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Maghsoudi M, Aghdam R, Eslahchi C. Removing the association of random gene sets and survival time in cancers with positive random bias using fixed-point gene set. Sci Rep 2023; 13:8663. [PMID: 37248269 DOI: 10.1038/s41598-023-35588-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 05/20/2023] [Indexed: 05/31/2023] Open
Abstract
Cancer research aims to identify genes that cause or control disease progression. Although a wide range of gene sets have been published, they are usually in poor agreement with one another. Furthermore, recent findings from a gene-expression cohort of different cancer types, known as positive random bias, showed that sets of genes chosen randomly are significantly associated with survival time much higher than expected. In this study, we propose a method based on Brouwer's fixed-point theorem that employs significantly survival-associated random gene sets and reveals a small fixed-point gene set for cancers with a positive random bias property. These sets significantly correspond to cancer-related pathways with biological relevance for the progression and metastasis of the cancer types they represent. Our findings show that our proposed significant gene sets are biologically related to each cancer type available in the cancer genome atlas with the positive random bias property, and by using these sets, positive random bias is significantly more reduced in comparison with state-of-the-art methods in this field. The random bias property is removed in 8 of these 17 cancer types, and the number of random sets of genes associated with survival time is significantly reduced in the remaining 9 cancers.
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Affiliation(s)
- Maryam Maghsoudi
- School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
| | - Rosa Aghdam
- School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Changiz Eslahchi
- School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran.
- Department of Computer and Data Sciences, Faculty of Mathematical Sciences, Shahid Beheshti University, Tehran, Iran.
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2
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Identification of potential biomarkers for papillary thyroid carcinoma by comprehensive bioinformatics analysis. Mol Cell Biochem 2023:10.1007/s11010-022-04606-x. [PMID: 36635603 DOI: 10.1007/s11010-022-04606-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 10/28/2022] [Indexed: 01/14/2023]
Abstract
To perform bioinformatics analysis on the papillary thyroid carcinoma (PTC) gene chip dataset to explore new biological markers for PTC. The gene expression profiles of GSE3467 and GSE6004 chip data were collected by GEO2R, and the differentially expressed genes (DEGs) were selected for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Protein-protein interaction (PPI) relationship analysis was achieved using STRING, and the hub genes were obtained using the Cytoscape software. GEPIA was used to validate the expressions of the hub genes in the normal and tumor tissues and to conduct survival analyses. Pertinent genetic pathology results were fetched using the HPA database. Finally, the key genes were clinically verified by reverse transcription-polymerase chain reaction. 97 genes were jointly up-regulated and 107 genes were jointly down-regulated in GSE3467 and GSE6004. GO function enrichment analysis revealed that the DEGs were involved in the regulation of calcium ion transport into cytosol, integrin binding, and cell adhesion molecule binding. KEGG pathway enrichment analysis indicated that the DEGs were chiefly associated with thyroid cancer and non-small cell lung cancer. According to the PPI network, 30 key target genes were identified. Only the expressions of ANK2, TLE1, and TCF4 matched between the normal and tumor tissues, and were associated with disease prognosis. When compared with the normal thyroid tissues, the protein and mRNA expressions of ANK2, TLE1, and TCF4 were down-regulated in PTC. Significant differences exist in overall gene expression between the thyroid tissues of patients with PTC and those of healthy people. Furthermore, the differential genes ANK2, TLE1, and TCF4 are expected to be reliable molecular markers for the mechanism study and diagnosis of PTC.
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3
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Zhang W, Shang X, Liu N, Ma X, Yang R, Xia H, Zhang Y, Zheng Q, Wang X, Liu Y. ANK2 as a novel predictive biomarker for immune checkpoint inhibitors and its correlation with antitumor immunity in lung adenocarcinoma. BMC Pulm Med 2022; 22:483. [PMID: 36539782 PMCID: PMC9768990 DOI: 10.1186/s12890-022-02279-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Immune checkpoint inhibitors (ICIs) have been shown to significantly improve the survival of patients with advanced lung adenocarcinoma (LUAD). However, only limited proportion of patients could benefit from ICIs. Novel biomarkers with strong predictability are needed for clinicians to maximize the efficacy of ICIs. Our study aimed to identify potential biomarkers predicting ICIs efficacy in LUAD. METHODS The Cancer Genome Atlas (TCGA) PanCancer Atlas studies in cBioportal were used to evaluate the mutation frequency of ANK2 across multiple cancers. Clinical and mutational data for LUAD from ICIs-treated cohorts (Hellmann et al. and Rizvi et al.) were collected to explore the correlation between ANK2 mutation and clinical outcomes. In addition, the relationship between ANK2 expression and clinical outcomes was analyzed using LUAD data from TCGA and Gene Expression Omnibus. Furthermore, the impact of ANK2 mutation and expression on the tumor immune microenvironment of LUAD was analyzed using TCGA and TISIDB databases. RESULTS Patients with ANK2 mutation benefited more from ICIs. In ICIs-treated cohort, prolonged progression-free survival (PFS) (median PFS: NR (not reached) vs. 5.42 months, HR (hazard ratio) 0.31, 95% CI 0.18-0.54; P = 0.0037), improved complete response rate (17.65% vs. 1.85%, P = 0.0402), and improved objective response rate (64.71% vs. 24.07%, P = 0.0033) were observed in LUAD patients with ANK2 mutation compared to their wild-type counterparts. Regarding ANK2 expression, it was observed that ANK2 expression was decreased in LUAD (P < 0.05) and a higher level of ANK2 expression was associated with longer overall survival (HR 0.69, 95% CI 0.52-0.92; P = 0.012) in TCGA LUAD cohort. Moreover, ANK2 mutation or higher ANK2 expression correlated with enhanced antitumor immunity and "hot" tumor microenvironment in LUAD, which could be potential mechanisms that ANK2 mutation facilitated ICIs therapy and patients with higher ANK2 expression survived longer. CONCLUSION Our findings suggest that ANK2 mutation or increased ANK2 expression may serve as a favorable biomarker for the efficacy of ICIs in patients with LUAD.
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Affiliation(s)
- Wengang Zhang
- grid.452402.50000 0004 1808 3430Department of Medical Oncology, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, 250012 Shandong China
| | - Xiaoling Shang
- grid.452402.50000 0004 1808 3430Department of Medical Oncology, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, 250012 Shandong China
| | - Ni Liu
- grid.452402.50000 0004 1808 3430Department of Medical Oncology, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, 250012 Shandong China
| | - Xinchun Ma
- grid.452402.50000 0004 1808 3430Department of Medical Oncology, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, 250012 Shandong China
| | - Rui Yang
- grid.452402.50000 0004 1808 3430Department of Medical Oncology, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, 250012 Shandong China
| | - Handai Xia
- grid.452402.50000 0004 1808 3430Department of Medical Oncology, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, 250012 Shandong China
| | - Yuqing Zhang
- grid.452402.50000 0004 1808 3430Department of Medical Oncology, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, 250012 Shandong China
| | - Qi Zheng
- grid.452402.50000 0004 1808 3430Department of Medical Oncology, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, 250012 Shandong China
| | - Xiuwen Wang
- grid.452402.50000 0004 1808 3430Department of Medical Oncology, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, 250012 Shandong China
| | - Yanguo Liu
- grid.452402.50000 0004 1808 3430Department of Medical Oncology, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, 250012 Shandong China
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4
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Mather RL, Parolia A, Carson SE, Venalainen E, Roig-Carles D, Jaber M, Chu SC, Alborelli I, Wu R, Lin D, Nabavi N, Jachetti E, Colombo MP, Xue H, Pucci P, Ci X, Hawkes C, Li Y, Pandha H, Ulitsky I, Marconett C, Quagliata L, Jiang W, Romero I, Wang Y, Crea F. The evolutionarily conserved long non-coding RNA LINC00261 drives neuroendocrine prostate cancer proliferation and metastasis via distinct nuclear and cytoplasmic mechanisms. Mol Oncol 2021; 15:1921-1941. [PMID: 33793068 PMCID: PMC8253100 DOI: 10.1002/1878-0261.12954] [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: 03/06/2020] [Revised: 01/21/2021] [Accepted: 03/30/2021] [Indexed: 12/19/2022] Open
Abstract
Metastatic neuroendocrine prostate cancer (NEPC) is a highly aggressive disease, whose incidence is rising. Long noncoding RNAs (lncRNAs) represent a large family of disease- and tissue-specific transcripts, most of which are still functionally uncharacterized. Thus, we set out to identify the highly conserved lncRNAs that play a central role in NEPC pathogenesis. To this end, we performed transcriptomic analyses of donor-matched patient-derived xenograft models (PDXs) with immunohistologic features of prostate adenocarcinoma (AR+ /PSA+ ) or NEPC (AR- /SYN+ /CHGA+ ) and through differential expression analyses identified lncRNAs that were upregulated upon neuroendocrine transdifferentiation. These genes were prioritized for functional assessment based on the level of conservation in vertebrates. Here, LINC00261 emerged as the top gene with over 3229-fold upregulation in NEPC. Consistently, LINC00261 expression was significantly upregulated in NEPC specimens in multiple patient cohorts. Knockdown of LINC00261 in PC-3 cells dramatically attenuated its proliferative and metastatic abilities, which are explained by parallel downregulation of CBX2 and FOXA2 through distinct molecular mechanisms. In the cell cytoplasm, LINC00261 binds to and sequesters miR-8485 from targeting the CBX2 mRNA, while inside the nucleus, LINC00261 functions as a transcriptional scaffold to induce SMAD-driven expression of the FOXA2 gene. For the first time, these results demonstrate hyperactivation of the LINC00261-CBX2-FOXA2 axes in NEPC to drive proliferation and metastasis, and that LINC00261 may be utilized as a therapeutic target and a biomarker for this incurable disease.
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Affiliation(s)
- Rebecca L Mather
- Cancer Research Group-School of Life Health and Chemical Sciences, The Open University, Milton Keynes, UK
| | - Abhijit Parolia
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Sandra E Carson
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Erik Venalainen
- Experimental Therapeutics, BC Cancer Research Centre, Vancouver, Canada
| | - David Roig-Carles
- Cancer Research Group-School of Life Health and Chemical Sciences, The Open University, Milton Keynes, UK
| | - Mustapha Jaber
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Shih-Chun Chu
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | - Rebecca Wu
- Experimental Therapeutics, BC Cancer Research Centre, Vancouver, Canada
| | - Dong Lin
- Experimental Therapeutics, BC Cancer Research Centre, Vancouver, Canada.,The Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, Canada.,Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
| | - Noushin Nabavi
- Experimental Therapeutics, BC Cancer Research Centre, Vancouver, Canada
| | - Elena Jachetti
- Molecular Immunology Unit, Department of Research, Fondazione IRCCS Istituto Nazionale Tumori, Milano, Italy
| | - Mario P Colombo
- Molecular Immunology Unit, Department of Research, Fondazione IRCCS Istituto Nazionale Tumori, Milano, Italy
| | - Hui Xue
- Experimental Therapeutics, BC Cancer Research Centre, Vancouver, Canada
| | - Perla Pucci
- Cancer Research Group-School of Life Health and Chemical Sciences, The Open University, Milton Keynes, UK
| | - Xinpei Ci
- The Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, Canada.,Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
| | - Cheryl Hawkes
- Cancer Research Group-School of Life Health and Chemical Sciences, The Open University, Milton Keynes, UK
| | - Yinglei Li
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, China
| | - Hardev Pandha
- Department of Clinical and Experimental Medicine, Faculty of Health and Medical Science, University of Surrey, Guildford, UK
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Crystal Marconett
- Departments of Surgery, Biochemistry and Molecular Medicine, Norris Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Luca Quagliata
- Institute of Pathology, University Hospital Basel, Switzerland
| | - Wei Jiang
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, China
| | - Ignacio Romero
- Cancer Research Group-School of Life Health and Chemical Sciences, The Open University, Milton Keynes, UK
| | - Yuzhuo Wang
- Experimental Therapeutics, BC Cancer Research Centre, Vancouver, Canada.,The Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, Canada.,Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
| | - Francesco Crea
- Cancer Research Group-School of Life Health and Chemical Sciences, The Open University, Milton Keynes, UK
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5
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Schabort JJ, Nam AR, Lee KH, Kim SW, Lee JE, Cho JY. ANK2 Hypermethylation in Canine Mammary Tumors and Human Breast Cancer. Int J Mol Sci 2020; 21:ijms21228697. [PMID: 33218035 PMCID: PMC7698701 DOI: 10.3390/ijms21228697] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/16/2020] [Accepted: 11/16/2020] [Indexed: 12/12/2022] Open
Abstract
Canine mammary tumors (CMT) constitute the most common tumor types found in female dogs. Understanding this cancer through extensive research is important not only for clinical veterinary applications, but also in the scope of comparative oncology. The use of DNA methylation as a biomarker has been noted for numerous cancers in the form of both tissue and liquid biopsies, yet the study of methylation in CMT has been limited. By analyzing our canine methyl-binding domain sequencing (MBD-seq) data, we identified intron regions of canine ANK2 and EPAS1 as differentially methylated regions (DMGs) in CMT. Subsequently, we established quantitative methylation specific PCR (qMSP) of ANK2 and EPAS1 to validate the target hypermethylation in CMT tissue, as well as cell free DNA (cfDNA) from CMT plasma. Both ANK2 and EPAS1 were hypermethylated in CMT and highlighted as potential tissue biomarkers in CMT. ANK2 additionally showed significant hypermethylation in the plasma cfDNA of CMT, indicating that it could be a potential liquid biopsy biomarker as well. A similar trend towards hypermethylation was indicated in HBC at a specific CpG of the ANK2 target on the orthologous human region, which validates the comparative approach using aberrant methylation in CMT.
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Affiliation(s)
- Johannes J. Schabort
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, 08826 Seoul, Korea; (J.J.S.); (A.-R.N.); (K.-H.L.)
| | - A-Reum Nam
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, 08826 Seoul, Korea; (J.J.S.); (A.-R.N.); (K.-H.L.)
| | - Kang-Hoon Lee
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, 08826 Seoul, Korea; (J.J.S.); (A.-R.N.); (K.-H.L.)
| | - Seok Won Kim
- Division of Breast Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul 06351, Korea; (S.W.K.); (J.E.L.)
| | - Jeong Eon Lee
- Division of Breast Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul 06351, Korea; (S.W.K.); (J.E.L.)
| | - Je-Yoel Cho
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, 08826 Seoul, Korea; (J.J.S.); (A.-R.N.); (K.-H.L.)
- Correspondence: ; Tel.: +82-02-880-1268
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6
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Xu Q, Jia X, Wu Q, Shi L, Ma Z, Ba N, Zhao H, Xia X, Zhang Z. Esomeprazole affects the proliferation, metastasis, apoptosis and chemosensitivity of gastric cancer cells by regulating lncRNA/circRNA-miRNA-mRNA ceRNA networks. Oncol Lett 2020; 20:329. [PMID: 33101498 PMCID: PMC7577076 DOI: 10.3892/ol.2020.12193] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 09/07/2020] [Indexed: 12/11/2022] Open
Abstract
Recently, proton pump inhibitors have become a hot research topic in the field of cancer drug research. However, the specific anti-tumor effect and underlying mechanisms of esomeprazole (ESO) in gastric cancer (GC) have remained elusive. In the present study, the toxic effects of ESO on the GC cell line AGS were investigated. MTT assays confirmed that ESO inhibited the proliferation of AGS cells and significantly enhanced their chemosensitivity. Transwell assays were performed to determine the anti-metastatic effects of ESO in AGS cells. Flow cytometry demonstrated that ESO induced cell apoptosis and caused cell cycle arrest in the S and G2/M phases. Furthermore, the differential expression of 948 long non-coding RNAs (lncRNAs), 114 circular RNAs (circRNAs), 1,197 mRNAs and 199 microRNAs (miRNAs) was detected in AGS cells via microarray analysis and RNA-sequencing. The top 10 differently expressed genes were mostly located on chromosomes 10 and 19. In addition, Gene Ontology analysis indicated that the genes were accumulated in functional terms associated with DNA replication, the cell cycle and the apoptotic signaling pathway. Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed a variety of significantly dysregulated signaling pathways and targets, including the EGFR tyrosine kinase inhibitor resistance pathway, forkhead box O signaling pathway, p53 signaling pathway and platinum drug resistance pathway. Subsequently, the interactions of microtubule-associated protein 2 (MAP2), homeodomain-interacting protein kinase 2 (HIPK2) and ankyrin 2 (ANK2) were noted in a competing endogenous RNA (ceRNA) network, which may be important targets of ESO, exerting an anti-tumor effect in AGS cells. Collectively, ESO affects the proliferation, metastasis, apoptosis and chemosensitivity of gastric cancer cells by regulating long non-coding RNA/circRNA-miRNA-mRNA ceRNA networks.
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Affiliation(s)
- Qian Xu
- Department of Oncology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Xiyun Jia
- Department of Oncology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Qian Wu
- Department of Gastroenterology, Huanghe Central Hospital, Zhengzhou, Henan 450003, P.R. China
| | - Lei Shi
- Department of Clinical Pharmacy, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Zihan Ma
- Department of Oncology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Nan Ba
- Department of Oncology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Han Zhao
- Department of Oncology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Xingzhou Xia
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Zisen Zhang
- Department of Oncology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
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7
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Genetic heterogeneity and prognostic impact of recurrent ANK2 and TP53 mutations in mantle cell lymphoma: a multi-centre cohort study. Sci Rep 2020; 10:13359. [PMID: 32770099 PMCID: PMC7414214 DOI: 10.1038/s41598-020-70310-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 07/21/2020] [Indexed: 12/13/2022] Open
Abstract
The molecular features of mantle cell lymphoma (MCL), including its increased incidence, and complex therapies have not been investigated in detail, particularly in East Asian populations. In this study, we performed targeted panel sequencing (TPS) and whole-exome sequencing (WES) to investigate the genetic alterations in Korean MCL patients. We obtained a total of 53 samples from MCL patients from five Korean university hospitals between 2009 and 2016. We identified the recurrently mutated genes such as SYNE1, ATM, KMT2D, CARD11, ANK2, KMT2C, and TP53, which included some known drivers of MCL. The mutational profiles of our cohort indicated genetic heterogeneity. The significantly enriched pathways were mainly involved in gene expression, cell cycle, and programmed cell death. Multivariate analysis revealed that ANK2 mutations impacted the unfavourable overall survival (hazard ratio [HR] 3.126; P = 0.032). Furthermore, TP53 mutations were related to worse progression-free survival (HR 7.813; P = 0.043). Among the recurrently mutated genes with more than 15.0% frequency, discrepancies were found in only 5 genes from 4 patients, suggesting comparability of the TPS to WES in practical laboratory settings. We provide the unbiased genetic landscape that might contribute to MCL pathogenesis and recurrent genes conferring unfavourable outcomes.
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8
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Obergasteiger J, Frapporti G, Pramstaller PP, Hicks AA, Volta M. A new hypothesis for Parkinson's disease pathogenesis: GTPase-p38 MAPK signaling and autophagy as convergence points of etiology and genomics. Mol Neurodegener 2018; 13:40. [PMID: 30071902 PMCID: PMC6090926 DOI: 10.1186/s13024-018-0273-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 07/19/2018] [Indexed: 02/07/2023] Open
Abstract
The combination of genetics and genomics in Parkinson´s disease has recently begun to unveil molecular mechanisms possibly underlying disease onset and progression. In particular, catabolic processes such as autophagy have been increasingly gaining relevance as post-mortem evidence and experimental models suggested a participation in neurodegeneration and alpha-synuclein Lewy body pathology. In addition, familial Parkinson´s disease linked to LRRK2 and alpha-synuclein provided stronger correlation between etiology and alterations in autophagy. More detailed cellular pathways are proposed and genetic risk factors that associate with idiopathic Parkinson´s disease provide further clues in dissecting contributions of single players. Nevertheless, the fine-tuning of these processes remains elusive, as the initial stages of the pathways are not yet clarified.In this review, we collect literature evidence pointing to autophagy as the common, downstream target of Parkinsonian dysfunctions and augment current knowledge on the factors that direct the subsequent steps. Cell and molecular biology evidence indicate that p38 signaling underlies neurodegeneration and autoptic observations suggest a participation in neuropathology. Moreover, alpha-synuclein and LRRK2 also appear involved in the p38 pathway with additional roles in the regulation of GTPase signaling. Small GTPases are critical modulators of p38 activation and thus, their functional interaction with aSyn and LRRK2 could explain much of the detailed mechanics of autophagy in Parkinson´s disease.We propose a novel hypothesis for a more comprehensive working model where autophagy is controlled by upstream pathways, such as GTPase-p38, that have been so far underexplored in this context. In addition, etiological factors (LRRK2, alpha-synuclein) and risk loci might also combine in this common mechanism, providing a powerful experimental setting to dissect the cause of both familial and idiopathic disease.
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Affiliation(s)
- Julia Obergasteiger
- Institute for Biomedicine, Eurac Research – Affiliated Institute of the University of Lübeck, Via Galvani 31, 39100 Bolzano, Italy
| | - Giulia Frapporti
- Institute for Biomedicine, Eurac Research – Affiliated Institute of the University of Lübeck, Via Galvani 31, 39100 Bolzano, Italy
| | - Peter P. Pramstaller
- Institute for Biomedicine, Eurac Research – Affiliated Institute of the University of Lübeck, Via Galvani 31, 39100 Bolzano, Italy
- Department of Neurology, General Central Hospital, Via Böhler 5, 39100 Bolzano, Italy
- Department of Neurology, University of Lübeck, Ratzeburger Allee, 23538 Lübeck, Germany
| | - Andrew A. Hicks
- Institute for Biomedicine, Eurac Research – Affiliated Institute of the University of Lübeck, Via Galvani 31, 39100 Bolzano, Italy
| | - Mattia Volta
- Institute for Biomedicine, Eurac Research – Affiliated Institute of the University of Lübeck, Via Galvani 31, 39100 Bolzano, Italy
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9
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Scumaci D, Oliva A, Concolino A, Curcio A, Fiumara CV, Tammè L, Campuzano O, Pascali VL, Coll M, Iglesias A, Berne P, Casu G, Olivo E, Ausania F, Ricci P, Indolfi C, Brugada J, Brugada R, Cuda G. Integration of "Omics" Strategies for Biomarkers Discovery and for the Elucidation of Molecular Mechanisms Underlying Brugada Syndrome. Proteomics Clin Appl 2018; 12:e1800065. [PMID: 29956481 DOI: 10.1002/prca.201800065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/26/2018] [Indexed: 12/31/2022]
Abstract
PURPOSE The Brugada syndrome (BrS) is a severe inherited cardiac disorder. Given the high genetic and phenotypic heterogeneity of this disease, three different "omics" approaches are integrated in a synergic way to elucidate the molecular mechanisms underlying the pathophysiology of BrS as well as for identifying reliable diagnostic/prognostic markers. EXPERIMENTAL DESIGN The profiling of plasma Proteome and MiRNome is perfomed in a cohort of Brugada patients that were preliminary subjected to genomic analysis to assess a peculiar gene mutation profile. RESULTS The integrated analysis of "omics" data unveiled a cooperative activity of mutated genes, deregulated miRNAs and proteins in orchestrating transcriptional and post-translational events that are critical determining factors for the development of the Brugada pattern. CONCLUSIONS AND CLINICAL RELEVANCE This study provides the basis to shed light on the specific molecular fingerprints underlying BrS development and to gain further insights on the pathogenesis of this life-threatening cardiac disease.
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Affiliation(s)
- Domenica Scumaci
- Laboratory of Proteomics, Research Center of Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100, Catanzaro, Italy
| | - Antonio Oliva
- Fondazione Policlinico A. Gemelli IRCCS, Roma, Università Cattolica del Sacro Cuore, Large Francesco Vito 1, 00168, Rome, Italy
| | - Antonio Concolino
- Laboratory of Proteomics, Research Center of Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100, Catanzaro, Italy
| | - Antonio Curcio
- Division of Cardiology, Department of Medical and Surgical Science, University "Magna Graecia" of Catanzaro, 88100, Catanzaro, Italy
| | - Claudia Vincenza Fiumara
- Laboratory of Proteomics, Research Center of Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100, Catanzaro, Italy
| | - Laura Tammè
- Laboratory of Proteomics, Research Center of Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100, Catanzaro, Italy
| | - Oscar Campuzano
- Cardiovascular Genetics Center, Gencardio Institut d'Investigacions Biomèdiques de Girona,, 17290, Girona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV) 17007, Girona, Spain.,Department of Medical Sciences, School of Medicine, University of Girona, 17004, Girona, Spain
| | - Vincenzo L Pascali
- Fondazione Policlinico A. Gemelli IRCCS, Roma, Università Cattolica del Sacro Cuore, Large Francesco Vito 1, 00168, Rome, Italy
| | - Monica Coll
- Cardiovascular Genetics Center, Gencardio Institut d'Investigacions Biomèdiques de Girona,, 17290, Girona, Spain
| | - Anna Iglesias
- Cardiovascular Genetics Center, Gencardio Institut d'Investigacions Biomèdiques de Girona,, 17290, Girona, Spain
| | - Paola Berne
- Unità Operativa Complessa di Cardiologia Ospedale "San Francesco", 08100, Nuoro, Italy
| | - Gavino Casu
- Unità Operativa Complessa di Cardiologia Ospedale "San Francesco", 08100, Nuoro, Italy
| | - Erika Olivo
- Laboratory of Proteomics, Research Center of Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100, Catanzaro, Italy
| | - Francesco Ausania
- Fondazione Policlinico A. Gemelli, IRCCS, Università Cattolica del Sacro Cuore, Roma
| | - Pietrantonio Ricci
- Department of Medical Sciences, School of Medicine, University of Girona, 17004, Girona, Spain.,Institute of Legal Medicine, University "Magna Graecia" of Catanzaro, 88100, Catanzaro, Italy
| | - Ciro Indolfi
- Division of Cardiology, Department of Medical and Surgical Science, University "Magna Graecia" of Catanzaro, 88100, Catanzaro, Italy
| | - Josep Brugada
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV) 17007, Girona, Spain.,Arrhythmia's Unit, Hospital Clinic, 08036, Barcelona, Spain
| | - Ramon Brugada
- Cardiovascular Genetics Center, Gencardio Institut d'Investigacions Biomèdiques de Girona,, 17290, Girona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV) 17007, Girona, Spain.,Department of Medical Sciences, School of Medicine, University of Girona, 17004, Girona, Spain.,Cardiology Service, Hospital Josep Trueta, 17007, Girona, Spain
| | - Giovanni Cuda
- Laboratory of Proteomics, Research Center of Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100, Catanzaro, Italy
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10
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Cao W, Wei W, Zhan Z, Xie D, Xie Y, Xiao Q. Regulation of drug resistance and metastasis of gastric cancer cells via the microRNA647-ANK2 axis. Int J Mol Med 2018; 41:1958-1966. [PMID: 29328428 PMCID: PMC5810220 DOI: 10.3892/ijmm.2018.3381] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 11/22/2017] [Indexed: 12/11/2022] Open
Abstract
Due to a lack of effective methods for early diagnosis, the majority of patients with gastric cancer (GC) are diagnosed during the late stages of the disease, which are often accompanied by metastasis. For these patients, despite being considered an important therapeutic modality in the treatment of cancer, chemotherapy is usually not effective due to multidrug resistance (MDR). The expression levels of MDR/metastasis-associated genes are regulated by numerous microRNAs (miRNAs/miRs). The expression of miR-647 in GC tissues and SGC7901/VCR cell line (drug resistance to vincristine) was detected by qRT-PCR. The effect of overexpression of miR-647 on drug resistance was evaluated by measuring the half maximal inhibitory concentration (IC50) value of SGC-7901/VCR to vincristine and tumor growth in vivo. Moreover, drug-induced cell apoptosis and cell cycle were evaluated by flow cytometry, as well as the ability of cell migration and invasiveness detected by wound healing and transwell assay. Furthermore, underlying targets of miR-647 were predicted by TargetScan and MicroRNA; meanwhile, the expression of ANK2, FAK, MMP2, MMP12,CD44,SNAIL1 were observed by qRT-PCR and western blot analysis. The present study established that the expression levels of miR-647 were downregulated in GC tissues from patients with metastasis and in the vincristine-resistant SGC7901 (SGC-7901/VCR) GC cell line. The IC50 value for vincristine was significantly decreased, whereas the proportion of cells in G0/G1 phase and the drug-induced apoptotic rate were significantly increased following upregulation of miR-647. Furthermore, the results demonstrated that miR-647 overexpression led to decreased migration and invasion of SGC-7901/VCR cells. Overexpression of miR-647 was also demonstrated to sensitize tumors to chemotherapy in vivo. In addition, miR-647 overexpression was able to reduce the expression levels of ankyrin-B, focal adhesion kinase, matrix metalloproteinase (MMP)2, MMP12, cluster of differentiation 44 and snail family transcriptional repressor 1. In conclusion, these findings demonstrated that miR-647 may function as a novel target to ameliorate drug resistance and metastasis of GC cells.
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Affiliation(s)
- Wenlong Cao
- Department of Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Weiyuan Wei
- Department of Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Zexu Zhan
- Department of Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Dongyi Xie
- Department of Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Yubo Xie
- Department of Anaesthesiology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Qiang Xiao
- Department of Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
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11
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Cao W, Wei W, Zhan Z, Xie D, Xie Y, Xiao Q. Role of miR-647 in human gastric cancer suppression. Oncol Rep 2017; 37:1401-1411. [PMID: 28098914 PMCID: PMC5364874 DOI: 10.3892/or.2017.5383] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 01/03/2017] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) regulate various oncogenes concomitantly, resulting in tumor suppression. They regulate proliferation and migration pathways in tumor development, suggesting a potential therapeutic role. In the present study, we found that miR-647 was markedly downregulated in gastric cancer (GC), and was significantly correlated with reduced tumor size and metastasis. In addition, miR-647 was also reduced in GC cell lines. Furthermore, overexpression of miR-647 in the GC cell lines inhibited cell proliferation, promoted cell cycle arrest at the G0/G1 phase and induced cell apoptosis. miR-647 also significantly inhibited tumor growth in vivo. Notably, we found that miR-647 overexpression suppressed the migration and invasion of the cancer cells, particularly liver metastasis in nude mice. miR-647 also reduced the expression levels of genes associated with proliferation and metastasis in tumors, including ANK2, FAK, MMP2, MMP12, CD44 and SNAIL1. Overall, our findings demonstrated that miR-647 exerts powerful antitumorigenic effects in vitro and in vivo, and may represent a promising therapeutic agent against GC.
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Affiliation(s)
- Wenlong Cao
- Department of Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Weiyuan Wei
- Department of Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Zexu Zhan
- Department of Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Dongyi Xie
- Department of Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Yubo Xie
- Department of Anaesthesiology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Qiang Xiao
- Department of Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
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12
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Ely EE, Guzman MA, Calvey LS, Batanian JR. Masked hypodiploidy in anaplastic meningiomas by duplication of the original clone found in atypical meningiomas: illustration of the evolution of genetic alterations. Neuropathology 2014; 34:353-9. [PMID: 24612240 DOI: 10.1111/neup.12112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 01/23/2014] [Accepted: 01/30/2014] [Indexed: 11/30/2022]
Abstract
Meningiomas are common, usually benign neoplasms of the central nervous system. Atypical and anaplastic meningiomas can be aggressive, show more rapid growth, and a greater propensity to recur following resection. General consensus believes that genetic abnormalities leading to anaplastic transformation are present at initial tumor presentation; however, this has not been demonstrated by array-comparative genome hybridization. We confirm the hypothesis by showing the evolution of genetic alterations in the transformation of an atypical meningioma to an anaplastic meningioma. Additionally, we provide potential genes responsible for malignant transformation of meningiomas, which, with further research, may provide diagnostic and therapeutic implications.
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Affiliation(s)
- Erin E Ely
- Department of Pathology, Saint Louis University, Saint Louis, Missouri, USA
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