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Jalali P, Yaghoobi A, Rezaee M, Zabihi MR, Piroozkhah M, Aliyari S, Salehi Z. Decoding common genetic alterations between Barrett's esophagus and esophageal adenocarcinoma: A bioinformatics analysis. Heliyon 2024; 10:e31194. [PMID: 38803922 PMCID: PMC11128929 DOI: 10.1016/j.heliyon.2024.e31194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 05/12/2024] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
Background Esophageal adenocarcinoma (EAC) is a common cancer with a poor prognosis in advanced stages. Therefore, early EAC diagnosis and treatment have gained attention in recent decades. It has been found that various pathological changes, particularly Barrett's Esophagus (BE), can occur in the esophageal tissue before the development of EAC. In this study, we aimed to identify the molecular contributor in BE to EAC progression by detecting the essential regulatory genes that are differentially expressed in both BE and EAC. Materials and methods We conducted a comprehensive bioinformatics analysis to detect BE and EAC-associated genes. The common differentially expressed genes (DEGs) and common single nucleotide polymorphisms (SNPs) were detected using the GEO and DisGeNET databases, respectively. Then, hub genes and the top modules within the protein-protein interaction network were identified. Moreover, the co-expression network of the top module by the HIPPIE database was constructed. Additionally, the gene regulatory network was constructed based on miRNAs and circRNAs. Lastly, we inspected the DGIdb database for possible interacted drugs. Results Our microarray dataset analysis identified 92 common DEGs between BE and EAC with significant enrichment in skin and epidermis development genes. The study also identified 22 common SNPs between BE and EAC. The top module of PPI network analysis included SCEL, KRT6A, SPRR1A, SPRR1B, SPRR3, PPL, SPRR2B, EVPL, and CSTA. We constructed a ceRNA network involving three specific mRNAs, 23 miRNAs, and 101 selected circRNAs. According to the results from the DGIdb database, TD101 was found to interact with the KRT6A gene. Conclusion The present study provides novel potential candidate genes that may be involved in the molecular association between Esophageal adenocarcinoma and Barrett's Esophagus, resulting in developing the diagnostic tools and therapeutic targets to prevent progression of BE to EAC.
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Affiliation(s)
- Pooya Jalali
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Yaghoobi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Malihe Rezaee
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zabihi
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Moein Piroozkhah
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shahram Aliyari
- Division of Applied Bioinformatics, German Cancer Research Center DKFZ Heidelberg, Iran
| | - Zahra Salehi
- Hematology, Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran
- Research Institute for Oncology, Hematology and Cell Therapy, Tehran University of Medical Sciences, Tehran, Iran
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Li J, Lu Y, Yang D, Ren M, Yin Y, Zhao Y, He S. Differentially expressed genes of esophageal tissue in male acute and chronic sleep deprivation mice. GENES, BRAIN, AND BEHAVIOR 2024; 23:e12896. [PMID: 38662955 PMCID: PMC11045192 DOI: 10.1111/gbb.12896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/21/2024] [Accepted: 04/06/2024] [Indexed: 04/29/2024]
Abstract
Gastroesophageal reflux disease (GERD) is associated with sleep disturbances. However, mechanisms underlying these interactions remain unclear. Male acute and chronic sleep deprivation (SD) mice were used for this study. Mice in the chronic SD group exhibited anxiety- and depression-like behaviors. We further performed high-throughput genome sequencing and bioinformatics analysis to screen for featured differentially expressed genes (DEGs) in the esophageal tissue. The acute SD group, comprised 25 DEGs including 14 downregulated and 11 upregulated genes. Compared with the acute SD group, more DEGs were present in the chronic SD group, with a total of 169 DEGs, including 88 downregulated and 81 upregulated genes. Some DEGs that were closely related to GERD and associated esophageal diseases were significantly different in the chronic SD group. Quantitative real-time polymerase chain reaction verified the downregulation of Krt4, Krt13, Krt15 and Calml3 and upregulation of Baxl1 and Per3. Notably, these DEGs are involved in biological processes, which might be the pathways of the neuroregulatory mechanisms of DEGs expression.
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Affiliation(s)
- Jing Li
- Department of GastroenterologyFirst Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
- Shannxi Clinical Research Center of Digestive Disease (Cancer Devision)Xi'anChina
| | - Yifan Lu
- Department of NeurobiologySchool of Basic Medicine, Fourth Military Medical UniversityXi'anChina
| | - Dingding Yang
- Department of NeurobiologySchool of Basic Medicine, Fourth Military Medical UniversityXi'anChina
| | - Mudan Ren
- Department of GastroenterologyFirst Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
- Shannxi Clinical Research Center of Digestive Disease (Cancer Devision)Xi'anChina
| | - Yan Yin
- Department of GastroenterologyFirst Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
- Shannxi Clinical Research Center of Digestive Disease (Cancer Devision)Xi'anChina
| | - Yan Zhao
- Department of GastroenterologyFirst Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
- Shannxi Clinical Research Center of Digestive Disease (Cancer Devision)Xi'anChina
| | - Shuixiang He
- Department of GastroenterologyFirst Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
- Shannxi Clinical Research Center of Digestive Disease (Cancer Devision)Xi'anChina
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Stabenau KA, Samuels TL, Lam TK, Mathison AJ, Wells C, Altman KW, Battle MA, Johnston N. Pepsinogen/Proton Pump Co-Expression in Barrett's Esophageal Cells Induces Cancer-Associated Changes. Laryngoscope 2023; 133:59-69. [PMID: 35315085 DOI: 10.1002/lary.30109] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/27/2022] [Accepted: 03/04/2022] [Indexed: 02/02/2023]
Abstract
EDUCATIONAL OBJECTIVE At the conclusion of this presentation, participants should better understand the carcinogenic potential of pepsin and proton pump expression in Barrett's esophagus. OBJECTIVE Barrett's esophagus (BE) is a well-known risk factor for esophageal adenocarcinoma (EAC). Gastric H+ /K+ ATPase proton pump and pepsin expression has been demonstrated in some cases of BE; however, the contribution of local pepsin and proton pump expression to carcinogenesis is unknown. In this study, RNA sequencing was used to examine global transcriptomic changes in a BE cell line ectopically expressing pepsinogen and/or gastric H+ /K+ ATPase proton pumps. STUDY DESIGN In vitro translational. METHODS BAR-T, a human BE cell line devoid of expression of pepsinogen or proton pumps, was transduced by lentivirus-encoding pepsinogen (PGA5) and/or gastric proton pump subunits (ATP4A, ATP4B). Changes relative to the parental line were assessed by RNA sequencing. RESULTS Top canonical pathways associated with protein-coding genes differentially expressed in pepsinogen and/or proton pump expressing BAR-T cells included those involved in the tumor microenvironment and epithelial-mesenchymal transition. Top upstream regulators of coding transcripts included TGFB1 and ERBB2, which are associated with the pathogenesis and prognosis of BE and EAC. Top upstream regulators of noncoding transcripts included p300-CBP, I-BET-151, and CD93, which have previously described associations with EAC or carcinogenesis. The top associated disease of both coding and noncoding transcripts was cancer. CONCLUSIONS These data support the carcinogenic potential of pepsin and proton pump expression in BE and reveal molecular pathways affected by their expression. Further study is warranted to investigate the role of these pathways in carcinogenesis associated with BE. LEVEL OF EVIDENCE NA Laryngoscope, 133:59-69, 2023.
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Affiliation(s)
- Kaleigh A Stabenau
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Tina L Samuels
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Tina K Lam
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Angela J Mathison
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Clive Wells
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Kenneth W Altman
- Department of Otolaryngology, Geisinger Health System, Danville, California, USA
| | - Michele A Battle
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Nikki Johnston
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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Su W, Feng B, Hu L, Guo X, Yu M. MUC3A promotes the progression of colorectal cancer through the PI3K/Akt/mTOR pathway. BMC Cancer 2022; 22:602. [PMID: 35655161 PMCID: PMC9161576 DOI: 10.1186/s12885-022-09709-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/27/2022] [Indexed: 12/17/2022] Open
Abstract
AbstractMucin 3A (MUC3A) is overexpressed in colorectal cancer (CRC) and associated with poor prognosis, but the related mechanism remains unclear. Our study found that MUC3A promotes the progression of CRC by activating the PI3K/Akt/mTOR signaling pathway. Knockout of MUC3A significantly inhibited the proliferation of CRC cells and induced G1 phase arrest by upregulating p21 protein, an important cell cycle regulator. Moreover, knockout of MUC3A significantly inhibited invasion ability and enhanced the sensitivity to the chemotherapeutic agent 5-FU. Furthermore, we found that knockout of MUC3A repressed the PI3K/Akt/mTOR pathway through RNA-seq. Treatment with the PI3K/Akt/mTOR pathway inhibitor rapamycin successfully eliminated the difference in proliferation, invasion and chemoresistance between MUC3A knockout cells and control cells. Our study suggests that MUC3A is a potential oncogene that promotes the proliferation, invasion, and chemotherapy resistance of CRC. Moreover, CRC patients with high expression of MUC3A may benefit from rapamycin treatment.
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Barrett's Metaplasia Progression towards Esophageal Adenocarcinoma: An Attempt to Select a Panel of Molecular Sensors and to Reflect Clinical Alterations by Experimental Models. Int J Mol Sci 2022; 23:ijms23063312. [PMID: 35328735 PMCID: PMC8955539 DOI: 10.3390/ijms23063312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 02/06/2023] Open
Abstract
The molecular processes that predispose the development of Barrett’s esophagus (BE) towards esophageal adenocarcinoma (EAC) induced by gastrointestinal reflux disease (GERD) are still under investigation. In this study, based on a scientific literature screening and an analysis of clinical datasets, we selected a panel of 20 genes covering BE- and EAC-specific molecular markers (FZD5, IFNGR1, IL1A, IL1B, IL1R1, IL1RN, KRT4, KRT8, KRT15, KRT18, NFKBIL1, PTGS1, PTGS2, SOCS3, SOX4, SOX9, SOX15, TIMP1, TMEM2, TNFRSF10B). Furthermore, we aimed to reflect these alterations within an experimental and translational in vitro model of BE to EAC progression. We performed a comparison between expression profiles in GSE clinical databases with an in vitro model of GERD involving a BE cell line (BAR-T) and EAC cell lines (OE33 and OE19). Molecular responses of cells treated with acidified bile mixture (BM) at concentration of 100 and 250 μM for 30 min per day were evaluated. We also determined a basal mRNA expression within untreated, wild type cell lines on subsequent stages of BE and EAC development. We observed that an appropriately optimized in vitro model based on the combination of BAR-T, OE33 and OE19 cell lines reflects in 65% and more the clinical molecular alterations observed during BE and EAC development. We also confirmed previous observations that exposure to BM (GERD in vitro) activated carcinogenesis in non-dysplastic cells, inducing molecular alternations in the advanced stages of BE. We conclude that it is possible to induce, to a high extent, the molecular profile observed clinically within appropriately and carefully optimized experimental models, triggering EAC development. This experimental scheme and molecular marker panel might be implemented in further research, e.g., aiming to develop and evaluate novel compounds and prodrugs targeting GERD as well as BE and EAC prevention and treatment.
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Yu SMW, Leventhal JS, Cravedi P. Totally tubular, dude: rethinking DKD pathogenesis in the wake of SGLT2i data. J Nephrol 2021; 34:629-631. [PMID: 32965657 DOI: 10.1007/s40620-020-00868-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Samuel Mon-Wei Yu
- Department of Medicine, Translational Transplant Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Paolo Cravedi
- Department of Medicine, Translational Transplant Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Jia R, Li Z, Liang W, Ji Y, Weng Y, Liang Y, Ning P. Identification of key genes unique to the luminal a and basal-like breast cancer subtypes via bioinformatic analysis. World J Surg Oncol 2020; 18:268. [PMID: 33066779 PMCID: PMC7568373 DOI: 10.1186/s12957-020-02042-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 09/30/2020] [Indexed: 01/11/2023] Open
Abstract
Background Breast cancer subtypes are statistically associated with prognosis. The search for markers of breast tumor heterogeneity and the development of precision medicine for patients are the current focuses of the field. Methods We used a bioinformatic approach to identify key disease-causing genes unique to the luminal A and basal-like subtypes of breast cancer. First, we retrieved gene expression data for luminal A breast cancer, basal-like breast cancer, and normal breast tissue samples from The Cancer Genome Atlas database. The differentially expressed genes unique to the 2 breast cancer subtypes were identified and subjected to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. We constructed protein–protein interaction networks of the differentially expressed genes. Finally, we analyzed the key modules of the networks, which we combined with survival data to identify the unique cancer genes associated with each breast cancer subtype. Results We identified 1114 differentially expressed genes in luminal A breast cancer and 1042 differentially expressed genes in basal-like breast cancer, of which the subtypes shared 500. We observed 614 and 542 differentially expressed genes unique to luminal A and basal-like breast cancer, respectively. Through enrichment analyses, protein–protein interaction network analysis, and module mining, we identified 8 key differentially expressed genes unique to each subtype. Analysis of the gene expression data in the context of the survival data revealed that high expression of NMUR1 and NCAM1 in luminal A breast cancer statistically correlated with poor prognosis, whereas the low expression levels of CDC7, KIF18A, STIL, and CKS2 in basal-like breast cancer statistically correlated with poor prognosis. Conclusions NMUR1 and NCAM1 are novel key disease-causing genes for luminal A breast cancer, and STIL is a novel key disease-causing gene for basal-like breast cancer. These genes are potential targets for clinical treatment.
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Affiliation(s)
- Rong Jia
- College of Computer and Information, Inner Mongolia Medical University, Hohhot, 010110, Inner Mongolia Autonomous Region, China
| | - Zhongxian Li
- College of Computer and Information, Inner Mongolia Medical University, Hohhot, 010110, Inner Mongolia Autonomous Region, China
| | - Wei Liang
- College of Computer and Information, Inner Mongolia Medical University, Hohhot, 010110, Inner Mongolia Autonomous Region, China
| | - Yucheng Ji
- College of Computer and Information, Inner Mongolia Medical University, Hohhot, 010110, Inner Mongolia Autonomous Region, China
| | - Yujie Weng
- College of Computer and Information, Inner Mongolia Medical University, Hohhot, 010110, Inner Mongolia Autonomous Region, China
| | - Ying Liang
- College of Computer and Information, Inner Mongolia Medical University, Hohhot, 010110, Inner Mongolia Autonomous Region, China
| | - Pengfei Ning
- College of Computer and Information, Inner Mongolia Medical University, Hohhot, 010110, Inner Mongolia Autonomous Region, China.
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