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Song J, Kim D, Jung J, Choi E, Lee Y, Jeong Y, Lee B, Lee S, Shim Y, Won Y, Cho H, Jang DK, Kang HW, Joo JWJ, Jang W. Elucidating immunological characteristics of the adenoma-carcinoma sequence in colorectal cancer patients in South Korea using a bioinformatics approach. Sci Rep 2024; 14:10105. [PMID: 38698020 PMCID: PMC11066069 DOI: 10.1038/s41598-024-56078-2] [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: 08/03/2023] [Accepted: 03/01/2024] [Indexed: 05/05/2024] Open
Abstract
Colorectal cancer (CRC) is one of the top five most common and life-threatening malignancies worldwide. Most CRC develops from advanced colorectal adenoma (ACA), a precancerous stage, through the adenoma-carcinoma sequence. However, its underlying mechanisms, including how the tumor microenvironment changes, remain elusive. Therefore, we conducted an integrative analysis comparing RNA-seq data collected from 40 ACA patients who visited Dongguk University Ilsan Hospital with normal adjacent colons and tumor samples from 18 CRC patients collected from a public database. Differential expression analysis identified 21 and 79 sequentially up- or down-regulated genes across the continuum, respectively. The functional centrality of the continuum genes was assessed through network analysis, identifying 11 up- and 13 down-regulated hub-genes. Subsequently, we validated the prognostic effects of hub-genes using the Kaplan-Meier survival analysis. To estimate the immunological transition of the adenoma-carcinoma sequence, single-cell deconvolution and immune repertoire analyses were conducted. Significant composition changes for innate immunity cells and decreased plasma B-cells with immunoglobulin diversity were observed, along with distinctive immunoglobulin recombination patterns. Taken together, we believe our findings suggest underlying transcriptional and immunological changes during the adenoma-carcinoma sequence, contributing to the further development of pre-diagnostic markers for CRC.
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Affiliation(s)
- Jaeseung Song
- Department of Life Sciences, Dongguk University, Seoul, 04620, South Korea
| | - Daeun Kim
- Department of Life Sciences, Dongguk University, Seoul, 04620, South Korea
| | - Junghyun Jung
- Department of Life Sciences, Dongguk University, Seoul, 04620, South Korea
- Division of AI Software Convergence, Dongguk University-Seoul, Seoul, 04620, South Korea
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Hollywood, CA, USA
| | - Eunyoung Choi
- Department of Life Sciences, Dongguk University, Seoul, 04620, South Korea
| | - Yubin Lee
- Department of Life Sciences, Dongguk University, Seoul, 04620, South Korea
| | - Yeonbin Jeong
- Department of Life Sciences, Dongguk University, Seoul, 04620, South Korea
| | - Byungjo Lee
- Department of Life Sciences, Dongguk University, Seoul, 04620, South Korea
| | - Sora Lee
- Department of Life Sciences, Dongguk University, Seoul, 04620, South Korea
| | - Yujeong Shim
- Department of Life Sciences, Dongguk University, Seoul, 04620, South Korea
| | - Youngtae Won
- Department of Life Sciences, Dongguk University, Seoul, 04620, South Korea
| | - Hyeki Cho
- Department of Internal Medicine, Dongguk University Ilsan Hospital, Dongguk University College of Medicine, Goyang, 10326, South Korea
| | - Dong Kee Jang
- Department of Internal Medicine, Seoul Metropolitan Government Seoul National University Boramae Medical Center, Seoul, 07061, South Korea
| | - Hyoun Woo Kang
- Department of Internal Medicine, Dongguk University Ilsan Hospital, Dongguk University College of Medicine, Goyang, 10326, South Korea.
- Department of Internal Medicine, Seoul Metropolitan Government Seoul National University Boramae Medical Center, Seoul, 07061, South Korea.
| | - Jong Wha J Joo
- Division of AI Software Convergence, Dongguk University-Seoul, Seoul, 04620, South Korea.
| | - Wonhee Jang
- Department of Life Sciences, Dongguk University, Seoul, 04620, South Korea.
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Kula A, Dawidowicz M, Mielcarska S, Świętochowska E, Waniczek D. Prognostic Value of HHLA2 in Patients with Solid Tumors: A Meta-Analysis. Int J Mol Sci 2024; 25:4760. [PMID: 38731979 PMCID: PMC11083681 DOI: 10.3390/ijms25094760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
HHLA2 is a checkpoint from the B7 family that can play a co-stimulatory or co-inhibitory role in cancer, depending on the binding receptor. The aim of this meta-analysis was to assess the relationship between HHLA2 levels and its impact on the prognosis of patients with solid cancers. The study used data from PubMed, Embase, Web of Science (WOS), Cochrane and SCOPUS databases. The R studio software was used for the data analysis. The study assessed overall survival (OS), disease-specific survival (DSS), progression-free survival (PFS), recurrence-free survival (RFS), and disease-free survival (DFS) by pooling appropriate hazard ratios (HR). Eighteen studies (2880 patients' data) were included. High expression of HHLA2 was associated with worse OS (HR = 1.58, 95% CI: 1.23-2.03), shorter RFS (HR = 1.95, 95% CI: 1.38-2.77) and worse DFS (HR = 1.45, 95% CI: 1.01-2.09) in patients with solid cancers. The current study suggests that high expression of HHLA2 is associated with poorer prognosis in patients with solid cancers.
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Affiliation(s)
- Agnieszka Kula
- Department of Oncological Surgery, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-808 Katowice, Poland;
| | - Miriam Dawidowicz
- Department of Oncological Surgery, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-808 Katowice, Poland;
| | - Sylwia Mielcarska
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-800 Zabrze, Poland; (S.M.); (E.Ś.)
| | - Elżbieta Świętochowska
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-800 Zabrze, Poland; (S.M.); (E.Ś.)
| | - Dariusz Waniczek
- Department of Oncological Surgery, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-808 Katowice, Poland;
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Stricker E, Peckham-Gregory EC, Scheurer ME. HERVs and Cancer-A Comprehensive Review of the Relationship of Human Endogenous Retroviruses and Human Cancers. Biomedicines 2023; 11:936. [PMID: 36979914 PMCID: PMC10046157 DOI: 10.3390/biomedicines11030936] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/03/2023] [Accepted: 03/10/2023] [Indexed: 03/30/2023] Open
Abstract
Genomic instability and genetic mutations can lead to exhibition of several cancer hallmarks in affected cells such as sustained proliferative signaling, evasion of growth suppression, activated invasion, deregulation of cellular energetics, and avoidance of immune destruction. Similar biological changes have been observed to be a result of pathogenic viruses and, in some cases, have been linked to virus-induced cancers. Human endogenous retroviruses (HERVs), once external pathogens, now occupy more than 8% of the human genome, representing the merge of genomic and external factors. In this review, we outline all reported effects of HERVs on cancer development and discuss the HERV targets most suitable for cancer treatments as well as ongoing clinical trials for HERV-targeting drugs. We reviewed all currently available reports of the effects of HERVs on human cancers including solid tumors, lymphomas, and leukemias. Our review highlights the central roles of HERV genes, such as gag, env, pol, np9, and rec in immune regulation, checkpoint blockade, cell differentiation, cell fusion, proliferation, metastasis, and cell transformation. In addition, we summarize the involvement of HERV long terminal repeat (LTR) regions in transcriptional regulation, creation of fusion proteins, expression of long non-coding RNAs (lncRNAs), and promotion of genome instability through recombination.
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Affiliation(s)
- Erik Stricker
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77047, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77047, USA
| | | | - Michael E. Scheurer
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77047, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77047, USA
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Hu S, Wang X, Wang T, Wang L, Liu L, Ren W, Liu X, Zhang W, Liao W, Liao Z, Zou R, Zhang X. Differential enrichment of H3K9me3 in intrahepatic cholangiocarcinoma. BMC Med Genomics 2022; 15:185. [PMID: 36028818 PMCID: PMC9414128 DOI: 10.1186/s12920-022-01338-1] [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: 05/04/2022] [Accepted: 08/23/2022] [Indexed: 12/05/2022] Open
Abstract
Background Intrahepatic cholangiocarcinoma (ICC) is a malignant tumor, which poses a serious threat to human health. Histone 3 lysine 9 trimethylation (H3K9me3) is a post-translational modification involved in regulating a broad range of biological processes and has been considered as potential therapeutic target in types of cancer. However, there is limited research on investigating profiles of histone modification H3K9me3 in ICC patients. Methods In this study, we applied the ChIP-seq technique to investigate the effect of H3K9me3 on ICC. Anti-H3K9me3 antibody was used for ChIP-seq in ICC (RBE cell lines) and HIBEpic (normal cell lines). MACS2 (peak-calling tools) was then used to identify the peaks recorded in RBE and HIBEpic cell lines. Gene expression, mutation and clinical data were downloaded from TCGA and cBioPortal databases. Results H3K9me3 exhibited abnormal methylation and influenced the process of abnormal gene expression in patients suffering from ICC. The Wnt/β-Catenin signaling pathway (also known as simply the WNT signaling pathway) was enriched in H3K9me3-regulated genes. Conclusions We are the first to report that H3K9me3 may play an important role in the progression of ICC. It promotes the understanding of epigenetic molecular mechanisms for ICC. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01338-1.
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Affiliation(s)
- Sheng Hu
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Kunming Medical University, No. 374, Dianmain Road, Kunming, China
| | - Xuejun Wang
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Kunming Medical University, No. 374, Dianmain Road, Kunming, China
| | - Tao Wang
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Kunming Medical University, No. 374, Dianmain Road, Kunming, China
| | - Lianmin Wang
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Kunming Medical University, No. 374, Dianmain Road, Kunming, China
| | - Lixin Liu
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Kunming Medical University, No. 374, Dianmain Road, Kunming, China
| | - Wenjun Ren
- Department of Cardiovascular Surgery, The First People's Hospital of Yunnan Province, Kunming, China.,Department of Thoracic Surgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xiaoyong Liu
- Department of Cardiology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Weihan Zhang
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Kunming Medical University, No. 374, Dianmain Road, Kunming, China
| | - Weiran Liao
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Kunming Medical University, No. 374, Dianmain Road, Kunming, China
| | - Zhoujun Liao
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Kunming Medical University, No. 374, Dianmain Road, Kunming, China
| | - Renchao Zou
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Kunming Medical University, No. 374, Dianmain Road, Kunming, China.
| | - Xiaowen Zhang
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Kunming Medical University, No. 374, Dianmain Road, Kunming, China.
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Mocan LP, Ilieș M, Melincovici CS, Spârchez M, Crăciun R, Nenu I, Horhat A, Tefas C, Spârchez Z, Iuga CA, Mocan T, Mihu CM. Novel approaches in search for biomarkers of cholangiocarcinoma. World J Gastroenterol 2022; 28:1508-1525. [PMID: 35582128 PMCID: PMC9048460 DOI: 10.3748/wjg.v28.i15.1508] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/12/2021] [Accepted: 03/06/2022] [Indexed: 02/06/2023] Open
Abstract
Cholangiocarcinoma (CCA) arises from the ductular epithelium of the biliary tree, either within the liver (intrahepatic CCA) or more commonly from the extrahepatic bile ducts (extrahepatic CCA). This disease has a poor prognosis and a growing worldwide prevalence. The poor outcomes of CCA are partially explained by the fact that a final diagnosis is challenging, especially the differential diagnosis between hepatocellular carcinoma and intrahepatic CCA, or distal CCA and pancreatic head adenocarcinoma. Most patients present with an advanced disease, unresectable disease, and there is a lack in non-surgical therapeutic modalities. Not least, there is an acute lack of prognostic biomarkers which further complicates disease management. Therefore, there is a dire need to find alternative diagnostic and follow-up pathways that can lead to an accurate result, either singlehandedly or combined with other methods. In the "-omics" era, this goal can be attained by various means, as it has been successfully demonstrated in other primary tumors. Numerous variants can reach a biomarker status ranging from circulating nucleic acids to proteins, metabolites, extracellular vesicles, and ultimately circulating tumor cells. However, given the relatively heterogeneous data, extracting clinical meaning from the inconsequential noise might become a tall task. The current review aims to navigate the nascent waters of the non-invasive approach to CCA and provide an evidence-based input to aid clinical decisions and provide grounds for future research.
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Affiliation(s)
- Lavinia-Patricia Mocan
- Department of Histology, Faculty of Medicine, "Iuliu Hațieganu" University of Medicine and Pharmacy, Cluj-Napoca 400012, Romania
| | - Maria Ilieș
- Department of Proteomics and Metabolomics, MedFUTURE Research Center for Advanced Medicine, "Iuliu Hațieganu" University of Medicine and Pharmacy, Cluj-Napoca 400349, Romania
| | - Carmen Stanca Melincovici
- Department of Histology, Faculty of Medicine, "Iuliu Hațieganu" University of Medicine and Pharmacy, Cluj-Napoca 400012, Romania
| | - Mihaela Spârchez
- 2nd Pediatrics Department, Faculty of Medicine, "Iuliu Hațieganu" University of Medicine and Pharmacy, Cluj-Napoca 400012, Romania
| | - Rareș Crăciun
- 3rd Medical Department, Faculty of Medicine, "Iuliu Hațieganu" University of Medicine and Pharmacy, Cluj-Napoca 400012, Romania
- Department of Gastroenterology, "Prof. dr. Octavian Fodor" Institute for Gastroenterology and Hepatology, Cluj-Napoca 400162, Romania
| | - Iuliana Nenu
- 3rd Medical Department, Faculty of Medicine, "Iuliu Hațieganu" University of Medicine and Pharmacy, Cluj-Napoca 400012, Romania
- Department of Gastroenterology, "Prof. dr. Octavian Fodor" Institute for Gastroenterology and Hepatology, Cluj-Napoca 400162, Romania
| | - Adelina Horhat
- 3rd Medical Department, Faculty of Medicine, "Iuliu Hațieganu" University of Medicine and Pharmacy, Cluj-Napoca 400012, Romania
- Department of Gastroenterology, "Prof. dr. Octavian Fodor" Institute for Gastroenterology and Hepatology, Cluj-Napoca 400162, Romania
| | - Cristian Tefas
- 3rd Medical Department, Faculty of Medicine, "Iuliu Hațieganu" University of Medicine and Pharmacy, Cluj-Napoca 400012, Romania
- Department of Gastroenterology, "Prof. dr. Octavian Fodor" Institute for Gastroenterology and Hepatology, Cluj-Napoca 400162, Romania
| | - Zeno Spârchez
- 3rd Medical Department, Faculty of Medicine, "Iuliu Hațieganu" University of Medicine and Pharmacy, Cluj-Napoca 400012, Romania
- Department of Gastroenterology, "Prof. dr. Octavian Fodor" Institute for Gastroenterology and Hepatology, Cluj-Napoca 400162, Romania
| | - Cristina Adela Iuga
- Department of Proteomics and Metabolomics, MedFUTURE Research Center for Advanced Medicine, "Iuliu Hațieganu" University of Medicine and Pharmacy, Cluj-Napoca 400349, Romania
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, "Iuliu Hațieganu" University of Medicine and Pharmacy, Cluj-Napoca 400012, Romania
| | - Tudor Mocan
- 3rd Medical Department, Faculty of Medicine, "Iuliu Hațieganu" University of Medicine and Pharmacy, Cluj-Napoca 400012, Romania
- Department of Gastroenterology, "Prof. dr. Octavian Fodor" Institute for Gastroenterology and Hepatology, Cluj-Napoca 400162, Romania
| | - Carmen Mihaela Mihu
- Department of Histology, Faculty of Medicine, "Iuliu Hațieganu" University of Medicine and Pharmacy, Cluj-Napoca 400012, Romania
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