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Rai S, Singh MP, Sinha A, Srivastava A, Datta D, Srivastava S. Unravelling a novel CTNND1-RAB6A fusion transcript: Implications in colon cancer cell migration. Int J Biol Macromol 2024; 262:129981. [PMID: 38336316 DOI: 10.1016/j.ijbiomac.2024.129981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 01/22/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024]
Abstract
The interchange of DNA sequences between genes may occur because of chromosomal rearrangements leading to the formation of chimeric genes. These chimeric genes have been linked to various cancers, accumulated significant interest in recent times. We used paired-end RNA-seq. data of four CRC and one normal sample generated from our previous study. The STAR-Fusion pipeline was utilized to identify the fusion genes unique to CRC. The in-silico identified fusion gene(s) were explored for their diagnostic, prognostic and therapeutic biomarker potential using TCGA-datasets, then validated through PCR and DNA sequencing. Further, cell line-based studies were performed to gain functional insights of the novel fusion transcript CTNND1-RAB6A, which was amplified in one sample. Sequencing revealed that there was a total loss of the CTNND1 gene, whereas RAB6A retained its coding sequence. Further, RAB6A was functionally characterized for its oncogenic potential in HCT116 cell line. RAB6A under-expression was found to be significantly associated with increased cell migration and is proposed to be regulated via the RAB6A-ECR1-Liprin-α axis. We conclude that RAB6A gene may play significant role in CRC oncogenesis, and could be used as a potential biomarker and therapeutic target in future for better management of a subset of CRCs harbouring this fusion.
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Affiliation(s)
- Sandhya Rai
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Teliyarganj-Prayagraj, U.P. 211004, India
| | - Manish Pratap Singh
- Department of Zoology, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, (U.P.) 273009, India
| | - Abhipsa Sinha
- Division of cancer biology, CSIR-Central Drug Research Institute, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226031, India
| | - Ankit Srivastava
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Teliyarganj-Prayagraj, U.P. 211004, India
| | - Dipak Datta
- Division of cancer biology, CSIR-Central Drug Research Institute, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226031, India
| | - Sameer Srivastava
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Teliyarganj-Prayagraj, U.P. 211004, India.
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Salamini-Montemurri M, Lamas-Maceiras M, Lorenzo-Catoira L, Vizoso-Vázquez Á, Barreiro-Alonso A, Rodríguez-Belmonte E, Quindós-Varela M, Cerdán ME. Identification of lncRNAs Deregulated in Epithelial Ovarian Cancer Based on a Gene Expression Profiling Meta-Analysis. Int J Mol Sci 2023; 24:10798. [PMID: 37445988 PMCID: PMC10341812 DOI: 10.3390/ijms241310798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/19/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023] Open
Abstract
Epithelial ovarian cancer (EOC) is one of the deadliest gynecological cancers worldwide, mainly because of its initially asymptomatic nature and consequently late diagnosis. Long non-coding RNAs (lncRNA) are non-coding transcripts of more than 200 nucleotides, whose deregulation is involved in pathologies such as EOC, and are therefore envisaged as future biomarkers. We present a meta-analysis of available gene expression profiling (microarray and RNA sequencing) studies from EOC patients to identify lncRNA genes with diagnostic and prognostic value. In this meta-analysis, we include 46 independent cohorts, along with available expression profiling data from EOC cell lines. Differential expression analyses were conducted to identify those lncRNAs that are deregulated in (i) EOC versus healthy ovary tissue, (ii) unfavorable versus more favorable prognosis, (iii) metastatic versus primary tumors, (iv) chemoresistant versus chemosensitive EOC, and (v) correlation to specific histological subtypes of EOC. From the results of this meta-analysis, we established a panel of lncRNAs that are highly correlated with EOC. The panel includes several lncRNAs that are already known and even functionally characterized in EOC, but also lncRNAs that have not been previously correlated with this cancer, and which are discussed in relation to their putative role in EOC and their potential use as clinically relevant tools.
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Affiliation(s)
- Martín Salamini-Montemurri
- Centro Interdisciplinar de Química e Bioloxía (CICA), As Carballeiras, s/n, Campus de Elviña, Universidade da Coruña, 15071 A Coruña, Spain
- Facultade de Ciencias, A Fraga, s/n, Campus de A Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
| | - Mónica Lamas-Maceiras
- Centro Interdisciplinar de Química e Bioloxía (CICA), As Carballeiras, s/n, Campus de Elviña, Universidade da Coruña, 15071 A Coruña, Spain
- Facultade de Ciencias, A Fraga, s/n, Campus de A Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
| | - Lidia Lorenzo-Catoira
- Centro Interdisciplinar de Química e Bioloxía (CICA), As Carballeiras, s/n, Campus de Elviña, Universidade da Coruña, 15071 A Coruña, Spain
- Facultade de Ciencias, A Fraga, s/n, Campus de A Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
| | - Ángel Vizoso-Vázquez
- Centro Interdisciplinar de Química e Bioloxía (CICA), As Carballeiras, s/n, Campus de Elviña, Universidade da Coruña, 15071 A Coruña, Spain
- Facultade de Ciencias, A Fraga, s/n, Campus de A Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
| | - Aida Barreiro-Alonso
- Centro Interdisciplinar de Química e Bioloxía (CICA), As Carballeiras, s/n, Campus de Elviña, Universidade da Coruña, 15071 A Coruña, Spain
- Facultade de Ciencias, A Fraga, s/n, Campus de A Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
| | - Esther Rodríguez-Belmonte
- Centro Interdisciplinar de Química e Bioloxía (CICA), As Carballeiras, s/n, Campus de Elviña, Universidade da Coruña, 15071 A Coruña, Spain
- Facultade de Ciencias, A Fraga, s/n, Campus de A Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
| | - María Quindós-Varela
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
- Complexo Hospitalario Universitario de A Coruña (CHUAC), Servizo Galego de Saúde (SERGAS), 15006 A Coruña, Spain
| | - M Esperanza Cerdán
- Centro Interdisciplinar de Química e Bioloxía (CICA), As Carballeiras, s/n, Campus de Elviña, Universidade da Coruña, 15071 A Coruña, Spain
- Facultade de Ciencias, A Fraga, s/n, Campus de A Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
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Melone V, Salvati A, Palumbo D, Giurato G, Nassa G, Rizzo F, Palo L, Giordano A, Incoronato M, Vitale M, Mian C, Di Biase I, Cristiano S, Narciso V, Cantile M, Di Mauro A, Tatangelo F, Tafuto S, Modica R, Pivonello C, Salvatore M, Colao A, Weisz A, Tarallo R. Identification of functional pathways and molecular signatures in neuroendocrine neoplasms by multi-omics analysis. J Transl Med 2022; 20:306. [PMID: 35794609 PMCID: PMC9258165 DOI: 10.1186/s12967-022-03511-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 06/28/2022] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Neuroendocrine neoplasms (NENs) represent a heterogeneous class of rare tumors with increasing incidence. They are characterized by the ability to secrete peptide hormones and biogenic amines but other reliable biomarkers are lacking, making diagnosis and identification of the primary site very challenging. While in some NENs, such as the pancreatic ones, next generation sequencing technologies allowed the identification of new molecular hallmarks, our knowledge of the molecular profile of NENs from other anatomical sites is still poor. METHODS Starting from the concept that NENs from different organs may be clinically and genetically correlated, we applied a multi-omics approach by combining multigene panel testing, CGH-array, transcriptome and miRNome profiling and computational analyses, with the aim to highlight common molecular and functional signatures of gastroenteropancreatic (GEP)-NENs and medullary thyroid carcinomas (MTCs) that could aid diagnosis, prognosis and therapy. RESULTS By comparing genomic and transcriptional profiles, ATM-dependent signaling emerged among the most significant pathways at multiple levels, involving gene variations and miRNA-mediated regulation, thus representing a novel putative druggable pathway in these cancer types. Moreover, a set of circulating miRNAs was also selected as possible diagnostic/prognostic biomarkers useful for clinical management of NENs. CONCLUSIONS These findings depict a complex molecular and functional landscape of NENs, shedding light on novel therapeutic targets and disease biomarkers to be exploited.
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Affiliation(s)
- Viola Melone
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, via S. Allende, 84081, Baronissi, SA, Italy
| | - Annamaria Salvati
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, via S. Allende, 84081, Baronissi, SA, Italy
- Medical Genomics Program and Division of Oncology, AOU 'S. Giovanni di Dio e Ruggi d'Aragona' University of Salerno, Rete Oncologica Campana, 84131, Salerno, Italy
| | - Domenico Palumbo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, via S. Allende, 84081, Baronissi, SA, Italy
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, via S. Allende, 84081, Baronissi, SA, Italy
- Medical Genomics Program and Division of Oncology, AOU 'S. Giovanni di Dio e Ruggi d'Aragona' University of Salerno, Rete Oncologica Campana, 84131, Salerno, Italy
- Genome Research Center for Health, 84081, Baronissi, SA, Italy
| | - Giovanni Nassa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, via S. Allende, 84081, Baronissi, SA, Italy
- Medical Genomics Program and Division of Oncology, AOU 'S. Giovanni di Dio e Ruggi d'Aragona' University of Salerno, Rete Oncologica Campana, 84131, Salerno, Italy
- Genome Research Center for Health, 84081, Baronissi, SA, Italy
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, via S. Allende, 84081, Baronissi, SA, Italy
- Medical Genomics Program and Division of Oncology, AOU 'S. Giovanni di Dio e Ruggi d'Aragona' University of Salerno, Rete Oncologica Campana, 84131, Salerno, Italy
- Genome Research Center for Health, 84081, Baronissi, SA, Italy
| | - Luigi Palo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, via S. Allende, 84081, Baronissi, SA, Italy
| | - Alessandro Giordano
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, via S. Allende, 84081, Baronissi, SA, Italy
| | | | - Mario Vitale
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, SA, Italy
| | - Caterina Mian
- Endocrinology Unit, Department of Medicine (DIMED), University of Padua, Padua, Italy
| | - Immacolata Di Biase
- MeriGen Diagnostic & c sas, traversa M. Pietravalle 11, 80131, Naples, Italy
| | - Stefano Cristiano
- MeriGen Diagnostic & c sas, traversa M. Pietravalle 11, 80131, Naples, Italy
| | - Viviana Narciso
- MeriGen Diagnostic & c sas, traversa M. Pietravalle 11, 80131, Naples, Italy
| | - Monica Cantile
- Pathology Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Via Mariano Semmola, 80131, Naples, Italy
| | - Annabella Di Mauro
- Pathology Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Via Mariano Semmola, 80131, Naples, Italy
| | - Fabiana Tatangelo
- Pathology Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Via Mariano Semmola, 80131, Naples, Italy
| | - Salvatore Tafuto
- Sarcomas and Rare Tumors Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Via Mariano Semmola, 80131, Naples, Italy
| | - Roberta Modica
- Department of Clinical Medicine and Surgery, Endocrinology Unit, Federico II University, Naples, Italy
| | - Claudia Pivonello
- Department of Clinical Medicine and Surgery, Endocrinology Unit, Federico II University, Naples, Italy
| | - Marco Salvatore
- IRCCS Synlab SDN s.p.a, Via Gianturco 113, 80143, Naples, Italy
| | - Annamaria Colao
- Department of Clinical Medicine and Surgery, Endocrinology Unit, Federico II University, Naples, Italy
- UNESCO Chair for Health Education and Sustainable Development, Federico II University, Naples, Italy
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, via S. Allende, 84081, Baronissi, SA, Italy.
- Medical Genomics Program and Division of Oncology, AOU 'S. Giovanni di Dio e Ruggi d'Aragona' University of Salerno, Rete Oncologica Campana, 84131, Salerno, Italy.
- Genome Research Center for Health, 84081, Baronissi, SA, Italy.
| | - Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, via S. Allende, 84081, Baronissi, SA, Italy.
- Medical Genomics Program and Division of Oncology, AOU 'S. Giovanni di Dio e Ruggi d'Aragona' University of Salerno, Rete Oncologica Campana, 84131, Salerno, Italy.
- Genome Research Center for Health, 84081, Baronissi, SA, Italy.
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