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Werba G, Weissinger D, Kawaler EA, Zhao E, Kalfakakou D, Dhara S, Wang L, Lim HB, Oh G, Jing X, Beri N, Khanna L, Gonda T, Oberstein P, Hajdu C, Loomis C, Heguy A, Sherman MH, Lund AW, Welling TH, Dolgalev I, Tsirigos A, Simeone DM. Author Correction: Single-cell RNA sequencing reveals the effects of chemotherapy on human pancreatic adenocarcinoma and its tumor microenvironment. Nat Commun 2023; 14:3912. [PMID: 37400453 DOI: 10.1038/s41467-023-39680-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023] Open
Affiliation(s)
- Gregor Werba
- Department of Surgery, NYU Langone Health, New York, NY, 10016, USA
| | - Daniel Weissinger
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, 10016, USA
| | - Emily A Kawaler
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, 10016, USA
| | - Ende Zhao
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, 10016, USA
| | | | - Surajit Dhara
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, 10016, USA
| | - Lidong Wang
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, 10016, USA
| | - Heather B Lim
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, 10016, USA
| | - Grace Oh
- Department of Surgery, NYU Langone Health, New York, NY, 10016, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, 10016, USA
| | - Xiaohong Jing
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, 10016, USA
| | - Nina Beri
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, 10016, USA
- Department of Medicine, NYU Langone Health, New York, NY, 10016, USA
| | - Lauren Khanna
- Department of Medicine, NYU Langone Health, New York, NY, 10016, USA
| | - Tamas Gonda
- Department of Medicine, NYU Langone Health, New York, NY, 10016, USA
| | - Paul Oberstein
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, 10016, USA
- Department of Medicine, NYU Langone Health, New York, NY, 10016, USA
| | - Cristina Hajdu
- Department of Pathology, NYU Langone Health, New York, NY, 10016, USA
| | - Cynthia Loomis
- Department of Pathology, NYU Langone Health, New York, NY, 10016, USA
| | - Adriana Heguy
- Department of Pathology, NYU Langone Health, New York, NY, 10016, USA
| | - Mara H Sherman
- Department of Cell, Developmental and Cancer Biology, Oregon Health Sciences University, Portland, OR, 97239, USA
| | - Amanda W Lund
- Department of Pathology, NYU Langone Health, New York, NY, 10016, USA
- Department of Dermatology, NYU Langone Health, New York, NY, 10016, USA
| | | | - Igor Dolgalev
- Department of Pathology, NYU Langone Health, New York, NY, 10016, USA
| | - Aristotelis Tsirigos
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, 10016, USA.
- Department of Pathology, NYU Langone Health, New York, NY, 10016, USA.
| | - Diane M Simeone
- Department of Surgery, NYU Langone Health, New York, NY, 10016, USA.
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, 10016, USA.
- Department of Pathology, NYU Langone Health, New York, NY, 10016, USA.
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Werba G, Weissinger D, Kawaler EA, Zhao E, Kalfakakou D, Dhara S, Wang L, Lim HB, Oh G, Jing X, Beri N, Khanna L, Gonda T, Oberstein P, Hajdu C, Loomis C, Heguy A, Sherman MH, Lund AW, Welling TH, Dolgalev I, Tsirigos A, Simeone DM. Single-cell RNA sequencing reveals the effects of chemotherapy on human pancreatic adenocarcinoma and its tumor microenvironment. Nat Commun 2023; 14:797. [PMID: 36781852 PMCID: PMC9925748 DOI: 10.1038/s41467-023-36296-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 01/25/2023] [Indexed: 02/15/2023] Open
Abstract
The tumor microenvironment (TME) in pancreatic ductal adenocarcinoma (PDAC) is a complex ecosystem that drives tumor progression; however, in-depth single cell characterization of the PDAC TME and its role in response to therapy is lacking. Here, we perform single-cell RNA sequencing on freshly collected human PDAC samples either before or after chemotherapy. Overall, we find a heterogeneous mixture of basal and classical cancer cell subtypes, along with distinct cancer-associated fibroblast and macrophage subpopulations. Strikingly, classical and basal-like cancer cells exhibit similar transcriptional responses to chemotherapy and do not demonstrate a shift towards a basal-like transcriptional program among treated samples. We observe decreased ligand-receptor interactions in treated samples, particularly between TIGIT on CD8 + T cells and its receptor on cancer cells, and identify TIGIT as the major inhibitory checkpoint molecule of CD8 + T cells. Our results suggest that chemotherapy profoundly impacts the PDAC TME and may promote resistance to immunotherapy.
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Affiliation(s)
- Gregor Werba
- Department of Surgery, NYU Langone Health, New York, New York, 10016, USA
| | - Daniel Weissinger
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, 10016, USA
| | - Emily A Kawaler
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, 10016, USA
| | - Ende Zhao
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, 10016, USA
| | - Despoina Kalfakakou
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, 10016, USA
| | - Surajit Dhara
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, 10016, USA
| | - Lidong Wang
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, 10016, USA
| | - Heather B Lim
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, 10016, USA
| | - Grace Oh
- Department of Surgery, NYU Langone Health, New York, New York, 10016, USA.,Perlmutter Cancer Center, NYU Langone Health, New York, New York, 10016, USA
| | - Xiaohong Jing
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, 10016, USA
| | - Nina Beri
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, 10016, USA.,Department of Medicine, NYU Langone Health, New York, New York, 10016, USA
| | - Lauren Khanna
- Department of Medicine, NYU Langone Health, New York, New York, 10016, USA
| | - Tamas Gonda
- Department of Medicine, NYU Langone Health, New York, New York, 10016, USA
| | - Paul Oberstein
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, 10016, USA.,Department of Medicine, NYU Langone Health, New York, New York, 10016, USA
| | - Cristina Hajdu
- Department of Pathology, NYU Langone Health, New York, New York, 10016, USA
| | - Cynthia Loomis
- Department of Pathology, NYU Langone Health, New York, New York, 10016, USA
| | - Adriana Heguy
- Department of Pathology, NYU Langone Health, New York, New York, 10016, USA
| | - Mara H Sherman
- Department of Cell, Developmental and Cancer Biology, Oregon Health Sciences University, Portland, Oregon, 97239, USA
| | - Amanda W Lund
- Department of Pathology, NYU Langone Health, New York, New York, 10016, USA.,Department of Dermatology, NYU Langone Health, New York, New York, 10016, USA
| | - Theodore H Welling
- Department of Surgery, NYU Langone Health, New York, New York, 10016, USA
| | - Igor Dolgalev
- Department of Pathology, NYU Langone Health, New York, New York, 10016, USA
| | - Aristotelis Tsirigos
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, 10016, USA. .,Department of Pathology, NYU Langone Health, New York, New York, 10016, USA.
| | - Diane M Simeone
- Department of Surgery, NYU Langone Health, New York, New York, 10016, USA. .,Perlmutter Cancer Center, NYU Langone Health, New York, New York, 10016, USA. .,Department of Pathology, NYU Langone Health, New York, New York, 10016, USA.
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Oberstein PE, Rahma O, Beri N, Stoll-D'Astice A, Kawaler EA, Dolgalev I, Werba G, Cardo-Ruffino V, Böllenrücher N, Costa AD, Nazeer S, Squires M, Nowak J, Bar-Sagi D, Wolpin B, Simeone DM, Dougan SK. Abstract PR005: Primary results of PanCAN-SR1, a phase 1b study evaluating Gemcitabine, nab-Paclitaxel, Canakinumab, and Spartalizumab to target IL-1β and PD-1 in metastatic pancreatic cancer with correlative tissue and blood biomarker analysis. Cancer Res 2022. [DOI: 10.1158/1538-7445.panca22-pr005] [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: 11/17/2022]
Abstract
Abstract
In preclinical work, the inflammatory cytokine IL-1β was shown to be upregulated in pancreatic cancer tumors and to contribute to activation of pancreatic stellate cells and immunosuppression (Das et al 2020). We conducted an open-label multicenter Phase Ib study evaluating gemcitabine, nab-paclitaxel, canakinumab (ACZ885), a high-affinity human anti-interleukin-1β (IL-1β) mAb, and spartalizumab (PDR001), a PD-1 mAb. Eligible subjects had previously untreated metastatic PDA and RECIST measurable disease. The primary objective was to confirm recommended phase II dose by evaluating the incidence of dose limiting toxicities (DLTs) in the first 56 days of dosing in at least 6 evaluable subjects utilizing a Bayesian logistic regression model. Subjects underwent baseline and on-study tissue and blood collection for correlative translational research. Results: 10 subjects were enrolled between Nov 2020 and Mar 2021. At the primary data cut off of May 23, 2021, 6 subjects were evaluable for DLT. There were no DLTs, the recommended Phase II dose was established as: gemcitabine (1000mg/m2 IV) day 1,8,15; nab-paclitaxel (125mg/m2 IV) day 1,8,15; canakinumab (250mg SC) day 1, spartalizumab (400mg IV) day 1; of each 28 day cycle. At the time of an updated database extraction on June 1, 2022, 2 subjects remain on study. Adverse events were consistent with those typically seen with chemotherapy. The most common Grade 3/4 AEs were neutropenia (60%) and anemia (50%), with no fatal AEs. One patient discontinued spartalizumab due to grade 3 pneumonitis. In preliminary efficacy analysis (n=10), there are 3 confirmed PRs, 5 subjects with stable disease, 2 subjects with progression as best response. Individual site data estimates that the 12 month OS rate is 60%; updated RR, PFS and OS data will be reported. Activation of CD8 T cells in peripheral blood and increased serum levels of IFN-induced chemokines CXCL9/10 were observed in both responder and non-responder patients. Using an in vitro suppression assay, we showed that baseline serum from responders could induce myeloid derived suppressor cells, an effect that was abrogated with treatment. Single cell transcriptional profiling, multiplex immunofluorescence and spatial transcriptomics also revealed treatment-dependent shifts in T cell activation state and myeloid cells in the tumors of patients experiencing clinical response. Conclusions: PanCAN-SR1 established the Phase II dose of canakinumab and spartalizumab with chemotherapy in first line metastatic PDA, based upon favorable benefit-risk assessment. Based on our comprehensive analysis of 10 patients treated with combination therapy including IL-1b blockade, we hypothesize that the definitive role of anti-IL-1b in human patients with pancreatic cancer is to reduce systemic immune suppression and to reduce immunosuppressive myeloid cell activation in the tumor. The clinical utility of targeting IL-1β in pancreatic cancer is being evaluated in a randomized Phase II/III study through the Precision Promise clinical trial network. NCT04581343.
Citation Format: Paul E. Oberstein, Osama Rahma, Nina Beri, Amy Stoll-D'Astice, Emily A. Kawaler, Igor Dolgalev, Gregor Werba, Victoire Cardo-Ruffino, Naïma Böllenrücher, Andressa Dias Costa, Saloney Nazeer, Matthew Squires, Jonathan Nowak, Dafna Bar-Sagi, Brian Wolpin, Diane M Simeone, Stephanie K Dougan. Primary results of PanCAN-SR1, a phase 1b study evaluating Gemcitabine, nab-Paclitaxel, Canakinumab, and Spartalizumab to target IL-1β and PD-1 in metastatic pancreatic cancer with correlative tissue and blood biomarker analysis [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr PR005.
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Weissinger D, Kawaler EA, Werba G, Zhao E, Kalfakakou D, Dhara S, Oh G, Jing X, Beri N, Khanna L, Gonda T, Oberstein PE, Hajdu C, Loomis C, Heguy A, Sherman MH, Lund AW, Welling TH, Dolgalev I, Tsirigos A, Simeone DM. Abstract PR010: Single-cell sequencing elucidates the effects of chemotherapy on cancer cell heterogeneity and the tumor microenvironment of human pancreatic adenocarcinoma. Cancer Res 2022. [DOI: 10.1158/1538-7445.panca22-pr010] [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: 11/17/2022]
Abstract
Abstract
The tumor microenvironment (TME) in pancreatic ductal adenocarcinoma (PDAC) is a complex ecosystem that drives tumor progression. Improving our understanding of the PDAC TME and its role in response to therapy via in-depth single cell characterization will have broad clinical implications for biomarker development and therapeutic design. In this study, we performed single-cell RNA sequencing on freshly collected human PDAC samples of primary (n=16) or metastatic (n=11) origin, either before (n=20) or after (n=7) chemotherapy. We found a heterogeneous mixture of basal and classical Moffitt cancer cell subtypes in all samples, along with distinct cancer-associated fibroblast (CAF) and tumor-associated macrophage (TAM) subpopulations. We identified the major CAF subpopulations as inflammatory CAFs (iCAFs) and myofibroblastic CAFs (myCAFs); within these subpopulations were a very few cells expressing immunogenic features which have previously been associated with antigen presenting CAFs (apCAFs). Tumor-associated macrophages (TAMs) could be categorized into two major subpopulations, C1QC+ TAMs or SPP1+ TAMs, each with distinct functional characteristics. For example, phagocytosis-associated gene sets were enriched in C1QC+ TAMs, while angiogenesis-associated gene sets were enriched in SPP1+ TAMs. Comparison of naïve and chemotherapy treated primary PDAC samples revealed that classical and basal-like cancer cells exhibited similar transcriptional responses to chemotherapy; this contrasts with some previous reports which posited a shift towards a basal-like transcriptional program among treated samples. We further noted that treated samples evinced fewer ligand-receptor interactions, particularly between TIGIT on CD8+ T cells and its ligand on cancer cells. We also identified TIGIT, not PD1, as the major inhibitory checkpoint molecule of CD8+ T cells in the PDAC TME. Altogether, our results suggest that chemotherapy impacts the PDAC TME and may further reduce response to immunotherapy.
Citation Format: Daniel Weissinger, Emily A. Kawaler, Gregor Werba, Ende Zhao, Despoina Kalfakakou, Surajit Dhara, Grace Oh, Xiaohong Jing, Nina Beri, Lauren Khanna, Tamas Gonda, Paul E. Oberstein, Cristina Hajdu, Cynthia Loomis, Adriana Heguy, Mara H. Sherman, Amanda W. Lund, Theodore H. Welling, Igor Dolgalev, Aristotelis Tsirigos, Diane M. Simeone. Single-cell sequencing elucidates the effects of chemotherapy on cancer cell heterogeneity and the tumor microenvironment of human pancreatic adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr PR010.
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Affiliation(s)
- Daniel Weissinger
- 1Perlmutter Cancer Center, New York University Langone Health, New York, NY,
| | - Emily A. Kawaler
- 1Perlmutter Cancer Center, New York University Langone Health, New York, NY,
| | - Gregor Werba
- 2Department of Surgery, New York University Langone Health, New York, NY,
| | - Ende Zhao
- 1Perlmutter Cancer Center, New York University Langone Health, New York, NY,
| | - Despoina Kalfakakou
- 1Perlmutter Cancer Center, New York University Langone Health, New York, NY,
| | - Surajit Dhara
- 1Perlmutter Cancer Center, New York University Langone Health, New York, NY,
| | - Grace Oh
- 2Department of Surgery, New York University Langone Health, New York, NY,
| | - Xiaohong Jing
- 1Perlmutter Cancer Center, New York University Langone Health, New York, NY,
| | - Nina Beri
- 3Department of Medicine, New York University Langone Health, New York, NY,
| | - Lauren Khanna
- 3Department of Medicine, New York University Langone Health, New York, NY,
| | - Tamas Gonda
- 3Department of Medicine, New York University Langone Health, New York, NY,
| | - Paul E. Oberstein
- 3Department of Medicine, New York University Langone Health, New York, NY,
| | - Cristina Hajdu
- 4Department of Pathology, New York University Langone Health, New York, NY,
| | - Cynthia Loomis
- 4Department of Pathology, New York University Langone Health, New York, NY,
| | - Adriana Heguy
- 4Department of Pathology, New York University Langone Health, New York, NY,
| | - Mara H. Sherman
- 5Department of Cell, Developmental and Cancer Biology, Oregon Health Sciences University, Portland, OR,
| | - Amanda W. Lund
- 4Department of Pathology, New York University Langone Health, New York, NY,
| | | | - Igor Dolgalev
- 4Department of Pathology, New York University Langone Health, New York, NY,
| | - Aristotelis Tsirigos
- 6Applied Bioinformatics Laboratories, New York University Langone Health, New York, NY
| | - Diane M. Simeone
- 2Department of Surgery, New York University Langone Health, New York, NY,
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Berger AA, Kawaler EA, Dao F, Misirlioglu S, Fernandez EA, Olvera N, Van Oudenhove E, DeLair D, Levine DA. The role of CTNNB1 mutations and matrix metalloproteinases (MMPs) in anti-angiogenesis treatment of endometrial carcinoma. Gynecol Oncol 2022; 167:323-333. [PMID: 36150916 DOI: 10.1016/j.ygyno.2022.09.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 04/24/2022] [Revised: 09/08/2022] [Accepted: 09/10/2022] [Indexed: 11/04/2022]
Abstract
OBJECTIVE Treatment options and associated biomarkers for advanced and recurrent disease are limited. Endometrial cancers (ECs) with CTNNB1 exon 3 mutations appear to have preferential response to bevacizumab, an anti-angiogenesis treatment, though the mechanism of action is unknown. We aim to identify mediators of bevacizumab-responsive endometrial cancers. METHODS We analyzed RNA expression from TCGA and protein expression from CPTAC to identify likely targets for β-catenin overactivity. We then transiently and stably overexpressed β-catenin in EC cells to confirm the results suggested by our in silico analysis. We performed corroborative experiments by silencing CTNNB1 in mutated cell lines to demonstrate functional specificity. We implanted transduced cells into xenograft models to study microvessel density. RESULTS CTNNB1-mutated ECs were associated with increased β-catenin and MMP7 protein abundance (P < 0.001), but not VEGF-A protein abundance. Overexpressing β-catenin in EC cells did not increase VEGF-A abundance but did increase expression and secretion of MMP7 (P < 0.03). Silencing CTNNB1 in CTNNB1-mutated cells decreased MMP7 gene expression in EC (P < 0.0001). Microvessel density was not increased. CONCLUSIONS These data provide a mechanistic understanding for bevacizumab-response in CTNNB1-mutated ECs demonstrated in GOG-86P. We hypothesize that overexpressed and secreted MMP7 potentially digests VEGFR-1, releasing VEGF-A, and increasing its availability. These activities may drive the formation of permeable vessels, which contributes to tumor progression, metastasis, and immune suppression. This mechanism is unique to EC and advocates for further clinical trials evaluating this treatment-related biomarker.
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Affiliation(s)
- Amnon A Berger
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, United States of America; Department of Anesthesia, Critical Care and Pain Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, United States of America
| | - Emily A Kawaler
- Vilcek Institute of Graduate Biomedical Sciences, New York University Grossman School of Medicine, New York, NY, United States of America
| | - Fanny Dao
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, United States of America
| | - Selim Misirlioglu
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, United States of America
| | | | - Narciso Olvera
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, United States of America
| | - Elke Van Oudenhove
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, United States of America
| | - Deborah DeLair
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, United States of America
| | - Douglas A Levine
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, United States of America; Merck Research Laboratories, Rahway, NJ, United States of America.
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6
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Everett JN, Dettwyler SA, Jing X, Stender C, Schmitter M, Baptiste A, Chun J, Kawaler EA, Khanna LG, Gross SA, Gonda TA, Beri N, Oberstein PE, Simeone DM. Impact of comprehensive family history and genetic analysis in the multidisciplinary pancreatic tumor clinic setting. Cancer Med 2022; 12:2345-2355. [PMID: 35906821 PMCID: PMC9939217 DOI: 10.1002/cam4.5059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/25/2022] [Accepted: 06/29/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Genetic testing is recommended for all pancreatic ductal adenocarcinoma (PDAC) patients. Prior research demonstrates that multidisciplinary pancreatic cancer clinics (MDPCs) improve treatment- and survival-related outcomes for PDAC patients. However, limited information exists regarding the utility of integrated genetics in the MDPC setting. We hypothesized that incorporating genetics in an MDPC serving both PDAC patients and high-risk individuals (HRI) could: (1) improve compliance with guideline-based genetic testing for PDAC patients, and (2) optimize HRI identification and PDAC surveillance participation to improve early detection and survival. METHODS Demographics, genetic testing results, and pedigrees were reviewed for PDAC patients and HRI at one institution over 45 months. Genetic testing analyzed 16 PDAC-associated genes at minimum. RESULTS Overall, 969 MDPC subjects were evaluated during the study period; another 56 PDAC patients were seen outside the MDPC. Among 425 MDPC PDAC patients, 333 (78.4%) completed genetic testing; 29 (8.7%) carried a PDAC-related pathogenic germline variant (PGV). Additionally, 32 (9.6%) met familial pancreatic cancer (FPC) criteria. These PDAC patients had 191 relatives eligible for surveillance or genetic testing. Only 2/56 (3.6%) non-MDPC PDAC patients completed genetic testing (p < 0.01). Among 544 HRI, 253 (46.5%) had a known PGV or a designation of FPC, and were eligible for surveillance at baseline; of the remainder, 15/291 (5.2%) were eligible following genetic testing and PGV identification. CONCLUSION Integrating genetics into the multidisciplinary setting significantly improved genetic testing compliance by reducing logistical barriers for PDAC patients, and clarified cancer risks for their relatives while conserving clinical resources. Overall, we identified 206 individuals newly eligible for surveillance or genetic testing (191 relatives of MDPC PDAC patients, and 15 HRI from this cohort), enabling continuity of care for PDAC patients and at-risk relatives in one clinic.
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Affiliation(s)
- Jessica N. Everett
- Department of MedicineNew York University Langone HealthNew York CityNew YorkUSA,Department of SurgeryNew York University Langone HealthNew York CityNew YorkUSA,Perlmutter Cancer CenterNew York University Langone HealthNew York CityNew YorkUSA
| | - Shenin A. Dettwyler
- Perlmutter Cancer CenterNew York University Langone HealthNew York CityNew YorkUSA
| | - Xiaohong Jing
- Perlmutter Cancer CenterNew York University Langone HealthNew York CityNew YorkUSA
| | - Cody Stender
- Perlmutter Cancer CenterNew York University Langone HealthNew York CityNew YorkUSA
| | - Madeleine Schmitter
- Perlmutter Cancer CenterNew York University Langone HealthNew York CityNew YorkUSA
| | - Ariele Baptiste
- Perlmutter Cancer CenterNew York University Langone HealthNew York CityNew YorkUSA
| | - Jennifer Chun
- Perlmutter Cancer CenterNew York University Langone HealthNew York CityNew YorkUSA
| | - Emily A. Kawaler
- Applied Bioinformatics LaboratoriesNew York University Langone HealthNew York CityNew YorkUSA
| | - Lauren G. Khanna
- Department of MedicineNew York University Langone HealthNew York CityNew YorkUSA
| | - Seth A. Gross
- Department of MedicineNew York University Langone HealthNew York CityNew YorkUSA
| | - Tamas A. Gonda
- Department of MedicineNew York University Langone HealthNew York CityNew YorkUSA
| | - Nina Beri
- Department of MedicineNew York University Langone HealthNew York CityNew YorkUSA,Department of SurgeryNew York University Langone HealthNew York CityNew YorkUSA
| | - Paul E. Oberstein
- Department of MedicineNew York University Langone HealthNew York CityNew YorkUSA,Department of SurgeryNew York University Langone HealthNew York CityNew YorkUSA
| | - Diane M. Simeone
- Department of MedicineNew York University Langone HealthNew York CityNew YorkUSA,Perlmutter Cancer CenterNew York University Langone HealthNew York CityNew YorkUSA,Department of PathologyNew York University Langone HealthNew York CityNew YorkUSA
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7
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Blumenberg L, Kawaler EA, Cornwell M, Smith S, Ruggles KV, Fenyö D. BlackSheep: A Bioconductor and Bioconda Package for Differential Extreme Value Analysis. J Proteome Res 2021; 20:3767-3773. [PMID: 34165986 PMCID: PMC8256816 DOI: 10.1021/acs.jproteome.1c00190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
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Unbiased assays such as shotgun proteomics and RNA-seq provide high-resolution
molecular characterization of tumors. These assays measure molecules with highly varied
distributions, making interpretation and hypothesis testing challenging. Samples with
the most extreme measurements for a molecule can reveal the most interesting biological
insights yet are often excluded from analysis. Furthermore, rare disease subtypes are,
by definition, underrepresented in cancer cohorts. To provide a strategy for identifying
molecules aberrantly enriched in small sample cohorts, we present BlackSheep, a package
for nonparametric description and differential analysis of genome-wide data, available
from Bioconductor (https://www.bioconductor.org/packages/release/bioc/html/blacksheepr.html) and
Bioconda (https://bioconda.github.io/recipes/blksheep/README.html). BlackSheep is a
complementary tool to other differential expression analysis methods, which is
particularly useful when analyzing small subgroups in a larger cohort.
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Affiliation(s)
- Lili Blumenberg
- Vilcek Institute of Graduate Biomedical Sciences, New York University Grossman School of Medicine, New York, New York 10016, United States.,Division of Translational Medicine, Department of Medicine, New York University Grossman School of Medicine, New York, New York 10016, United States.,Institute for Systems Genetics, New York University Grossman School of Medicine, New York, New York 10016, United States
| | - Emily A Kawaler
- Vilcek Institute of Graduate Biomedical Sciences, New York University Grossman School of Medicine, New York, New York 10016, United States.,Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York 10016, United States.,Institute for Systems Genetics, New York University Grossman School of Medicine, New York, New York 10016, United States
| | - MacIntosh Cornwell
- Vilcek Institute of Graduate Biomedical Sciences, New York University Grossman School of Medicine, New York, New York 10016, United States.,Division of Translational Medicine, Department of Medicine, New York University Grossman School of Medicine, New York, New York 10016, United States.,Institute for Systems Genetics, New York University Grossman School of Medicine, New York, New York 10016, United States
| | - Shaleigh Smith
- Vilcek Institute of Graduate Biomedical Sciences, New York University Grossman School of Medicine, New York, New York 10016, United States
| | - Kelly V Ruggles
- Division of Translational Medicine, Department of Medicine, New York University Grossman School of Medicine, New York, New York 10016, United States.,Institute for Systems Genetics, New York University Grossman School of Medicine, New York, New York 10016, United States
| | - David Fenyö
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York 10016, United States.,Institute for Systems Genetics, New York University Grossman School of Medicine, New York, New York 10016, United States
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8
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Kawaler EA, Dou Y, Zhou DC, Gritsenko MA, Rodland KD, Ding L, Zhang B, Liu T, Fenyö D. Abstract 6580: Proteogenomic characterization of endometrial carcinoma. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-6580] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Endometrial cancer (EC) is the sixth most common cancer in women globally and is one of the few cancers for which mortality is increasing; to address the need to develop new methods for the diagnosis and treatment of this disease, we performed a comprehensive proteogenomic characterization of 95 endometrial carcinomas.
We prospectively collected 83 endometrioid and 12 serous tumors, along with 49 normal tissue samples, for multi-omic characterization. Each sample underwent whole exome sequencing, whole genome sequencing, total RNA and miRNA sequencing, and DNA methylation array analyses. In addition, we evaluated all samples for protein, phosphorylation, and acetylation levels using an integrated, isobaric tandem mass tag labeling–based quantitative proteomics workflow. This dataset, publicly available through the Genomic Data Commons, CPTAC data portal, and other sources, provides a valuable resource for researchers and clinicians.
Our analyses of these tumors revealed, among other things, a potential role for circRNAs in the epithelial-mesenchymal transition and new information about proteomic markers of clinical and genomic tumor subgroups, including relationships to known druggable pathways. We found possible new consequences of perturbations to the Wnt/β-catenin pathway, particularly CTNNB1 hotspot mutations; moreover, from the genome-wide acetylation survey, we found potential regulatory mechanisms linking Wnt signaling and histone acetylation. Phosphorylation data analysis suggests an elevated DNA damage response in serous tumors, which we hypothesize may be targetable by certain FDA-approved drugs. We found that TP53 hotspot mutations play unique trans-acting roles as compared to the same mutations in colon and ovarian cancers. We also characterized aspects of the tumor immune landscape, including immunogenic alterations, neoantigens, common cancer/testis antigens, and the immune microenvironment, all of which can inform immunotherapy decisions; of particular translational interest, we identified a subset of patients who, despite having high amounts of microsatellite instability, exhibit biomarkers which suggest that immunotherapy would be an ineffective treatment for their disease.
By integrating global measurements of protein abundance, phosphorylation, and acetylation with next-generation genomics and transcriptomics, we have provided novel insights into biological processes underlying the development of endometrial cancers and generated strong hypotheses for new approaches to personalized treatment of individuals with endometrial cancer.
Citation Format: Emily A. Kawaler, Yongchao Dou, Daniel Cui Zhou, Marina A. Gritsenko, Karin D. Rodland, Li Ding, Bing Zhang, Tao Liu, David Fenyö, Clinical Proteomic Tumor Analysis Consortium. Proteogenomic characterization of endometrial carcinoma [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 6580.
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Affiliation(s)
| | | | | | | | | | - Li Ding
- 3Washington University in St. Louis, St. Louis, MO
| | - Bing Zhang
- 2Baylor College of Medicine, Houston, TX
| | - Tao Liu
- 4Pacific Northwest National Laboratory, Richland, WA
| | - David Fenyö
- 1New York University Langone Health, New York, NY
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9
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Gillette MA, Satpathy S, Cao S, Dhanasekaran SM, Vasaikar SV, Krug K, Petralia F, Li Y, Liang WW, Reva B, Krek A, Ji J, Song X, Liu W, Hong R, Yao L, Blumenberg L, Savage SR, Wendl MC, Wen B, Li K, Tang LC, MacMullan MA, Avanessian SC, Kane MH, Newton CJ, Cornwell M, Kothadia RB, Ma W, Yoo S, Mannan R, Vats P, Kumar-Sinha C, Kawaler EA, Omelchenko T, Colaprico A, Geffen Y, Maruvka YE, da Veiga Leprevost F, Wiznerowicz M, Gümüş ZH, Veluswamy RR, Hostetter G, Heiman DI, Wyczalkowski MA, Hiltke T, Mesri M, Kinsinger CR, Boja ES, Omenn GS, Chinnaiyan AM, Rodriguez H, Li QK, Jewell SD, Thiagarajan M, Getz G, Zhang B, Fenyö D, Ruggles KV, Cieslik MP, Robles AI, Clauser KR, Govindan R, Wang P, Nesvizhskii AI, Ding L, Mani DR, Carr SA. Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma. Cell 2020; 182:200-225.e35. [PMID: 32649874 PMCID: PMC7373300 DOI: 10.1016/j.cell.2020.06.013] [Citation(s) in RCA: 338] [Impact Index Per Article: 84.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 03/06/2020] [Accepted: 06/03/2020] [Indexed: 12/24/2022]
Abstract
To explore the biology of lung adenocarcinoma (LUAD) and identify new therapeutic opportunities, we performed comprehensive proteogenomic characterization of 110 tumors and 101 matched normal adjacent tissues (NATs) incorporating genomics, epigenomics, deep-scale proteomics, phosphoproteomics, and acetylproteomics. Multi-omics clustering revealed four subgroups defined by key driver mutations, country, and gender. Proteomic and phosphoproteomic data illuminated biology downstream of copy number aberrations, somatic mutations, and fusions and identified therapeutic vulnerabilities associated with driver events involving KRAS, EGFR, and ALK. Immune subtyping revealed a complex landscape, reinforced the association of STK11 with immune-cold behavior, and underscored a potential immunosuppressive role of neutrophil degranulation. Smoking-associated LUADs showed correlation with other environmental exposure signatures and a field effect in NATs. Matched NATs allowed identification of differentially expressed proteins with potential diagnostic and therapeutic utility. This proteogenomics dataset represents a unique public resource for researchers and clinicians seeking to better understand and treat lung adenocarcinomas.
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Affiliation(s)
- Michael A Gillette
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA; Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, 02115, USA.
| | - Shankha Satpathy
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.
| | - Song Cao
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | | | - Suhas V Vasaikar
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Karsten Krug
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yize Li
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Wen-Wei Liang
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Boris Reva
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jiayi Ji
- Department of Population Health Science and Policy; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Xiaoyu Song
- Department of Population Health Science and Policy; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Wenke Liu
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Runyu Hong
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Lijun Yao
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Lili Blumenberg
- Institute for Systems Genetics and Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Sara R Savage
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Michael C Wendl
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Bo Wen
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kai Li
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Lauren C Tang
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA; Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Melanie A MacMullan
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA; Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA, 90089, USA
| | - Shayan C Avanessian
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - M Harry Kane
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | | | - MacIntosh Cornwell
- Institute for Systems Genetics and Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Ramani B Kothadia
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Weiping Ma
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Seungyeul Yoo
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rahul Mannan
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Pankaj Vats
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | | | - Emily A Kawaler
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Tatiana Omelchenko
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Antonio Colaprico
- Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
| | - Yifat Geffen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Yosef E Maruvka
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | | | - Maciej Wiznerowicz
- Poznan University of Medical Sciences, Poznań, 61-701, Poland; International Institute for Molecular Oncology, Poznań, 60-203, Poland
| | - Zeynep H Gümüş
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rajwanth R Veluswamy
- Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - David I Heiman
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Matthew A Wyczalkowski
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Christopher R Kinsinger
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Emily S Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Qing Kay Li
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins Medical Institutions, Baltimore, MD, 21224, USA
| | - Scott D Jewell
- Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Mathangi Thiagarajan
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Gad Getz
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - David Fenyö
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Kelly V Ruggles
- Institute for Systems Genetics and Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Marcin P Cieslik
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Karl R Clauser
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Ramaswamy Govindan
- Division of Oncology and Siteman Cancer Center, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Li Ding
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Steven A Carr
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.
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10
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Dou Y, Kawaler EA, Cui Zhou D, Gritsenko MA, Huang C, Blumenberg L, Karpova A, Petyuk VA, Savage SR, Satpathy S, Liu W, Wu Y, Tsai CF, Wen B, Li Z, Cao S, Moon J, Shi Z, Cornwell M, Wyczalkowski MA, Chu RK, Vasaikar S, Zhou H, Gao Q, Moore RJ, Li K, Sethuraman S, Monroe ME, Zhao R, Heiman D, Krug K, Clauser K, Kothadia R, Maruvka Y, Pico AR, Oliphant AE, Hoskins EL, Pugh SL, Beecroft SJI, Adams DW, Jarman JC, Kong A, Chang HY, Reva B, Liao Y, Rykunov D, Colaprico A, Chen XS, Czekański A, Jędryka M, Matkowski R, Wiznerowicz M, Hiltke T, Boja E, Kinsinger CR, Mesri M, Robles AI, Rodriguez H, Mutch D, Fuh K, Ellis MJ, DeLair D, Thiagarajan M, Mani DR, Getz G, Noble M, Nesvizhskii AI, Wang P, Anderson ML, Levine DA, Smith RD, Payne SH, Ruggles KV, Rodland KD, Ding L, Zhang B, Liu T, Fenyö D. Proteogenomic Characterization of Endometrial Carcinoma. Cell 2020; 180:729-748.e26. [PMID: 32059776 PMCID: PMC7233456 DOI: 10.1016/j.cell.2020.01.026] [Citation(s) in RCA: 247] [Impact Index Per Article: 61.8] [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: 05/29/2019] [Revised: 11/11/2019] [Accepted: 01/16/2020] [Indexed: 02/07/2023]
Abstract
We undertook a comprehensive proteogenomic characterization of 95 prospectively collected endometrial carcinomas, comprising 83 endometrioid and 12 serous tumors. This analysis revealed possible new consequences of perturbations to the p53 and Wnt/β-catenin pathways, identified a potential role for circRNAs in the epithelial-mesenchymal transition, and provided new information about proteomic markers of clinical and genomic tumor subgroups, including relationships to known druggable pathways. An extensive genome-wide acetylation survey yielded insights into regulatory mechanisms linking Wnt signaling and histone acetylation. We also characterized aspects of the tumor immune landscape, including immunogenic alterations, neoantigens, common cancer/testis antigens, and the immune microenvironment, all of which can inform immunotherapy decisions. Collectively, our multi-omic analyses provide a valuable resource for researchers and clinicians, identify new molecular associations of potential mechanistic significance in the development of endometrial cancers, and suggest novel approaches for identifying potential therapeutic targets.
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Affiliation(s)
- Yongchao Dou
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Emily A Kawaler
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Daniel Cui Zhou
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Chen Huang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lili Blumenberg
- Department of Medicine, NYU School of Medicine, New York, NY 10016, USA
| | - Alla Karpova
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Sara R Savage
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shankha Satpathy
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Wenke Liu
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Yige Wu
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Bo Wen
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhi Li
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Song Cao
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Jamie Moon
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Zhiao Shi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - MacIntosh Cornwell
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Matthew A Wyczalkowski
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Rosalie K Chu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Suhas Vasaikar
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hua Zhou
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Qingsong Gao
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Kai Li
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sunantha Sethuraman
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Rui Zhao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - David Heiman
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Karsten Krug
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Karl Clauser
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ramani Kothadia
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yosef Maruvka
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexander R Pico
- Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Amanda E Oliphant
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Emily L Hoskins
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Samuel L Pugh
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Sean J I Beecroft
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - David W Adams
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Jonathan C Jarman
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Andy Kong
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hui-Yin Chang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Boris Reva
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yuxing Liao
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dmitry Rykunov
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Antonio Colaprico
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Division of Biostatistics, Department of Public Health Science, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Xi Steven Chen
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Division of Biostatistics, Department of Public Health Science, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Andrzej Czekański
- Department of Oncology, Wroclaw Medical University, 50-367 Wrocław, Poland; Wroclaw Comprehensive Cancer Center, 53-413 Wrocław, Poland
| | - Marcin Jędryka
- Department of Oncology, Wroclaw Medical University, 50-367 Wrocław, Poland; Wroclaw Comprehensive Cancer Center, 53-413 Wrocław, Poland
| | - Rafał Matkowski
- Department of Oncology, Wroclaw Medical University, 50-367 Wrocław, Poland; Wroclaw Comprehensive Cancer Center, 53-413 Wrocław, Poland
| | - Maciej Wiznerowicz
- Poznan University of Medical Sciences, 61-701 Poznań, Poland; University Hospital of Lord's Transfiguration, 60-569 Poznań, Poland; International Institute for Molecular Oncology, 60-203 Poznań, Poland
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Emily Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Christopher R Kinsinger
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - David Mutch
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Katherine Fuh
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Matthew J Ellis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Deborah DeLair
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA
| | - Mathangi Thiagarajan
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - D R Mani
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gad Getz
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael Noble
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Matthew L Anderson
- College of Medicine Obstetrics & Gynecology, University of South Florida Health, Tampa, FL 33620, USA
| | - Douglas A Levine
- Gynecologic Oncology, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Kelly V Ruggles
- Department of Medicine, NYU School of Medicine, New York, NY 10016, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR 97221, USA.
| | - Li Ding
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA.
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
| | - David Fenyö
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA.
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