutated in cancer, and defects may serve as a putative predictive biomarker. However, the functional impact of most ATM variants is not well known. In this study, we examined the relationship between ATM variants and ATM protein expression to better discern ATM functional defects in patients (pts) with advanced cancer. Methods: We retrospectively identified pts seen at MD Anderson Cancer Center who had ATM variants detected on CLIA-certified next generation sequencing (NGS) assays. ATM immunohistochemistry (IHC) was performed on available tumors. We then prospectively assessed ATM IHC on tumors from pts who were referred for DNA damage repair inhibitor (DDRi) trials. Functional classification of the variants was performed via published in silico tools and/or precision oncology decision support (PODS). An IHC cut-off of 100% loss in tumor cell nuclei defined ATM loss of protein (LOP). Results: Of 1394 ATM-mutant tumors identified retrospectively, ATM alterations were classified as 16% (N = 216) inactivating, 12% (N = 163) potentially inactivating, 71% (N = 993) variant of unknown significance (VUS), and 2% (N = 22) benign. Coding variants were seen across the ATM exonic structure/splice sites, and 20 individual variants were shared in > 10 pts. 263/297 available retrospective tumor samples had interpretable IHC results; 27% (N = 72) had ATM LOP. LOP was most prevalent in tumors with inactivating ATM variants (39/100, 39%); but, importantly, LOP was seen in 20% (N = 33/162) of potentially inactivating/VUS, thus better clarifying their functional impact. In the prospective cohort of 217 pt tumors, 17% (N = 37) had ATM LOP. 29% (N = 62/217) of this cohort also had ATM variants. ATM LOP was seen in 48% of tumors with inactivating variants (N = 14/29), 25% of tumors with potentially/VUS(N = 9/36), and 9% (N = 14/156) of tumors without ATM variants identified. ATM LOP was detected most commonly in colorectal (24%; N = 8/34), cholangiocarcinoma (20%; N = 6/30), prostate (16%; N = 16/104) and pancreatic (9%; N = 1/11) cancers among this cohort of pts referred for DDRi trials. Conclusions: ATM coding variants occurred across the gene, with certain variants shared across tumor types. The functional impact of most ATM variants was VUS, and ATM LOP can help clarify function in up to 25% of these VUS. Also, ATM LOP can be seen even in tumors without ATM variants identified, suggesting epigenetic or post-translational loss. Future prospective studies assessing predictive capability of paired DNA and protein-level profiling of ATM are warranted.
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Affiliation(s)
| | - Jinesh S. Gheeya
- University of Texas Health Science Center at Houston, Houston, TX
| | | | | | - Khalida M Wani
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Hung Le
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Erick Campbell
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Nora Sylvia Sanchez
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy/University of Texas MD Anderson Cancer Center, Houston, TX
| | - Dong Yang
- University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | - Vijaykumar Holla
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Kenna Rael Shaw
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Wei-Lien Wang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Timothy A Yap
- The University of Texas MD Anderson Cancer Center, Houston, TX
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10
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Johnson DH, Hailemichael Y, Foo WC, Hess KR, Haymaker CL, Wani KM, Lazar AJ, Saberian CM, Bentebibel SE, Burton EM, Abu-Sbeih H, Wang Y, Hwu P, Diab A. Interleukin-6 is potential target to de-couple checkpoint inhibitor-induced colitis from antitumor immunity. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.2616] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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
2616 Background: A deep understanding of the immunobiology of checkpoint inhibitor (CPI) induced immune related toxicities, such as immune related enterocolitis (irEC), and how these compare to the immune signatures in tumors could lead to the development of strategies that de-couple autoimmunity from anti-tumor immunity. Methods: Total RNA from patient-matched irEC and normal colon FFPE tissue from patients [n = 12] receiving CPIs were profiled with the 770 gene NanoString nCounter PanCancer Immune Profiling Panel (NanoPCIP). The mean fold change in gene expression from normal vs. irEC inflamed colonic tissue and baseline vs. on-treatment tumor samples from patients responding or non-responding to ipilimumab based therapy were analyzed. C57BL/6 mice with B16.BL6 melanoma tumors were treated with systemic anti-IL-6 + anti-CTLA-4 vs. anti-CTLA4 alone vs. placebo and tumor size was measured. Results: In patients with irEC, the highest significantly upregulated differentially expressed gene (DEG) in inflamed colon tissue encoded for IL-6 (Fold change +24.1). None of the significant and highest upregulated DEGs in the colitis, including IL-6, were significantly upregulated in responding tumors. Interestingly, IL-6 was also the highest upregulated DEG in non-responding tumors numerically. When comparing mean fold changes across these analyses, the gene with the largest difference in upregulatation between colitis and responding tumors was IL-6; the other highest upregulated genes in colitis encoded for neutrophil and monocyte chemotactic molecules. In our mouse models, the addition of IL-6 blockade to anti-CTLA-4 therapy significantly improved tumor shrinkage compared to anti-CTLA-4 alone. Conclusions: Our data demonstrates that IL-6-mediated inflammation may be more prevalent in irEC and tumors not responding to CPIs than in tumors responding, and blocking IL-6 enhances CPI anti-melanoma activity. Targeting IL-6 may ameliorate irEC without hindering anti-tumor immunity.
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Affiliation(s)
| | | | - Wai Chin Foo
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Kenneth R. Hess
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Khalida M Wani
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | | | - Yinghong Wang
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Patrick Hwu
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Adi Diab
- The University of Texas MD Anderson Cancer Center, Houston, TX
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11
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Roszik J, Ring KL, Wani KM, Lazar AJ, Yemelyanova AV, Soliman PT, Frumovitz M, Jazaeri AA. Gene Expression Analysis Identifies Novel Targets for Cervical Cancer Therapy. Front Immunol 2018; 9:2102. [PMID: 30283446 PMCID: PMC6156434 DOI: 10.3389/fimmu.2018.02102] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [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] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 08/28/2018] [Indexed: 01/17/2023] Open
Abstract
Although there has been significant progress in prevention and treatment of cervical cancer, this malignancy is still a leading cause of cancer death for women. Anti-angiogenesis and immunotherapy approaches have been providing survival benefits, however, response rates and durability of response need to be improved. There is a clear need for combination therapies that increase effectiveness of these agents and further improve patient outcome. Previous studies have largely focused on gene expression and molecular pathways in untreated cervix cancer. The goal of this study was to evaluate cancer-specific molecular pathways and their correlation with tumor immune profile in recurrent cervical cancer. Tumor and adjacent normal tissues were used to identify potential combination therapy targets. We found that DNA damage repair pathway genes were significantly overexpressed in the tumor. Based on our results and other recent investigations, we suggest that combination immune checkpoint and PARP inhibitor therapy is a high priority consideration for patients with recurrent, previously treated cervical cancer. We also show that multiple epithelial-mesenchymal transition-related genes, including MAP2K4, ID2, JAK1, FGF2, PIK3R1, AKT3, FGF13, and STAT3 may be potential targets. Interestingly, high-throughput analysis of Cancer Genome Atlas data identified distinct targets, including Fatty acid synthase FASN and Matrix Metallopeptidase 1 MMP1 as novel, promising combination therapy partners.
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Affiliation(s)
- Jason Roszik
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Kari L. Ring
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Virginia Health System, Charlottesville, VA, United States
| | - Khalida M. Wani
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Alexander J. Lazar
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Anna V. Yemelyanova
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Pamela T. Soliman
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Michael Frumovitz
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Amir A. Jazaeri
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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12
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Zaky W, Patil SS, Park M, Liu D, Wang WL, Wani KM, Calle S, Ketonen L, Khatua S. Ganglioglioma in children and young adults: single institution experience and review of the literature. J Neurooncol 2018; 139:739-747. [PMID: 29882043 DOI: 10.1007/s11060-018-2921-6] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 06/01/2018] [Indexed: 11/26/2022]
Abstract
BACKGROUND Ganglioglioma (GG) is a rare mixed glial-neuronal neoplasm accounting for 0.5-5% of all pediatric central nervous system (CNS) tumors. Rarity of this tumor has precluded defining robust treatment guidelines. This retrospective study evaluates the prognostic factors and outcomes of this rare neoplasm. PATIENTS AND METHODS Retrospective analysis of 55 patients with GG was conducted to describe clinical findings, and outcomes. Kaplan-Meier survival and Cox-regression analyses were performed to assess the overall survival (OS) and progression-free survival (PFS). RESULTS The mean age at diagnosis was 11.8 years (range 1-21 years) with a median follow-up period of 9.5 years. 53 patients (92.7%) had low grade GG and 2 patients had anaplastic GG. 25 patients had tumor progression, whose median PFS was 12 years. Six patients with low grade GG progressed to a higher grade, with median survival of 9.1 month after transformation. The 5 and 10 year PFS were 65 and 57%, respectively. The 5 and 10 year OS was 96 and 86% respectively. 8 of the 19 (42%) samples tested demonstrated positivity for the BRAF V600E mutation. Multivariate Cox regression analyses showed location and extent of resection were significant factors for PFS and presence of metastatsis attained significance for OS. CONCLUSION This is the one of the largest retrospective study of pediatric GG. Identifying clinical variables, which could stratify these tumors into low- and high-risk groups might help to profile a risk-based therapeutic strategy. Collaborative multiinstitutional prospective studies are warranted to delineate treatment consensus and investigate prognostic factors.
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Affiliation(s)
- Wafik Zaky
- Department of Pediatric Patient Care, UT MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 87, Houston, TX, 77030, USA
| | - Shekhar S Patil
- Department of Internal Medicine, McGovern Medical School, UT Health Science Center, 7440 Cambridge Street, Houston, TX, 77054, USA
| | - Minjeong Park
- Department of Biostatistics, UT MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Diane Liu
- Department of Biostatistics, UT MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Wei-Lien Wang
- Department of Pathology, UT MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
- Department of Translational Molecular Pathology, UT MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Khalida M Wani
- Department of Translational Molecular Pathology, UT MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Susana Calle
- Department of Diagnostic Radiology, UT MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Leena Ketonen
- Department of Diagnostic Radiology, UT MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Soumen Khatua
- Department of Pediatric Patient Care, UT MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 87, Houston, TX, 77030, USA.
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13
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Olar A, Goodman LD, Wani KM, Boehling NS, Sharma DS, Mody RR, Gumin J, Claus EB, Lang FF, Cloughesy TF, Lai A, Aldape KD, DeMonte F, Sulman EP. A gene expression signature predicts recurrence-free survival in meningioma. Oncotarget 2018; 9:16087-16098. [PMID: 29662628 PMCID: PMC5882319 DOI: 10.18632/oncotarget.24498] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 02/01/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Meningioma is the most common primary brain tumor and has a variable risk of local recurrence. While World Health Organization (WHO) grade generally correlates with recurrence, there is substantial within-grade variation of recurrence risk. Current risk stratification does not accurately predict which patients are likely to benefit from adjuvant radiation therapy (RT). We hypothesized that tumors at risk for recurrence have unique gene expression profiles (GEP) that could better select patients for adjuvant RT. METHODS We developed a recurrence predictor by machine learning modeling using a training/validation approach. RESULTS Three publicly available AffymetrixU133 gene expression datasets (GSE9438, GSE16581, GSE43290) combining 127 primary, non-treated meningiomas of all grades served as the training set. Unsupervised variable selection was used to identify an 18-gene GEP model (18-GEP) that separated recurrences. This model was validated on 62 primary, non-treated cases with similar grade and clinical variable distribution as the training set. When applied to the validation set, 18-GEP separated recurrences with a misclassification error rate of 0.25 (log-rank p=0.0003). 18-GEP was predictive for tumor recurrence [p=0.0008, HR=4.61, 95%CI=1.89-11.23)] and was predictive after adjustment for WHO grade, mitotic index, sex, tumor location, and Simpson grade [p=0.0311, HR=9.28, 95%CI=(1.22-70.29)]. The expression signature included genes encoding proteins involved in normal embryonic development, cell proliferation, tumor growth and invasion (FGF9, SEMA3C, EDNRA), angiogenesis (angiopoietin-2), cell cycle regulation (CDKN1A), membrane signaling (tetraspanin-7, caveolin-2), WNT-pathway inhibitors (DKK3), complement system (C1QA) and neurotransmitter regulation (SLC1A3, Secretogranin-II). CONCLUSIONS 18-GEP accurately stratifies patients with meningioma by recurrence risk having the potential to guide the use of adjuvant RT.
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Affiliation(s)
- Adriana Olar
- Medical University of South Carolina & Hollings Cancer Center, Departments of Pathology and Laboratory Medicine & Neurosurgery, Charleston, SC, USA
| | - Lindsey D. Goodman
- Neurosciences Graduate Group, Perlman School of Medicine, University of Pennsylvania, Department of Biology, Philadelphia, PA, USA
| | - Khalida M. Wani
- The University of Texas MD Anderson Cancer Center, Department of Translational Molecular Pathology, Houston, TX, USA
| | | | - Devi S. Sharma
- The University of California at Los Angeles, Department of Neurology, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Reema R. Mody
- The University of California at Los Angeles, Department of Neurology, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Joy Gumin
- The University of Texas MD Anderson Cancer Center, Department of Neurosurgery, Houston, TX, USA
| | - Elizabeth B. Claus
- Brigham and Women’s Hospital, Harvard Medical School, Department of Neurosurgery, Boston, MA, USA
- School of Public Health, Yale University, Department of Biostatistics, New Haven, CT, USA
| | - Frederick F. Lang
- The University of Texas MD Anderson Cancer Center, Department of Neurosurgery, Houston, TX, USA
| | - Timothy F. Cloughesy
- The University of California at Los Angeles, Department of Neurology, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Albert Lai
- The University of California at Los Angeles, Department of Neurology, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Kenneth D. Aldape
- MacFeeters-Hamilton Brain Tumour Centre, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Franco DeMonte
- The University of Texas MD Anderson Cancer Center, Department of Neurosurgery, Houston, TX, USA
| | - Erik P. Sulman
- The University of Texas MD Anderson Cancer Center, Department of Translational Molecular Pathology, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center, Departments of Radiation Oncology and Genomic Medicine, Houston, TX, USA
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14
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Yam C, Xu X, Davies MA, Gimotty PA, Morrissette JJD, Tetzlaff MT, Wani KM, Liu S, Deng W, Buckley M, Zhao J, Amaravadi RK, Haas NB, Kudchadkar RR, Pavlick AC, Sosman JA, Tawbi H, Walker L, Schuchter LM, Karakousis GC, Gangadhar TC. A Multicenter Phase I Study Evaluating Dual PI3K and BRAF Inhibition with PX-866 and Vemurafenib in Patients with Advanced BRAF V600-Mutant Solid Tumors. Clin Cancer Res 2017; 24:22-32. [PMID: 29051322 DOI: 10.1158/1078-0432.ccr-17-1807] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/29/2017] [Accepted: 10/12/2017] [Indexed: 01/12/2023]
Abstract
Purpose: The objectives of the study were to evaluate the safety of daily oral PX-866 in combination with twice daily vemurafenib and to identify potential predictive biomarkers for this novel combination.Experimental Design: We conducted a phase I, open-label, dose-escalation study in patients with advanced BRAF V600-mutant solid tumors. PX-866 was administered on a continuous schedule in combination with vemurafenib. Patients underwent a baseline and on-treatment biopsy after 1-week of PX-866 monotherapy for biomarker assessment.Results: Twenty-four patients were enrolled. The most common treatment-related adverse events were gastrointestinal side effects. One dose-limiting toxicity (DLT) of grade 3 rash and one DLT of grade 3 pancreatitis were observed in cohort 2 (PX-866 6 mg daily; vemurafenib 960 mg twice daily) and cohort 3 (PX-866 8 mg daily; vemurafenib 960 mg twice daily), respectively. Of 23 response-evaluable patients, seven had confirmed partial responses (PR), 10 had stable disease, and six had disease progression. Decreases in intratumoral pAKT expression were observed following treatment with PX-866. Patients who achieved PRs had higher rates of PTEN loss by IHC (80% vs. 58%) and pathogenic PTEN mutations and/or deletions (57% vs. 25%). Two patients with durable PRs had an increase in intratumoral CD8+ T-cell infiltration following treatment with PX-866.Conclusions: PX-866 was well tolerated at its maximum tolerated single-agent dose when given in combination with a modified dose of vemurafenib (720 mg twice daily). Response to treatment appeared to be associated with PTEN loss and treatment with PX-866 seemed to increase CD8+ T-cell infiltration in some patients. Clin Cancer Res; 24(1); 22-32. ©2017 AACR.
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Affiliation(s)
- Clinton Yam
- Abramson Cancer Center and the Division of Hematology & Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xiaowei Xu
- Abramson Cancer Center and the Division of Hematology & Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Michael A Davies
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Phyllis A Gimotty
- Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jennifer J D Morrissette
- Center for Personalized Diagnostics, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Khalida M Wani
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shujing Liu
- Abramson Cancer Center and the Division of Hematology & Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Wanleng Deng
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Meghan Buckley
- Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jianhua Zhao
- Center for Personalized Diagnostics, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ravi K Amaravadi
- Abramson Cancer Center and the Division of Hematology & Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Naomi B Haas
- Abramson Cancer Center and the Division of Hematology & Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | | | | | - Hussein Tawbi
- The University of Texas MD Anderson Cancer Center, Houston, Texas.,The University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Luke Walker
- Cascadian Therapeutics (formerly Oncothyreon) Inc., Seattle, Washington
| | - Lynn M Schuchter
- Abramson Cancer Center and the Division of Hematology & Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Giorgos C Karakousis
- Abramson Cancer Center and the Division of Hematology & Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Tara C Gangadhar
- Abramson Cancer Center and the Division of Hematology & Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
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15
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Olar A, Wani KM, Wilson CD, Zadeh G, DeMonte F, Jones DTW, Pfister SM, Sulman EP, Aldape KD. Global epigenetic profiling identifies methylation subgroups associated with recurrence-free survival in meningioma. Acta Neuropathol 2017; 133:431-444. [PMID: 28130639 PMCID: PMC5600514 DOI: 10.1007/s00401-017-1678-x] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [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: 11/19/2016] [Revised: 01/16/2017] [Accepted: 01/17/2017] [Indexed: 12/14/2022]
Abstract
Meningioma is the most common primary brain tumor and carries a substantial risk of local recurrence. Methylation profiles of meningioma and their clinical implications are not well understood. We hypothesized that aggressive meningiomas have unique DNA methylation patterns that could be used to better stratify patient management. Samples (n = 140) were profiled using the Illumina HumanMethylation450BeadChip. Unsupervised modeling on a training set (n = 89) identified 2 molecular methylation subgroups of meningioma (MM) with significantly different recurrence-free survival (RFS) times between the groups: a prognostically unfavorable subgroup (MM-UNFAV) and a prognostically favorable subgroup (MM-FAV). This finding was validated in the remaining 51 samples and led to a baseline meningioma methylation classifier (bMMC) defined by 283 CpG loci (283-bMMC). To further optimize a recurrence predictor, probes subsumed within the baseline classifier were subject to additional modeling using a similar training/validation approach, leading to a 64-CpG loci meningioma methylation predictor (64-MMP). After adjustment for relevant clinical variables [WHO grade, mitotic index, Simpson grade, sex, location, and copy number aberrations (CNAs)] multivariable analyses for RFS showed that the baseline methylation classifier was not significant (p = 0.0793). The methylation predictor, however, was significantly associated with tumor recurrence (p < 0.0001). CNAs were extracted from the 450k intensity profiles. Tumor samples in the MM-UNFAV subgroup showed an overall higher proportion of CNAs compared to the MM-FAV subgroup tumors and the CNAs were complex in nature. CNAs in the MM-UNFAV subgroup included recurrent losses of 1p, 6q, 14q and 18q, and gain of 1q, all of which were previously identified as indicators of poor outcome. In conclusion, our analyses demonstrate robust DNA methylation signatures in meningioma that correlate with CNAs and stratify patients by recurrence risk.
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Affiliation(s)
- Adriana Olar
- Departments of Pathology and Laboratory Medicine and Neurosurgery, Medical University of South Carolina and Hollings Cancer Center, 171 Ashley Ave., MSC 908, Charleston, SC, 29425, USA.
| | - Khalida M Wani
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 2130 W Holcombe Blvd., Houston, TX, 77030, USA
| | - Charmaine D Wilson
- Center for Nursing Research, The University of Texas School of Nursing, 6901 Bertner St., Houston, TX, 77030, USA
| | - Gelareh Zadeh
- Princess Margaret Cancer Centre, MacFeeters-Hamilton Brain Tumour Centre, College Street 101, Toronto, M5G 1L7, ON, Canada
| | - Franco DeMonte
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - David T W Jones
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Network (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Network (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
| | - Erik P Sulman
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 2130 W Holcombe Blvd., Houston, TX, 77030, USA
- Departments of Radiation Oncology and Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Kenneth D Aldape
- Princess Margaret Cancer Centre, MacFeeters-Hamilton Brain Tumour Centre, College Street 101, Toronto, M5G 1L7, ON, Canada
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16
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Chen G, McQuade JL, Panka DJ, Hudgens CW, Amin-Mansour A, Mu XJ, Bahl S, Jané-Valbuena J, Wani KM, Reuben A, Creasy CA, Jiang H, Cooper ZA, Roszik J, Bassett RL, Joon AY, Simpson LM, Mouton RD, Glitza IC, Patel SP, Hwu WJ, Amaria RN, Diab A, Hwu P, Lazar AJ, Wargo JA, Garraway LA, Tetzlaff MT, Sullivan RJ, Kim KB, Davies MA. Clinical, Molecular, and Immune Analysis of Dabrafenib-Trametinib Combination Treatment for BRAF Inhibitor-Refractory Metastatic Melanoma: A Phase 2 Clinical Trial. JAMA Oncol 2017; 2:1056-64. [PMID: 27124486 DOI: 10.1001/jamaoncol.2016.0509] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
IMPORTANCE Combined treatment with dabrafenib and trametinib (CombiDT) achieves clinical responses in only about 15% of patients with BRAF inhibitor (BRAFi)-refractory metastatic melanoma in contrast to the higher response rate observed in BRAFi-naïve patients. Identifying correlates of response and mechanisms of resistance in this population will facilitate clinical management and rational therapeutic development. OBJECTIVE To determine correlates of benefit from CombiDT therapy in patients with BRAFi-refractory metastatic melanoma. DESIGN, SETTING, AND PARTICIPANTS Single-center, single-arm, open-label phase 2 trial of CombiDT treatment in patients with BRAF V600 metastatic melanoma resistant to BRAFi monotherapy conducted between September 2012 and October 2014 at the University of Texas MD Anderson Cancer Center. Key eligibility criteria for participants included BRAF V600 metastatic melanoma, prior BRAFi monotherapy, measurable disease (RECIST 1.1), and tumor accessible for biopsy. INTERVENTIONS Patients were treated with dabrafenib (150 mg, twice daily) and trametinib (2 mg/d) continuously until disease progression or intolerance. All participants underwent a mandatory baseline biopsy, and optional biopsy specimens were obtained on treatment and at disease progression. Whole-exome sequencing, reverse transcription polymerase chain reaction analysis for BRAF splicing, RNA sequencing, and immunohistochemical analysis were performed on tumor samples, and blood was analyzed for levels of circulating BRAF V600. MAIN OUTCOMES AND MEASURES The primary end point was overall response rate (ORR). Progression-free survival (PFS) and overall survival (OS) were secondary clinical end points. RESULTS A total of 28 patients were screened, and 23 enrolled. Among evaluable patients, the confirmed ORR was 10%; disease control rate (DCR) was 45%, and median PFS was 13 weeks. Clinical benefit was associated with duration of prior BRAFi therapy greater than 6 months (DCR, 73% vs 11% for ≤6 months; P = .02) and decrease in circulating BRAF V600 at day 8 of cycle 1 (DCR, 75% vs 18% for no decrease; P = .02) but not with pretreatment mitogen-activated protein kinase (MAPK) pathway mutations or activation. Biopsy specimens obtained during treatment demonstrated that CombiDT therapy failed to achieve significant MAPK pathway inhibition or immune infiltration in most patients. CONCLUSIONS AND RELEVANCE The baseline presence of MAPK pathway alterations was not associated with benefit from CombiDT in patients with BRAFi-refractory metastatic melanoma. Failure to inhibit the MAPK pathway provides a likely explanation for the limited clinical benefit of CombiDT in this setting. Circulating BRAF V600 is a promising early biomarker of clinical response. TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT01619774.
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Affiliation(s)
- Guo Chen
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Jennifer L McQuade
- Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston
| | - David J Panka
- Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Courtney W Hudgens
- Departments of Pathology and Translational and Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston
| | | | | | | | | | - Khalida M Wani
- Departments of Pathology and Translational and Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston
| | - Alexandre Reuben
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston7Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston
| | - Caitlyn A Creasy
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Hong Jiang
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston7Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston
| | - Zachary A Cooper
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston7Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston
| | - Jason Roszik
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Roland L Bassett
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston
| | - Aron Y Joon
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston
| | - Lauren M Simpson
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Rosalind D Mouton
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Isabella C Glitza
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Sapna P Patel
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Wen-Jen Hwu
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Rodabe N Amaria
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Adi Diab
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Alexander J Lazar
- Departments of Pathology and Translational and Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston
| | - Jennifer A Wargo
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston7Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston
| | | | - Michael T Tetzlaff
- Departments of Pathology and Translational and Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston
| | | | - Kevin B Kim
- California Pacific Medical Center Research Institute, San Francisco
| | - Michael A Davies
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston11Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston
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17
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Tetzlaff MT, Curry JL, Yin V, Pattanaprichakul P, Manonukul J, Uiprasertkul M, Manyam GC, Wani KM, Aldape K, Zhang L, Prieto VG, Esmaeli B. Distinct pathways in the pathogenesis of sebaceous carcinomas implicated by differentially expressed microRNAs. JAMA Ophthalmol 2016. [PMID: 26203913 DOI: 10.1001/jamaophthalmol.2015.2310] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
IMPORTANCE The molecular-genetic alterations contributing to the pathogenesis of sebaceous carcinoma and sebaceous adenoma remain poorly understood. Given that sebaceous carcinoma is associated with substantial morbidity and mortality, there is a critical need to delineate the pathways driving sebaceous carcinoma and candidate molecules for targeted therapy. OBJECTIVE To describe differentially expressed microRNAs (miRNAs) in a series of periocular sebaceous carcinomas compared with sebaceous adenomas in order to identify pathways driving the pathogenesis of sebaceous carcinoma. DESIGN, SETTING, AND PARTICIPANTS Thirty sebaceous carcinomas and 23 sebaceous adenomas (including 11 that were confirmed to be related to Muir-Torre syndrome and 6 that were confirmed to be sporadic) were obtained from archives (from 48 patients) of 2 institutions (University of Texas MD Anderson Cancer Center, Houston, and Siriraj Hospital, Mahidol University, Bangkok, Thailand) and profiled. MAIN OUTCOMES AND MEASURES Expression of miRNAs was determined using total RNA from formalin-fixed, paraffin-embedded tissue and real-time reverse transcription-polymerase chain reaction performed in a microfluidics card containing 378 unique miRNAs. Fold change was determined using the ΔΔCt method (reference probe, RNU48). Median centering was used to normalize the data. Two-sample t tests were used to identify differentially expressed miRNAs. The false discovery rate was assessed by β-uniform mixture analysis of P values from the t statistics. Significance was defined by this estimated false discovery rate. RESULTS Serial testing and validation confirmed overexpression of 2 miRNAs previously reported to be oncogenic, miR-486-5p (4.4-fold; P = 2.4 × 10-8) and miR-184 (3.5-fold; P = 1.7 × 10-6), in sebaceous carcinoma compared with sebaceous adenoma and downregulation of 2 miRNAs previously reported to have tumor-suppressive properties, miR-211 (-5.8-fold; P = 2.3 × 10-9) and miR-518d (-4.5-fold; 6.7 × 10-5), in sebaceous carcinoma compared with sebaceous adenoma. CONCLUSIONS AND RELEVANCE Sebaceous carcinoma exhibits an miRNA expression profile distinct from that of sebaceous adenoma, implicating dysregulation of NF-κB and PTEN (targets of miR-486-5p) and TGF-β signaling (target of miR-211) in the pathogenesis of sebaceous carcinoma. The identification of miRNAs whose expression is altered in sebaceous carcinoma compared with sebaceous adenoma provides a novel entry point for a more comprehensive understanding of the molecular-genetic alterations pivotal to the development of sebaceous carcinoma.
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Affiliation(s)
- Michael T Tetzlaff
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston
| | - Jonathan L Curry
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston
| | - Vivian Yin
- Orbital Oncology and Ophthalmic Plastic Surgery, Department of Plastic Surgery, University of Texas MD Anderson Cancer Center, Houston
| | - Penvadee Pattanaprichakul
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston3Department of Dermatology, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Jane Manonukul
- Department of Dermatology, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Mongkol Uiprasertkul
- Department of Dermatology, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Ganiraju C Manyam
- Department of Biostatistics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston
| | - Khalida M Wani
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston
| | - Kenneth Aldape
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston
| | - Li Zhang
- Department of Biostatistics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston
| | - Victor G Prieto
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston
| | - Bita Esmaeli
- Orbital Oncology and Ophthalmic Plastic Surgery, Department of Plastic Surgery, University of Texas MD Anderson Cancer Center, Houston
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18
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Haydu LE, Calderone TL, Miller J, Bassett RL, Joon A, Zhang J, Morgan MB, Shaw KR, Cooper ZA, Burton EM, Siroy A, Wani KM, Stingo F, Baladandayuthapani V, Tetzlaff MT, Wargo JA, Lazar AJF, Davies MA, Gershenwald JE. Comparison of DNA and RNA analyte extraction and melanin removal methods from formalin-fixed, paraffin-embedded (FFPE) melanoma. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.15_suppl.e20002] [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: 11/20/2022] Open
Affiliation(s)
| | | | - John Miller
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Aron Joon
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jianhua Zhang
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Kenna Rael Shaw
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Alan Siroy
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Khalida M Wani
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Franceso Stingo
- The University of Texas MD Anderson Cancer Center, Houston, TX
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19
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Olar A, Wani KM, Alfaro-Munoz KD, Heathcock LE, van Thuijl HF, Gilbert MR, Armstrong TS, Sulman EP, Cahill DP, Vera-Bolanos E, Yuan Y, Reijneveld JC, Ylstra B, Wesseling P, Aldape KD. IDH mutation status and role of WHO grade and mitotic index in overall survival in grade II-III diffuse gliomas. Acta Neuropathol 2015; 129:585-96. [PMID: 25701198 DOI: 10.1007/s00401-015-1398-z] [Citation(s) in RCA: 235] [Impact Index Per Article: 26.1] [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: 10/01/2014] [Revised: 02/11/2015] [Accepted: 02/12/2015] [Indexed: 12/31/2022]
Abstract
Diffuse gliomas are up till now graded based upon morphology. Recent findings indicate that isocitrate dehydrogenase (IDH) mutation status defines biologically distinct groups of tumors. The role of tumor grade and mitotic index in patient outcome has not been evaluated following stratification by IDH mutation status. To address this, we interrogated 558 WHO grade II-III diffuse gliomas for IDH1/2 mutations and investigated the prognostic impact of WHO grade within IDH-mutant and IDH-wild type tumor subsets independently. The prognostic impact of grade was modest in IDH-mutant [hazard ratio (HR) = 1.21, 95 % confidence interval (CI) = 0.91-1.61] compared to IDH-wild type tumors (HR = 1.74, 95 % CI = 0.95-3.16). Using a dichotomized mitotic index cut-off of 4/1000 tumor cells, we found that while mitotic index was significantly associated with outcome in IDH-wild type tumors (log-rank p < 0.0001, HR = 4.41, 95 % CI = 2.55-7.63), it was not associated with outcome in IDH-mutant tumors (log-rank p = 0.5157, HR = 1.10, 95 % CI = 0.80-1.51), and could demonstrate a statistical interaction (p < 0.0001) between IDH mutation and mitotic index (i.e., suggesting that the effect of mitotic index on patient outcome is dependent on IDH mutation status). Patient age, an established prognostic factor in diffuse glioma, was significantly associated with outcome only in the IDH-wild type subset, and consistent with prior data, 1p/19q co-deletion conferred improved outcome in the IDH-mutant cohort. These findings suggest that stratification of grade II-III gliomas into subsets defined by the presence or absence of IDH mutation leads to subgroups with distinct prognostic characteristics. Further evaluation of grading criteria and prognostic markers is warranted within IDH-mutant versus IDH-wild type diffuse grade II-III gliomas as independent entities.
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Affiliation(s)
- Adriana Olar
- Department of Pathology, G1.3510, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA,
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20
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Olar A, Wani KM, Sulman EP, Mansouri A, Zadeh G, Wilson CD, DeMonte F, Fuller GN, Aldape KD. Mitotic Index is an Independent Predictor of Recurrence-Free Survival in Meningioma. Brain Pathol 2014; 25:266-75. [PMID: 25040885 DOI: 10.1111/bpa.12174] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Accepted: 07/03/2014] [Indexed: 12/22/2022] Open
Abstract
While World Health Organization (WHO) grading of meningioma stratifies patients according to recurrence risk overall, there is substantial within-grade heterogeneity with respect to recurrence-free survival (RFS). Most meningiomas are graded according to mitotic counts per unit area on hematoxylin and eosin sections, a method potentially confounded by tumor cellularity, as well as potential limitations of accurate mitotic figure detection on routine histology. To refine mitotic figure assessment, we evaluated 363 meningiomas with phospho-histone H3 (Ser10) and determined the mitotic index (number of mitoses per 1000 tumor cells). The median mitotic indices among WHO grade I (n = 268), grade II (n = 84) and grade III (n = 11) tumors were 1, 4 and 12. Classification and regression tree analysis to categorize cut-offs identified three subgroups defined by mitotic indices of 0-2, 3-4 and ≥5, which on univariate analysis were associated with RFS (P < 0.01). In multivariate analysis, mitotic index subgrouped in this manner was significantly associated with RFS (P < 0.01) after adjustment for Simpson grade, WHO grade and MIB-1 index. Mitotic index was then examined within individual WHO grade, showing that for grade I and grade II meningiomas, mitotic index can add additional information to RFS risk. The results suggest that the use of a robust mitotic marker in meningioma could refine risk stratification.
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Affiliation(s)
- Adriana Olar
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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21
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Wani KM, Niyogi AK. Environment and silicosis in glass factories. Indian J Public Health 1968; 12:131-9. [PMID: 5732714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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