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Liu S, Zhong H, Zhu J, Wu Y, Deng Y, Wu L. Regulome-wide association study identifies genetically driven accessible regions associated with pancreatic cancer risk. Int J Cancer 2024; 154:670-678. [PMID: 37850323 PMCID: PMC10842605 DOI: 10.1002/ijc.34761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 09/04/2023] [Accepted: 09/21/2023] [Indexed: 10/19/2023]
Abstract
Genome-wide association studies (GWAS) have identified two dozen genetic variants that are associated with the risk of pancreatic ductal adenocarcinoma (PDAC), a deadly malignancy. However, a majority of these variants are located in noncoding regions of the genome, which limits the translation of GWAS findings into clinical applications. The regulome-wide association study (RWAS) is a recently developed method for identifying TF binding-induced accessibility regions for diseases. However, their potential connection to PDAC has yet to be fully explored. We evaluated the associations between genetically predicted levels of chromatin accessibility and risk of PDAC by using pan-cancer chromatin accessibility genetic prediction models. Our analysis included 8275 cases and 6723 controls from the PanScan (I, II, and III) and PanC4 consortia. To further refine our results, we also integrated genes associated to allele-specific accessibility quantitative trait loci (as-aQTL) and TF motifs located in the as-aQTL. We found that 50 chromatin accessibility features were associated with PDAC risk at a false discovery rate (FDR) of less than 0.05. A total of 28 RWAS peaks were identified as conditionally significant. By integrating the results from as-aQTL, motif analysis, and RWAS, we identified candidate causal regulatory elements for two potential chromatin accessibility regions (THCA_89956 and ESCA_89167) that are associated with PDAC risk. Our study identified chromatin accessibility features in noncoding genomic regions that are associated with PDAC risk. We also predicted the associated genes and disrupt motifs. Our findings provide new insights into the regulatory mechanisms of noncoding regions for pancreatic tumorigenesis.
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Affiliation(s)
- Shuai Liu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Hua Zhong
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Jingjing Zhu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Yong Wu
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, David Geffen School of Medicine at UCLA
| | - Youping Deng
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Lang Wu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA
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Giarrizzo M, LaComb JF, Bialkowska AB. The Role of Krüppel-like Factors in Pancreatic Physiology and Pathophysiology. Int J Mol Sci 2023; 24:ijms24108589. [PMID: 37239940 DOI: 10.3390/ijms24108589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/04/2023] [Accepted: 05/06/2023] [Indexed: 05/28/2023] Open
Abstract
Krüppel-like factors (KLFs) belong to the family of transcription factors with three highly conserved zinc finger domains in the C-terminus. They regulate homeostasis, development, and disease progression in many tissues. It has been shown that KLFs play an essential role in the endocrine and exocrine compartments of the pancreas. They are necessary to maintain glucose homeostasis and have been implicated in the development of diabetes. Furthermore, they can be a vital tool in enabling pancreas regeneration and disease modeling. Finally, the KLF family contains proteins that act as tumor suppressors and oncogenes. A subset of members has a biphasic function, being upregulated in the early stages of oncogenesis and stimulating its progression and downregulated in the late stages to allow for tumor dissemination. Here, we describe KLFs' function in pancreatic physiology and pathophysiology.
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Affiliation(s)
- Michael Giarrizzo
- Department of Medicine, Renaissance School of Medicine at Stony Brook University, Stony Brook, NY 11794, USA
| | - Joseph F LaComb
- Department of Medicine, Renaissance School of Medicine at Stony Brook University, Stony Brook, NY 11794, USA
| | - Agnieszka B Bialkowska
- Department of Medicine, Renaissance School of Medicine at Stony Brook University, Stony Brook, NY 11794, USA
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Sun N, Kabir M, Lee Y, Xie L, Hu X, Velez J, Chen X, Kaniskan HÜ, Jin J. Discovery of the First Lactate Dehydrogenase Proteolysis Targeting Chimera Degrader for the Treatment of Pancreatic Cancer. J Med Chem 2023; 66:596-610. [PMID: 36538511 PMCID: PMC9969998 DOI: 10.1021/acs.jmedchem.2c01505] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Lactate dehydrogenase (LDH) is a key glycolytic enzyme and biomarker of aggressive cancers. LDHA and LDHB are two main LDH subunits, and both are frequently overexpressed in tumors and essential for tumor growth. A number of LDHA/B small-molecule inhibitors have been developed. Here, we report the discovery of the first LDH proteolysis targeting chimera (PROTAC) degrader, compound 22 (MS6105). 22 potently degraded LDHA in a time- and ubiquitin-proteasome system-dependent manner. Using an unbiased global proteomic study, we confirmed that 22 degraded both LDHA and LDHB significantly. 22 was significantly more potent than the parent LDH inhibitor in suppressing the growth of both quasi-mesenchymal state and epithelial state pancreatic cancer cell lines. Furthermore, 22 was bioavailable in mice through intraperitoneal injection. Overall, 22 could be a valuable chemical tool for the research community to explore pathophysiological functions of LDH in vitro and in vivo.
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Affiliation(s)
- Ning Sun
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Md Kabir
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Youngeun Lee
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Ling Xie
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Xiaoping Hu
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Julia Velez
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Xian Chen
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - H Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
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Kondratyeva LG, Safina DR, Chernov IP, Kopantzev EP, Kostrov SV, Sverdlov ED. PDX1, a key factor in pancreatic embryogenesis, can exhibit antimetastatic activity in pancreatic ductal adenocarcinoma. Cancer Manag Res 2019; 11:7077-7087. [PMID: 31440095 PMCID: PMC6666369 DOI: 10.2147/cmar.s209940] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/25/2019] [Indexed: 12/12/2022] Open
Abstract
Background: In cancer biology, metastasizing is one of the most poorly studied processes. Pancreatic ductal adenocarcinoma (PDAC) is characterized by early metastasis, which is the leading cause of death. The PDX1 protein is crucial for the development of cancer, and its low levels are characteristic of the most aggressive PDAC tumors. The PDX1 is a mediator of initiation and progression of PDAC. However, further studies are needed to elucidate the role of PDX1 in the cancer metastasis. Purpose: To confirm the hypothesis that PDX1 in PDAC plays suppressor role of epithelial–mesenchymal transition (EMT), and to study its possible ability to inhibit metastasis. Methods: A PDX1-overexpressing PDAC cell line was obtained by lentiviral transduction of PANC-1 cells. PDX1 overexpression was confirmed by RT-PCR and Western blotting. Effects of PDX1 ectopic expression on cell proliferation and motility were determined in PANC-1 cells using MTS, cell cycle analysis, transwell and wound-healing assay. EMT genes expression was analyzed in PDX1-overexpressing and Control PANC-1. Finally, the migration potential of pancreatic cancer cells expressing PDX1 was evaluated using a zebrafish embryo model. Results: The motility of human PDAC cells PANC-1 considerably decreased at ectopic expression of PDX1. The decreased expression of ZEB1, the key factor of EMT, and almost unchanged expression of the genes that characterize the epithelial state suggest a decrease in the EMT ability. Suppression of PDX1 expression by siRNA knockdown restored the PANC1 motility. Conclusion: The results obtained suggest a possible therapeutic use of PDX1 delivery into PDAC patients with a reduced or absent expression of PDX1 in the most aggressive tumors.
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Affiliation(s)
- Liya G Kondratyeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Dina R Safina
- Institute of Molecular Genetics Russian Academy of Sciences, Moscow, Russia
| | - Igor P Chernov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Eugene P Kopantzev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Sergey V Kostrov
- Institute of Molecular Genetics Russian Academy of Sciences, Moscow, Russia
| | - Eugene D Sverdlov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia.,Institute of Molecular Genetics Russian Academy of Sciences, Moscow, Russia
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Zinovyeva MV, Nikolaev LG, Kondratyeva LG, Vinogradova TV, Sverdlov ED. Correlation between Expression of KLF5 and ZEB1 Transcription Factor Genes in Pancreatic Cancer. DOKL BIOCHEM BIOPHYS 2018; 481:219-221. [PMID: 30168064 DOI: 10.1134/s1607672918040129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Indexed: 11/23/2022]
Abstract
The mRNA content of the transcription factors KLF5 and ZEB1 was studied in pancreatic tumor tissues and in fetal and normal pancreas. Transcription of these factors was not high and similar in normal and fetal pancreatic tissues but greatly increased in the pancreatic ductal adenocarcinoma tissues. A significant positive correlation between the KLF5 and ZEB1 transcription levels in the pancreatic tumor tissues was observed.
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Affiliation(s)
- M V Zinovyeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - L G Nikolaev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - L G Kondratyeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - T V Vinogradova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - E D Sverdlov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
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Abstract
Pancreatic cancers arise through a series of genetic events both inherited and acquired. Inherited genetic changes, both high penetrance and low penetrance, are an important component of pancreatic cancer risk, and may be used to characterize populations who will benefit from early detection. Furthermore, pancreatic cancer patients with inherited mutations may be particularly sensitive to certain targeted agents, providing an opportunity to personalized treatment. Family history of pancreatic cancer is one of the strongest risk factors for the disease, and is associated with an increased risk of caners at other sites, including but not limited to breast, ovarian and colorectal cancer. The goal of this chapter is to discuss the importance of family history of pancreatic cancer, and the known genes that account for a portion of the familial clustering of pancreatic cancer.
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Affiliation(s)
- Fei Chen
- Department of Epidemiology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Nicholas J Roberts
- Department of Pathology, Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins Medical Institution, Baltimore, MD, USA
| | - Alison P Klein
- Department of Epidemiology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Department of Pathology, Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins Medical Institution, Baltimore, MD, USA.
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