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Gong D, Adomako-Bonsu AG, Wang M, Li J. Three specific gut bacteria in the occurrence and development of colorectal cancer: a concerted effort. PeerJ 2023; 11:e15777. [PMID: 37554340 PMCID: PMC10405800 DOI: 10.7717/peerj.15777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 06/29/2023] [Indexed: 08/10/2023] Open
Abstract
Colorectal cancer (CRC), which develops from the gradual evolution of tubular adenomas and serrated polyps in the colon and rectum, has a poor prognosis and a high mortality rate. In addition to genetics, lifestyle, and chronic diseases, intestinal integrity and microbiota (which facilitate digestion, metabolism, and immune regulation) could promote CRC development. For example, enterotoxigenic Bacteroides fragilis, genotoxic Escherichia coli (pks+ E. coli), and Fusobacterium nucleatum, members of the intestinal microbiota, are highly correlated in CRC. This review describes the roles and mechanisms of these three bacteria in CRC development. Their interaction during CRC initiation and progression has also been proposed. Our view is that in the precancerous stage of colorectal cancer, ETBF causes inflammation, leading to potential changes in intestinal ecology that may provide the basic conditions for pks+ E. coli colonization and induction of oncogenic mutations, when cancerous intestinal epithelial cells can further recruit F. nucleatum to colonise the lesion site and F. nucleatum may contribute to CRC advancement by primarily the development of cancer cells, stemization, and proliferation, which could create new and tailored preventive, screening and therapeutic interventions. However, there is the most dominant microbiota in each stage of CRC development, not neglecting the possibility that two or even all three bacteria could be engaged at any stage of the disease. The relationship between the associated gut microbiota and CRC development may provide important information for therapeutic strategies to assess the potential use of the associated gut microbiota in CRC studies, antibiotic therapy, and prevention strategies.
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Affiliation(s)
- Dengmei Gong
- Institute of Zoonosis, College of Public Health, Zunyi Medical University, Zunyi, Guizhou, China
| | - Amma G Adomako-Bonsu
- Institute of Toxicology and Pharmacology, University Medical School Schleswig-Holstein, Kiel, Germany
| | - Maijian Wang
- Gastrointestinal Surgery, Affiliate Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Jida Li
- Institute of Zoonosis, College of Public Health, Zunyi Medical University, Zunyi, Guizhou, China
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2
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Ghafouri‐Fard S, Harsij A, Farahzadi H, Hussen BM, Taheri M, Mokhtari M. A concise review on the role of MIR100HG in human disorders. J Cell Mol Med 2023; 27:2278-2289. [PMID: 37487022 PMCID: PMC10424294 DOI: 10.1111/jcmm.17875] [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: 04/25/2023] [Revised: 07/12/2023] [Accepted: 07/18/2023] [Indexed: 07/26/2023] Open
Abstract
MIR100HG is a long non-coding RNA (lncRNA) encoded by a locus on chr11:122,028,203-122,556,721. This gene can regulate cell proliferation, apoptosis, cell cycle transition and cell differentiation. MIR100HG was firstly identified through a transcriptome analysis and found to regulate differentiation of human neural stem cells. It is functionally related with a number of signalling pathways such as TGF-β, Wnt, Hippo and ERK/MAPK signalling pathways. Dysregulation of MIR100HG has been detected in a diversity of cancers in association with clinical outcomes. Moreover, it has a role in the pathophysiology of dilated cardiomyopathy, intervertebral disk degeneration and pulmonary fibrosis. The current study summarizes the role of these lncRNAs in human disorders.
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Affiliation(s)
- Soudeh Ghafouri‐Fard
- Department of Medical Genetics, School of MedicineShahid Beheshti University of Medical SciencesTehranIran
| | - Atefeh Harsij
- Phytochemistry Research CentreShahid Beheshti University of Medical SciencesTehranIran
| | - Hossein Farahzadi
- Phytochemistry Research CentreShahid Beheshti University of Medical SciencesTehranIran
| | - Bashdar Mahmud Hussen
- Department of Clinical Analysis, College of PharmacyHawler Medical UniversityErbilIraq
| | - Mohammad Taheri
- Urology and Nephrology Research CentreShahid Beheshti University of Medical SciencesTehranIran
- Institute of Human GeneticsJena University HospitalJenaGermany
| | - Majid Mokhtari
- Skull Base Research Centre, Loghman Hakim HospitalShahid Beheshti University of Medical SciencesTehranIran
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Zhou M, Hou P, Yan C, Chen L, Li K, Wang Y, Zhao J, Su J, Sun J. Cell-free DNA 5-hydroxymethylcytosine profiles of long non-coding RNA genes enable early detection and progression monitoring of human cancers. Clin Epigenetics 2021; 13:197. [PMID: 34689838 PMCID: PMC8543867 DOI: 10.1186/s13148-021-01183-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/11/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND 5-Hydroxymethylcytosine (5hmC) is a significant DNA epigenetic modification. However, the 5hmC modification alterations in genomic regions encoding long non-coding RNA (lncRNA) and their clinical significance remain poorly characterized. RESULTS A three-phase discovery-modeling-validation study was conducted to explore the potential of the plasma-derived 5hmC modification level in genomic regions encoding lncRNAs as a superior alternative biomarker for cancer diagnosis and surveillance. Genome-wide 5hmC profiles in the plasma circulating cell-free DNA of 1632 cancer and 1379 non-cancerous control samples from different cancer types and multiple centers were repurposed and characterized. A large number of altered 5hmC modifications were distributed at genomic regions encoding lncRNAs in cancerous compared with healthy subjects. Furthermore, most 5hmC-modified lncRNA genes were cancer-specific, with only a relatively small number of 5hmC-modified lncRNA genes shared by various cancer types. A 5hmC-LncRNA diagnostic score (5hLD-score) comprising 39 tissue-shared 5hmC-modified lncRNA gene markers was developed using elastic net regularization. The 5hLD-score was able to accurately distinguish tumors from healthy controls with an area under the curve (AUC) of 0.963 [95% confidence interval (CI) 0.940-0.985] and 0.912 (95% CI 0.837-0.987) in the training and internal validation cohorts, respectively. Results from three independent validations confirmed the robustness and stability of the 5hLD-score with an AUC of 0.851 (95% CI 0.786-0.916) in Zhang's non-small cell lung cancer cohort, AUC of 0.887 (95% CI 0.852-0.922) in Tian's esophageal cancer cohort, and AUC of 0.768 (95% CI 0.746-0.790) in Cai's hepatocellular carcinoma cohort. In addition, a significant association was identified between the 5hLD-score and the progression from hepatitis to liver cancer. Finally, lncRNA genes modified by tissue-specific 5hmC alteration were again found to be capable of identifying the origin and location of tumors. CONCLUSION The present study will contribute to the ongoing effort to understand the transcriptional programs of lncRNA genes, as well as facilitate the development of novel invasive genomic tools for early cancer detection and surveillance.
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Affiliation(s)
- Meng Zhou
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Ping Hou
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Congcong Yan
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Lu Chen
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Ke Li
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Yiran Wang
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Jingting Zhao
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Jianzhong Su
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
| | - Jie Sun
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
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Knockdown of lncRNA PVT1 inhibits the proliferation and accelerates the apoptosis of colorectal cancer cells via the miR‑761/MAPK1 axis. Mol Med Rep 2021; 24:794. [PMID: 34515320 DOI: 10.3892/mmr.2021.12434] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 08/03/2021] [Indexed: 11/05/2022] Open
Abstract
Colorectal cancer (CRC) is associated with high morbidity rates. Long non‑coding RNAs (lncRNAs) participate in the development of CRC. However, the potential roles of lncRNA plasmacytoma variant translocation 1 (PVT1) in CRC remain unknown. Therefore, the aim of the present study was to investigate the potential roles of PVT1 in CRC. Reverse transcription‑quantitative PCR and western blot analyses were conducted to determine the mRNA and protein expression levels. The cellular behaviors were detected using 5‑Ethynyl‑2'‑deoxyuridine, Cell Counting Kit‑8 and flow cytometry assays. The interaction between PVT1 and microRNA (miR)‑761 or MAPK1 was confirmed using a dual‑luciferase reporter assay. Moreover, the Pearson's method was applied for correlation analysis. The results demonstrated that the expression levels of PVT1 and MAPK1 were upregulated, while miR‑761 was downregulated in CRC tissues. The expression of PVT1 was positively correlated with MAPK1 and negatively correlated with miR‑761. In addition, PVT1 sponged miR‑761 to upregulate MAPK1 expression. It was found that the knockdown of PVT1 expression inhibited the proliferation and promoted the apoptosis of CRC cells, which was more potent in cells transfected with miR‑761. The regulatory role of small interfering RNA‑PVT1 on the expression of apoptosis‑related genes was reduced by MAPK1. Collectively, the present results suggested that knockdown of PVT1 may inhibit the progression of CRC by regulating the miR‑761/MAPK1 axis, which may provide a promising biomarker for the treatment of CRC.
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Seo I, Lee HW, Byun SJ, Park JY, Min H, Lee SH, Lee JS, Kim S, Bae SU. Neoadjuvant chemoradiation alters biomarkers of anticancer immunotherapy responses in locally advanced rectal cancer. J Immunother Cancer 2021; 9:jitc-2020-001610. [PMID: 33692216 PMCID: PMC7949478 DOI: 10.1136/jitc-2020-001610] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Neoadjuvant chemoradiation therapy (CRT) is a widely used preoperative treatment strategy for locally advanced rectal cancer (LARC). However, a few studies have evaluated the molecular changes caused by neoadjuvant CRT in these cancer tissues. Here, we aimed to investigate changes in immunotherapy-related immunogenic effects in response to preoperative CRT in LARC. METHODS We analyzed 60 pairs of human LARC tissues before and after irradiation from three independent LARC cohorts, including a LARC patient RNA sequencing (RNA-seq) dataset from our cohort and GSE15781 and GSE94104 datasets. RESULTS Gene ontology analysis showed that preoperative CRT significantly enriched the immune response in LARC tissues. Moreover, gene set enrichment analysis revealed six significantly enriched Kyoto Encyclopedia of Genes and Genomes pathways associated with downregulated genes, including mismatch repair (MMR) genes, in LARC tissues after CRT in all three cohorts. Radiation also induced apoptosis and downregulated various MMR system-related genes in three colorectal cancer cells. One patient with LARC showed a change in microsatellite instability (MSI) status after CRT, as demonstrated by the loss of MMR protein and PCR for MSI. Moreover, CRT significantly increased tumor mutational burden in LARC tissues. CIBERSORT analysis revealed that the proportions of M2 macrophages and CD8 T cells were significantly increased after CRT in both the RNA-seq dataset and GSE94104. Notably, preoperative CRT increased various immune biomarker scores, such as the interferon-γ signature, the cytolytic activity and the immune signature. CONCLUSIONS Taken together, our findings demonstrated that neoadjuvant CRT modulated the immune-related characteristics of LARC, suggesting that neoadjuvant CRT may enhance the responsiveness of LARC to immunotherapy.
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Affiliation(s)
- Incheol Seo
- Department of Microbiology, Dongguk University College of Medicine, Gyeongju, Gyeongsangbuk-do, Korea (the Republic of)
| | - Hye Won Lee
- Department of Pathology, Keimyung University Dongsan Medical Center, Daegu, Korea (the Republic of).,Institute for Cancer Research, Keimyung University, Daegu, Korea (the Republic of)
| | - Sang Jun Byun
- Department of Radiation Oncology, Keimyung University School of Medicine, Daegu, Korea (the Republic of)
| | - Jee Young Park
- Department of Pathology, Keimyung University Dongsan Medical Center, Daegu, Korea (the Republic of).,Department of Immunology, Keimyung University School of Medicine, Daegu, Korea (the Republic of)
| | - Hyeonji Min
- Department of Immunology, Keimyung University School of Medicine, Daegu, Korea (the Republic of)
| | - Sung Hwan Lee
- Department of Surgery, CHA University - Bundang Campus, Seongnam, Gyeonggi-do, Korea (the Republic of).,Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ju-Seog Lee
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Shin Kim
- Department of Immunology, Keimyung University School of Medicine, Daegu, Korea (the Republic of) .,Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Institute of Medical Science & Institute for Cancer Research, Keimyung University, Daegu, Korea (the Republic of)
| | - Sung Uk Bae
- Institute of Medical Science & Institute for Cancer Research, Keimyung University, Daegu, Korea (the Republic of) .,Department of Surgery, Keimyung University Dongsan Medical Center, Daegu, Korea (the Republic of)
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Wylezinski LS, Shaginurova GI, Spurlock Iii CF. Longitudinal assessment and stability of long non-coding RNA gene expression profiles measured in human peripheral whole blood collected into PAXgene blood RNA tubes. BMC Res Notes 2020; 13:531. [PMID: 33183338 PMCID: PMC7664084 DOI: 10.1186/s13104-020-05360-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 10/26/2020] [Indexed: 12/18/2022] Open
Abstract
Objective Long non-coding RNAs (lncRNAs) are emerging as novel biomarkers for a variety of chronic conditions including autoimmune disease. PAXgene Blood RNA tubes are routinely used in clinical research and molecular diagnostic development to capture RNA profiles in peripheral whole blood. While the stability of mRNA expression profiles captured using PAXgene tubes has been documented previously, no previous work has determined the stability of lncRNA expression profiles observed in PAXgene tubes stored at − 80 °C. Here we sought to determine the effects on lncRNA expression profiles following − 80 °C storage of total RNA templates, cDNA synthesized using fresh or frozen total RNA template, and the impact of freeze–thaw cycles on both total RNA and cDNA obtained from PAXgene tubes. Results We find that storage of whole blood in PAXgene tubes, total RNA and cDNA for up to 1 year at − 80 °C or up to ten total RNA or cDNA freeze–thaw cycles do not significantly alter lncRNA expression profiles compared to baseline. As monthly expression profiles were determined, some month to month lncRNA expression variability was observed. However, all monthly observations fell within the 95% confidence interval calculated at baseline.
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Affiliation(s)
- Lukasz S Wylezinski
- IQuity, Inc, 111, 10th Avenue South, Suite 100, Nashville, TN, 37203, USA.,Decode Health, Inc, 209 10th Avenue South, Suite 404, Nashville, TN, USA.,Department of Medicine, Vanderbilt University School of Medicine, 1161 21st Avenue South, Medical Center North T3113, Nashville, TN, USA
| | | | - Charles F Spurlock Iii
- IQuity, Inc, 111, 10th Avenue South, Suite 100, Nashville, TN, 37203, USA. .,Decode Health, Inc, 209 10th Avenue South, Suite 404, Nashville, TN, USA. .,Department of Medicine, Vanderbilt University School of Medicine, 1161 21st Avenue South, Medical Center North T3113, Nashville, TN, USA.
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