1
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Li T, Yan Z, Wang W, Zhang R, Gan W, Lv S, Zeng Z, Hou Y, Yang M. SEMA6B Overexpression Predicts Poor Prognosis and Correlates With the Tumor Immunosuppressive Microenvironment in Colorectal Cancer. Front Mol Biosci 2021; 8:687319. [PMID: 34938771 PMCID: PMC8687481 DOI: 10.3389/fmolb.2021.687319] [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: 03/29/2021] [Accepted: 11/03/2021] [Indexed: 12/24/2022] Open
Abstract
Background: Semaphorin 6b (SEMA6B) is a member of the semaphorin axon-guidance family and has been demonstrated to both induce and inhibit tumor progression. However, the role of SEMA6B in colorectal cancer (CRC) has remained unclear. This study sought to explore the promising prognostic biomarker for CRC and to understand the expression pattern, clinical significance, immune effects, and biological functions of SEMA6B. Methods: SEMA6B expression in CRC was evaluated via multiple gene and protein expression databases and we identified its prognostic value through The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Correlations between SEMA6B expression and components of the tumor immune microenvironment were analyzed by packages implemented in R, Tumor Immune Estimation Resource (TIMER), Gene Expression Profiling Interactive Analysis (GEPIA), and Tumor-Immune System Interactions database (TISIDB). RNA interference was performed to silence the expression of SEMA6B to explore its biological roles in the colon cancer cell lines HCT116 and LoVo. Results: The messenger RNA (mRNA) level of SEMA6B and the protein expression were higher in CRC tissues than adjacent normal tissues from multiple CRC datasets. High SEMA6B expression was significantly associated with dismal survival. Multivariate Cox regression analysis demonstrated that SEMA6B was an independent prognostic factor for progression-free survival (PFS). The nomogram showed a favorable predictive ability in PFS. Functional enrichment analysis and the Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data (ESTIMATE) algorithm revealed that the gene cluster associated with the high SEMA6B group were prominently involved in immune responses and inflammatory activities. Notably, SEMA6B expression was positively correlated with infiltrating levels of CD4+ T cells, macrophages, myeloid-derived suppressor cells (MDSCs), regulatory T cells (Tregs), neutrophils, and dendritic cells. Moreover, SEMA6B expression displayed strong correlations with diverse marker sets of immunosuppressive cells in CRC. Integrative analysis revealed that immunosuppressive molecules and immune checkpoints were markedly upregulated in CRC samples with high SEMA6B expression. Furthermore, knockdown of SMEA6B in colon cancer cells significantly inhibited cell proliferation, migration, invasion and reduced the mRNA levels of immunosuppressive molecules. Conclusion: Our findings provide evidence that high SEMA6B expression correlated with adverse prognosis and the tumor immunosuppressive microenvironment in CRC patients. Therefore, SEMA6B may serve as a novel prognostic biomarker for CRC, which offers further insights into developing CRC-targeted immunotherapies.
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Affiliation(s)
- Tiegang Li
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zheng Yan
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Weiqi Wang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Rixin Zhang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenqiang Gan
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Silin Lv
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zifan Zeng
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yufang Hou
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Min Yang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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2
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Feng M, Duan R, Gao Y, Zhang H, Qiao Y, Li Q, Zhao F. Role of Epstein-Barr Virus and Human Papillomavirus Coinfection in Cervical Intraepithelial Neoplasia in Chinese Women Living With HIV. Front Cell Infect Microbiol 2021; 11:703259. [PMID: 34557425 PMCID: PMC8453025 DOI: 10.3389/fcimb.2021.703259] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/19/2021] [Indexed: 01/04/2023] Open
Abstract
Given that only a small percentage of human papillomavirus (HPV)-positive women develop cancer, HPV is necessary but insufficient for carcinogenesis. Mucosally transmitted viral cofactors appear to contribute to HPV-related cervical cancer, such as Epstein-Barr virus (EBV), but previous studies have shown inconsistent outcomes. The exact role of EBV in cervical cancer remains unclear, and more studies are needed to determine its involvement. In this study, we describe the prevalence of EBV and HPV coinfection in HIV-positive women and explore how abnormal host immune status induced by viral coinfections modulates epithelial gene expression. We found a significant correlation between EBV-HPV coinfection and the incidence of high-grade cervical intraepithelial neoplasia (CIN2+). RNA sequencing indicated that CIN tissues coinfected with EBV and HPV led to significant changes in the gene expression of epithelial differentiation and development compared to normal tissues with HPV infection alone. In particular, several differentially expressed genes (DEGs) are closely associated with cancer, such as CACNG4, which was confirmed to be upregulated at both the mRNA and protein levels. Therefore, these findings provide some evidence that EBV may act as a cofactor or mediator in HPV-related cervical cancer. Specific genes or proteins, such as CACNG4, may serve as biomarkers that can risk stratify patients based on pathological changes in the cervix.
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Affiliation(s)
- Min Feng
- Institute of Medical Biology, Chinese Academy of Medicine Sciences and Peking Union Medical College, Kunming, China
| | - Rufei Duan
- Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University/Yunnan Cancer Hospital/Yunnan Cancer Center, Kunming, China.,Department of Cancer Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yang Gao
- Institute of Medical Biology, Chinese Academy of Medicine Sciences and Peking Union Medical College, Kunming, China
| | - Han Zhang
- Institute of Medical Biology, Chinese Academy of Medicine Sciences and Peking Union Medical College, Kunming, China
| | - Youlin Qiao
- Department of Cancer Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qihan Li
- Institute of Medical Biology, Chinese Academy of Medicine Sciences and Peking Union Medical College, Kunming, China
| | - Fanghui Zhao
- Department of Cancer Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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3
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De Marco C, Zoppoli P, Rinaldo N, Morganella S, Morello M, Zuccalà V, Carriero MV, Malanga D, Chirillo R, Bruni P, Malzoni C, Di Vizio D, Venturella R, Zullo F, Rizzuto A, Ceccarelli M, Ciliberto G, Viglietto G. Genome-wide analysis of copy number alterations led to the characterisation of PDCD10 as oncogene in ovarian cancer. Transl Oncol 2021; 14:101013. [PMID: 33516089 PMCID: PMC7846933 DOI: 10.1016/j.tranon.2021.101013] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/04/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022] Open
Abstract
We have identified 201 altered chromosomal bands and 3300 altered genes in human ovarian cancer samples. The gene encoding for PDCD10 was selected for further studies. PDCD10 was found to be over-expressed in primary cancer samples and in the corresponding metastatic lesions. High PDCD10 expression correlates with grade, nodal involvement or advanced FIGO stage. PDCD10 is involved in the control of cell growth and motility in vitro as well as tumorigenicity in vivo.
Copy Number Alterations (CNAs) represent the most common genetic alterations identified in ovarian cancer cells, being responsible for the extensive genomic instability observed in this cancer. Here we report the identification of CNAs in a cohort of Italian patients affected by ovarian cancer performed by SNP-based array. Our analysis allowed the identification of 201 significantly altered chromosomal bands (70 copy number gains; 131 copy number losses). The 3300 genes subjected to CNA identified here were compared to those present in the TCGA dataset. The analysis allowed the identification of 11 genes with increased CN and mRNA expression (PDCD10, EBAG9, NUDCD1, ENY2, CSNK2A1, TBC1D20, ZCCHC3, STARD3, C19orf12, POP4, UQCRFS1). PDCD10 was selected for further studies because of the highest frequency of CNA. PDCD10 was found, by immunostaining of three different Tissue Micro Arrays, to be over-expressed in the majority of ovarian primary cancer samples and in metastatic lesions. Moreover, significant correlations were found in specific subsets of patients, between increased PDCD10 expression and grade (p < 0.005), nodal involvement (p < 0.05) or advanced FIGO stage (p < 0.01). Finally, manipulation of PDCD10 expression by shRNA in ovarian cancer cells (OVCAR-5 and OVCA429) demonstrated a positive role for PDCD10 in the control of cell growth and motility in vitro and tumorigenicity in vivo. In conclusion, this study allowed the identification of novel genes subjected to copy number alterations in ovarian cancer. In particular, the results reported here point to a prominent role of PDCD10 as a bona fide oncogene.
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Affiliation(s)
- Carmela De Marco
- Department of Experimental and Clinical Medicine, "Magna Graecia", University Catanzaro, Italy.
| | - Pietro Zoppoli
- Department of Experimental and Clinical Medicine, "Magna Graecia", University Catanzaro, Italy
| | - Nicola Rinaldo
- Biogem Scarl, Institute for Genetic Research "G. Salvatore", Ariano Irpino (AV), Italy
| | - Sandro Morganella
- Biogem Scarl, Institute for Genetic Research "G. Salvatore", Ariano Irpino (AV), Italy
| | - Matteo Morello
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles (CA), USA
| | - Valeria Zuccalà
- Pathology Unit, "Pugliese-Ciaccio" Hospital, Catanzaro, Italy
| | | | - Donatella Malanga
- Department of Experimental and Clinical Medicine, "Magna Graecia", University Catanzaro, Italy
| | - Roberta Chirillo
- Department of Experimental and Clinical Medicine, "Magna Graecia", University Catanzaro, Italy
| | - Paola Bruni
- Casa di Cura "Malzoni-Villa dei Platani", Avellino, Italy
| | | | - Dolores Di Vizio
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles (CA), USA
| | - Roberta Venturella
- Unit of Obstetrics and Gynaecology, "Magna Graecia" University of Catanzaro, Italy
| | - Fulvio Zullo
- Unit of Obstetrics and Gynaecology, "Magna Graecia" University of Catanzaro, Italy
| | - Antonia Rizzuto
- Department of Medical and Surgical Sciences, "Magna Graecia", Catanzaro, Italy
| | - Michele Ceccarelli
- Biogem Scarl, Institute for Genetic Research "G. Salvatore", Ariano Irpino (AV), Italy
| | | | - Giuseppe Viglietto
- Department of Experimental and Clinical Medicine, "Magna Graecia", University Catanzaro, Italy.
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4
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Jeong SJ, Lee KH, Nam AR, Cho JY. Genome-Wide Methylation Profiling in Canine Mammary Tumor Reveals miRNA Candidates Associated with Human Breast Cancer. Cancers (Basel) 2019; 11:E1466. [PMID: 31569550 PMCID: PMC6827104 DOI: 10.3390/cancers11101466] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/27/2019] [Accepted: 09/18/2019] [Indexed: 12/19/2022] Open
Abstract
Genome-wide methylation profiling is used in breast cancer (BC) studies, because DNA methylation is a crucial epigenetic regulator of gene expression, involved in many diseases including BC. We investigated genome-wide methylation profiles in both canine mammary tumor (CMT) tissues and peripheral blood mononuclear cells (PBMCs) using reduced representation bisulfite sequencing (RRBS) and found unique CMT-enriched methylation signatures. A total of 2.2-4.2 million cytosine-phosphate-guanine (CpG) sites were analyzed in both CMT tissues and PBMCs, which included 40,000 and 28,000 differentially methylated regions (DMRs) associated with 341 and 247 promoters of differentially methylated genes (DMGs) in CMT tissues and PBMCs, respectively. Genes related to apoptosis and ion transmembrane transport were hypermethylated, but cell proliferation and oncogene were hypomethylated in tumor tissues. Gene ontology analysis using DMGs in PBMCs revealed significant methylation changes in the subset of immune cells and host defense system-related genes, especially chemokine signaling pathway-related genes. Moreover, a number of CMT tissue-enriched DMRs were identified from the promoter regions of various microRNAs (miRNAs), including cfa-mir-96 and cfa-mir-149, which were reported as cancer-associated miRNAs in humans. We also identified novel miRNAs associated with CMT which can be candidates for new miRNAs associated with human BC. This study may provide new insight for a better understanding of aberrant methylation associated with both human BC and CMT, as well as possible targets for methylation-based BC diagnostic markers.
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Affiliation(s)
- Su-Jin Jeong
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.
| | - Kang-Hoon Lee
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.
| | - A-Reum Nam
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Je-Yoel Cho
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.
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5
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Morozov AV, Karpov VL. Proteasomes and Several Aspects of Their Heterogeneity Relevant to Cancer. Front Oncol 2019; 9:761. [PMID: 31456945 PMCID: PMC6700291 DOI: 10.3389/fonc.2019.00761] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 07/29/2019] [Indexed: 01/19/2023] Open
Abstract
The life of every organism is dependent on the fine-tuned mechanisms of protein synthesis and breakdown. The degradation of most intracellular proteins is performed by the ubiquitin proteasome system (UPS). Proteasomes are central elements of the UPS and represent large multisubunit protein complexes directly responsible for the protein degradation. Accumulating data indicate that there is an intriguing diversity of cellular proteasomes. Different proteasome forms, containing different subunits and attached regulators have been described. In addition, proteasomes specific for a particular tissue were identified. Cancer cells are highly dependent on the proper functioning of the UPS in general, and proteasomes in particular. At the same time, the information regarding the role of different proteasome forms in cancer is limited. This review describes the functional and structural heterogeneity of proteasomes, their association with cancer as well as several established and novel proteasome-directed therapeutic strategies.
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Affiliation(s)
- Alexey V. Morozov
- Laboratory of Regulation of Intracellular Proteolysis, W.A. Engelhardt Institute of Molecular Biology RAS, Moscow, Russia
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6
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Gene selection using hybrid binary black hole algorithm and modified binary particle swarm optimization. Genomics 2019; 111:669-686. [DOI: 10.1016/j.ygeno.2018.04.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 04/04/2018] [Accepted: 04/09/2018] [Indexed: 12/11/2022]
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7
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Strelnikov VV, Zaletaev DV. Evolution of cancer DNA methylotyping. Epigenomics 2019; 11:857-859. [PMID: 31144518 DOI: 10.2217/epi-2019-0079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Vladimir V Strelnikov
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, Russia.,Molecular & Cell Genetics Department, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitry V Zaletaev
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, Russia.,Molecular & Cell Genetics Department, Pirogov Russian National Research Medical University, Moscow, Russia.,Medical Genetics Laboratory, IM Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
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8
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Tanas AS, Sigin VO, Kalinkin AI, Litviakov NV, Slonimskaya EM, Ibragimova MK, Ignatova EO, Simonova OA, Kuznetsova EB, Kekeeva TV, Larin SS, Poddubskaya EV, Trotsenko ID, Rudenko VV, Karandasheva KO, Petrova KD, Tsyganov MM, Deryusheva IV, Kazantseva PV, Doroshenko AV, Tarabanovskaya NA, Chesnokova GG, Sekacheva MI, Nemtsova MV, Izhevskaya VL, Kutsev SI, Zaletaev DV, Strelnikov VV. Genome-wide methylotyping resolves breast cancer epigenetic heterogeneity and suggests novel therapeutic perspectives. Epigenomics 2019; 11:605-617. [PMID: 30729807 DOI: 10.2217/epi-2018-0213] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aim: To provide a breast cancer (BC) methylotype classification by genome-wide CpG islands bisulfite DNA sequencing. Materials & methods: XmaI-reduced representation bisulfite sequencing DNA methylation sequencing method was used to profile DNA methylation of 110 BC samples and 6 normal breast samples. Intrinsic DNA methylation BC subtypes were elicited by unsupervised hierarchical cluster analysis, and cluster-specific differentially methylated genes were identified. Results & conclusion: Overall, six distinct BC methylotypes were identified. BC cell lines constitute a separate group extremely highly methylated at the CpG islands. In turn, primary BC samples segregate into two major subtypes, highly and moderately methylated. Highly and moderately methylated superclusters, each incorporate three distinct epigenomic BC clusters with specific features, suggesting novel perspectives for personalized therapy.
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Affiliation(s)
- Alexander S Tanas
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, Russia.,Molecular & Cell Genetics Department, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Vladimir O Sigin
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, Russia
| | - Alexey I Kalinkin
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, Russia.,Medical Genetics Laboratory, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Nikolai V Litviakov
- Laboratory of Oncovirology, Cancer Research Institute, Tomsk National Research Medical Center, Tomsk, Russia
| | - Elena M Slonimskaya
- Department of General Oncology, Cancer Research Institute, Tomsk National Research Medical Center, Tomsk, Russia
| | - Marina K Ibragimova
- Laboratory of Oncovirology, Cancer Research Institute, Tomsk National Research Medical Center, Tomsk, Russia
| | - Ekaterina O Ignatova
- Clinical Pharmacology & Chemotherapy, Federal State Budgetary institution «N.N. Blokhin National Medical Research Center of Oncology» of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Olga A Simonova
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, Russia
| | - Ekaterina B Kuznetsova
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, Russia.,Medical Genetics Laboratory, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Tatiana V Kekeeva
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, Russia
| | - Sergey S Larin
- Gene Therapy Laboratory, Institute of Gene Biology, Moscow, Russia.,Molecular Immunology Laboratory, Federal Scientific Clinical Centre of Pediatric Hematology Oncology Immunology Named after Dmitry Rogachev, Moscow, Russia
| | - Elena V Poddubskaya
- Clinic of Personalized Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,VitaMed LLC, Moscow, Russia
| | | | - Viktoria V Rudenko
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, Russia
| | | | - Kseniya D Petrova
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, Russia.,Department of Biological and Medical Physics, Moscow Institute of Physics & Technology (State University), Dolgoprudny, Moscow Region, Russia
| | - Matvey M Tsyganov
- Laboratory of Oncovirology, Cancer Research Institute, Tomsk National Research Medical Center, Tomsk, Russia
| | - Irina V Deryusheva
- Laboratory of Oncovirology, Cancer Research Institute, Tomsk National Research Medical Center, Tomsk, Russia
| | - Polina V Kazantseva
- Department of General Oncology, Cancer Research Institute, Tomsk National Research Medical Center, Tomsk, Russia
| | - Artem V Doroshenko
- Department of General Oncology, Cancer Research Institute, Tomsk National Research Medical Center, Tomsk, Russia
| | - Natalia A Tarabanovskaya
- Department of General Oncology, Cancer Research Institute, Tomsk National Research Medical Center, Tomsk, Russia
| | - Galina G Chesnokova
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, Russia
| | - Marina I Sekacheva
- Clinic of Personalized Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Marina V Nemtsova
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, Russia.,Medical Genetics Laboratory, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Vera L Izhevskaya
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, Russia
| | - Sergey I Kutsev
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, Russia.,Molecular & Cell Genetics Department, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitry V Zaletaev
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, Russia.,Molecular & Cell Genetics Department, Pirogov Russian National Research Medical University, Moscow, Russia.,Medical Genetics Laboratory, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Vladimir V Strelnikov
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, Russia.,Molecular & Cell Genetics Department, Pirogov Russian National Research Medical University, Moscow, Russia
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9
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Baldin AV, Grishina AN, Korolev DO, Kuznetsova EB, Golovastova MO, Kalpinskiy AS, Alekseev BY, Kaprin AD, Zinchenko DV, Savvateeva LV, Varshavsky VA, Zernii EY, Vinarov AZ, Bazhin AV, Philippov PP, Zamyatnin AA. Autoantibody against arrestin-1 as a potential biomarker of renal cell carcinoma. Biochimie 2018; 157:26-37. [PMID: 30389514 DOI: 10.1016/j.biochi.2018.10.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 10/25/2018] [Indexed: 12/28/2022]
Abstract
Renal cell carcinoma (RCC) is the second-most common uronephrological cancer. In the absence of specific symptoms, early diagnosis of RCC is challenging. Monitoring of the aberrant expression of tumour-associated antigens (TAAs) and related autoantibody response is considered as a novel approach of RCC diagnostics. The aim of this study was to examine the aberrant expression of arrestin-1 in renal tumours, to investigate the possible epigenetic mechanism underlying arrestin-1 expression, and to assess the frequency of anti-arrestin-1 autoantibody response. Immunohistochemistry was used to assess the presence of arrestin-1 in primary tumours and metastases of 39 patients with RCC and renal oncocytoma. Bisulfite sequencing was employed to analyse the methylation status of the promoter of the SAG gene encoding arrestin-1. Western blot analysis was performed to detect autoantibodies against arrestin-1 in serum samples of 36 RCC and oncocytoma patients. Arrestin-1 was found to be expressed in RCC (58.7% of cases) and renal oncocytoma (90% of cases) cells, while being absent in healthy kidney. The expression of arrestin-1 in RCC metastases was more prominent than in primary tumours. Hypomethylation of the SAG gene promoter is unlikely to be the mechanism for the aberrant expression of arrestin-1. Autoantibodies against arrestin-1 were detected in sera of 75% of RCC patients. Taken together, our findings suggest employment of autoantibody against arrestin-1 as biomarker of RCC.
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Affiliation(s)
- Alexey V Baldin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991, Moscow, Russia.
| | - Alena N Grishina
- Anatomic Pathology Department, Sechenov First Moscow State Medical University, 119991, Moscow, Russia.
| | - Dmitry O Korolev
- Institute of Uronephrology and Human Reproductive Health, Sechenov First Moscow State Medical University, 119991, Moscow, Russia
| | - Ekaterina B Kuznetsova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991, Moscow, Russia; Research Centre for Medical Genetics, 115522, Moscow, Russia.
| | - Marina O Golovastova
- Department of Cell Signalling, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Alexey S Kalpinskiy
- P.A. Hertzen Moscow Oncology Research Center, National Medical Research Center of Radiology, 125284, Moscow, Russia
| | - Boris Y Alekseev
- P.A. Hertzen Moscow Oncology Research Center, National Medical Research Center of Radiology, 125284, Moscow, Russia
| | - Andrey D Kaprin
- P.A. Hertzen Moscow Oncology Research Center, National Medical Research Center of Radiology, 125284, Moscow, Russia.
| | - Dmitry V Zinchenko
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia.
| | - Lyudmila V Savvateeva
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991, Moscow, Russia
| | - Vladimir A Varshavsky
- Anatomic Pathology Department, Sechenov First Moscow State Medical University, 119991, Moscow, Russia
| | - Evgeni Yu Zernii
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991, Moscow, Russia; Department of Cell Signalling, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia.
| | - Andrey Z Vinarov
- Institute of Uronephrology and Human Reproductive Health, Sechenov First Moscow State Medical University, 119991, Moscow, Russia.
| | - Alexandr V Bazhin
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, Germany.
| | - Pavel P Philippov
- Department of Cell Signalling, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Andrey A Zamyatnin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991, Moscow, Russia; Department of Cell Signalling, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia.
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10
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Gentile S. hERG1 potassium channel in cancer cells: a tool to reprogram immortality. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016; 45:649-655. [PMID: 27649700 DOI: 10.1007/s00249-016-1169-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 07/21/2016] [Accepted: 08/30/2016] [Indexed: 12/12/2022]
Abstract
It has been well established that changes in ion fluxes across cellular membranes as a function of time is fundamental in maintaining cellular homeostasis of every living cell. Consequently, dysregulation of ion channels activity is a critical event in pathological conditions of several tissues, including cancer. Nevertheless, the role of ion channels in cancer biology is still not well understood and very little is known about the possible therapeutic opportunities offered by the use of the vast collection of drugs that target ion channels. In this review, we focus on the recent advances in understanding the role of the voltage-gated hERG1 potassium channel in cancer and on the effects of pharmacologic manipulation of the hERG1 in cancer cells aiming to provide insights into the biochemical signaling and cellular processes that are altered by using these drugs.
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Identification of important long non-coding RNAs and highly recurrent aberrant alternative splicing events in hepatocellular carcinoma through integrative analysis of multiple RNA-Seq datasets. Mol Genet Genomics 2015; 291:1035-51. [PMID: 26711644 DOI: 10.1007/s00438-015-1163-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 12/16/2015] [Indexed: 01/04/2023]
Abstract
Hepatocellular carcinoma (HCC) is an aggressive and deadly cancer. The molecular pathogenesis of the disease remains poorly understood. To better understand HCC biology and explore potential biomarkers and therapeutic targets, we investigated the whole transcriptome of HCC. Considering the genetic heterogeneity of HCC, four datasets from four studies consisting of 15 pairs of HCC and adjacent normal samples were analyzed. We observed that the number of lncRNAs expressed in each HCC sample was consistently greater than the adjacent normal sample. Moreover, 15 lncRNAs were identified expressed in five to seven HCC tissues but were not detected in any adjacent normal tissue. Differential expression analysis detected 35 up- and 80 down-regulated lncRNAs in HCC samples compared with adjacent normal samples. In addition, five differentially expressed lncRNAs were predicted to play a role in oxidation and reduction process. With regard to splicing alterations, we identified nine highly recurrent differential splicing events belonging to eight genes USO1, RPS24, CCDC50, THNSL2, NUMB, FN1 (two events), SLC39A14 and NR1I3. Of them, splicing alterations of SLC39A14 and NR1I3 were reported for the association with HCC for the first time. The splicing dysregulation in HCC may be influenced by three splicing factors ESRP2, CELF2 and SRSF5 which were significantly down-regulated in HCC samples. This study revealed uncharacterized aspects of HCC transcriptome and identified important lncRNAs and splicing isoforms with the potential to serve as biomarkers and therapeutic targets for the disease.
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Simonova OA, Kuznetsova EB, Poddubskaya EV, Kekeeva TV, Kerimov RA, Trotsenko ID, Tanas AS, Rudenko VV, Alekseeva EA, Zaletayev DV, Strelnikov VV. DNA methylation in the promoter regions of the laminin family genes in normal and breast carcinoma tissues. Mol Biol 2015. [DOI: 10.1134/s0026893315040160] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Purohit A, Sadanandam A, Myneni P, Singh RK. Semaphorin 5A mediated cellular navigation: connecting nervous system and cancer. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1846:485-93. [PMID: 25263940 PMCID: PMC4261006 DOI: 10.1016/j.bbcan.2014.09.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 09/19/2014] [Accepted: 09/21/2014] [Indexed: 12/30/2022]
Abstract
The ultraprecise wiring of neurons banks on the instructions provided by guidance cue proteins that steer them to their appropriate target tissue during neuronal development. Semaphorins are one such family of proteins. Semaphorins are known to play major physiological roles during the development of various organs including the nervous, cardiovascular, and immune systems. Their role in different pathologies including cancer remains an intense area of investigation. This review focuses on a novel member of this family of proteins, semaphorin 5A, which is much less explored in comparison to its other affiliates. Recent reports suggest that semaphorins play important roles in the pathology of cancer by affecting angiogenesis, tumor growth and metastasis. We will firstly give a general overview of the semaphorin family and its receptors. Next, we discuss their roles in cellular movements and how that makes them a connecting link between the nervous system and cancer. Finally, we focus our discussion on semaphorin 5A to summarize the prevailing knowledge for this molecule in developmental biology and carcinogenesis.
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Affiliation(s)
- Abhilasha Purohit
- Department of Pathology Microbiology, 985950, Nebraska Medical Center, Omaha, NE 68198-5900, USA
| | - Anguraj Sadanandam
- The Institute of Cancer Research, Division of Molecular Pathology, London, UK
| | - Pavan Myneni
- Department of Pathology Microbiology, 985950, Nebraska Medical Center, Omaha, NE 68198-5900, USA
| | - Rakesh K Singh
- Department of Pathology Microbiology, 985950, Nebraska Medical Center, Omaha, NE 68198-5900, USA.
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Bartošík M, Fojta M, Paleček E. Electrochemical detection of 5-methylcytosine in bisulfite-treated DNA. Electrochim Acta 2012. [DOI: 10.1016/j.electacta.2012.05.115] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Abstract
Detection of differential gene expression using microarray technology has received considerable interest in cancer research studies. Recently, many researchers discovered that oncogenes may be activated in some but not all samples in a given disease group. The existing statistical tools for detecting differentially expressed genes in a subset of the disease group mainly include cancer outlier profile analysis (COPA), outlier sum (OS), outlier robust t-statistic (ORT) and maximum ordered subset t-statistics (MOST). In this study, another approach named Least Sum of Ordered Subset Square t-statistic (LSOSS) is proposed. The results of our simulation studies indicated that LSOSS often has more power than previous statistical methods. When applied to real human breast and prostate cancer data sets, LSOSS was competitive in terms of the biological relevance of top ranked genes. Furthermore, a modified hierarchical clustering method was developed to classify the heterogeneous gene activation patterns of human breast cancer samples based on the significant genes detected by LSOSS. Three classes of gene activation patterns, which correspond to estrogen receptor (ER)+, ER− and a mixture of ER+ and ER−, were detected and each class was assigned a different gene signature.
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Affiliation(s)
- Yupeng Wang
- Department of Animal and Diary Science, University of Georgia, Athens, GA 30602, USA
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Tanas AS, Shkarupo VV, Kuznetsova EB, Zaletayev DV, Strelnikov VV. Novel tools for unbiased DNA differential methylation screening. Epigenomics 2010; 2:325-33. [DOI: 10.2217/epi.10.3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
DNA differential methylation screening approaches may be hypothesis driven (preselection of the loci to screen) or unbiased (screening precedes mapping of differentially methylated loci). The latter allow for the identification of sequences demonstrating ‘nonclassical’ methylation behavior in cancer and, thus, widen our concept of tumor biology. Extensive employment of unbiased screening methods is hampered by the troublesome procedures involved in physically mapping the identified differentially methylated DNA fragments. In this special report, we describe a positive experience of optimizing two screening methods, methylation-sensitive arbitrarily primed PCR and amplification of intermethylated sites, with a special focus on simplification, or even exclusion, of sequencing procedures. With our modifications, unbiased screening of DNA differential methylation acquires an easy-to-use workflow, including sophisticated experimental design, high-resolution analysis and simple genomic mapping of the fragments of interest.
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Affiliation(s)
- Alexander S Tanas
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moskvorechie Street 1, Moscow 115478, Russia
| | - Viktoria V Shkarupo
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moskvorechie Street 1, Moscow 115478, Russia
- IM Sechenov Moscow Medical Academy, Moscow, Russia
| | - Ekaterina B Kuznetsova
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moskvorechie Street 1, Moscow 115478, Russia
- IM Sechenov Moscow Medical Academy, Moscow, Russia
| | - Dmitry V Zaletayev
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moskvorechie Street 1, Moscow 115478, Russia
- IM Sechenov Moscow Medical Academy, Moscow, Russia
| | - Vladimir V Strelnikov
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moskvorechie Street 1, Moscow 115478, Russia
- IM Sechenov Moscow Medical Academy, Moscow, Russia
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DNA hypermethylation of tumors from non-small cell lung cancer (NSCLC) patients is associated with gender and histologic type. Lung Cancer 2009; 69:172-9. [PMID: 19945765 DOI: 10.1016/j.lungcan.2009.11.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Revised: 08/25/2009] [Accepted: 11/03/2009] [Indexed: 01/20/2023]
Abstract
BACKGROUND We previously identified a number of genes which were methylated significantly more frequently in the tumor compared to the non-cancerous lung tissues from non-small cell lung cancer (NSCLC) patients. Detection of methylation profiles of genes in NSCLC could provide insight into differential pathways to malignancy and lead to strategies for better treatment of individuals with NSCLC. METHODS We determined the DNA methylation status of 27 genes using quantitative MethyLight assays in lung tumor samples from 117 clinically well-characterized NSCLC patients. RESULTS Hypermethylation was detected in one of more of the genes in 106 (91%) of 117 cases and was detected at high levels (percentage methylation reference (PMR)> or =4%) in 79% of NSCLC cases. Methylation of APC, CCND2, KCNH5 and, RUNX was significantly more frequent in adenocarcinomas compared to squamous cell carcinomas (SCC), while methylation of CDKN2A was more common in SCC. Hypermethylation of KCNH5, KCNH8, and RARB was more frequent in females compared to males. Hypermethylation of APC and CCND2 was inversely associated with proliferation score assessed by Ki-67 level. CONCLUSIONS Our findings of differential gene hypermethylation frequencies in tumor tissues from patients with adenocarcinoma or squamous cell cancers and in females compared to males suggests that further investigation is warranted in order to more fully understand the potential disparate pathways and/or risk factors for NSCLC associated with histologic type and gender.
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