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Mandić K, Milutin Gašperov N, Božinović K, Dediol E, Krasić J, Sinčić N, Grce M, Sabol I, Barešić A. Integrative analysis in head and neck cancer reveals distinct role of miRNome and methylome as tumour epigenetic drivers. Sci Rep 2024; 14:9062. [PMID: 38643268 PMCID: PMC11032388 DOI: 10.1038/s41598-024-59312-z] [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: 01/11/2024] [Accepted: 04/09/2024] [Indexed: 04/22/2024] Open
Abstract
Head and neck cancer is the sixth most common malignancy worldwide, with the relatively low 5-year survival rate, mainly because it is diagnosed at a late stage. Infection with HPV is a well known aetiology, which affects the nature of these cancers and patients' survival. Besides, it is considered that the main driving force for this type of cancer could be epigenetics. In this study we aimed to find potential epigenetic biomarkers, by integrating miRNome, methylome, and transcriptome analyses. From the fresh head and neck cancer tissue samples, we chose a group for miRNome, methylome and transcriptome profiling, in comparison to adequate control samples. Bioinformatics analyses are performed in R v4.2.2. Count normalisation and group differential expression for mRNA and the previously obtained miRNA count data was performed with DESeq2 v1.36. Gene set enrichment analysis was performed and visualised using gProfiler2 v0.2.1 Identification of miRNA targets was performed by querying in miRTarBase using multiMiR v1.18.0. Annotation of CpG sites merging into islands was obtained from RnBeads.hg19 v1.28.0. package. For the integrative analysis we performed kmeans clustering using stats v4.2.2 package, using 8-12 clusters and nstart 100. We found that transcriptome analysis divides samples into cancers and controls clusters, with no relation to HPV status or cancer anatomical location. Differentially expressed genes (n = 2781) were predominantly associated with signalling pathways of tumour progression. We identified a cluster of genes under the control of the transcription factor E2F that are significantly underexpressed in cancer tissue, as well as T cell immunity genes and genes related to regulation of transcription. Among overexpressed genes in tumours we found those that belong to cell cycle regulation and vasculature. A small number of genes were found significantly differentially expressed in HPV-positive versus HPV-negative tumours (for example NEFH, ZFR2, TAF7L, ZNF541, and TYMS). In this comprehensive study on an overlapping set of samples where the integration of miRNome, methylome and transcriptome analysis were performed for head and neck cancer, we demonstrated that the majority of genes were associated exclusively with miRNome or methylome and, to a lesser extent, under the control of both epigenetic mechanisms.
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Affiliation(s)
- Katarina Mandić
- Division of Electronics, Ruđer Bošković Institute, Zagreb, Croatia
| | | | - Ksenija Božinović
- Division of Molecular Medicine, Ruđer Bošković Institute, Zagreb, Croatia
| | - Emil Dediol
- Department of Maxillofacial Surgery, Clinical Hospital Dubrava, Zagreb, Croatia
| | - Jure Krasić
- Department of Medical Biology, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Nino Sinčić
- Department of Medical Biology, University of Zagreb School of Medicine, Zagreb, Croatia
- Centre of Excellence in Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, Zagreb, Croatia
- Biomedical Research Centre Šalata, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Magdalena Grce
- Division of Molecular Medicine, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ivan Sabol
- Division of Molecular Medicine, Ruđer Bošković Institute, Zagreb, Croatia.
| | - Anja Barešić
- Division of Electronics, Ruđer Bošković Institute, Zagreb, Croatia
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2
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Anić P, Golubić Talić J, Božinović K, Dediol E, Mravak-Stipetić M, Grce M, Milutin Gašperov N. Methylation of Immune Gene Promoters in Oral and Oropharyngeal Cancer. Int J Mol Sci 2023; 24:ijms24097698. [PMID: 37175405 PMCID: PMC10178514 DOI: 10.3390/ijms24097698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/13/2023] [Accepted: 04/18/2023] [Indexed: 05/15/2023] Open
Abstract
The proportion of oral and oropharyngeal squamous cell carcinoma (OOSCC) that can be attributed to human papillomavirus (HPV) infection is growing nowadays. A potential factor indicating the occurrence of HPV-positive OSCC is a change in the degree of methylation of gene promoters that play a key role in the immune response. In this study, we investigated the difference in the methylation of EDARADD, GBP4, HAVCR2, HLA DPB1, IL12RB1, MARCO, and SIGLEC12 gene promoters in samples of healthy oral mucosa versus samples of oral and oropharyngeal cancer. The presence of HPV infection in samples was examined earlier. To determine the difference in methylation of those gene promotors, isolated and bisulfite-modified DNA was analysed by the methylation-specific PCR method. The investigated gene promoters were found to be more hypomethylated in the oral and oropharyngeal cancer samples in comparison to normal tissue. The proportion of unmethylated gene promoters was similar in HPV-positive and HPV-negative cancers, although the data should be confirmed on a larger set of samples. To conclude, in samples of healthy oral mucosa, the investigated gene promoters were found to be methylated in a high percentage (73.3% to 100%), while in oral and oropharyngeal cancer samples, they were methylated in a low percentage (11.1% to 37%), regardless of HPV infection.
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Affiliation(s)
- Petra Anić
- Research Department, Srebrnjak Children's Hospital, 10000 Zagreb, Croatia
| | | | - Ksenija Božinović
- Department of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Emil Dediol
- Department of Maxillofacial Surgery, Clinical Hospital Dubrava, 10000 Zagreb, Croatia
| | - Marinka Mravak-Stipetić
- Department of Oral Medicine, School of Dental Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Magdalena Grce
- Department of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
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3
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Li Z, Xia Z, Yu Y, Cai L, Jian W, Wang T, Xue W, Wang X, Wang B, Zhang P, Yao W, Zhang C, Wang C. A pyroptosis-associated signature plays a role in prognosis prediction in clear cell renal cell carcinoma. BMC Med Genomics 2022; 15:204. [PMID: 36163033 PMCID: PMC9513884 DOI: 10.1186/s12920-022-01339-0] [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: 10/19/2021] [Accepted: 08/24/2022] [Indexed: 12/24/2022] Open
Abstract
Background Approximately 90% of renal malignancies are RCCs (renal cell carcinomas), and the primary subtype in histology is ccRCC (clear cell RCC). In recent years, pyroptosis has been considered a kind of inflammation-related programmed cell death that participates in the invasion, metastasis, and proliferation of tumour cells, thereby influencing tumour prognosis. Nonetheless, the expression level of pyroptosis-associated genes in RCCs and their relationship with prognosis remain obscure. Results In our research, 44 regulators of pyroptosis that were differentially expressed between normal kidney and ccRCC tissues were identified. ccRCC cases were categorized into 2 subgroups according to prognostic-related DEGs (differentially expressed genes), and there was a significant difference in OS (overall survival) between them. The prognostic value of pyroptosis-associated genes was assessed as a signature based on a cohort from TCGA (The Cancer Genome Atlas). Following Cox regression with DEGs and LASSO (least absolute shrinkage and selection operator), a 6-gene signature was established, and all ccRCC cases in the cohort from TCGA were categorized into an LR (low-risk) or HR (high-risk) group (P < 0.001). In combination with clinical features, risk scores were considered a predictive factor of OS in ccRCC. KEGG (Kyoto Encyclopedia of Genes and Genomes) and GO (Gene Ontology) analyses suggest increased immunity and enrichment of genes related to immunity in the HR group. Conclusions Our findings indicate that genes related to pyroptosis have an important role in tumour immunity and may be used to predict the prognosis of ccRCC. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01339-0.
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Affiliation(s)
- Zhiyuan Li
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Zhinan Xia
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Yipeng Yu
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Licheng Cai
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Wengang Jian
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Tengda Wang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Wei Xue
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Xingyuan Wang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Bowen Wang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Peng Zhang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Wenhao Yao
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Cheng Zhang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China. .,Department of Urology, The Fourth Affiliated Hospital Zhejiang University School of Medicine, Yiwu City, 322000, China.
| | - Chunyang Wang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China.
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Fan X, Jiao L, Jin T. Activation and Immune Regulation Mechanisms of PYHIN Family During Microbial Infection. Front Microbiol 2022; 12:809412. [PMID: 35145495 PMCID: PMC8822057 DOI: 10.3389/fmicb.2021.809412] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/09/2021] [Indexed: 11/29/2022] Open
Abstract
The innate immune system defenses against pathogen infections via patten-recognition receptors (PRRs). PRRs initiate immune responses by recognizing pathogen-associated molecular patterns (PAMPs), including peptidoglycan, lipopolysaccharide, and nucleic acids. Several nucleic acid sensors or families have been identified, such as RIG-I-like receptors (RLRs), Toll-like receptors (TLRs), cyclic GMP-AMP synthase (cGAS), and PYHIN family receptors. In recent years, the PYHIN family cytosolic DNA receptors have increased attention because of their important roles in initiating innate immune responses. The family members in humans include Absent in melanoma 2 (AIM2), IFN-γ inducible protein 16 (IFI16), interferon-inducible protein X (IFIX), and myeloid cell nuclear differentiation antigen (MNDA). The PYHIN family members are also identified in mice, including AIM2, p202, p203, p204, and p205. Herein, we summarize recent advances in understanding the activation and immune regulation mechanisms of the PYHIN family during microbial infection. Furthermore, structural characterizations of AIM2, IFI16, p202, and p204 provide more accurate insights into the signaling mechanisms of PYHIN family receptors. Overall, the molecular details will facilitate the development of reagents to defense against viral infections.
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Affiliation(s)
- Xiaojiao Fan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Lianying Jiao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an, China
- Institute of Molecular and Translational Medicine, Translational Medicine Institute, Xi’an Jiaotong University Health Science Center, Xi’an, China
- *Correspondence: Lianying Jiao,
| | - Tengchuan Jin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- CAS Center for Excellence in Molecular Cell Science, Shanghai, China
- Tengchuan Jin,
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5
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Human Papillomaviruses-Associated Cancers: An Update of Current Knowledge. Viruses 2021; 13:v13112234. [PMID: 34835040 PMCID: PMC8623401 DOI: 10.3390/v13112234] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 12/21/2022] Open
Abstract
Human papillomaviruses (HPVs), which are small, double-stranded, circular DNA viruses infecting human epithelial cells, are associated with various benign and malignant lesions of mucosa and skin. Intensive research on the oncogenic potential of HPVs started in the 1970s and spread across Europe, including Croatia, and worldwide. Nowadays, the causative role of a subset of oncogenic or high-risk (HR) HPV types, led by HPV-16 and HPV-18, of different anogenital and head and neck cancers is well accepted. Two major viral oncoproteins, E6 and E7, are directly involved in the development of HPV-related malignancies by targeting synergistically various cellular pathways involved in the regulation of cell cycle control, apoptosis, and cell polarity control networks as well as host immune response. This review is aimed at describing the key elements in HPV-related carcinogenesis and the advances in cancer prevention with reference to past and on-going research in Croatia.
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6
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Wu Z, Chen L, Jin C, Xu J, Zhang X, Yao Y. A novel pyroptosis-associated gene signature for immune status and prognosis of cutaneous melanoma. PeerJ 2021; 9:e12304. [PMID: 34721986 PMCID: PMC8520690 DOI: 10.7717/peerj.12304] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/22/2021] [Indexed: 12/24/2022] Open
Abstract
Background Cutaneous melanoma (CM) is a life-threatening destructive malignancy. Pyroptosis significantly correlates with programmed tumor cell death and its microenvironment through active host-tumor crosstalk. However, the prognostic value of pyroptosis-associated gene signatures in CM remains unclear. Methods Gene profiles and clinical data of patients with CM were downloaded from The Cancer Genome Atlas (TCGA) to identify differentially expressed genes associated with pyroptosis and overall survival (OS). We constructed a prognostic gene signature using LASSO analysis, then applied immune cell infiltration scores and Kaplan-Meier, Cox, and pathway enrichment analyses to determine the roles of the gene signature in CM. A validation cohort was collected from the Gene Expression Omnibus (GEO) database. Results Four pyroptosis-associated genes were identified and incorporated into a prognostic gene signature. Integrated bioinformatics findings showed that the signature correlated with patient survival and was associated with tumor growth and metastasis. The results of Gene Set Enrichment Analysis of a risk signature indicated that several enriched pathways are associated with cancer and immunity. The risk signature for immune status significantly correlated with tumor stem cells, the immune microenvironment, immune cell infiltration and immune subtypes. The expression of four pyroptosis genes significantly correlated with the OS of patients with CM and was related to the sensitivity of cancer cells to several antitumor drugs. A signature comprising four genes associated with pyroptosis offers a novel approach to the prognosis and survival of patients with CM and will facilitate the development of individualized therapy.
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Affiliation(s)
- Zhengyuan Wu
- Yuhang First People's Hospital, Hangzhou, China.,The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Leilei Chen
- Yuhang First People's Hospital, Hangzhou, China
| | - Chaojie Jin
- Yuhang First People's Hospital, Hangzhou, China
| | - Jing Xu
- Yuhang First People's Hospital, Hangzhou, China
| | | | - Yi Yao
- Yuhang First People's Hospital, Hangzhou, China
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7
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Singh R, Ramsuran V, Naranbhai V, Yende-Zuma N, Garrett N, Mlisana K, Dong KL, Walker BD, Abdool Karim SS, Carrington M, Ndung'u T. Epigenetic Regulation of BST-2 Expression Levels and the Effect on HIV-1 Pathogenesis. Front Immunol 2021; 12:669241. [PMID: 34025670 PMCID: PMC8131512 DOI: 10.3389/fimmu.2021.669241] [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: 02/18/2021] [Accepted: 04/20/2021] [Indexed: 11/23/2022] Open
Abstract
HIV-1 must overcome host antiviral restriction factors for efficient replication. We hypothesized that elevated levels of bone marrow stromal cell antigen 2 (BST-2), a potent host restriction factor that interferes with HIV-1 particle release in some human cells and is antagonized by the viral protein Vpu, may associate with viral control. Using cryopreserved samples, from HIV-1 seronegative and seropositive Black women, we measured in vitro expression levels of BST-2 mRNA using a real-time PCR assay and protein levels were validated by Western blotting. The expression level of BST-2 showed an association with viral control within two independent cohorts of Black HIV infected females (r=-0.53, p=0.015, [n =21]; and r=-0.62, p=0.0006, [n=28]). DNA methylation was identified as a mechanism regulating BST-2 levels, where increased BST-2 methylation results in lower expression levels and associates with worse HIV disease outcome. We further demonstrate the ability to regulate BST-2 levels using a DNA hypomethylation drug. Our results suggest BST-2 as a factor for potential therapeutic intervention against HIV and other diseases known to involve BST-2.
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Affiliation(s)
- Ravesh Singh
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.,Africa Health Research Institute (AHRI), Durban, South Africa.,Department of Microbiology, National Health Laboratory Services, KZN Academic Complex, Inkosi Albert Luthuli Central Hospital, Durban, South Africa
| | - Veron Ramsuran
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, United States.,Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, Bethesda, MD, United States.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Vivek Naranbhai
- The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, United States.,Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, Bethesda, MD, United States.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Nonhlanhla Yende-Zuma
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Nigel Garrett
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Koleka Mlisana
- Department of Microbiology, National Health Laboratory Services, KZN Academic Complex, Inkosi Albert Luthuli Central Hospital, Durban, South Africa
| | - Krista L Dong
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Bruce D Walker
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.,Africa Health Research Institute (AHRI), Durban, South Africa.,The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, United States
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Mary Carrington
- The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, United States.,Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, Bethesda, MD, United States
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.,Africa Health Research Institute (AHRI), Durban, South Africa.,The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, United States.,Max Planck Institute for Infection Biology, Chariteplatz, Berlin, Germany.,Division of Infection and Immunity, University College London, London, United Kingdom
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8
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Wang B, Bhattacharya M, Roy S, Tian Y, Yin Q. Immunobiology and structural biology of AIM2 inflammasome. Mol Aspects Med 2020; 76:100869. [PMID: 32660715 DOI: 10.1016/j.mam.2020.100869] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/29/2020] [Accepted: 06/05/2020] [Indexed: 12/15/2022]
Abstract
Absent in melanoma 2 (AIM2) is a cytoplasmic sensor that upon recognizing double-stranded DNA assembles with apoptosis-associated speck-like protein containing a CARD (ASC) and procaspase-1 to form the multi-protein complex AIM2 inflammasome. Double-stranded DNA from bacterial, viral, or host cellular origins triggers AIM2 inflammasome assembly and activation, ultimately resulting in secretion of proinflammatory cytokines and pyroptotic cell death in order to eliminate microbial infection. Many pathogens therefore evade or suppress AIM2 inflammasome to establish infection. On the other hand, AIM2 activation is tightly controlled by multiple cellular factors to prevent autoinflammation. Extensive structural studies have captured the molecular details of multiple steps in AIM2 inflammasome assembly. The structures collectively revealed a nucleated polymerization mechanism that not only pervades each step of AIM2 inflammasome assembly, but also underlies assembly of other inflammasomes and complexes in immune signaling. In this article, we briefly review the identification of AIM2 as a cytoplasmic DNA sensor, summarize the importance of AIM2 inflammasome in infections and diseases, and discuss the molecular mechanisms of AIM2 assembly, activation, and regulation using recent cellular, biochemical, and structural results.
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Affiliation(s)
- Bing Wang
- Department of Biological Science, Florida State University, Tallahassee, FL, 32301, USA
| | - Madhurima Bhattacharya
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32301, USA
| | - Sayantan Roy
- Department of Biological Science, Florida State University, Tallahassee, FL, 32301, USA
| | - Yuan Tian
- Department of Biological Science, Florida State University, Tallahassee, FL, 32301, USA
| | - Qian Yin
- Department of Biological Science, Florida State University, Tallahassee, FL, 32301, USA; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32301, USA.
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9
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Tiwari R, de la Torre JC, McGavern DB, Nayak D. Beyond Tethering the Viral Particles: Immunomodulatory Functions of Tetherin ( BST-2). DNA Cell Biol 2019; 38:1170-1177. [PMID: 31502877 DOI: 10.1089/dna.2019.4777] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Host response to viral infection is a highly regulated process involving engagement of various host factors, cytokines, chemokines, and stimulatory signals that pave the way for an antiviral immune response. The response is manifested in terms of viral sequestration, phagocytosis, and inhibition of genome replication, and, finally, if required, lymphocyte-mediated clearance of virally infected cells. During this process, cross-talk between viral and host factors can shape disease outcomes and immunopathology. Bone marrow stromal antigen 2 (BST-2), also know as tetherin, is induced by type I interferon produced in response to viral infections, as well as in certain cancers. BST-2 has been shown to be a host restriction factor of virus multiplication through its ability to physically tether budding virions and restrict viral spread. However, BST-2 has other roles in the host antiviral response. This review focuses on the diverse functions of BST-2 and its downstream signaling pathways in regulating host immune responses.
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Affiliation(s)
- Ritudhwaj Tiwari
- Discipline of Bioscience and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Juan C de la Torre
- Department of Immunology and Microbial Science IMM-6, The Scripps Research Institute, La Jolla, California
| | - Dorian B McGavern
- Viral Immunology & Intravital Imaging Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Debasis Nayak
- Discipline of Bioscience and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
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10
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Matz KM, Guzman RM, Goodman AG. The Role of Nucleic Acid Sensing in Controlling Microbial and Autoimmune Disorders. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 345:35-136. [PMID: 30904196 DOI: 10.1016/bs.ircmb.2018.08.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Innate immunity, the first line of defense against invading pathogens, is an ancient form of host defense found in all animals, from sponges to humans. During infection, innate immune receptors recognize conserved molecular patterns, such as microbial surface molecules, metabolites produces during infection, or nucleic acids of the microbe's genome. When initiated, the innate immune response activates a host defense program that leads to the synthesis proteins capable of pathogen killing. In mammals, the induction of cytokines during the innate immune response leads to the recruitment of professional immune cells to the site of infection, leading to an adaptive immune response. While a fully functional innate immune response is crucial for a proper host response and curbing microbial infection, if the innate immune response is dysfunctional and is activated in the absence of infection, autoinflammation and autoimmune disorders can develop. Therefore, it follows that the innate immune response must be tightly controlled to avoid an autoimmune response from host-derived molecules, yet still unencumbered to respond to infection. In this review, we will focus on the innate immune response activated from cytosolic nucleic acids, derived from the microbe or host itself. We will depict how viruses and bacteria activate these nucleic acid sensing pathways and their mechanisms to inhibit the pathways. We will also describe the autoinflammatory and autoimmune disorders that develop when these pathways are hyperactive. Finally, we will discuss gaps in knowledge with regard to innate immune response failure and identify where further research is needed.
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Affiliation(s)
- Keesha M Matz
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, United States
| | - R Marena Guzman
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, United States
| | - Alan G Goodman
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, United States; Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, WA, United States.
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11
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AIM2 is a potential therapeutic target in human renal carcinoma and suppresses its invasion and metastasis via enhancing autophagy induction. Exp Cell Res 2018; 370:561-570. [DOI: 10.1016/j.yexcr.2018.07.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 07/11/2018] [Accepted: 07/12/2018] [Indexed: 12/19/2022]
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12
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Shao Q, Lin Z, Wu X, Tang J, Lu S, Feng D, Cheng C, Qing L, Yao K, Chen Y. Transcriptome sequencing of neurologic diseases associated genes in HHV-6A infected human astrocyte. Oncotarget 2018; 7:48070-48080. [PMID: 27344170 PMCID: PMC5217001 DOI: 10.18632/oncotarget.10127] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Accepted: 06/01/2016] [Indexed: 01/21/2023] Open
Abstract
Human Herpesvirus 6 (HHV-6) has been involved in the development of several central nervous system (CNS) diseases, such as Alzheimer's disease, multiple sclerosis and glioma. In order to identify the pathogenic mechanism of HHV-6A infection, we carried out mRNA-seq study of human astrocyte HA1800 cell with HHV-6A GS infection. Using mRNA-seq analysis of HA1800-control cells with HA1800-HHV-6A GS cells, we identified 249 differentially expressed genes. After investigating these candidate genes, we found seven genes associated with two or more CNS diseases: CTSS, PTX3, CHI3L1, Mx1, CXCL16, BIRC3, and BST2. This is the first transcriptome sequencing study which showed the significant association of these genes between HHV-6A infection and neurologic diseases. We believe that our findings can provide a new perspective to understand the pathogenic mechanism of HHV-6A infection and neurologic diseases.
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Affiliation(s)
- Qing Shao
- Department of Immunology, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China.,Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Zhe Lin
- Department of Immunology, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Xiaohui Wu
- Genetic Data Analysis Group, Shanghai Biotechnology Corporation, Shanghai, People's Republic of China
| | - Junwei Tang
- Liver Transplantation Center of The First Affiliated Hospital and Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Shuai Lu
- Department of Immunology, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Dongju Feng
- Department of Immunology, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Ci Cheng
- Department of Immunology, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Lanqun Qing
- Department of Immunology, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Kun Yao
- Department of Immunology, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Yun Chen
- Department of Immunology, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
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13
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Lugrin J, Martinon F. The AIM2 inflammasome: Sensor of pathogens and cellular perturbations. Immunol Rev 2017; 281:99-114. [DOI: 10.1111/imr.12618] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jérôme Lugrin
- Service of Adult Intensive Care Medicine; Lausanne University Hospital; Epalinges Switzerland
| | - Fabio Martinon
- Department of Biochemistry; University of Lausanne; Epalinges Switzerland
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14
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Choubey D. Absent in melanoma 2 proteins in the development of cancer. Cell Mol Life Sci 2016; 73:4383-4395. [PMID: 27328971 PMCID: PMC11108365 DOI: 10.1007/s00018-016-2296-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 06/04/2016] [Accepted: 06/16/2016] [Indexed: 12/19/2022]
Abstract
Recent studies utilizing chemical-induced colitis-associated and sporadic colon cancer in mouse models indicated a protective role for absent in melanoma 2 (Aim2) in colon epithelial cells. Accordingly, mutations in the human AIM2 gene have been found in colorectal cancer (CRC), and reduced expression of AIM2 in CRC is associated with its progression. Furthermore, the overexpression of AIM2 protein in human cancer cell lines inhibits cell proliferation. Interferon-inducible Aim2 and AIM2 are members of the PYHIN (PYRIN and HIN domain-containing) protein family and share ~57 % amino acid identity. The family also includes murine p202, human PYRIN-only protein 3, and IFI16, which negatively regulate Aim2/AIM2 functions. Because the CRC incidence and mortality rates are higher among men compared with women and the expression of Aim2/AIM2 proteins and their regulators is dependent upon age, gender, and sex hormones, we discuss the potential roles of Aim2/AIM2 in the development of cancer. An improved understanding of the biological functions of the AIM2 in the development of CRC will likely identify new therapeutic approaches to treat patients.
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Affiliation(s)
- Divaker Choubey
- Research Service, Cincinnati VA Medical Center, 3200 Vine Street, ML-151, Cincinnati, OH, 45220, USA.
- Department of Environmental Health, University of Cincinnati, 160 Panzeca Way, P. O. Box-670056, Cincinnati, OH, 45267, USA.
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15
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Sharma P, Bhunia S, Poojary SS, Tekcham DS, Barbhuiya MA, Gupta S, Shrivastav BR, Tiwari PK. Global methylation profiling to identify epigenetic signature of gallbladder cancer and gallstone disease. Tumour Biol 2016; 37:14687-14699. [DOI: 10.1007/s13277-016-5355-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 09/07/2016] [Indexed: 12/21/2022] Open
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16
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Mahauad-Fernandez WD, Okeoma CM. BST-2: at the crossroads of viral pathogenesis and oncogenesis. Future Virol 2016. [DOI: 10.2217/fvl.15.113] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
BST-2 is a moonlight protein with several protective and deleterious functions. Regulation of virus restriction and tumor aggressiveness are the most studied aspects of BST-2 function and thus, the main focus of this perspective. Virus inhibition roles of BST-2 have therapeutic potential that, if properly harnessed, could result in near broad spectrum antiviral. However, the involvement of BST-2 in cancer calls for additional studies on BST-2 biology and re-evaluation of the overall role of BST-2 in host protection, as it appears that BST-2 has pleiotropic effects in the host. Here, we analyze the antiviral and protumor roles of BST-2. We also discuss potential therapeutic options for BST-2 against viral infection and cancer.
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Affiliation(s)
- Wadie D Mahauad-Fernandez
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
- Interdisciplinary Program in Molecular & Cellular Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Chioma M Okeoma
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
- Interdisciplinary Program in Molecular & Cellular Biology, University of Iowa, Iowa City, IA 52242, USA
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17
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Mahauad-Fernandez WD, Okeoma CM. The role of BST-2/Tetherin in host protection and disease manifestation. IMMUNITY INFLAMMATION AND DISEASE 2015; 4:4-23. [PMID: 27042298 PMCID: PMC4768070 DOI: 10.1002/iid3.92] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 11/07/2015] [Accepted: 11/09/2015] [Indexed: 12/21/2022]
Abstract
Host cells respond to viral infections by activating immune response genes that are not only involved in inflammation, but may also predispose cells to cancerous transformation. One such gene is BST‐2, a type II transmembrane protein with a unique topology that endows it tethering and signaling potential. Through this ability to tether and signal, BST‐2 regulates host response to viral infection either by inhibiting release of nascent viral particles or in some models inhibiting viral dissemination. However, despite its antiviral functions, BST‐2 is involved in disease manifestation, a function linked to the ability of BST‐2 to promote cell‐to‐cell interaction. Therefore, modulating BST‐2 expression and/or activity has the potential to influence course of disease.
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Affiliation(s)
- Wadie D Mahauad-Fernandez
- Department of MicrobiologyCarver College of MedicineUniversity of IowaIowa CityIA52242USA; Interdisciplinary Program in Molecular and Cellular BiologyUniversity of IowaIowa CityIA52242USA
| | - Chioma M Okeoma
- Department of MicrobiologyCarver College of MedicineUniversity of IowaIowa CityIA52242USA; Interdisciplinary Program in Molecular and Cellular BiologyUniversity of IowaIowa CityIA52242USA
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18
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Singh V, Singh LC, Vasudevan M, Chattopadhyay I, Borthakar BB, Rai AK, Phukan RK, Sharma J, Mahanta J, Kataki AC, Kapur S, Saxena S. Esophageal Cancer Epigenomics and Integrome Analysis of Genome-Wide Methylation and Expression in High Risk Northeast Indian Population. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 19:688-99. [DOI: 10.1089/omi.2015.0121] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Virendra Singh
- National Institute of Pathology (ICMR), New Delhi, India
| | | | | | | | | | | | - Rup Kumar Phukan
- Regional Medical Research Centre (RMRC), Dibrugadh, Assam, India
| | | | - Jagadish Mahanta
- Regional Medical Research Centre (RMRC), Dibrugadh, Assam, India
| | | | - Sujala Kapur
- National Institute of Pathology (ICMR), New Delhi, India
| | - Sunita Saxena
- National Institute of Pathology (ICMR), New Delhi, India
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19
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Marzese DM, Hoon DS. Emerging technologies for studying DNA methylation for the molecular diagnosis of cancer. Expert Rev Mol Diagn 2015; 15:647-64. [PMID: 25797072 DOI: 10.1586/14737159.2015.1027194] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
DNA methylation is an epigenetic mechanism that plays a key role in regulating gene expression and other functions. Although this modification is seen in different sequence contexts, the most frequently detected DNA methylation in mammals involves cytosine-guanine dinucleotides. Pathological alterations in DNA methylation patterns are described in a variety of human diseases, including cancer. Unlike genetic changes, DNA methylation is heavily influenced by subtle modifications in the cellular microenvironment. In all cancers, aberrant DNA methylation is involved in the alteration of a large number of oncological pathways with relevant theranostic utility. Several technologies for DNA methylation mapping have been developed recently and successfully applied in cancer studies. The scope of these technologies varies from assessing a single cytosine-guanine locus to genome-wide distribution of DNA methylation. Here, we review the strengths and weaknesses of these approaches in the context of clinical utility for the molecular diagnosis of human cancers.
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Affiliation(s)
- Diego M Marzese
- Department of Molecular Oncology, Saint John's Health Center, John Wayne Cancer Institute, 2200 Santa Monica Blvd, Santa Monica, CA 90404, USA
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