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Tu YH, Juan HF, Huang HC. Context-dependent gene regulatory network reveals regulation dynamics and cell trajectories using unspliced transcripts. Brief Bioinform 2023; 24:6991202. [PMID: 36653899 DOI: 10.1093/bib/bbac633] [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: 10/18/2022] [Revised: 12/06/2022] [Accepted: 12/29/2022] [Indexed: 01/20/2023] Open
Abstract
Gene regulatory networks govern complex gene expression programs in various biological phenomena, including embryonic development, cell fate decisions and oncogenesis. Single-cell techniques are increasingly being used to study gene expression, providing higher resolution than traditional approaches. However, inferring a comprehensive gene regulatory network across different cell types remains a challenge. Here, we propose to construct context-dependent gene regulatory networks (CDGRNs) from single-cell RNA sequencing data utilizing both spliced and unspliced transcript expression levels. A gene regulatory network is decomposed into subnetworks corresponding to different transcriptomic contexts. Each subnetwork comprises the consensus active regulation pairs of transcription factors and their target genes shared by a group of cells, inferred by a Gaussian mixture model. We find that the union of gene regulation pairs in all contexts is sufficient to reconstruct differentiation trajectories. Functions specific to the cell cycle, cell differentiation or tissue-specific functions are enriched throughout the developmental process in each context. Surprisingly, we also observe that the network entropy of CDGRNs decreases along differentiation trajectories, indicating directionality in differentiation. Overall, CDGRN allows us to establish the connection between gene regulation at the molecular level and cell differentiation at the macroscopic level.
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Affiliation(s)
- Yueh-Hua Tu
- Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan
- Taiwan International Graduate Program on Bioinformatics, National Taiwan University, Taipei, 106, Taiwan
| | - Hsueh-Fen Juan
- Taiwan International Graduate Program on Bioinformatics, National Taiwan University, Taipei, 106, Taiwan
- Department of Life Science, National Taiwan University, Taipei, 106, Taiwan
| | - Hsuan-Cheng Huang
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei, 112, Taiwan
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2
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Sierra-Pagan JE, Garry DJ. The regulatory role of pioneer factors during cardiovascular lineage specification – A mini review. Front Cardiovasc Med 2022; 9:972591. [PMID: 36082116 PMCID: PMC9445115 DOI: 10.3389/fcvm.2022.972591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/03/2022] [Indexed: 11/15/2022] Open
Abstract
Cardiovascular disease (CVD) remains the number one cause of death worldwide. Ischemic heart disease contributes to heart failure and has considerable morbidity and mortality. Therefore, alternative therapeutic strategies are urgently needed. One class of epigenetic regulators known as pioneer factors has emerged as an important tool for the development of regenerative therapies for the treatment of CVD. Pioneer factors bind closed chromatin and remodel it to drive lineage specification. Here, we review pioneer factors within the cardiovascular lineage, particularly during development and reprogramming and highlight the implications this field of research has for the future development of cardiac specific regenerative therapies.
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Affiliation(s)
- Javier E. Sierra-Pagan
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - Daniel J. Garry
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, United States
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, United States
- Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota, Minneapolis, MN, United States
- *Correspondence: Daniel J. Garry
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3
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Wu A, Liu J, Zhang X, Niu C, Shu G, Yin G. Comprehensive Network Analysis of Dysregulated Genes Revealed MNX1‐AS1/ hsa‐miR‐4697‐3p/ HOXB13 Axis in OC Chemotherapy Response. Cancer Sci 2022; 113:2627-2641. [PMID: 35639251 PMCID: PMC9357658 DOI: 10.1111/cas.15447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 05/17/2022] [Accepted: 05/27/2022] [Indexed: 12/03/2022] Open
Abstract
Poor chemotherapy response is the main obstacle of ovarian cancer (OC) treatment. Platinum‐refractory and ‐resistant patients are associated with a worse outcome than platinum‐sensitive and partially sensitive patients, but the comprehensive similarities and differences among them are not yet clear. In this study, we analyzed the data of patients with different chemotherapy response in The Cancer Genome Atlas. We found a minority of altered genes were overlapped in refractory and resistant groups, as did the enriched pathways and Gene Ontology terms. We noticed that the neural signaling and drug metabolism enzymes were more significantly enriched and the protein–protein interaction supported these results. The transcription analysis highlighted PDX1 as the common and central transcription factor in both refractory and resistant groups. The competing endogenous RNA (ceRNA) network shared no common ceRNA pairs, indicating a major difference in noncoding RNA post‐transcriptional regulation. In the end, we validated the expression, regulation, binding, and effect on chemotherapy response for selected MNX1‐AS1/hsa‐miR‐4697‐3p/HOXB13 in OC cell lines. Our study offered a novel and comprehensive insight into chemotherapy response, and potential targets for improving chemotherapy response in OC.
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Affiliation(s)
- Anqi Wu
- Department of Pathology Xiangya Hospital School of Basic Medical Sciences Central South University Changsha 410013 China
- The Second Affiliated Hospital Department of Clinical Research Center Hengyang Medical School University of South China Hengyang 421001 China
| | - Jiaqi Liu
- Department of Pathology Xiangya Hospital School of Basic Medical Sciences Central South University Changsha 410013 China
| | - Xiaojun Zhang
- Department of Pathology Xiangya Hospital School of Basic Medical Sciences Central South University Changsha 410013 China
| | - Chenxi Niu
- Department of Pathology Xiangya Hospital School of Basic Medical Sciences Central South University Changsha 410013 China
| | - Guang Shu
- Department of Pathology Xiangya Hospital School of Basic Medical Sciences Central South University Changsha 410013 China
- Department of Histology and Embryology School of Basic Medical Sciences Central South University Changsha 410013 China
| | - Gang Yin
- Department of Pathology Xiangya Hospital School of Basic Medical Sciences Central South University Changsha 410013 China
- China‐Africa Research Center of Infectious Diseases School of Basic Medical sciences Central South University Changsha 410013 China
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4
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Molecular Mechanism of Pancreatic β-Cell Failure in Type 2 Diabetes Mellitus. Biomedicines 2022; 10:biomedicines10040818. [PMID: 35453568 PMCID: PMC9030375 DOI: 10.3390/biomedicines10040818] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 03/27/2022] [Accepted: 03/29/2022] [Indexed: 02/08/2023] Open
Abstract
Various important transcription factors in the pancreas are involved in the process of pancreas development, the differentiation of endocrine progenitor cells into mature insulin-producing pancreatic β-cells and the preservation of mature β-cell function. However, when β-cells are continuously exposed to a high glucose concentration for a long period of time, the expression levels of several insulin gene transcription factors are substantially suppressed, which finally leads to pancreatic β-cell failure found in type 2 diabetes mellitus. Here we show the possible underlying pathway for β-cell failure. It is likely that reduced expression levels of MafA and PDX-1 and/or incretin receptor in β-cells are closely associated with β-cell failure in type 2 diabetes mellitus. Additionally, since incretin receptor expression is reduced in the advanced stage of diabetes mellitus, incretin-based medicines show more favorable effects against β-cell failure, especially in the early stage of diabetes mellitus compared to the advanced stage. On the other hand, many subjects have recently suffered from life-threatening coronavirus infection, and coronavirus infection has brought about a new and persistent pandemic. Additionally, the spread of coronavirus infection has led to various limitations on the activities of daily life and has restricted economic development worldwide. It has been reported recently that SARS-CoV-2 directly infects β-cells through neuropilin-1, leading to apoptotic β-cell death and a reduction in insulin secretion. In this review article, we feature a possible molecular mechanism for pancreatic β-cell failure, which is often observed in type 2 diabetes mellitus. Finally, we are hopeful that coronavirus infection will decline and normal daily life will soon resume all over the world.
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5
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Hypermethylation of PDX1, EN2, and MSX1 predicts the prognosis of colorectal cancer. Exp Mol Med 2022; 54:156-168. [PMID: 35169223 PMCID: PMC8894425 DOI: 10.1038/s12276-022-00731-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 11/12/2021] [Accepted: 11/18/2021] [Indexed: 02/06/2023] Open
Abstract
Despite numerous observations regarding the relationship between DNA methylation changes and cancer progression, only a few genes have been verified as diagnostic biomarkers of colorectal cancer (CRC). To more practically detect methylation changes, we performed targeted bisulfite sequencing. Through co-analysis of RNA-seq, we identified cohort-specific DNA methylation markers: CpG islands of the intragenic regions of PDX1, EN2, and MSX1. We validated that these genes have oncogenic features in CRC and that their expression levels are increased in correlation with the hypermethylation of intragenic regions. The reliable depth of the targeted bisulfite sequencing data enabled us to design highly optimized quantitative methylation-specific PCR primer sets that can successfully detect subtle changes in the methylation levels of candidate regions. Furthermore, these methylation levels can divide CRC patients into two groups denoting good and poor prognoses. In this study, we present a streamlined workflow for screening clinically significant differentially methylated regions. Our discovery of methylation markers in the PDX1, EN2, and MSX1 genes suggests their promising performance as prognostic markers and their clinical application in CRC patients. An experimental strategy for detecting patterns of DNA modification reveals gene-specific alterations associated with worse outcomes in colorectal cancer patients. Many genomic regions undergo a process of chemical modification called methylation, which can strongly affect the expression of nearby genes. Many cancers exhibit abnormal methylation, and South Korean researchers led by Tae-You Kim of Seoul National University and Lark Kyun Kim of Yonsei University College of Medicine, Seoul, have developed a strategy for identifying such tumor-specific modifications. They identified a trio of genes that undergo excessive methylation in colorectal cancer, and show that this ‘signature’ is associated with more advanced metastatic tumors and shorter overall survival. The results from this study could give clinicians an additional diagnostic tool, and highlight the potential utility of performing such methylation profiling in other cancer types.
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Baumel-Alterzon S, Scott DK. Regulation of Pdx1 by oxidative stress and Nrf2 in pancreatic beta-cells. Front Endocrinol (Lausanne) 2022; 13:1011187. [PMID: 36187092 PMCID: PMC9521308 DOI: 10.3389/fendo.2022.1011187] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 08/26/2022] [Indexed: 01/05/2023] Open
Abstract
The beta-cell identity gene, pancreatic duodenal homeobox 1 (Pdx1), plays critical roles in many aspects of the life of beta-cells including differentiation, maturation, function, survival and proliferation. High levels of reactive oxygen species (ROS) are extremely toxic to cells and especially to beta-cells due to their relatively low expression of antioxidant enzymes. One of the major mechanisms for beta-cell dysfunction in type-2 diabetes results from oxidative stress-dependent inhibition of PDX1 levels and function. ROS inhibits Pdx1 by reducing Pdx1 mRNA and protein levels, inhibiting PDX1 nuclear localization, and suppressing PDX1 coactivator complexes. The nuclear factor erythroid 2-related factor (Nrf2) antioxidant pathway controls the redox balance and allows the maintenance of high Pdx1 levels. Therefore, pharmacological activation of the Nrf2 pathway may alleviate diabetes by preserving Pdx1 levels.
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Affiliation(s)
- Sharon Baumel-Alterzon
- Diabetes, Obesity and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- *Correspondence: Sharon Baumel-Alterzon,
| | - Donald K. Scott
- Diabetes, Obesity and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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Kondratyeva L, Chernov I, Kopantzev E, Didych D, Kuzmich A, Alekseenko I, Kostrov S, Sverdlov E. Pancreatic Lineage Specifier PDX1 Increases Adhesion and Decreases Motility of Cancer Cells. Cancers (Basel) 2021; 13:cancers13174390. [PMID: 34503200 PMCID: PMC8430990 DOI: 10.3390/cancers13174390] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 12/16/2022] Open
Abstract
Intercellular interactions involving adhesion factors are key operators in cancer progression. In particular, these factors are responsible for facilitating cell migration and metastasis. Strengthening of adhesion between tumor cells and surrounding cells or extracellular matrix (ECM), may provide a way to inhibit tumor cell migration. Recently, we demonstrated that PDX1 ectopic expression results in the reduction of pancreatic cancer line PANC-1 cell motility in vitro and in vivo, and we now provide experimental data confirming the hypothesis that suppression of migration may be related to the effect of PDX1 on cell adhesion. Cell migration analyses demonstrated decreased motility of pancreatic Colo357 and PANC-1 cell lines expressing PDX1. We observed decreased expression levels of genes associated with promoting cell migration and increased expression of genes negatively affecting cell motility. Expression of the EMT regulator genes was only mildly induced in cells expressing PDX1 during the simulation of the epithelial-mesenchymal transition (EMT) by the addition of TGFβ1 to the medium. PDX1-expressing cancer cell lines showed increased cell adhesion to collagen type I, fibronectin, and poly-lysine. We conclude that ectopic expression of PDX1 reduces the migration potential of cancer cells, by increasing the adhesive properties of cells and reducing the sensitivity to TGFβ1-induced EMT.
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Affiliation(s)
- Liya Kondratyeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Ulitsa Miklukho-Maklaya, 117997 Moscow, Russia; (I.C.); (E.K.); (D.D.); (A.K.); (I.A.)
- Correspondence: (L.K.); (E.S.)
| | - Igor Chernov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Ulitsa Miklukho-Maklaya, 117997 Moscow, Russia; (I.C.); (E.K.); (D.D.); (A.K.); (I.A.)
| | - Eugene Kopantzev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Ulitsa Miklukho-Maklaya, 117997 Moscow, Russia; (I.C.); (E.K.); (D.D.); (A.K.); (I.A.)
| | - Dmitry Didych
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Ulitsa Miklukho-Maklaya, 117997 Moscow, Russia; (I.C.); (E.K.); (D.D.); (A.K.); (I.A.)
| | - Alexey Kuzmich
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Ulitsa Miklukho-Maklaya, 117997 Moscow, Russia; (I.C.); (E.K.); (D.D.); (A.K.); (I.A.)
- Institute of Molecular Genetics of National Research Centre “Kurchatov Institute”, Ploshchad’ Akademika Kurchatova, 123182 Moscow, Russia;
| | - Irina Alekseenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Ulitsa Miklukho-Maklaya, 117997 Moscow, Russia; (I.C.); (E.K.); (D.D.); (A.K.); (I.A.)
- Institute of Molecular Genetics of National Research Centre “Kurchatov Institute”, Ploshchad’ Akademika Kurchatova, 123182 Moscow, Russia;
| | - Sergey Kostrov
- Institute of Molecular Genetics of National Research Centre “Kurchatov Institute”, Ploshchad’ Akademika Kurchatova, 123182 Moscow, Russia;
| | - Eugene Sverdlov
- Institute of Molecular Genetics of National Research Centre “Kurchatov Institute”, Ploshchad’ Akademika Kurchatova, 123182 Moscow, Russia;
- Correspondence: (L.K.); (E.S.)
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8
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Liot S, El Kholti N, Balas J, Genestier L, Verrier B, Valcourt U, Lambert E. Development of thymic tumor in [LSL:Kras G12D; Pdx1-CRE] mice, an adverse effect associated with accelerated pancreatic carcinogenesis. Sci Rep 2021; 11:15075. [PMID: 34302028 PMCID: PMC8302691 DOI: 10.1038/s41598-021-94566-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/08/2021] [Indexed: 12/18/2022] Open
Abstract
Pancreatic Ductal AdenoCarcinoma (PDAC) represents about 90% of pancreatic cancers. It is one of the most aggressive cancer, with a 5-year survival rate below 10% due to late diagnosis and poor therapeutic efficiency. This bad prognosis thus encourages intense research in order to better understand PDAC pathogenesis and molecular basis leading to the development of innovative therapeutic strategies. This research frequently involves the KC (LSL:KrasG12D;Pdx1-CRE) genetically engineered mouse model, which leads to pancreatic cancer predisposition. However, as frequently encountered in animal models, the KC mouse model also exhibits biases. Herein, we report a new adverse effect of KrasG12D mutation in KC mouse model. In our hands, 10% of KC mice developed clinical signs reaching pre-defined end-points between 100- and 150-days post-parturition, and associated with large thymic mass development. Histological and genetic analyses of this massive thymus enabled us (1) to characterize it as a highly proliferative thymic lymphoma and (2) to detect the unexpected recombination of the Lox-STOP-Lox cassette upstream KrasG12D allele and subsequent KRASG12D protein expression in all cells composing thymic masses. Finally, we highlighted that development of such thymic tumor was associated with accelerated pancreatic carcinogenesis, immune compartment disorganization, and in some cases, lung malignancies.
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Affiliation(s)
- Sophie Liot
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique (LBTI), UMR CNRS 5305, Université Claude Bernard Lyon 1, Institut de Biologie et Chimie Des Protéines, 7, passage du Vercors, 69367, Lyon Cedex 07, France
| | - Naïma El Kholti
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique (LBTI), UMR CNRS 5305, Université Claude Bernard Lyon 1, Institut de Biologie et Chimie Des Protéines, 7, passage du Vercors, 69367, Lyon Cedex 07, France
| | - Jonathan Balas
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique (LBTI), UMR CNRS 5305, Université Claude Bernard Lyon 1, Institut de Biologie et Chimie Des Protéines, 7, passage du Vercors, 69367, Lyon Cedex 07, France
| | - Laurent Genestier
- UR LIB « Lymphoma Immuno-Biology", Université Claude Bernard Lyon I, Lyon, France
| | - Bernard Verrier
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique (LBTI), UMR CNRS 5305, Université Claude Bernard Lyon 1, Institut de Biologie et Chimie Des Protéines, 7, passage du Vercors, 69367, Lyon Cedex 07, France
| | - Ulrich Valcourt
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique (LBTI), UMR CNRS 5305, Université Claude Bernard Lyon 1, Institut de Biologie et Chimie Des Protéines, 7, passage du Vercors, 69367, Lyon Cedex 07, France
| | - Elise Lambert
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique (LBTI), UMR CNRS 5305, Université Claude Bernard Lyon 1, Institut de Biologie et Chimie Des Protéines, 7, passage du Vercors, 69367, Lyon Cedex 07, France.
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Wu Y, Aegerter P, Nipper M, Ramjit L, Liu J, Wang P. Hippo Signaling Pathway in Pancreas Development. Front Cell Dev Biol 2021; 9:663906. [PMID: 34079799 PMCID: PMC8165189 DOI: 10.3389/fcell.2021.663906] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/12/2021] [Indexed: 12/17/2022] Open
Abstract
The Hippo signaling pathway is a vital regulator of pancreatic development and homeostasis, directing cell fate decisions, morphogenesis, and adult pancreatic cellular plasticity. Through loss-of-function research, Hippo signaling has been found to play key roles in maintaining the proper balance between progenitor cell renewal, proliferation, and differentiation in pancreatic organogenesis. Other studies suggest that overactivation of YAP, a downstream effector of the pathway, promotes ductal cell development and suppresses endocrine cell fate specification via repression of Ngn3. After birth, disruptions in Hippo signaling have been found to lead to de-differentiation of acinar cells and pancreatitis-like phenotype. Further, Hippo signaling directs pancreatic morphogenesis by ensuring proper cell polarization and branching. Despite these findings, the mechanisms through which Hippo governs cell differentiation and pancreatic architecture are yet to be fully understood. Here, we review recent studies of Hippo functions in pancreatic development, including its crosstalk with NOTCH, WNT/β-catenin, and PI3K/Akt/mTOR signaling pathways.
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Affiliation(s)
- Yifan Wu
- Department of Cell Systems and Anatomy, The University of Texas Health San Antonio, San Antonio, TX, United States.,Department of Obstetrics, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Pauline Aegerter
- Department of Cell Systems and Anatomy, The University of Texas Health San Antonio, San Antonio, TX, United States
| | - Michael Nipper
- Department of Cell Systems and Anatomy, The University of Texas Health San Antonio, San Antonio, TX, United States
| | - Logan Ramjit
- Department of Cell Systems and Anatomy, The University of Texas Health San Antonio, San Antonio, TX, United States
| | - Jun Liu
- Department of Cell Systems and Anatomy, The University of Texas Health San Antonio, San Antonio, TX, United States
| | - Pei Wang
- Department of Cell Systems and Anatomy, The University of Texas Health San Antonio, San Antonio, TX, United States
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10
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Creeden JF, Alganem K, Imami AS, Brunicardi FC, Liu SH, Shukla R, Tomar T, Naji F, McCullumsmith RE. Kinome Array Profiling of Patient-Derived Pancreatic Ductal Adenocarcinoma Identifies Differentially Active Protein Tyrosine Kinases. Int J Mol Sci 2020; 21:ijms21228679. [PMID: 33213062 PMCID: PMC7698519 DOI: 10.3390/ijms21228679] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/12/2020] [Accepted: 11/14/2020] [Indexed: 12/12/2022] Open
Abstract
Pancreatic cancer remains one of the most difficult malignancies to treat. Minimal improvements in patient outcomes and persistently abysmal patient survival rates underscore the great need for new treatment strategies. Currently, there is intense interest in therapeutic strategies that target tyrosine protein kinases. Here, we employed kinome arrays and bioinformatic pipelines capable of identifying differentially active protein tyrosine kinases in different patient-derived pancreatic ductal adenocarcinoma (PDAC) cell lines and wild-type pancreatic tissue to investigate the unique kinomic networks of PDAC samples and posit novel target kinases for pancreatic cancer therapy. Consistent with previously described reports, the resultant peptide-based kinome array profiles identified increased protein tyrosine kinase activity in pancreatic cancer for the following kinases: epidermal growth factor receptor (EGFR), fms related receptor tyrosine kinase 4/vascular endothelial growth factor receptor 3 (FLT4/VEGFR-3), insulin receptor (INSR), ephrin receptor A2 (EPHA2), platelet derived growth factor receptor alpha (PDGFRA), SRC proto-oncogene kinase (SRC), and tyrosine kinase non receptor 2 (TNK2). Furthermore, this study identified increased activity for protein tyrosine kinases with limited prior evidence of differential activity in pancreatic cancer. These protein tyrosine kinases include B lymphoid kinase (BLK), Fyn-related kinase (FRK), Lck/Yes-related novel kinase (LYN), FYN proto-oncogene kinase (FYN), lymphocyte cell-specific kinase (LCK), tec protein kinase (TEC), hemopoietic cell kinase (HCK), ABL proto-oncogene 2 kinase (ABL2), discoidin domain receptor 1 kinase (DDR1), and ephrin receptor A8 kinase (EPHA8). Together, these results support the utility of peptide array kinomic analyses in the generation of potential candidate kinases for future pancreatic cancer therapeutic development.
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Affiliation(s)
- Justin F. Creeden
- Department of Neurosciences, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (K.A.); (A.S.I.); (R.S.); (R.E.M.)
- Department of Cancer Biology, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (F.C.B.); (S.-H.L.)
- Department of Surgery, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA
- Correspondence: ; Tel.: +1-419-383-6474
| | - Khaled Alganem
- Department of Neurosciences, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (K.A.); (A.S.I.); (R.S.); (R.E.M.)
| | - Ali S. Imami
- Department of Neurosciences, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (K.A.); (A.S.I.); (R.S.); (R.E.M.)
| | - F. Charles Brunicardi
- Department of Cancer Biology, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (F.C.B.); (S.-H.L.)
- Department of Surgery, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA
| | - Shi-He Liu
- Department of Cancer Biology, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (F.C.B.); (S.-H.L.)
- Department of Surgery, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA
| | - Rammohan Shukla
- Department of Neurosciences, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (K.A.); (A.S.I.); (R.S.); (R.E.M.)
| | - Tushar Tomar
- PamGene International BV, 5200 BJ’s-Hertogenbosch, The Netherlands; (T.T.); (F.N.)
| | - Faris Naji
- PamGene International BV, 5200 BJ’s-Hertogenbosch, The Netherlands; (T.T.); (F.N.)
| | - Robert E. McCullumsmith
- Department of Neurosciences, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (K.A.); (A.S.I.); (R.S.); (R.E.M.)
- Neurosciences Institute, ProMedica, Toledo, OH 43606, USA
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11
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Zang HL, Huang GM, Ju HY, Tian XF. Integrative analysis of the inverse expression patterns in pancreas development and cancer progression. World J Gastroenterol 2019; 25:4727-4738. [PMID: 31528097 PMCID: PMC6718033 DOI: 10.3748/wjg.v25.i32.4727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 07/05/2019] [Accepted: 07/19/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND As the malignant tumor, pancreatic cancer with a meager 5-years survival rate has been widely concerning. However, the molecular mechanisms that result in malignant transformation of pancreatic cells remain elusive.
AIM To investigate the gene expression profiles in normal or malignant transformed pancreas development.
METHODS MaSigPro and ANOVA were performed on two pancreas development datasets downloaded from the Gene Expression Omnibus database. Six pancreatic cancer datasets collected from TCGA database were used to establish differentially expressed genes related to pancreas development and pancreatic cancer. Moreover, gene clusters with highly similar interpretation patterns between pancreas development and pancreatic cancer progression were established by self-organizing map and singular value decomposition. Additionally, the hypergeometric test was performed to compare the corresponding interpretation patterns. Abnormal regions of metabolic pathway were analyzed using the Sub-pathway-GM method.
RESULTS This study established the continuously upregulated and downregulated genes at different stages in pancreas development and progression of pancreatic cancer. Through analysis of the differentially expressed genes, we established the inverse and consistent direction development-cancer pattern associations. Based on the application of the Subpathway-GM analysis, we established 17 significant metabolic sub-pathways that were closely associated with pancreatic cancer. Of note, the most significant metabolites sub-pathway was related to glycerophospholipid metabolism.
CONCLUSION The inverse and consistent direction development-cancer pattern associations were established. There was a significant correlation in the inverse patterns, but not consistent direction patterns.
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Affiliation(s)
- Hong-Liang Zang
- Department of Hepatobiliary and Pancreatic Surgery, China-Japan Union Hospital of Jilin University, Changchun 130033, Jilin Province, China
| | - Guo-Min Huang
- Department of Hepatobiliary and Pancreatic Surgery, China-Japan Union Hospital of Jilin University, Changchun 130033, Jilin Province, China
| | - Hai-Ying Ju
- Department of Hematology, Jilin Province Blood Center, Changchun 130000, Jilin Province, China
| | - Xiao-Feng Tian
- Department of Hepatobiliary and Pancreatic Surgery, China-Japan Union Hospital of Jilin University, Changchun 130033, Jilin Province, China
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12
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Camolotto SA, Belova VK, Snyder EL. The role of lineage specifiers in pancreatic ductal adenocarcinoma. J Gastrointest Oncol 2018; 9:1005-1013. [PMID: 30603119 DOI: 10.21037/jgo.2018.05.04] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Over the last decade, multiple genomics studies have led to the identification of discrete molecular subtypes of pancreatic ductal adenocarcinoma. A general theme has emerged that most pancreatic ductal adenocarcinoma (PDAC) can be grouped into two major subtypes based on cancer cell autonomous properties: classical/pancreatic progenitor and basal-like/squamous. The classical/progenitor subtype expresses higher levels of lineage specifiers that regulate endodermal differentiation than the basal-like/squamous subtype. The basal-like/squamous subtype confers a worse prognosis, raising the possibility that loss of these lineage specifiers might enhance the malignant potential of PDAC. Here, we discuss several of these differentially expressed lineage specifiers and examine the evidence that they might play a functional role in PDAC biology.
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Affiliation(s)
| | - Veronika K Belova
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Eric L Snyder
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.,Department of Pathology, University of Utah, Salt Lake City, UT, USA
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13
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Kondratyeva LG, Chernov IP, Zinovyeva MV, Egorov VI, Kopantzev EP, Sverdlov ED. Heterogeneous Expression of Embryonal Development Master Regulator SOX9 in Patients with Pancreatic Cancer. DOKL BIOCHEM BIOPHYS 2018; 481:208-211. [PMID: 30168061 DOI: 10.1134/s1607672918040087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Indexed: 01/06/2023]
Abstract
The expression levels of the SOX9 gene in fetal, postnatal, and neoplastic pancreatic tissues were compared. In the fetal pancreatic samples, the mean relative level of the SOX9 gene expression was 8 times greater than the normal level. The tumor samples were divided into three groups depending on the SOX9 expression level. The first group showed a 6.5-fold increased expression level of SOX9 with respect to the normal one. The second and normal groups had approximately equal levels expression. The third group showed a 25-fold decreased expression level of SOX9. The discrepancy in the SOX9 expression, associated with the predominance of different functions of this master gene, depends on the poorly predictable individual factors and indicates that SOX9 should be excluded from the potential diagnostic biomarkers of pancreatic cancer.
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Affiliation(s)
- L G Kondratyeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - I P Chernov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - M V Zinovyeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - V I Egorov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - E P Kopantzev
- 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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