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Alahmari AA, Chaubey AH, Jonnakuti VS, Tisdale AA, Schwarz CD, Cornwell AC, Maraszek KE, Paterson EJ, Kim M, Venkat S, Gomez EC, Wang J, Gurova KV, Yalamanchili HK, Feigin ME. CPSF3 inhibition blocks pancreatic cancer cell proliferation through disruption of core histone mRNA processing. RNA 2024; 30:281-297. [PMID: 38191171 PMCID: PMC10870380 DOI: 10.1261/rna.079931.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 01/02/2024] [Indexed: 01/10/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with limited effective treatment options, potentiating the importance of uncovering novel drug targets. Here, we target cleavage and polyadenylation specificity factor 3 (CPSF3), the 3' endonuclease that catalyzes mRNA cleavage during polyadenylation and histone mRNA processing. We find that CPSF3 is highly expressed in PDAC and is associated with poor prognosis. CPSF3 knockdown blocks PDAC cell proliferation and colony formation in vitro and tumor growth in vivo. Chemical inhibition of CPSF3 by the small molecule JTE-607 also attenuates PDAC cell proliferation and colony formation, while it has no effect on cell proliferation of nontransformed immortalized control pancreatic cells. Mechanistically, JTE-607 induces transcriptional readthrough in replication-dependent histones, reduces core histone expression, destabilizes chromatin structure, and arrests cells in the S-phase of the cell cycle. Therefore, CPSF3 represents a potential therapeutic target for the treatment of PDAC.
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Affiliation(s)
- Abdulrahman A Alahmari
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, Alkharj 11942, Saudi Arabia
| | - Aditi H Chaubey
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Venkata S Jonnakuti
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
- Program in Quantitative and Computational Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Arwen A Tisdale
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Carla D Schwarz
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Abigail C Cornwell
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Kathryn E Maraszek
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Emily J Paterson
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Minsuh Kim
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Swati Venkat
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Eduardo Cortes Gomez
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Jianmin Wang
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Katerina V Gurova
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Hari Krishna Yalamanchili
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Michael E Feigin
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
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Venkat S, Feigin ME. Alternative Polyadenylation Characterizes Epithelial and Fibroblast Phenotypic Heterogeneity in Pancreatic Ductal Adenocarcinoma. Cancers (Basel) 2024; 16:640. [PMID: 38339391 PMCID: PMC10854489 DOI: 10.3390/cancers16030640] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 01/24/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Human tumors are characterized by extensive intratumoral transcriptional variability within the cancer cell and stromal compartments. This variation drives phenotypic heterogeneity, producing cell states with differential pro- and anti-tumorigenic properties. While bulk RNA sequencing cannot achieve cell-type-specific transcriptional granularity, single-cell sequencing has permitted an unprecedented view of these cell states. Despite this knowledge, we lack an understanding of the mechanistic drivers of this transcriptional and phenotypic heterogeneity. 3' untranslated region alternative polyadenylation (3' UTR-APA) drives gene expression alterations through regulation of 3' UTR length. These 3' UTR alterations modulate mRNA stability, protein expression and protein localization, resulting in cellular phenotypes including differentiation, cell proliferation, and migration. Therefore, we sought to determine whether 3' UTR-APA events could characterize phenotypic heterogeneity of tumor cell states. Here, we analyze the largest single-cell human pancreatic ductal adenocarcinoma (PDAC) dataset and resolve 3' UTR-APA patterns across PDAC cell states. We find that increased proximal 3' UTR-APA is associated with PDAC progression and characterizes a metastatic ductal epithelial subpopulation and an inflammatory fibroblast population. Furthermore, we find significant 3' UTR shortening events in cell-state-specific marker genes associated with increased expression. Therefore, we propose that 3' UTR-APA drives phenotypic heterogeneity in cancer.
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Affiliation(s)
| | - Michael E. Feigin
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
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Cornwell AC, Tisdale AA, Venkat S, Maraszek KE, Alahmari AA, George A, Attwood K, George M, Rempinski D, Franco-Barraza J, Seshadri M, Parker MD, Cortes Gomez E, Fountzilas C, Cukierman E, Steele NG, Feigin ME. Lorazepam Stimulates IL6 Production and Is Associated with Poor Survival Outcomes in Pancreatic Cancer. Clin Cancer Res 2023; 29:3793-3812. [PMID: 37587561 PMCID: PMC10502465 DOI: 10.1158/1078-0432.ccr-23-0547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/31/2023] [Accepted: 07/19/2023] [Indexed: 08/18/2023]
Abstract
PURPOSE This research investigates the association between benzodiazepines (BZD) and cancer patient survival outcomes, the pancreatic cancer tumor microenvironment, and cancer-associated fibroblast (CAF) signaling. EXPERIMENTAL DESIGN Multivariate Cox regression modeling was used to retrospectively measure associations between Roswell Park cancer patient survival outcomes and BZD prescription records. IHC, H&E, Masson's trichrome, RNAscope, and RNA sequencing were used to evaluate the impact of lorazepam (LOR) on the murine PDAC tumor microenvironment. ELISA and qPCR were used to determine the impact of BZDs on IL6 expression or secretion by human-immortalized pancreatic CAFs. PRESTO-Tango assays, reanalysis of PDAC single-cell sequencing/TCGA data sets, and GPR68 CRISPRi knockdown CAFs were used to determine the impact of BZDs on GPR68 signaling. RESULTS LOR is associated with worse progression-free survival (PFS), whereas alprazolam (ALP) is associated with improved PFS, in pancreatic cancer patients receiving chemotherapy. LOR promotes desmoplasia (fibrosis and extracellular matrix protein deposition), inflammatory signaling, and ischemic necrosis. GPR68 is preferentially expressed on human PDAC CAFs, and n-unsubstituted BZDs, such as LOR, significantly increase IL6 expression and secretion in CAFs in a pH and GPR68-dependent manner. Conversely, ALP and other GPR68 n-substituted BZDs decrease IL6 in human CAFs in a pH and GPR68-independent manner. Across many cancer types, LOR is associated with worse survival outcomes relative to ALP and patients not receiving BZDs. CONCLUSIONS We demonstrate that LOR stimulates fibrosis and inflammatory signaling, promotes desmoplasia and ischemic necrosis, and is associated with decreased pancreatic cancer patient survival.
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Affiliation(s)
- Abigail C. Cornwell
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Arwen A. Tisdale
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Swati Venkat
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Kathryn E. Maraszek
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Abdulrahman A. Alahmari
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, Alkharj, Saudi Arabia
| | - Anthony George
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Kristopher Attwood
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Madison George
- Department of Surgery, Henry Ford Pancreatic Cancer Center, Henry Ford Health, Detroit, Michigan
| | - Donald Rempinski
- Department of Surgery, Henry Ford Pancreatic Cancer Center, Henry Ford Health, Detroit, Michigan
| | - Janusz Franco-Barraza
- Cancer Signaling and Microenvironment Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
- Marvin and Concetta Greenberg Pancreatic Cancer Institute, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Mukund Seshadri
- Department of Oral Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Mark D. Parker
- Department of Physiology and Biophysics, University at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York
- Department of Ophthalmology, University at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York
| | - Eduardo Cortes Gomez
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
- Department of Biostatistics, State University of New York at Buffalo, Buffalo, New York
| | - Christos Fountzilas
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Edna Cukierman
- Cancer Signaling and Microenvironment Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
- Marvin and Concetta Greenberg Pancreatic Cancer Institute, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Nina G. Steele
- Department of Surgery, Henry Ford Pancreatic Cancer Center, Henry Ford Health, Detroit, Michigan
| | - Michael E. Feigin
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
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Patel A, Kozlowski K, Richardson K, Jalaeian H, Venkat S. Abstract No. 225 Comparison of Outcome of CT-Guided Lung Biopsy Using a 17-Gauge vs. 19-Gauge Biopsy Gun System. J Vasc Interv Radiol 2023. [DOI: 10.1016/j.jvir.2022.12.286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023] Open
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Alam S, Zunic A, Venkat S, Feigin ME, Atanassov BS. Regulation of Cyclin D1 Degradation by Ubiquitin-Specific Protease 27X Is Critical for Cancer Cell Proliferation and Tumor Growth. Mol Cancer Res 2022; 20:1751-1762. [PMID: 36001804 PMCID: PMC9722596 DOI: 10.1158/1541-7786.mcr-22-0259] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 07/25/2022] [Accepted: 08/23/2022] [Indexed: 01/15/2023]
Abstract
Cyclin D1 (CCND1) is a critical regulator of cell proliferation and its overexpression has been linked to the development and progression of several malignancies. CCND1 overexpression is recognized as a major mechanism of therapy resistance in several cancers; tumors that rely on CCND1 overexpression to evade cancer therapy are extremely sensitive to its ablation. Therefore, targeting CCND1 is a promising strategy for preventing tumor progression and combating therapy resistance in cancer patients. Although CCND1 itself is not a druggable target, it can be targeted indirectly by inhibiting its regulators. CCND1 steady-state levels are tightly regulated by ubiquitin-mediated degradation, and defects in CCND1 ubiquitination are associated with increased CCND1 protein levels in cancer. Here, we uncover a novel function of ubiquitin-specific protease 27X (USP27X), a deubiquitinating enzyme (DUB), in regulating CCND1 degradation in cancer. USP27X binds to and stabilizes CCND1 in a catalytically dependent manner by negatively regulating its ubiquitination. USP27X expression levels correlate with the levels of CCND1 in several HER2 therapy-resistant breast cancer cell lines, and its ablation leads to a severe reduction of CCND1 protein levels, inhibition of tumor growth, and resensitization to targeted therapy. Together, the results presented in our study are the first to expose USP27X as a major CCND1 deubiquitinase and provide a mechanistic explanation for how this DUB fosters tumor growth. IMPLICATIONS As a deubiquitinating enzyme, USP27X is a druggable target. Our study illuminates new avenues for therapeutic intervention in CCND1-driven cancers.
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Affiliation(s)
- Shamshad Alam
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Amanda Zunic
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Swati Venkat
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Michael E. Feigin
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Boyko S. Atanassov
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.,Corresponding author: Boyko S. Atanassov, Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY,14263, USA.
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Alahmari AA, Chaubey A, Tisdale A, Schwarz C, Cornwell A, Maraszek K, Paterson E, Kim M, Venkat S, Gomez EC, Wang J, Gurova K, Feigin ME. Abstract B042: Inhibition of CPSF3 attenuates pancreatic cancer cell proliferation through disruption of histone processing. Cancer Res 2022. [DOI: 10.1158/1538-7445.panca22-b042] [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
Treatment regimens of pancreatic ductal adenocarcinoma (PDAC) are limited and minimally effective which potentiates the importance of discovering novel potential drug targets. We discovered widespread dysregulation of alternative polyadenylation (APA) in PDAC patients. APA is a pre-mRNA processing mechanism that generates mRNAs isoforms with distinct 3’ untranslated regions (3’UTRs). These isoforms contribute to the expression and function of mRNAs and proteins. Our recent study revealed that APA alterations in PDAC drive dysregulation of PDAC-promoting genes and present a reliable prognostic marker. APA is controlled by a suite of genes, including cleavage and polyadenylation specificity factor 3 (CPSF3). Because CPSF3 is the endonuclease that catalyzes mRNA cleavage, we here sought to target CPSF3 in PDAC. We show that CPSF3 expression is significantly upregulated and associated with unfavorable prognosis in PDAC patients. Loss of CPSF3 decreases PDAC cell proliferation, clonogenicity and tumor growth. We show that CPSF3 loss causes APA changes of tumor-associated genes and validate the tumor suppressing activity of one APA-altered gene, FHL1. Using JTE-607, a chemical inhibitor of CPSF3, we find that PDAC cells are preferentially sensitive while non-transformed cell lines are resistant to CPSF3 inhibition. Notably, we show that JTE-607 decreases proliferation-dependent histone expression and disrupts nucleosome assembly. Finally, we find that JTE-607 arrests cells in early to mid S-phase of the cell cycle, resembling histone defect-induced cell cycle arrest. Overall, we reveal alternative polyadenylation and histone processing as two distinct mechanisms underlying CPSF3-induced attenuation of cell proliferation and identify CPSF3 as a potential therapeutic target in PDAC.
Citation Format: Abdulrahman A. Alahmari, Aditi Chaubey, Arwen Tisdale, Carla Schwarz, Abigail Cornwell, Kathryn Maraszek, Emily Paterson, Minsuh Kim, Swati Venkat, Eduardo Cortes Gomez, Jianmin Wang, Katerina Gurova, Michael E. Feigin. Inhibition of CPSF3 attenuates pancreatic cancer cell proliferation through disruption of histone processing [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 B042.
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Affiliation(s)
| | - Aditi Chaubey
- 1Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Arwen Tisdale
- 1Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Carla Schwarz
- 1Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | | | | | | | - Minsuh Kim
- 1Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Swati Venkat
- 1Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | | | - Jianmin Wang
- 1Roswell Park Comprehensive Cancer Center, Buffalo, NY
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Cornwell AC, Alahmari AA, Tisdale AA, Maraszek K, Venkat S, Feigin ME. Abstract C048: Benzodiazepines modify the pancreatic ductal adenocarcinoma tumor microenvironment. Cancer Res 2022. [DOI: 10.1158/1538-7445.panca22-c048] [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
Benzodiazepines (BZDs) are a class of drugs commonly prescribed to pancreatic ductal adenocarcinoma (PDAC) patients to treat anxiety, anticipatory nausea prior to chemotherapy, and insomnia. We discovered that approximately 1 in 4 pancreatic cancer patients are prescribed BZDs and that significant differences in survival outcomes are associated with the type of BZD prescribed. Lorazepam is associated with poorer recurrence-free survival (HR 3.83 (1.53,9.57)) while alprazolam is associated with improved recurrence-free survival (HR 0.38 (0.16,0.92)). We hypothesize that these differences in survival result from off-target activation of the proton-sensing GPCR, GPR68, by n-unsubstituted BZDs, such as lorazepam. GPR68 is preferentially expressed in PDAC cancer-associated fibroblasts (CAFs). We found that n-unsubstituted BZDs commonly prescribed to PDAC patients potentiate activation of GPR68 in the presence of acidity, subsequently promoting secretion of IL-6 by CAFs in a GPR68-dependent manner. Conversely, we found that n-substituted BZDs, such as alprazolam, decrease IL-6 secretion by CAFs in a GPR68-independent manner. Using a syngeneic KPC transplant model, we found that tumors from mice treated with lorazepam had increased expression of inflammatory signaling pathways and ECM-related genes by RNA sequencing. Histologically, lorazepam-treated tumors had increased levels of collagen, alpha-smooth muscle actin staining, and high levels of ischemic necrosis in the centers of the tumors. Overall, these findings indicate that benzodiazepines can modify the PDAC tumor microenvironment, which may subsequently impact chemotherapeutic efficacy and patient survival.
Citation Format: Abigail C. Cornwell, Abdulrahman A. Alahmari, Arwen A. Tisdale, Kathryn Maraszek, Swati Venkat, Michael E. Feigin. Benzodiazepines modify the pancreatic ductal adenocarcinoma tumor microenvironment [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 C048.
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Affiliation(s)
| | | | | | | | - Swati Venkat
- 1Roswell Park Comprehensive Cancer Center, Buffalo, NY
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Argmann C, Hou R, Ungaro RC, Irizar H, Al-Taie Z, Huang R, Kosoy R, Venkat S, Song WM, Di'Narzo AF, Losic B, Hao K, Peters L, Comella PH, Wei G, Atreja A, Mahajan M, Iuga A, Desai PT, Branigan P, Stojmirovic A, Perrigoue J, Brodmerkel C, Curran M, Friedman JR, Hart A, Lamousé-Smith E, Wehkamp J, Mehandru S, Schadt EE, Sands BE, Dubinsky MC, Colombel JF, Kasarskis A, Suárez-Fariñas M. Biopsy and blood-based molecular biomarker of inflammation in IBD. Gut 2022:gutjnl-2021-326451. [PMID: 36109152 PMCID: PMC10014487 DOI: 10.1136/gutjnl-2021-326451] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 08/22/2022] [Indexed: 12/13/2022]
Abstract
OBJECTIVE IBD therapies and treatments are evolving to deeper levels of remission. Molecular measures of disease may augment current endpoints including the potential for less invasive assessments. DESIGN Transcriptome analysis on 712 endoscopically defined inflamed (Inf) and 1778 non-inflamed (Non-Inf) intestinal biopsies (n=498 Crohn's disease, n=421 UC and 243 controls) in the Mount Sinai Crohn's and Colitis Registry were used to identify genes differentially expressed between Inf and Non-Inf biopsies and to generate a molecular inflammation score (bMIS) via gene set variance analysis. A circulating MIS (cirMIS) score, reflecting intestinal molecular inflammation, was generated using blood transcriptome data. bMIS/cirMIS was validated as indicators of intestinal inflammation in four independent IBD cohorts. RESULTS bMIS/cirMIS was strongly associated with clinical, endoscopic and histological disease activity indices. Patients with the same histologic score of inflammation had variable bMIS scores, indicating that bMIS describes a deeper range of inflammation. In available clinical trial data sets, both scores were responsive to IBD treatment. Despite similar baseline endoscopic and histologic activity, UC patients with lower baseline bMIS levels were more likely treatment responders compared with those with higher levels. Finally, among patients with UC in endoscopic and histologic remission, those with lower bMIS levels were less likely to have a disease flare over time. CONCLUSION Transcriptionally based scores provide an alternative objective and deeper quantification of intestinal inflammation, which could augment current clinical assessments used for disease monitoring and have potential for predicting therapeutic response and patients at higher risk of disease flares.
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Affiliation(s)
- Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ruixue Hou
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ryan C Ungaro
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Haritz Irizar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Zainab Al-Taie
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ruiqi Huang
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Roman Kosoy
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Won-Min Song
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Antonio F Di'Narzo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Sema4, Stamford, Connecticut, USA
| | - Bojan Losic
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Sema4, Stamford, Connecticut, USA
| | - Lauren Peters
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Phillip H Comella
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Gabrielle Wei
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ashish Atreja
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Milind Mahajan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Sema4, Stamford, Connecticut, USA
| | - Alina Iuga
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | | | | | | | | | - Mark Curran
- Janssen R&D, Spring House, Pennsylvania, USA
| | | | - Amy Hart
- Janssen R&D, Spring House, Pennsylvania, USA
| | | | - Jan Wehkamp
- Janssen R&D, Spring House, Pennsylvania, USA
| | - Saurabh Mehandru
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Sema4, Stamford, Connecticut, USA
| | - Bruce E Sands
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Marla C Dubinsky
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jean-Frederic Colombel
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Andrew Kasarskis
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Sema4, Stamford, Connecticut, USA
| | - Mayte Suárez-Fariñas
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA .,Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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9
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Doepner M, Lee I, Natale CA, Brathwaite R, Venkat S, Kim SH, Wei Y, Vakoc CR, Capell BC, Katzenellenbogen JA, Katzenellenbogen BS, Feigin ME, Ridky TW. Endogenous DOPA inhibits melanoma through suppression of CHRM1 signaling. Sci Adv 2022; 8:eabn4007. [PMID: 36054350 PMCID: PMC10848963 DOI: 10.1126/sciadv.abn4007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 07/14/2022] [Indexed: 05/18/2023]
Abstract
Melanoma risk is 30 times higher in people with lightly pigmented skin versus darkly pigmented skin. Using primary human melanocytes representing the full human skin pigment continuum and preclinical melanoma models, we show that cell-intrinsic differences between dark and light melanocytes regulate melanocyte proliferative capacity and susceptibility to malignant transformation, independent of melanin and ultraviolet exposure. These differences result from dihydroxyphenylalanine (DOPA), a melanin precursor synthesized at higher levels in melanocytes from darkly pigmented skin. We used both high-throughput pharmacologic and genetic in vivo CRISPR screens to determine that DOPA limits melanocyte and melanoma cell proliferation by inhibiting the muscarinic acetylcholine receptor M1 (CHRM1) signaling. Pharmacologic CHRM1 antagonism in melanoma leads to depletion of c-Myc and FOXM1, both of which are proliferation drivers associated with aggressive melanoma. In preclinical mouse melanoma models, pharmacologic inhibition of CHRM1 or FOXM1 inhibited tumor growth. CHRM1 and FOXM1 may be new therapeutic targets for melanoma.
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Affiliation(s)
- Miriam Doepner
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Inyoung Lee
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Christopher A. Natale
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Roderick Brathwaite
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Swati Venkat
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Sung Hoon Kim
- Department of Chemistry and Cancer Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yiliang Wei
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Brian C. Capell
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - John A. Katzenellenbogen
- Department of Chemistry and Cancer Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Benita S. Katzenellenbogen
- Departments of Molecular and Integrative Physiology and Cancer Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Michael E. Feigin
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Todd W. Ridky
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Doepner M, Natale C, Lee I, Brathwaite R, Venkat S, Kim S, Wei Y, Vakoc C, Katzenellenbogen J, Katzenellenbogen B, Feigin M, Ridky T. 653 Endogenous DOPA inhibits melanoma through suppression of CHRM1 signaling. J Invest Dermatol 2022. [DOI: 10.1016/j.jid.2022.05.664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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11
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Barton M, Puchferran C, Kattan A, Pennix T, Sanan A, Venkat S, Bhatia S, Zikria J. Abstract No. 386 Comparing pre-procedure imaging versus direct stick venography for low flow vascular arterio-venous malformations. J Vasc Interv Radiol 2022. [DOI: 10.1016/j.jvir.2022.03.467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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12
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Richardson K, Hernandez A, Venkat S, Jalaeian H, Bhatia S. Abstract No. 548 Does body habitus affect the outcome of CT-guided lung biopsies? J Vasc Interv Radiol 2022. [DOI: 10.1016/j.jvir.2022.03.530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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13
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Cornwell AC, Alahmari AA, Tisdale AA, Maraszek K, Venkat S, Feigin ME. Abstract PO-100: Lorazepam promotes desmoplasia and ischemic necrosis in murine pancreatic ductal adenocarcinoma. Cancer Res 2021. [DOI: 10.1158/1538-7445.panca21-po-100] [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
The goal of this research is to identify the effect of the GPR68-activator benzodiazepine (BZD) lorazepam on the pancreatic ductal adenocarcinoma (PDA) tumor microenvironment (TME). BZDs are commonly prescribed to PDA patients to treat anxiety and anticipatory nausea prior to chemotherapy. Certain types of BZDs are known to promote off-target activation of GPR68 under acidic conditions. We hypothesize that GPR68-activating BZDs will stimulate pro-fibrotic and pro-inflammatory signaling pathways by cancer-associated fibroblasts (CAFs), producing a more desmoplastic TME that will subsequently constrict the tumor vasculature, decreasing chemotherapeutic efficacy, and ultimately decreasing patient survival. Using a subcutaneous KPC allograft mouse model, we found that lorazepam modified the TME by significantly increasing α-SMA (smooth muscle actin) protein expression, collagen deposition, and ischemic necrosis. Preliminary, we found that treating tumor-bearing KPC mice with lorazepam similarly promoted ischemic necrosis. RNA sequencing of the lorazepam-treated allograft tumors indicated that CAF and ECM-related genes such as PDPN, LOX, SERPINB2, and ITGA11 were significantly upregulated. Pathway analysis revealed that lorazepam treatment promoted pathways related to inflammation, EMT, hypoxia, as well as known GPR68 downstream signaling pathways such as TNF-alpha signaling via NF-kB and IL6/JAK/STAT3 signaling. qRT-PCR of immortalized CAFs treated with lorazepam indicated that IL6 expression is increased by lorazepam in a GPR68-dependent manner at acidic pH, supporting that the promotion of IL6 expression we observed in vivo was likely GPR68 and CAF-dependent. To validate the clinical significance of our work, covariate adjusted analyses of pancreatic cancer patients who received chemotherapy at Roswell Park from 2004-2020 was performed. Patients taking GPR68 activator benzodiazepines versus non-activator benzodiazepines had poorer progression-free survival (HR 6.85(2.12,22.06)), suggesting that GPR68 activation by benzodiazepines may negatively impact survival. Overall, these findings suggest that lorazepam significantly modifies the PDA TME by promoting desmoplasia and ischemic necrosis, due in part to activation of GPR68. Future experimental work will determine if lorazepam negatively impacts survival and chemotherapeutic efficacy. Significance: This research may guide the development of new clinical recommendations for prescribing benzodiazepines to PDA patients, which will likely be applicable to other cancer types.
Citation Format: Abigail C. Cornwell, Abdulrahman A. Alahmari, Arwen A. Tisdale, Kathryn Maraszek, Swati Venkat, Michael E. Feigin. Lorazepam promotes desmoplasia and ischemic necrosis in murine pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the AACR Virtual Special Conference on Pancreatic Cancer; 2021 Sep 29-30. Philadelphia (PA): AACR; Cancer Res 2021;81(22 Suppl):Abstract nr PO-100.
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Affiliation(s)
| | | | | | | | - Swati Venkat
- Roswell Park Comprehensive Cancer Center, Buffalo, NY
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14
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Gosch M, Pils K, Venkat S, Singler K. [Aspects of multimodal pain therapy in old age]. Z Gerontol Geriatr 2021; 54:823-832. [PMID: 34319451 DOI: 10.1007/s00391-021-01952-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/21/2021] [Indexed: 11/29/2022]
Abstract
Chronic pain in older adults should be explained and treated on the basis of the biopsychosocial model. With its interdisciplinary and interprofessional approach, multimodal pain therapy is the method of choice. In old age freedom from pain is usually not the primary goal. It is more important to restore the quality of life of those affected and to maintain independence and autonomy with a versatile treatment offer. This article explains the basics of multimodal pain therapy and its special features in old age.
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Affiliation(s)
- M Gosch
- Medizinische Klinik 2, Schwerpunkt Geriatrie, Klinikum Nürnberg, Paracelsus Medizinische Privatuniversität Nürnberg, Prof. Ernst-Nathan-Str. 1, 90419, Nürnberg, Deutschland.
| | - K Pils
- Institut für Physikalische Medizin und Rehabilitation, Wiener Gesundheitsverbund - Klinik Favoriten, Kundratstr. 1, 1100, Wien, Österreich
| | - S Venkat
- Klinik für Psychosomatische Medizin und Psychotherapie, Schmerztagesklinik, Klinikum Nürnberg, Paracelsus Medizinische Privatuniversität Nürnberg, Prof. Ernst-Nathan-Str. 1, 90419, Nürnberg, Deutschland
| | - K Singler
- Medizinische Klinik 2, Schwerpunkt Geriatrie, Klinikum Nürnberg, Paracelsus Medizinische Privatuniversität Nürnberg, Prof. Ernst-Nathan-Str. 1, 90419, Nürnberg, Deutschland.,Institut für Biomedizin des Alterns, Friedrich-Alexander-Universität Erlangen-Nürnberg, Kobergerstr. 60, 90408, Nürnberg, Deutschland
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Venkat S, Alahmari AA, Feigin ME. Drivers of Gene Expression Dysregulation in Pancreatic Cancer. Trends Cancer 2021; 7:594-605. [PMID: 33618999 PMCID: PMC8217125 DOI: 10.1016/j.trecan.2021.01.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 01/15/2021] [Accepted: 01/22/2021] [Indexed: 12/21/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) remains a devastating disease with a poor prognosis. The functional consequences of common genetic aberrations and their roles in treatment strategies have been extensively reviewed. In addition to these genomic aberrations, consideration of non-genetic drivers of altered oncogene expression is essential to account for the diversity in PDAC phenotypes. In this review we seek to assess our current understanding of mechanisms of gene expression dysregulation. We focus on four drivers of gene expression dysregulation, including mutations, transcription factors, epigenetic regulators, and RNA stability/isoform regulation, in the context of PDAC pathogenesis. Recent studies provide much-needed insight into the role of gene expression dysregulation in dissecting tumor heterogeneity and stratifying patients for the development of personalized treatment strategies.
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Affiliation(s)
- Swati Venkat
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Abdulrahman A Alahmari
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA; Department of Medical Laboratory Sciences, Prince Sattam Bin Abdulaziz University, Alkharj, Saudi Arabia
| | - Michael E Feigin
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.
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Venkat S, Tisdale AA, Schwarz JR, Alahmari AA, Maurer HC, Olive KP, Eng KH, Feigin ME. Alternative polyadenylation drives oncogenic gene expression in pancreatic ductal adenocarcinoma. Genome Res 2020; 30:347-360. [PMID: 32029502 PMCID: PMC7111527 DOI: 10.1101/gr.257550.119] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 02/04/2020] [Indexed: 01/08/2023]
Abstract
Alternative polyadenylation (APA) is a gene regulatory process that dictates mRNA 3'-UTR length, resulting in changes in mRNA stability and localization. APA is frequently disrupted in cancer and promotes tumorigenesis through altered expression of oncogenes and tumor suppressors. Pan-cancer analyses have revealed common APA events across the tumor landscape; however, little is known about tumor type-specific alterations that may uncover novel events and vulnerabilities. Here, we integrate RNA-sequencing data from the Genotype-Tissue Expression (GTEx) project and The Cancer Genome Atlas (TCGA) to comprehensively analyze APA events in 148 pancreatic ductal adenocarcinomas (PDACs). We report widespread, recurrent, and functionally relevant 3'-UTR alterations associated with gene expression changes of known and newly identified PDAC growth-promoting genes and experimentally validate the effects of these APA events on protein expression. We find enrichment for APA events in genes associated with known PDAC pathways, loss of tumor-suppressive miRNA binding sites, and increased heterogeneity in 3'-UTR forms of metabolic genes. Survival analyses reveal a subset of 3'-UTR alterations that independently characterize a poor prognostic cohort among PDAC patients. Finally, we identify and validate the casein kinase CSNK1A1 (also known as CK1alpha or CK1a) as an APA-regulated therapeutic target in PDAC. Knockdown or pharmacological inhibition of CSNK1A1 attenuates PDAC cell proliferation and clonogenic growth. Our single-cancer analysis reveals APA as an underappreciated driver of protumorigenic gene expression in PDAC via the loss of miRNA regulation.
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Affiliation(s)
- Swati Venkat
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14263, USA
| | - Arwen A Tisdale
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14263, USA
| | - Johann R Schwarz
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14263, USA
| | - Abdulrahman A Alahmari
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14263, USA
| | - H Carlo Maurer
- Klinikum rechts der Isar, II. Medizinische Klinik, Technische Universität München, 81675 Munich, Germany
| | - Kenneth P Olive
- Herbert Irving Comprehensive Cancer Center, Department of Medicine, Division of Digestive and Liver Diseases, Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York 10032, USA
| | - Kevin H Eng
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14263, USA
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14263, USA
| | - Michael E Feigin
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14263, USA
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Mai T, Contreras F, Venkat S, Mohan P, Bhatia S. 4:12 PM Abstract No. 306 Survival benefits of drug-eluting bead transarterial chemoembolization in Barcelona Clinic Liver Cancer stage C hepatocellular carcinoma patients. J Vasc Interv Radiol 2020. [DOI: 10.1016/j.jvir.2019.12.359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Acharya V, Swersky A, Fox B, Tummala S, Miller Z, Venkat S, Kably I, Mohan P. Abstract No. 681 Angioplasty and/or stenting for transplant renal artery stenosis. J Vasc Interv Radiol 2020. [DOI: 10.1016/j.jvir.2019.12.740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Venkat S, Tisdale AA, Eng KH, Feigin ME. Abstract A14: Alternative polyadenylation drives oncogenic gene expression in pancreatic cancer. Cancer Res 2019. [DOI: 10.1158/1538-7445.panca19-a14] [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
Tumors can co-opt the mRNA processing machinery to dysregulate the expression of oncogenes and tumor suppressors. One such altered process, termed alternative polyadenylation (APA), is responsible for regulating 3’-untranslated region (UTR) length. APA is driven by a core set of factors that recognize a series of highly conserved sequences within the 3’-UTR on the pre-mRNA. The pre-mRNA is then cleaved before addition of the poly(A) tail. As most transcripts contain several polyadenylation sequences, the choice of where to cleave is a critical determinant of 3’-UTR length. The 3’-UTR contains regulatory sequences, including miRNA binding sites, that control mRNA stability, function, and subcellular localization. Therefore, altering the length of a 3’-UTR can have dramatic impacts on gene function and cellular phenotype. APA factor expression is altered in a variety of cancer types, resulting in dysregulated gene expression. For example, loss of the APA factor CFIm25 in glioblastoma increases cell proliferation through 3’-UTR shortening and upregulated expression of cyclin D1. Pan-cancer analyses have revealed that hundreds of transcripts undergo APA. How these changes in 3’-UTR length are mechanistically linked to changes in gene expression and function are complex and only now being functionally addressed. Despite recent efforts to interrogate APA events in human tumors, numerous critical gaps in knowledge remain. Several pan-cancer analyses have revealed common APA events across diverse tumor types. However, no large-scale, single tumor-type analysis has been reported. Furthermore, the role of APA in pancreatic ductal adenocarcinoma (PDA) has been largely unaddressed. An understanding of the gene-regulatory mechanisms driving PDA progression may provide novel targets for therapeutic intervention. We have performed a comprehensive analysis of differential APA events in normal pancreas and PDA tumors, and observe widespread 3’-UTR shortening in PDA, correlating with expression changes in known PDA drivers and alterations in cancer signaling networks. Experimental validation of candidate genes reveals APA as a novel mechanism of regulation for the PDA oncogene ALDOA, and other genes implicated in pancreatic cancer cell growth, migration, and invasion. Hierarchical clustering of APA events allowed the development of a prognostic signature, identifying patients with poor prognosis. We find that 3’-UTR shortening events drive a preferential loss of tumor suppressive miRNA binding sites, and validate these findings through experimental manipulation of 3’-UTRs in cultured cells. Finally, we identify the serine/threonine kinase casein kinase 1 alpha (CK1) as an APA-regulated, targetable factor driving pancreatic cancer cell growth; inhibition of CK1 attenuates cell proliferation, colony formation, and migration. Our study reveals new mechanisms of dysregulation for cancer promoting genes, highlights the prognostic value of APA analysis, and identifies new targetable factors for PDA.
Citation Format: Swati Venkat, Arwen A Tisdale, Kevin H. Eng, Michael E. Feigin. Alternative polyadenylation drives oncogenic gene expression in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2019 Sept 6-9; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2019;79(24 Suppl):Abstract nr A14.
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Affiliation(s)
- Swati Venkat
- Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | | | - Kevin H. Eng
- Roswell Park Comprehensive Cancer Center, Buffalo, NY
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Lencioni R, Doshi M, Venkat S, Scagnelli T, Narayanan G. 4:12 PM Abstract No. 139 Transarterial chemoembolization of hepatocellular carcinoma with a novel radiopaque drug-eluting bead. J Vasc Interv Radiol 2018. [DOI: 10.1016/j.jvir.2018.01.157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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Froud T, Mohan P, Venkat S, Lencioni R, Narayanan G. Abstract No. 494 Microwave ablation zone observations in a large series with recommendations for adjustments. J Vasc Interv Radiol 2018. [DOI: 10.1016/j.jvir.2018.01.539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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22
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Venkat S, Linstedt AD. Manganese-induced trafficking and turnover of GPP130 is mediated by sortilin. Mol Biol Cell 2017; 28:2569-2578. [PMID: 28768823 PMCID: PMC5597328 DOI: 10.1091/mbc.e17-05-0326] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/17/2017] [Accepted: 07/24/2017] [Indexed: 11/11/2022] Open
Abstract
By binding and directing the cycling Golgi protein GPP130 to lysosomes, the sorting receptor sortilin mediates the manganese-induced GPP130 down-regulation that protects against Shiga toxicosis. Elevated, nontoxic doses of manganese (Mn) protect against Shiga toxin-1–induced cell death via down-regulation of GPP130, a cycling Golgi membrane protein that serves as an endosome-to-Golgi trafficking receptor for the toxin. Mn binds to GPP130 in the Golgi and causes GPP130 to oligomerize/aggregate, and the complexes are diverted to lysosomes. In fact, based on experiments using the self-interacting FM domain, it appears generally true that aggregation of a Golgi protein leads to its lysosomal degradation. How such oligomers are selectively sorted out of the Golgi is unknown. Here we provide evidence that Mn-induced exit of GPP130 from the trans-Golgi network (TGN) toward lysosomes is mediated by the sorting receptor sortilin interacting with the lumenal stem domain of GPP130. In contrast, FM-induced lysosomal trafficking of the Golgi protein galactosyltransferase was sortilin independent and occurred even in the absence of its native lumenal domain. Thus sortilin-dependent as well as sortilin-independent sorting mechanisms target aggregated Golgi membrane proteins for lysosomal degradation.
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Affiliation(s)
- Swati Venkat
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Adam D Linstedt
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213
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Gogia A, Raina V, Deo S, Mohanti B, Shukla N, Venkat S. PO41 An overview of young breast cancer patients. Breast 2012. [DOI: 10.1016/s0960-9776(12)70052-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Venkat S. Emergency in the cowshed. West J Med 2011. [DOI: 10.1136/bmj.d4271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Schubert CS, Venkat S, Söllner W. Die Veränderung der gesundheitsbezogenen Lebensqualität bei chronischen Schmerzpatienten im Rahmen eines multimodalen Therapieprogramms – Ein Vergleich von Patienten mit der Diagnose "Anhaltende somatoforme Schmerzstörung" und anderen chronischen Schmerzpatienten. Psychother Psychosom Med Psychol 2009. [DOI: 10.1055/s-0029-1208201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Usha M, Deepak V, Venkat S, Gargi M. Treatment of severely mutilated incisors: a challenge to the pedodontist. J Indian Soc Pedod Prev Dent 2007; 25 Suppl:S34-6. [PMID: 17921639] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
Dental caries is the single most common chronic childhood disease. In early childhood caries, there is early carious involvement and gross destruction of the maxillary anterior teeth. This leads to difficulty in speech, decreased masticatory efficiency, development of abnormal tongue habits and subsequent malocclusion and psychological problems if esthetics are compromised. The restoration of severely decayed primary incisors is often a difficult procedure that presents a special challenge to pediatric dentists. This case report documents the restoration of severely mutilated lateral incisors in a patient with early childhood caries.
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Affiliation(s)
- M Usha
- Department of Pedodontics and Preventive Dentistry, V. S. Dental College and Hospital, V. V. Puram, Bangalore - 560 004, Karnataka, India.
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Venkat S, Apte SK, Chaubey RC, Chauhan PS. Radioadaptive response in human lymphocytes in vitro. J Environ Pathol Toxicol Oncol 2002; 20:165-75. [PMID: 11797826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
Exposure to low doses of radiation and/or chemicals can prime an organism to withstand the stress of a subsequent exposure to higher doses of the same agent. In the case of radiation, this phenomenon has been called radioadaptive response. Cytogenetic studies have been undertaken in human lymphocytes to investigate adaptive response (AR) to ionizing radiation, in particular to seek the role of variables such as priming dose, cell cycle stage, and age and gender of the donor. We demonstrated that pre-exposure of lymphocytes in whole blood cultures to very low doses in the range of about 1 cGy (priming or adaptive dose [AD]) reduced the frequency of micronuclei in binucleated cells induced by 100 cGy--that is, produced an AR in these cells in vitro. However, pre-exposure of cells to 10.0 cGy did not reduce the chromosomal damage (micronuclei) induced by the challenging dose (CD) of 100 cGy under the same protocol, thus exhibiting an inverse dose-response relationship. There was marked variability in the AR among the individuals investigated in the study. The extent of AR also depended on the stage of cell cycle exposed to the CD of radiation. Maximum AR was observed when CD of 100 cGy was given 4 hours after AD, 30 hours following the mitogenic stimulation of lymphocytes. The least AR was observed when CD was given 48 hours after stimulation. Interestingly, AR was also found to be dependent on the age of the donor, a decrease in AR being observed with an increasing age. No significant difference in AR was observed between male and female donors. To understand the molecular events underlying AR, protein synthesis patterns were studied in human lymphocytes subjected to mitogen, heat, or radiation stress. Heat shock (45 degrees C, for 15 min) induced 7 proteins with molecular weights ranging from 40 to 80 kDa, while treatment with phytohemagglutinin (40 microg/mL) showed induction of 2 proteins of molecular weights 38 and 48 kDa, respectively. However, exposure of human lymphocyte cultures to gamma radiation did not significantly induce synthesis of any protein, up to 800 cGy dose. Lack of induction of proteins by gamma radiation in human lymphocytes contrasts with the previous reports showing X-ray radiation-enhanced gene expression in melanoma cells and/or human tumor fibroblasts.
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Affiliation(s)
- S Venkat
- Cell Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India
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Venkat S, Chaubey RC, Chauhan PS. Radio-adaptive response in human lymphocytes in vitro. Indian J Exp Biol 1996; 34:909-12. [PMID: 9014534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
An attempt has been made to investigate the adaptive response to ionizing radiation in the human lymphocytes in vitro using cytochalasin-B blocked micronucleated binucleate cells (mn-BNCs) as a cytogenetic end point. Whole blood samples drawn from healthy donors, of either sex were irradiated in vitro at a dose of 1 cGy (adaptive or conditioning dose) Cobalt-60 gamma radiation (dose rate 1.12 cGy/min) at about 26 hr after mitogenic stimulation. After 31 hr of their initiation, groups of cultures were subsequently exposed to a challenging dose of 100 cGy gamma radiation (dose rate 82 cGy/min.). Eight males in the age group ranging from 25 to 55 years and eight females (age group 25 to 29 years), have been analysed during this study. Analysis of data revealed 40.6% reduction in the frequency of mn-BNCs among the males with a range from 25.7% to 54.7%. In case of females, also the per cent reduction varied from 26.3% to 49.0%, with a mean value of 33.7%. Pooling the data from males and females gave an overall reduction of 37.1% in the frequency of radiation induced mn-BNCs due to pre-exposure to 1 cGy radiation.
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Affiliation(s)
- S Venkat
- Cell Biology Division, Bhabha Atomic Research Centre, Bombay, India
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