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Izadifard M, Ahmadvand M, Pashaiefar H, Alimoghadam K, Kasaeian A, Barkhordar M, Seghatoleslami G, Vaezi M, Ghavamzadeh A, Yaghmaie M. Diagnosis of Cutaneous Acute Graft‑Versus‑Host Disease Through Circulating Plasma miR-638, miR-6511b-5p, miR-3613-5p, miR-455-3p, miR-5787, and miR-548a-3p as Prospective Noninvasive Biomarkers Following Allogeneic Hematopoietic Stem Cell Transplantation. Clin Transplant 2024; 38:e15371. [PMID: 39031894 DOI: 10.1111/ctr.15371] [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: 03/18/2024] [Revised: 05/15/2024] [Accepted: 05/22/2024] [Indexed: 07/22/2024]
Abstract
BACKGROUND There are currently no laboratory tests that can accurately predict the likelihood of developing acute graft-versus-host disease (aGVHD), a patient's response to treatment, or their survival chance. This research aimed to establish circulating miRNAs as diagnostic, prognostic, or predictive biomarkers of aGVHD. METHODS In a prospective cohort, we studied the incidence of cutaneous aGVHD in AML patients undergoing allo-HSCT at Shariati Hospital in Tehran, Iran during 2020-2023. Patients with cutaneous aGVHD were labeled as the case group, while patients without cutaneous aGVHD were selected as the control group. Accordingly, the expression levels of six significant miRNAs (miR-638, miR-6511b-5p, miR-3613-5p, miR-455-3p, miR-5787, miR-548a-3p) were evaluated by quantitative reverse transcription-polymerase chain reaction (RTqPCR) in three different time-points: before transplantation, on day 14 and day 21 after transplantation. RESULTS The levels of plasma miR-455-3p, miR-5787, miR-638, and miR-3613-5p were significantly downregulated, while miR-548a-3p, and miR-6511b-5p were significantly upregulated in individuals with cutaneous aGVHD in comparison to patients without GVHD. Additionally, the possibility for great diagnostic accuracy for cutaneous aGVHD was revealed by ROC curve analysis of differentially expressed miRNAs (DEMs). CONCLUSION The study findings encourage us to hypothesize that the aforementioned miRNAs may contribute to the predominance of aGVHD, particularly low-grade cutaneous aGVHD.
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Affiliation(s)
- Marzieh Izadifard
- Hematology, Oncology and Stem Cell Transplantation Research Center, Research Institute for Oncology, Hematology and Cell Therapy, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Ahmadvand
- Cell Therapy and Hematopoietic Stem Cell Transplantation Research Center, Research Institute for Oncology, Hematology, and Cell Therapy, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Pashaiefar
- Hematology, Oncology and Stem Cell Transplantation Research Center, Research Institute for Oncology, Hematology and Cell Therapy, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Kamran Alimoghadam
- Cell Therapy and Hematopoietic Stem Cell Transplantation Research Center, Research Institute for Oncology, Hematology, and Cell Therapy, Tehran University of Medical Sciences, Tehran, Iran
| | - Amir Kasaeian
- Hematology, Oncology and Stem Cell Transplantation Research Center, Research Institute for Oncology, Hematology and Cell Therapy, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Barkhordar
- Cell Therapy and Hematopoietic Stem Cell Transplantation Research Center, Research Institute for Oncology, Hematology, and Cell Therapy, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Mohammad Vaezi
- Hematology, Oncology and Stem Cell Transplantation Research Center, Research Institute for Oncology, Hematology and Cell Therapy, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Ardeshir Ghavamzadeh
- Hematology, Oncology and Stem Cell Transplantation Research Center, Research Institute for Oncology, Hematology and Cell Therapy, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
- ATMP Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Marjan Yaghmaie
- Hematology, Oncology and Stem Cell Transplantation Research Center, Research Institute for Oncology, Hematology and Cell Therapy, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
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Lagström S, Løvestad AH, Umu SU, Ambur OH, Nygård M, Rounge TB, Christiansen IK. HPV16 and HPV18 type-specific APOBEC3 and integration profiles in different diagnostic categories of cervical samples. Tumour Virus Res 2021; 12:200221. [PMID: 34175494 PMCID: PMC8287217 DOI: 10.1016/j.tvr.2021.200221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 04/09/2021] [Accepted: 06/07/2021] [Indexed: 12/14/2022] Open
Abstract
Human papillomavirus (HPV) 16 and 18 are the most predominant types in cervical cancer. Only a small fraction of HPV infections progress to cancer, indicating that additional factors and genomic events contribute to the carcinogenesis, such as minor nucleotide variation caused by APOBEC3 and chromosomal integration. We analysed intra-host minor nucleotide variants (MNVs) and integration in HPV16 and HPV18 positive cervical samples with different morphology. Samples were sequenced using an HPV whole genome sequencing protocol TaME-seq. A total of 80 HPV16 and 51 HPV18 positive samples passed the sequencing depth criteria of 300× reads, showing the following distribution: non-progressive disease (HPV16 n = 21, HPV18 n = 12); cervical intraepithelial neoplasia (CIN) grade 2 (HPV16 n = 27, HPV18 n = 9); CIN3/adenocarcinoma in situ (AIS) (HPV16 n = 27, HPV18 n = 30); cervical cancer (HPV16 n = 5). Similar numbers of MNVs in HPV16 and HPV18 samples were observed for most viral genes, with the exception of HPV18 E4 with higher numbers across clinical categories. APOBEC3 signatures were observed in HPV16 lesions, while similar mutation patterns were not detected for HPV18. The proportion of samples with integration was 13% for HPV16 and 59% for HPV18 positive samples, with a noticeable portion located within or close to cancer-related genes.
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Affiliation(s)
- Sonja Lagström
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway; Department of Research, Cancer Registry of Norway, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | - Sinan Uğur Umu
- Department of Research, Cancer Registry of Norway, Oslo, Norway
| | - Ole Herman Ambur
- Faculty of Health Sciences, OsloMet, Oslo Metropolitan University, Oslo, Norway
| | - Mari Nygård
- Department of Research, Cancer Registry of Norway, Oslo, Norway
| | - Trine B Rounge
- Department of Research, Cancer Registry of Norway, Oslo, Norway; Department of Informatics, University of Oslo, Oslo, Norway.
| | - Irene Kraus Christiansen
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway; Department of Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus University Hospital and University of Oslo, Lørenskog, Norway.
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Mandal P, Bhattacharjee B, Sen S, Bhattacharya A, Saha SS, Chowdhury RR, Mondal NR, Chakrabarty B, Chatterjee T, Roy S, Sengupta S. Predominance of genomically defined A lineage of HPV16 over D lineage in Indian patients from eastern India with squamous cell carcinoma of the cervix in association with distinct oncogenic phenotypes. Transl Oncol 2021; 15:101256. [PMID: 34717279 PMCID: PMC8564679 DOI: 10.1016/j.tranon.2021.101256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/28/2021] [Accepted: 10/22/2021] [Indexed: 11/25/2022] Open
Abstract
The HPV16 lineage A viruses are predominantly associated with cervical squamous cell carcinoma (SCC) in the eastern region of India. Among lineage A viruses, the E5(Y44L, I65V), E6(L83V) and LCR: C7577T variants are associated with SCC. The risk alleles are distributed among 10 clades comprising of 64 HPV16 genomes. Low integration, high episomal copy numbers and high E7 mRNA expression in SCC contrasts lineage A viruses from lineage D.
Human papillomavirus type-16 (HPV16) is classified into lineages, A, B, C and D and 10 sub-lineages portraying variable infectivity, persistence, and cytological outcomes, however, with geographical variations. Our objective was to delineate the distinctive features of lineages among cervical squamous cell carcinoma (SCC) in the eastern region of India. A total of 145 SCC cases and 24 non-malignant specimens, harboring episomal HPV16, were included. The presence of higher proportion of lineage A over D was observed among SCC cases (86.89% A1, 8.97% D1 and 4.14% D2), while only A1 sub-lineage viruses were found among control specimens. Among the A1 viruses, an association of variants in the E5 (Y44L, I65V), E6 (L83V) genes and LCR: C7577T with SCC, with combined Odd's ratio (95% CI) of 20.5(4.61–91.25) was observed. Network analyses revealed the presence of 10 clades of lineage A viruses comprising of 64 HPV16 genomes harboring the risk alleles. High episomal HPV16 DNA copy numbers (adjusted p-value= 0.0271) and E7 mRNA expression (p-value=0.000017) predominated in SCC with lineage A, over D. Our study highlights the distinctive modalities of oncogenicity among different HPV16 lineages.
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Affiliation(s)
- Paramita Mandal
- National Institute of Biomedical Genomics, P.O.: N.S.S., Kalyani, West Bengal 741251, India; Biomedical Genetics Laboratory, Department of Zoology, The University of Burdwan, Purba Burdwan, West Bengal 713104, India
| | - Bornali Bhattacharjee
- National Institute of Biomedical Genomics, P.O.: N.S.S., Kalyani, West Bengal 741251, India; Amity Institute of Biotechnology, Amity University Kolkata, Kolkata, India.
| | - Shrinka Sen
- National Institute of Biomedical Genomics, P.O.: N.S.S., Kalyani, West Bengal 741251, India; Department of Medical Genetics, University of British Columbia, 4500 Oak Street, Vancouver, British Columbia V6H 3N1, Canada
| | - Amrapali Bhattacharya
- National Institute of Biomedical Genomics, P.O.: N.S.S., Kalyani, West Bengal 741251, India; DBT-NIDAN Kendra on Rare Genetic Diseases, N. R. S. Medical College and Hospital, 138, A. J. C. Bose Road, Kolkata 700014, India
| | - Sweta Sharma Saha
- National Institute of Biomedical Genomics, P.O.: N.S.S., Kalyani, West Bengal 741251, India; Translational and Clinical Research Institute, Faculty of Medical Sciences, Centre for Cancer, Newcastle University, NE2 4HH, UK
| | | | | | | | | | | | - Sharmila Sengupta
- National Institute of Biomedical Genomics, P.O.: N.S.S., Kalyani, West Bengal 741251, India.
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Pulati N, Zhang Z, Gulimilamu A, Qi X, Yang J. HPV16+‐miRNAs in cervical cancer and the anti‐tumor role played by miR‐5701. J Gene Med 2019; 21:e3126. [PMID: 31498525 DOI: 10.1002/jgm.3126] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 08/15/2019] [Accepted: 08/30/2019] [Indexed: 12/19/2022] Open
Affiliation(s)
- Nuerbieke Pulati
- Department of Radiation OncologyPeople's Hospital of Xinjiang Uygur Autonomous Region Urumqi Xinjiang China
| | - Zegao Zhang
- Department of Radiation OncologyPeople's Hospital of Xinjiang Uygur Autonomous Region Urumqi Xinjiang China
| | - Aireti Gulimilamu
- Department of Radiation OncologyPeople's Hospital of Xinjiang Uygur Autonomous Region Urumqi Xinjiang China
| | - Xiaoli Qi
- Department of Radiation OncologyPeople's Hospital of Xinjiang Uygur Autonomous Region Urumqi Xinjiang China
| | - Jie Yang
- Department of Radiation OncologyPeople's Hospital of Xinjiang Uygur Autonomous Region Urumqi Xinjiang China
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5
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Mandal P, Saha SS, Sen S, Bhattacharya A, Bhattacharya NP, Bucha S, Sinha M, Chowdhury RR, Mondal NR, Chakravarty B, Chatterjee T, Roy S, Chattapadhyay A, Sengupta S. Cervical cancer subtypes harbouring integrated and/or episomal HPV16 portray distinct molecular phenotypes based on transcriptome profiling of mRNAs and miRNAs. Cell Death Discov 2019; 5:81. [PMID: 30937183 PMCID: PMC6433907 DOI: 10.1038/s41420-019-0154-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 02/03/2019] [Accepted: 02/13/2019] [Indexed: 12/12/2022] Open
Abstract
Heterogeneity in cervical cancers (CaCx) in terms of HPV16 physical status prompted us to investigate the mRNA and miRNA signatures among the different categories of CaCx samples. We performed microarray-based mRNA expression profiling and quantitative real-time PCR-based expression analysis of some prioritised miRNAs implicated in cancer-related pathways among various categories of cervical samples. Such samples included HPV16-positive CaCx cases that harboured either purely integrated HPV16 genomes (integrated) and those that harboured episomal viral genomes, either pure or concomitant with integrated viral genomes (episomal), which were compared with normal cervical samples that were either HPV negative or positive for HPV16. The mRNA expression profile differed characteristically between integrated and episomal CaCx cases for enriched biological pathways. miRNA expression profiles also differed among CaCx cases compared with controls (upregulation—miR-21, miR-16, miR-205, miR-323; downregulation—miR-143, miR-196b, miR-203, miR-34a; progressive upregulation—miR-21 and progressive downregulation—miR-143, miR-34a, miR-196b and miR-203) in the order of HPV-negative controls, HPV16-positive non-malignant samples and HPV16-positive CaCx cases. miR-200a was upregulated in HPV16-positive cervical tissues irrespective of histopathological status. Expression of majority of the predicted target genes was negatively correlated with their corresponding miRNAs, irrespective of the CaCx subtypes. E7 mRNA expression correlated positively with miR-323 expression among episomal cases and miR-203, among integrated cases. miR-181c expression was downregulated only among the episomal CaCx cases and negatively correlated with protein coding transcript of the proliferative target gene, CKS1B of the significantly enriched “G2/M DNA Damage Checkpoint Regulation” pathway among CaCx cases. Thus, the two CaCx subtypes are distinct entities at the molecular level, which could be differentially targeted for therapy. In fact, availability of a small molecule inhibitor of CKS1B, suggests that drugging CKS1B could be a potential avenue of treating the large majority of CaCx cases harbouring episomal HPV16.
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Affiliation(s)
- Paramita Mandal
- 1National Institute of Biomedical Genomics, Kalyani, West Bengal India.,6Present Address: Department of Zoology, The University of Burdwan, Burdwan, West Bengal India
| | - Sweta Sharma Saha
- 1National Institute of Biomedical Genomics, Kalyani, West Bengal India.,Present Address: Section of Haematology/Oncology, Department of Medicine, university of Chicago, 5841 S Maryland Ave MC 2115, Chicago, IL 60637 USA
| | - Shrinka Sen
- 1National Institute of Biomedical Genomics, Kalyani, West Bengal India.,8Present Address: Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru, Karnataka 560064 India
| | | | - Nitai P Bhattacharya
- 2Crystallography & Molecular Biology Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064 India
| | - Sudha Bucha
- 2Crystallography & Molecular Biology Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064 India
| | - Mithun Sinha
- 2Crystallography & Molecular Biology Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064 India.,9Present Address: Comprehensive Wound Center, Center for Regenerative Medicine and Cell Based Therapies, The Ohio State University, Columbus, OH USA
| | - Rahul Roy Chowdhury
- 3Department of Gynecology, Saroj Gupta Cancer Centre and Research Institute, Kolkata, India
| | - Nidhu Ranjan Mondal
- 3Department of Gynecology, Saroj Gupta Cancer Centre and Research Institute, Kolkata, India
| | - Biman Chakravarty
- 3Department of Gynecology, Saroj Gupta Cancer Centre and Research Institute, Kolkata, India
| | - Tanmay Chatterjee
- 3Department of Gynecology, Saroj Gupta Cancer Centre and Research Institute, Kolkata, India
| | - Sudipta Roy
- Sri Aurobindo Seva Kendra, 1H, Gariahat Road (S) Jodhpur Park, Kolkata, 700068 West Bengal India
| | | | - Sharmila Sengupta
- 1National Institute of Biomedical Genomics, Kalyani, West Bengal India
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6
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Du B, Wang X, Wu D, Wang T, Yang X, Wang J, Shi X, Chen L, Zhang W. MicroRNA expression profiles identify biomarkers for predicting the response to chemoradiotherapy in rectal cancer. Mol Med Rep 2018; 18:1909-1916. [PMID: 29956755 PMCID: PMC6072158 DOI: 10.3892/mmr.2018.9215] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/02/2017] [Indexed: 02/07/2023] Open
Abstract
Neoadjuvant chemoradiotherapy (nCRT) following surgery significantly improves the survival rate of patients with rectal cancer. However, nCRT is associated with significant adverse symptoms and high medical costs. Therefore, it is important to investigate potential biomarkers for the prediction of the response to nCRT in patients with rectal cancer. The present study identified candidate biomarkers for predicting a complete response (CR) to nCRT in patients with rectal cancer and investigated the associated mechanisms. Microarray data (accession no. GSE29298) was downloaded from the Gene Expression Omnibus database. Differentially expressed microRNAs (miRNAs/miR) were screened between the pathological CR (pCR) group and no pCR (incomplete response) group. miRNA target genes were predicted using the miRWalk 2.0 online tool and subjected to Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. Furthermore, a miRNA co‑regulatory network was constructed and disease‑associated genes were predicted. The results demonstrated that a total of 36 upregulated and 5 downregulated miRNAs were identified between the two groups. Among these differentially expressed miRNAs, miR‑548c‑5p, miR‑548d‑5p and miR‑663a were significantly associated with a CR to nCRT. The co‑regulatory network and pathway analysis indicated that miR‑548c‑5p and miR‑548d‑5p may function together through stem cell pluripotency and ubiquitin‑mediated proteolysis signaling pathways. Furthermore, the prediction of disease‑associated genes demonstrated that miR‑548c‑5p/miR‑548d‑5p and miR‑663a may regulate genes associated with rectal cancer, including mutated in colorectal cancers (MCC) and adenomatous polyposis coli (APC), and colorectal neoplasms, including interleukin‑6 signal transducer (IL6ST), cell cycle checkpoint kinase 2 (CHEK2), marker of proliferation Ki‑67 (MKI67), cadherin 7 (CDH7), calreticulin (CALR) and transforming growth factor β1 (TGFB1). Therefore, miR‑548c‑5p, miR‑548d‑5p and miR‑663a are promising candidate biomarkers for predicting a CR to nCRT. miR‑548c‑5p/miR‑548d‑5p may be associated with a CR by regulating IL6ST, CHEK2, MKI67 and MCC. In addition, it may function through the pluripotency of stem cells and ubiquitin‑mediated proteolysis signaling pathways. miR‑663a may be associated with a CR to nCRT by targeting CDH7, CALR, APC and TGFβ1. Thus, the miRNA biomarkers investigated in the present study may represent novel therapeutic targets for the prediction and eventual improvement of the response to nCRT in patients with rectal cancer.
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Affiliation(s)
- Binbin Du
- Department of Anorectal Surgery, Gansu Provincial Hospital, Lanzhou, Gansu 730000, P.R. China
| | - Xiaoying Wang
- Department of Anorectal Surgery, Gansu Provincial Hospital, Lanzhou, Gansu 730000, P.R. China
| | - Dewang Wu
- Department of Anorectal Surgery, Gansu Provincial Hospital, Lanzhou, Gansu 730000, P.R. China
| | - Tao Wang
- Department of Anorectal Surgery, Gansu Provincial Hospital, Lanzhou, Gansu 730000, P.R. China
| | - Xiongfei Yang
- Department of Anorectal Surgery, Gansu Provincial Hospital, Lanzhou, Gansu 730000, P.R. China
| | - Jiankai Wang
- Department of Radiotherapy, Gansu Provincial Hospital, Lanzhou, Gansu 730000, P.R. China
| | - Xinlong Shi
- Department of Anorectal Surgery, Gansu Provincial Hospital, Lanzhou, Gansu 730000, P.R. China
| | - Lingjuan Chen
- Department of Anorectal Surgery, Gansu Provincial Hospital, Lanzhou, Gansu 730000, P.R. China
| | - Weisheng Zhang
- Department of Anorectal Surgery, Gansu Provincial Hospital, Lanzhou, Gansu 730000, P.R. China
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Ellwanger JH, Zambra FMB, Guimarães RL, Chies JAB. MicroRNA-Related Polymorphisms in Infectious Diseases-Tiny Changes With a Huge Impact on Viral Infections and Potential Clinical Applications. Front Immunol 2018; 9:1316. [PMID: 29963045 PMCID: PMC6010531 DOI: 10.3389/fimmu.2018.01316] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/28/2018] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are single-stranded sequences of non-coding RNA with approximately 22 nucleotides that act posttranscriptionally on gene expression. miRNAs are important gene regulators in physiological contexts, but they also impact the pathogenesis of various diseases. The role of miRNAs in viral infections has been explored by different authors in both population-based as well as in functional studies. However, the effect of miRNA polymorphisms on the susceptibility to viral infections and on the clinical course of these diseases is still an emerging topic. Thus, this review will compile and organize the findings described in studies that evaluated the effects of genetic variations on miRNA genes and on their binding sites, in the context of human viral diseases. In addition to discussing the basic aspects of miRNAs biology, we will cover the studies that investigated miRNA polymorphisms in infections caused by hepatitis B virus, hepatitis C virus, human immunodeficiency virus, Epstein–Barr virus, and human papillomavirus. Finally, emerging topics concerning the importance of miRNA genetic variants will be presented, focusing on the context of viral infectious diseases.
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Affiliation(s)
- Joel Henrique Ellwanger
- Laboratório de Imunobiologia e Imunogenética, Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Francis Maria Báo Zambra
- Laboratório de Imunobiologia e Imunogenética, Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Rafael Lima Guimarães
- Departamento de Genética, Universidade Federal do Pernambuco (UFPE), Recife, Brazil.,Laboratório de Imunopatologia Keizo Asami (LIKA), Universidade Federal de Pernambuco (UFPE), Recife, Brazil
| | - José Artur Bogo Chies
- Laboratório de Imunobiologia e Imunogenética, Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
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Matboli M, Shafei AE, Azazy AE, Reda M, El-Khazragy N, Nagy AA, Ali MA, Sobhi M, Abdel-Rahman O. Clinical evaluation of circulating miR-548a-3p and -20a expression in malignant pleural mesothelioma patients. Biomark Med 2018; 12:129-139. [PMID: 29338319 DOI: 10.2217/bmm-2017-0224] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
AIM miRNAs may act as promising diagnostic and prognostic biomarkers of mesothelioma. This study integrates serum miR-548a-3p and miR-20a expression based on in silico data analysis followed by clinical validation in malignant mesothelioma patients (malignant pleural mesothelioma [MPM]). PATIENTS & METHODS Serum miR-548a-3p and miR-20a level was assessed in the serum of patients with MPM, chronic asbestos exposure and healthy volunteers by quantitative real-time PCR. RESULTS The expression of serum miR-548a-3p and miR-20a was positive in 91.6 and 96.7% MPM patients, respectively. Both miRNAs were able to segregate between cases and controls. The sensitivity of the combined chosen serum miRNAs reached 100% in the diagnosis of MPM. CONCLUSION The current work revealed that sera miR-548a-3p and miR-20a may serve as promising novel diagnostic tools for MPM.
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Affiliation(s)
- Marwa Matboli
- Medical Biochemistry & Molecular Biology Department, Faculty of Medicine, Ain Shams University, Medical Ain Shams Research Center (MASRI). PO Box 11381, Abbassia, Cairo, Egypt
| | - Ayman E Shafei
- Biomedical Research Department, Armed Forces College of Medicine, Cairo, Egypt
| | | | - Maged Reda
- Armed Forces College of Medicine, Cairo, Egypt
| | - Nashwa El-Khazragy
- Department of Clinical Pathology, Oncology Diagnostic Unit, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Ahmed Aly Nagy
- Clinical Oncology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Mahmoud A Ali
- Biomedical Research Department, Armed Forces College of Medicine, Cairo, Egypt
| | - Mohamed Sobhi
- Clinical Oncology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Omar Abdel-Rahman
- Clinical Oncology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
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9
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Liu J, Liu F, Li X, Song X, Zhou L, Jie J. Screening key genes and miRNAs in early-stage colon adenocarcinoma by RNA-sequencing. Tumour Biol 2017; 39:1010428317714899. [PMID: 28714374 DOI: 10.1177/1010428317714899] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Colon adenocarcinoma is the third leading cause of cancer-related deaths across the world, developing novel and non-invasive diagnostic and prognostic biomarkers for the early-stage colon adenocarcinoma at molecular level is essential. In our study, RNA-sequencing was performed to identify the differentially expressed genes and miRNAs (DEmiRNAs) in early-stage colon adenocarcinoma compared to tissues of precancerous lesions, colonic intraepithelial neoplasia. The DEmiRNA-target interaction network was constructed and functional annotation of targets of DEmiRNAs was performed. The Cancer Genome Atlas was used to verify the expression of selected differentially expressed genes. The receiver operating characteristic analyses of selected differentially expressed genes was performed. In total, 865 differentially expressed genes, 26 DEmiRNAs, and 329 DEmiRNA-target pairs were obtained. Based on the early-stage colon adenocarcinoma network, miR-548c-5p, miR-548i, and miR-548am-5p were the top three DEmiRNAs that covered most differentially expressed genes. NTRK2, DTNA, and BTG2 were the top three differentially expressed genes regulated by most DEmiRNAs. Cancer and colorectal cancer pathways were two significantly enriched pathways in early-stage colon adenocarcinoma. The common differentially expressed genes in both the pathways were AXIN2, Smad2, Smad4, PIK3R1, and BCL2. The expression levels of eight differentially expressed genes (NTRK2, DTNA, BTG2, COL11A1, Smad2, Smad4, PIK3R1, and BCL2) in The Cancer Genome Atlas database were compatible with our RNA-sequencing. All these eight differentially expressed genes and AXIN2 had the potential diagnosis value for Colon adenocarcinoma. In conclusion, a total of ten differentially expressed genes (NTRK2, DTNA, BTG2, COLCA1, COL11A1, AXIN2, Smad2, Smad4, PIK3R1, and BCL2) and four DEmiRNAs (miR-548c-5p, miR-548i, mir-424-5p, and miR-548am-5p) may be involved in the pathogenesis of early-stage colon adenocarcinoma which may make a contribution for developing new diagnostic and therapeutic strategies for early-stage colon adenocarcinoma.
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Affiliation(s)
- Jixi Liu
- Department of Gastroenterology, China-Japan Friendship Hospital, Beijing, China
| | - Fang Liu
- Department of Gastroenterology, China-Japan Friendship Hospital, Beijing, China
| | - Xiaoou Li
- Department of Gastroenterology, China-Japan Friendship Hospital, Beijing, China
| | - Xin Song
- Department of Gastroenterology, China-Japan Friendship Hospital, Beijing, China
| | - Lei Zhou
- Department of Gastroenterology, China-Japan Friendship Hospital, Beijing, China
| | - Jianzheng Jie
- Department of Gastroenterology, China-Japan Friendship Hospital, Beijing, China
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Sen S, Mandal P, Bhattacharya A, Kundu S, Roy Chowdhury R, Mondal NR, Chatterjee T, Chakravarty B, Roy S, Sengupta S. Impact of viral and host DNA methylations on HPV16-related cervical cancer pathogenesis. Tumour Biol 2017; 39:1010428317699799. [PMID: 28459195 DOI: 10.1177/1010428317699799] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Epigenetic alterations within human papillomavirus (HPV) and host cellular genomes are known to occur during cervical carcinogenesis. Our objective was to analyse the influence of (1) methylation within two immunostimulatory CpG motifs within HPV16 E6 and E7 genes around the viral late promoter and their correlation, if any, with expression deregulation of host receptor (TLR9) and DNA methyltransferases (DNMT1, DNMT3A and DNMT3B) and (2) global DNA methylation levels within CpGs of the repetitive Alu sequences, on cervical cancer (CaCx) pathogenesis. Significantly higher proportions of CaCx samples portrayed methylation in immunostimulatory CpG motifs, compared to HPV16-positive non-malignant samples, with cases harbouring episomal HPV16 showing decreased methylation compared to those with viral integration. A significant linear trend of TLR9 upregulation was recorded in the order of HPV-negative controls < HPV16-positive non-malignant samples < HPV16-positive CaCx cases. TLR9 upregulation in cases with episomal HPV16 was again higher among those with non-methylated immunostimulatory CpG motifs. Comparison of cases with HPV-negative controls revealed that DNMT3A was significantly downregulated only among integrated cases, DNMT3B was significantly overexpressed among both categories of cases, although at variable levels, while DNMT1 failed to show any deregulated expression among the cases. Global host DNA hypomethylation, also showed a significant linear increasing trend through the progressive CaCx development stages mentioned above and was most prominently higher among cases with episomal HPV16 as opposed to viral integration. Thus, HPV16 and host methylations appear to influence CaCx pathogenesis, with differential molecular signatures among CaCx cases with episomal and integrated HPV16.
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Affiliation(s)
- Shrinka Sen
- 1 National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Paramita Mandal
- 1 National Institute of Biomedical Genomics, Kalyani, West Bengal, India
- 2 Department of Zoology, University of Burdwan, Burdwan, West Bengal, India
| | | | - Sudip Kundu
- 1 National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Rahul Roy Chowdhury
- 3 Department of Gynecology, Saroj Gupta Cancer Centre and Research Institute, Kolkata, West Bengal, India
| | - Nidhu Ranjan Mondal
- 3 Department of Gynecology, Saroj Gupta Cancer Centre and Research Institute, Kolkata, West Bengal, India
| | - Tanmay Chatterjee
- 3 Department of Gynecology, Saroj Gupta Cancer Centre and Research Institute, Kolkata, West Bengal, India
| | - Biman Chakravarty
- 3 Department of Gynecology, Saroj Gupta Cancer Centre and Research Institute, Kolkata, West Bengal, India
| | - Sudipta Roy
- 4 Sri Aurobindo Seva Kendra, Kolkata, West Bengal, India
| | - Sharmila Sengupta
- 1 National Institute of Biomedical Genomics, Kalyani, West Bengal, India
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Sharma Saha S, Roy Chowdhury R, Mondal NR, Chakravarty B, Chatterjee T, Roy S, Sengupta S. Identification of genetic variation in the lncRNA HOTAIR associated with HPV16-related cervical cancer pathogenesis. Cell Oncol (Dordr) 2016; 39:559-572. [PMID: 27683269 DOI: 10.1007/s13402-016-0298-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2016] [Indexed: 01/17/2023] Open
Abstract
PURPOSE Previously, over-expression of the long noncoding RNA (lncRNA) HOTAIR has been found to be associated with the invasive and metastatic capacities of several epithelial cancers, including cervical cancer (CaCx). Here, we aimed at identifying functionally relevant genetic variants that may be employed to differentiate between clinically distinct CaCx subtypes, i.e., those exhibiting high HOTAIR levels and molecular signatures of metastasis and those lacking such signatures in the presence of low HOTAIR expression levels. METHODS Genomic DNA isolated from various cervical tissue samples (characterized by histopathology and HPV status) was used for HOTAIR amplicon sequencing, followed by validation of the findings by Sanger sequencing. The impact of the genetic variants found on the secondary structure of HOTAIR and the concomitant alterations in miRNA binding sites were determined through in silico analysis, followed by miRNA expression analysis by quantitative real-time PCR and confirmation of miRNA binding using a luciferase reporter assay. RESULTS We found that rs2366152C was over-represented [ORage-adjusted = 2.58 (1.23-5.57); p = 0.014] in low HOTAIR expressing HPV positive CaCx cases compared to HPV negative controls. This genetic variant showed the propensity of a secondary structure alteration and gain of a miR-22 binding site in HOTAIR, which was found to be concordant with miR-22 over-expression in low HOTAIR CaCx cases compared to controls. We found that miR-22 expression negatively correlated with HOTAIR and E7 expression in HPV16 positive cases and in an E7 transfected HPV negative CaCx-derived cell line (C33A), but was not altered in high HOTAIR cases compared to controls. Reduced luciferase activity of a HOTAIR rs2366152C expression plasmid in C33A cells through miR-22 co-transfection confirmed the ability of miR-22 to specifically target rs2366152C-harbouring HOTAIR lncRNA in CaCx cells, ultimately leading to its down-regulation. CONCLUSIONS Our data indicate that rs2366152C not only has the potential to serve as a marker for singling out CaCx cases lacking metastatic molecular signatures, but also to explain the functional inactivation of HOTAIR in these cases, including the mechanism of its down-regulation.
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Affiliation(s)
- Sweta Sharma Saha
- National Institute of Biomedical Genomics, Netaji Subhas Sanatorium, 2nd Floor, P.O.: N.S.S, Kalyani, 741251, West Bengal, India
| | - Rahul Roy Chowdhury
- Department of Gynecology, Saroj Gupta Cancer Centre and Research Institute, Kolkata, India
| | - Nidhu Ranjan Mondal
- Department of Gynecology, Saroj Gupta Cancer Centre and Research Institute, Kolkata, India
| | - Biman Chakravarty
- Department of Gynecology, Saroj Gupta Cancer Centre and Research Institute, Kolkata, India
| | - Tanmay Chatterjee
- Department of Gynecology, Saroj Gupta Cancer Centre and Research Institute, Kolkata, India
| | - Sudipta Roy
- Sri Aurobindo Seva Kendra, 1H, Gariahat Road (S) Jodhpur Park, Kolkata, 700068, West Bengal, India
| | - Sharmila Sengupta
- National Institute of Biomedical Genomics, Netaji Subhas Sanatorium, 2nd Floor, P.O.: N.S.S, Kalyani, 741251, West Bengal, India.
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Zhao G, Wang T, Huang QK, Pu M, Sun W, Zhang ZC, Ling R, Tao KS. MicroRNA-548a-5p promotes proliferation and inhibits apoptosis in hepatocellular carcinoma cells by targeting Tg737. World J Gastroenterol 2016; 22:5364-5373. [PMID: 27340352 PMCID: PMC4910657 DOI: 10.3748/wjg.v22.i23.5364] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 04/04/2016] [Accepted: 05/04/2016] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate whether Tg737 is regulated by microRNA-548a-5p (miR-548a-5p), and correlates with hepatocellular carcinoma (HCC) cell proliferation and apoptosis.
METHODS: Assays of loss of function of Tg737 were performed by the colony formation assay, CCK assay and cell cycle assay in HCC cell lines. The interaction between miR-548a-5p and its downstream target, Tg737, was evaluated by a dual-luciferase reporter assay and quantitative real-time polymerase chain reaction. Tg737 was then up-regulated in HCC cells to evaluate its effect on miR-548a-5p regulation. HepG2 cells stably overexpressing miR-548a-5p or miR-control were also subcutaneously inoculated into nude mice to evaluate the effect of miR-548a-5p up-regulation on in vivo tumor growth. As the final step, the effect of miR-548a-5p on the apoptosis induced by cisplatin was evaluated by flow cytometry.
RESULTS: Down-regulation of Tg737, which is a target gene of miR-548a-5p, accelerated HCC cell proliferation, and miR-548a-5p promoted HCC cell proliferation in vitro and in vivo. Like the down-regulation of Tg737, overexpression of miR-548a-5p in HCC cell lines promoted cell proliferation, increased colony forming ability and hampered cell apoptosis. In addition, miR-548a-5p overexpression increased HCC cell growth in vivo. MiR-548a-5p down-regulated Tg737 expression through direct contact with its 3’ untranslated region (UTR), and miR-548a-5p expression was negatively correlated with Tg737 levels in HCC specimens. Restoring Tg737 (without the 3’UTR) significantly hampered miR-548a-5p induced cell proliferation, and rescued the miR-548a-5p induced cell proliferation inhibition and apoptosis induced by cisplatin.
CONCLUSION: MiR-548a-5p negatively regulates the tumor inhibitor gene Tg737 and promotes tumorigenesis in vitro and in vivo, indicating its potential as a novel therapeutic target for HCC.
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Sharma S, Mandal P, Sadhukhan T, Roy Chowdhury R, Ranjan Mondal N, Chakravarty B, Chatterjee T, Roy S, Sengupta S. Bridging Links between Long Noncoding RNA HOTAIR and HPV Oncoprotein E7 in Cervical Cancer Pathogenesis. Sci Rep 2015; 5:11724. [PMID: 26152361 PMCID: PMC4495428 DOI: 10.1038/srep11724] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 06/03/2015] [Indexed: 12/21/2022] Open
Abstract
Human Papillomavirus (HPV) type 16 oncoprotein E7 plays a major role in cervical carcinogenesis by interacting with and functionally inactivating various host regulatory molecules. Long noncoding RNA (lncRNA) HOTAIR is one such regulator that recruits chromatin remodelling complex PRC2, creating gene silencing H3K27 me3 marks. Hence, we hypothesized that HOTAIR could be a potential target of E7, in HPV16 related cervical cancers (CaCx). We identified significant linear trend of progressive HOTAIR down-regulation through HPV negative controls, HPV16 positive non-malignants and CaCx samples. Majority of CaCx cases portrayed HOTAIR down-regulation in comparison to HPV negative controls, with corresponding up-regulation of HOTAIR target, HOXD10, and enrichment of cancer related pathways. However, a small subset had significantly higher HOTAIR expression, concomitant with high E7 expression and enrichment of metastatic pathways. Expression of HOTAIR and PRC2-complex members (EZH2 and SUZ12), showed significant positive correlation with E7 expression in CaCx cases and E7 transfected C33A cell line, suggestive of interplay between E7 and HOTAIR. Functional inactivation of HOTAIR by direct interaction with E7 could also be predicted by in silico analysis and confirmed by RNA-Immunoprecipitation. Our study depicts one of the causal mechanisms of cervical carcinogenesis by HPV16 E7, through modulation of HOTAIR expression and function.
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Affiliation(s)
- Sweta Sharma
- National Institute of Biomedical Genomics, Netaji Subhas Sanatorium, 2 Floor, P.O. N.S.S, Kalyani 741251, West Bengal, India
| | - Paramita Mandal
- National Institute of Biomedical Genomics, Netaji Subhas Sanatorium, 2 Floor, P.O. N.S.S, Kalyani 741251, West Bengal, India
| | - Tamal Sadhukhan
- National Institute of Biomedical Genomics, Netaji Subhas Sanatorium, 2 Floor, P.O. N.S.S, Kalyani 741251, West Bengal, India
| | - Rahul Roy Chowdhury
- Department of Gynecology, Saroj Gupta Cancer Centre and Research Institute, Kolkata,India
| | - Nidhu Ranjan Mondal
- Department of Gynecology, Saroj Gupta Cancer Centre and Research Institute, Kolkata,India
| | - Biman Chakravarty
- Department of Gynecology, Saroj Gupta Cancer Centre and Research Institute, Kolkata,India
| | - Tanmay Chatterjee
- Department of Gynecology, Saroj Gupta Cancer Centre and Research Institute, Kolkata,India
| | - Sudipta Roy
- Sri Aurobindo Seva Kendra, 1H, Gariahat Road (S) Jodhpur Park, Kolkata-700068, West Bengal, India
| | - Sharmila Sengupta
- National Institute of Biomedical Genomics, Netaji Subhas Sanatorium, 2 Floor, P.O. N.S.S, Kalyani 741251, West Bengal, India
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Role of microRNAs in cancers of the female reproductive tract: insights from recent clinical and experimental discovery studies. Clin Sci (Lond) 2014; 128:153-80. [PMID: 25294164 DOI: 10.1042/cs20140087] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
microRNAs (miRNAs) are small RNA molecules that represent the top of the pyramid of many tumorigenesis cascade pathways as they have the ability to affect multiple, intricate, and still undiscovered downstream targets. Understanding how miRNA molecules serve as master regulators in these important networks involved in cancer initiation and progression open up significant innovative areas for therapy and diagnosis that have been sadly lacking for deadly female reproductive tract cancers. This review will highlight the recent advances in the field of miRNAs in epithelial ovarian cancer, endometrioid endometrial cancer and squamous-cell cervical carcinoma focusing on studies associated with actual clinical information in humans. Importantly, recent miRNA profiling studies have included well-characterized clinical specimens of female reproductive tract cancers, allowing for studies correlating miRNA expression with clinical outcomes. This review will summarize the current thoughts on the role of miRNA processing in unique miRNA species present in these cancers. In addition, this review will focus on current data regarding miRNA molecules as unique biomarkers associated with clinically significant outcomes such as overall survival and chemotherapy resistance. We will also discuss why specific miRNA molecules are not recapitulated across multiple studies of the same cancer type. Although the mechanistic contributions of miRNA molecules to these clinical phenomena have been confirmed using in vitro and pre-clinical mouse model systems, these studies are truly only the beginning of our understanding of the roles miRNAs play in cancers of the female reproductive tract. This review will also highlight useful areas for future research regarding miRNAs as therapeutic targets in cancers of the female reproductive tract.
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