1
|
Vieira IA, Viola GD, Pezzi EH, Kowalski TW, Fernandes BV, Andreis TF, Bom N, Sonnenstrahl G, Rocha YMDA, Corrêa BDS, Donatti LM, Sant’Anna GDS, Corleta HVE, Brum IS, Rosset C, Vianna FSL, Macedo GS, Palmero EI, Ashton-Prolla P. Exploring the frequency of a TP53 polyadenylation signal variant in tumor DNA from patients diagnosed with lung adenocarcinomas, sarcomas and uterine leiomyomas. Genet Mol Biol 2024; 46:e20230133. [PMID: 38252059 PMCID: PMC10802224 DOI: 10.1590/1678-4685-gmb-2023-0133] [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: 05/19/2023] [Accepted: 11/16/2023] [Indexed: 01/23/2024] Open
Abstract
The TP53 3'UTR variant rs78378222 A>C has been detected in different tumor types as a somatic alteration that reduces p53 expression through modification of polyadenylation and miRNA regulation. Its prevalence is not yet known in all tumors. Herein, we examine tumor tissue prevalence of rs7837822 in Brazilian cohorts of patients from south and southeast regions diagnosed with lung adenocarcinoma (LUAD, n=586), sarcoma (SARC, n=188) and uterine leiomyoma (ULM, n=41). The minor allele (C) was identified in heterozygosity in 6/586 LUAD tumors (prevalence = 1.02 %) and none of the SARC and ULM samples. Additionally, next generation sequencing analysis revealed that all variant-positive tumors (n=4) with sample availability had additional pathogenic or likely pathogenic somatic variants in the TP53 coding regions. Among them, 3/4 (75 %) had the same pathogenic or likely pathogenic sequence variant (allele frequency <0.05 in tumor DNA) namely c.751A>C (p.Ile251Leu). Our results indicate a low somatic prevalence of rs78378222 in LUAD, ULM and SARC tumors from Brazilian patients, which suggests that no further analysis of this variant in the specific studied regions of Brazil is warranted. However, these findings should not exclude tumor molecular testing of this TP53 3'UTR functional variant for different populations.
Collapse
Affiliation(s)
- Igor Araujo Vieira
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade do Vale do Rio dos Sinos (UNISINOS), Escola de Saúde, São Leopoldo, RS, Brazil
| | - Guilherme Danielski Viola
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
| | - Eduarda Heidrich Pezzi
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
| | - Thayne Woycinck Kowalski
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul (UFRGS), Laboratório de Genética Médica e Populacional, Porto Alegre, RS, Brazil
- Instituto Nacional de Genética Médica Populacional (INAGEMP), Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Serviço de Genética Médica, Sistema Nacional de Informações sobre Agentes Teratogênicos (SIAT), Porto Alegre, RS, Brazil
- Complexo de Ensino Superior de Cachoeirinha (CESUCA), Cachoeirinha, RS, Brazil
| | - Bruna Vieira Fernandes
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
| | - Tiago Finger Andreis
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
| | - Natascha Bom
- Universidade do Vale do Rio dos Sinos (UNISINOS), Curso de Graduação em Biomedicina, São Leopoldo, RS, Brazil
| | - Giulianna Sonnenstrahl
- Universidade do Vale do Rio dos Sinos (UNISINOS), Curso de Graduação em Biomedicina, São Leopoldo, RS, Brazil
| | - Yasminne Marinho de Araújo Rocha
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
| | - Bruno da Silveira Corrêa
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
| | - Luiza Mezzomo Donatti
- Universidade Federal do Rio Grande do Sul, Instituto de Ciências Básicas da Saúde, Departamento de Fisiologia, Laboratório de Biologia Molecular Endócrino e Tumoral, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Ciências Biológicas: Fisiologia, Porto Alegre, RS, Brazil
| | - Gabriela dos Santos Sant’Anna
- Universidade Federal do Rio Grande do Sul, Instituto de Ciências Básicas da Saúde, Departamento de Fisiologia, Laboratório de Biologia Molecular Endócrino e Tumoral, Porto Alegre, RS, Brazil
| | - Helena von Eye Corleta
- Universidade Federal do Rio Grande do Sul, Instituto de Ciências Básicas da Saúde, Departamento de Fisiologia, Laboratório de Biologia Molecular Endócrino e Tumoral, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Serviço de Ginecologia e Obstetrícia, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Departamento de Ginecologia e Obstetrícia, Porto Alegre, RS, Brazil
| | - Ilma Simoni Brum
- Universidade Federal do Rio Grande do Sul, Instituto de Ciências Básicas da Saúde, Departamento de Fisiologia, Laboratório de Biologia Molecular Endócrino e Tumoral, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Ciências Biológicas: Fisiologia, Porto Alegre, RS, Brazil
| | - Clévia Rosset
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul (UFRGS), Programa de Pós-Graduação em Ciências Médicas: Medicina (PPGCM), Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Unidade de Pesquisa Laboratorial (UPL), Porto Alegre, RS, Brazil
| | - Fernanda Sales Luiz Vianna
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul (UFRGS), Laboratório de Genética Médica e Populacional, Porto Alegre, RS, Brazil
- Instituto Nacional de Genética Médica Populacional (INAGEMP), Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Serviço de Genética Médica, Sistema Nacional de Informações sobre Agentes Teratogênicos (SIAT), Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul (UFRGS), Programa de Pós-Graduação em Ciências Médicas: Medicina (PPGCM), Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Imunobiologia e Imunogenética, Porto Alegre, RS, Brazil
| | - Gabriel S. Macedo
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Programa de Medicina Personalizada, Porto Alegre, RS, Brazil
| | - Edenir Inez Palmero
- Instituto Nacional de Câncer (INCA), Departamento de Genética, Rio de Janeiro, RJ, Brazil
- Hospital de Câncer de Barretos, Centro de Pesquisa em Oncologia Molecular, Barretos, SP, Brazil
| | - Patricia Ashton-Prolla
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul (UFRGS), Programa de Pós-Graduação em Ciências Médicas: Medicina (PPGCM), Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Programa de Medicina Personalizada, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Serviço de Genética Médica, Porto Alegre, RS, Brazil
| |
Collapse
|
2
|
Erdem M, Cicek M, Erson-Bensan AE. Versatile RNA: overlooked gems of the transcriptome. FEBS J 2023; 290:4843-4851. [PMID: 36719259 DOI: 10.1111/febs.16742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/16/2023] [Accepted: 01/30/2023] [Indexed: 02/01/2023]
Abstract
The critical role of RNA, its use and targetability concerning different aspects of human health are gaining more attention because our understanding of the versatility of RNA has dramatically evolved over the last decades. We now appreciate that RNA is far more critical than a messenger molecule and possesses many complicated functions. As a multifunctional molecule with its sequence, flexible structures and enzymatic abilities, RNA is genuinely powerful. Mammalian transcriptomes consist of a dynamically regulated plethora of coding and noncoding RNA types. However, some aspects of RNA metabolism remain to be explored. In this Viewpoint, we focus on the transcriptome's unconventional and possibly overlooked aspects to emphasize the importance of RNA in mammalian systems.
Collapse
Affiliation(s)
- Murat Erdem
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Mustafa Cicek
- Department of Biology, Kamil Ozdag Faculty of Science, Karamanoglu Mehmetbey University, Karaman, Turkey
| | | |
Collapse
|
3
|
Dioken DN, Ozgul I, Koksal Bicakci G, Gol K, Can T, Erson-Bensan AE. Differential expression of mRNA 3'-end isoforms in cervical and ovarian cancers. Heliyon 2023; 9:e20035. [PMID: 37810050 PMCID: PMC10559779 DOI: 10.1016/j.heliyon.2023.e20035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 07/26/2023] [Accepted: 09/08/2023] [Indexed: 10/10/2023] Open
Abstract
Early diagnosis and therapeutic targeting are continuing challenges for gynecological cancers. Here, we focus on cancer transcriptomes and describe the differential expression of 3'UTR isoforms in patients using an algorithm to detect differential poly(A) site usage. We find primarily 3'UTR shortening cases in cervical cancers compared with the normal cervix. We show differential expression of alternate 3'-end isoforms of FOXP1, VPS4B, and OGT in HPV16-positive patients who develop high-grade cervical lesions compared with the infected but non-progressing group. In contrast, in ovarian cancers, 3'UTR lengthening is more evident compared with normal ovary tissue. Nevertheless, highly malignant ovarian tumors have unique 3'UTR shortening events (e.g., CHRAC1, SLC16A1, and TOP2A), some of which correlate with upregulated protein levels in tumors. Overall, our study shows isoform level deregulation in gynecological cancers and highlights the complexity of the transcriptome. This transcript diversity could help identify novel cancer genes and provide new possibilities for diagnosis and therapy.
Collapse
Affiliation(s)
- Didem Naz Dioken
- Department of Biological Sciences, Middle East Technical University (METU), Dumlupinar Blv No: 1 Universiteler Mah., Cankaya, Ankara, 06800, Turkiye
| | - Ibrahim Ozgul
- Department of Biological Sciences, Middle East Technical University (METU), Dumlupinar Blv No: 1 Universiteler Mah., Cankaya, Ankara, 06800, Turkiye
| | - Gozde Koksal Bicakci
- Department of Biological Sciences, Middle East Technical University (METU), Dumlupinar Blv No: 1 Universiteler Mah., Cankaya, Ankara, 06800, Turkiye
| | - Kemal Gol
- Gynecology Clinic, Ugur Mumcu Cad 17/2, Cankaya, Ankara, Turkiye
| | - Tolga Can
- Department of Computer Engineering, Middle East Technical University (METU), Dumlupinar Blv No: 1, Universiteler Mah., Ankara, 06800, Turkiye
| | - Ayse Elif Erson-Bensan
- Department of Biological Sciences, Middle East Technical University (METU), Dumlupinar Blv No: 1 Universiteler Mah., Cankaya, Ankara, 06800, Turkiye
| |
Collapse
|
4
|
Chen Z, Pi H, Zheng W, Guo X, Shi C, Wang Z, Zhang J, Qu X, Liu L, Shen H, Lu Y, Chen M, Zhang W, Sun R, Fan Y. The 3' Non-Coding Sequence Negatively Regulates PD-L1 Expression, and Its Regulators Are Systematically Identified in Pan-Cancer. Genes (Basel) 2023; 14:1620. [PMID: 37628671 PMCID: PMC10454350 DOI: 10.3390/genes14081620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
The 3'-untranslated region (3'-UTR) of PD-L1 is significantly longer than the coding sequences (CDSs). However, its role and regulators have been little studied. We deleted whole 3'-UTR region by CRISPR-Cas9. Prognostic analysis was performed using online tools. Immune infiltration analysis was performed using the Timer and Xcell packages. Immunotherapy response prediction and Cox regression was performed using the R software. MicroRNA network analysis was conducted by the Cytoscape software. The level of PD-L1 was significantly and dramatically up-regulated in cells after deleting the 3'-UTR. Additionally, we discovered a panel of 43 RNA-binding proteins (RBPs) whose expression correlates with PD-L1 in the majority of cancer cell lines and tumor tissues. Among these RBPs, PARP14 is widely associated with immune checkpoints, the tumor microenvironment, and immune-infiltrating cells in various cancer types. We also identified 38 microRNAs whose individual expressions are associated with PD-L1 across different cancers. Notably, miR-3139, miR-4761, and miR-15a-5p showed significant associations with PD-L1 in most cancer types. Furthermore, we revealed 21 m6A regulators that strongly correlate with PD-L1. Importantly, by combining the identified RBP and m6A regulators, we established an immune signature consisting of RBMS1, QKI, ZC3HAV1, and RBM38. This signature can be used to predict the responsiveness of cancer patients to immune checkpoint blockade treatment. We demonstrated the critical role of the 3'-UTR in the regulation of PD-L1 and identified a significant number of potential PD-L1 regulators across various types of cancer. The biomarker signature generated from our findings shows promise in predicting patient prognosis. However, further biological investigation is necessary to explore the potential of these PD-L1 regulators.
Collapse
Affiliation(s)
- Zike Chen
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong 226001, China; (Z.C.); (Z.W.); (J.Z.); (X.Q.); (L.L.); (M.C.)
| | - Hui Pi
- Department of Pathophysiology, School of Medicine, Nantong University, Nantong 226001, China;
| | - Wen Zheng
- Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong 226001, China; (W.Z.); (X.G.); (C.S.)
| | - Xiaohong Guo
- Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong 226001, China; (W.Z.); (X.G.); (C.S.)
| | - Conglin Shi
- Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong 226001, China; (W.Z.); (X.G.); (C.S.)
| | - Zhiyang Wang
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong 226001, China; (Z.C.); (Z.W.); (J.Z.); (X.Q.); (L.L.); (M.C.)
| | - Jie Zhang
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong 226001, China; (Z.C.); (Z.W.); (J.Z.); (X.Q.); (L.L.); (M.C.)
| | - Xuanhao Qu
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong 226001, China; (Z.C.); (Z.W.); (J.Z.); (X.Q.); (L.L.); (M.C.)
| | - Lehan Liu
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong 226001, China; (Z.C.); (Z.W.); (J.Z.); (X.Q.); (L.L.); (M.C.)
| | - Haoliang Shen
- The Intensive Care Unit, Affiliated Hospital of Nantong University, Nantong 226001, China; (H.S.); (Y.L.)
| | - Yang Lu
- The Intensive Care Unit, Affiliated Hospital of Nantong University, Nantong 226001, China; (H.S.); (Y.L.)
| | - Miaomiao Chen
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong 226001, China; (Z.C.); (Z.W.); (J.Z.); (X.Q.); (L.L.); (M.C.)
| | - Weibing Zhang
- Nantong Center for Disease Control and Prevention, Nantong 226001, China;
| | - Rong Sun
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong 226001, China; (Z.C.); (Z.W.); (J.Z.); (X.Q.); (L.L.); (M.C.)
| | - Yihui Fan
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong 226001, China; (Z.C.); (Z.W.); (J.Z.); (X.Q.); (L.L.); (M.C.)
- Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong 226001, China; (W.Z.); (X.G.); (C.S.)
| |
Collapse
|
5
|
De Paolo R, Sarti S, Bernardi S, Cucco F, Tavosanis A, Pitto L, Poliseno L. Differential impact of BRAFV600E isoforms on tumorigenesis in a zebrafish model of melanoma. Cell Biosci 2023; 13:121. [PMID: 37393328 DOI: 10.1186/s13578-023-01064-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 06/05/2023] [Indexed: 07/03/2023] Open
Abstract
BRAFV600E comes as two main splicing variants. The well-studied ref isoform and the recently discovered X1 isoform are co-expressed in cancer cells and differ in terms of 3'UTR length and sequence, as well as C-term protein sequence. Here, we use a melanoma model in zebrafish to study the role played by each isoform in larval pigmentation, nevi formation, and their progression into melanoma tumours. We show that both BRAFV600E-ref and BRAFV600E-X1 proteins promote larval pigmentation and nevi formation, while melanoma-free survival curves performed in adult fish indicate that BRAFV600E-ref protein is a much stronger melanoma driver that BRAFV600E-X1 protein. Crucially, we also show that the presence of the 3'UTR suppresses the effect of ref protein. Our data highlight the necessity to undertake a systematic study of BRAFV600E isoforms, in order to uncover the full spectrum of their kinase-(in)dependent and coding-(in)dependent functions, hence to develop more informed strategies for therapeutic targeting.
Collapse
Affiliation(s)
- Raffaella De Paolo
- Institute of Clinical Physiology, CNR, Pisa, Italy
- Oncogenomics Unit, Core Research Laboratory (CRL), ISPRO, Via Moruzzi 1, 56124, Pisa, Italy
| | - Samanta Sarti
- Institute of Clinical Physiology, CNR, Pisa, Italy
- Oncogenomics Unit, Core Research Laboratory (CRL), ISPRO, Via Moruzzi 1, 56124, Pisa, Italy
- Department of Radiation Oncology, Columbia University Irving Medical Center, New York, USA
| | - Sara Bernardi
- Institute of Clinical Physiology, CNR, Pisa, Italy
- Oncogenomics Unit, Core Research Laboratory (CRL), ISPRO, Via Moruzzi 1, 56124, Pisa, Italy
- Department of Molecular Medicine and Neurobiology, IRCCS Fondazione Stella Maris, Pisa, Italy
| | | | - Andrea Tavosanis
- Institute of Clinical Physiology, CNR, Pisa, Italy
- Oncogenomics Unit, Core Research Laboratory (CRL), ISPRO, Via Moruzzi 1, 56124, Pisa, Italy
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Laura Poliseno
- Institute of Clinical Physiology, CNR, Pisa, Italy.
- Oncogenomics Unit, Core Research Laboratory (CRL), ISPRO, Via Moruzzi 1, 56124, Pisa, Italy.
| |
Collapse
|
6
|
Marranci A, Prantera A, Masotti S, De Paolo R, Baldanzi C, Podda MS, Mero S, Vitiello M, Franchin C, Laezza M, Comelli L, Arrigoni G, Cervelli T, Del Pozzo G, Poliseno L. PARP1 negatively regulates MAPK signaling by impairing BRAF-X1 translation. J Hematol Oncol 2023; 16:33. [PMID: 37013641 PMCID: PMC10071733 DOI: 10.1186/s13045-023-01428-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/17/2023] [Indexed: 04/05/2023] Open
Abstract
In human cells BRAF oncogene is invariably expressed as a mix of two coding transcripts: BRAF-ref and BRAF-X1. These two mRNA isoforms, remarkably different in the sequence and length of their 3'UTRs, are potentially involved in distinct post-transcriptional regulatory circuits. Herein, we identify PARP1 among the mRNA Binding Proteins that specifically target the X1 3'UTR in melanoma cells. Mechanistically, PARP1 Zinc Finger domain down-regulates BRAF expression at the translational level. As a consequence, it exerts a negative impact on MAPK pathway, and sensitizes melanoma cells to BRAF and MEK inhibitors, both in vitro and in vivo. In summary, our study unveils PARP1 as a negative regulator of the highly oncogenic MAPK pathway in melanoma, through the modulation of BRAF-X1 expression.
Collapse
Affiliation(s)
- Andrea Marranci
- Institute of Clinical Physiology (IFC), CNR, Via Moruzzi 1, 56124, Pisa, Italy.
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Via Moruzzi 1, 56124, Pisa, Italy.
- Fondazione Pisana per la Scienza ONLUS, 56017, Pisa, Italy.
| | - Antonella Prantera
- Institute of Clinical Physiology (IFC), CNR, Via Moruzzi 1, 56124, Pisa, Italy
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Via Moruzzi 1, 56124, Pisa, Italy
- University of Siena, Siena, Italy
| | - Simona Masotti
- Institute of Clinical Physiology (IFC), CNR, Via Moruzzi 1, 56124, Pisa, Italy
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Via Moruzzi 1, 56124, Pisa, Italy
| | - Raffaella De Paolo
- Institute of Clinical Physiology (IFC), CNR, Via Moruzzi 1, 56124, Pisa, Italy
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Via Moruzzi 1, 56124, Pisa, Italy
- University of Siena, Siena, Italy
| | - Caterina Baldanzi
- Institute of Clinical Physiology (IFC), CNR, Via Moruzzi 1, 56124, Pisa, Italy
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Via Moruzzi 1, 56124, Pisa, Italy
- University of Siena, Siena, Italy
| | - Maurizio S Podda
- Institute of Clinical Physiology (IFC), CNR, Via Moruzzi 1, 56124, Pisa, Italy
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Via Moruzzi 1, 56124, Pisa, Italy
- University of Siena, Siena, Italy
| | - Serena Mero
- Institute of Clinical Physiology (IFC), CNR, Via Moruzzi 1, 56124, Pisa, Italy
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Via Moruzzi 1, 56124, Pisa, Italy
- Molecular Medicine and Neurobiology, IRCCS Fondazione Stella Maris, 56128, Pisa, Italy
| | - Marianna Vitiello
- Institute of Clinical Physiology (IFC), CNR, Via Moruzzi 1, 56124, Pisa, Italy
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Via Moruzzi 1, 56124, Pisa, Italy
- Genetics, Department of Biology, University of Pisa, 56126, Pisa, Italy
| | - Cinzia Franchin
- Department of Biomedical Sciences, University of Padova, Padua, Italy
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, Padua, Italy
| | - Mariavittoria Laezza
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso", CNR, Naples, Italy
| | - Laura Comelli
- Institute of Clinical Physiology (IFC), CNR, Via Moruzzi 1, 56124, Pisa, Italy
| | - Giorgio Arrigoni
- Department of Biomedical Sciences, University of Padova, Padua, Italy
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, Padua, Italy
| | - Tiziana Cervelli
- Institute of Clinical Physiology (IFC), CNR, Via Moruzzi 1, 56124, Pisa, Italy
| | - Giovanna Del Pozzo
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso", CNR, Naples, Italy
| | - Laura Poliseno
- Institute of Clinical Physiology (IFC), CNR, Via Moruzzi 1, 56124, Pisa, Italy.
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Via Moruzzi 1, 56124, Pisa, Italy.
| |
Collapse
|
7
|
Khan AA, Kim N, Korstanje R, Choi S. Loss-of-function mutation in Pcsk1 increases serum APOA1 level and LCAT activity in mice. Lab Anim Res 2022; 38:1. [PMID: 34996527 PMCID: PMC8739671 DOI: 10.1186/s42826-021-00111-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/29/2021] [Indexed: 01/20/2023] Open
Abstract
Background The convertase subtilisin/kexin family 1 gene (PCSK1) has been associated in various human genetics studies with a wide spectrum of metabolic phenotypes, including early-onset obesity, hyperphagia, diabetes insipidus, and others. Despite the evident influence of PCSK1 on obesity and the known functions of other PCSKs in lipid metabolism, the role of PCSK1 specifically in lipid and cholesterol metabolism remains unclear. This study evaluated the effect of loss of PCSK1 function on high-density lipoprotein (HDL) metabolism in mice. Results HDL cholesterol, apolipoprotein A1 (APOA1) levels in serum and liver, and the activities of two enzymes (lecithin-cholesterol acyltransferase, LCAT and phospholipid transfer protein, PLTP) were evaluated in 8-week-old mice with a non-synonymous single nucleotide mutation leading to an amino acid substitution in PCSK1, which results in a loss of protein’s function. Mutant mice had similar serum HDL cholesterol concentration but increased levels of serum total and mature APOA1, and LCAT activity in comparison to controls. Conclusions This study presents the first evaluation of the role of PCSK1 in HDL metabolism using a loss-of-function mutant mouse model. Further investigations will be needed to determine the underlying molecular mechanism.
Collapse
Affiliation(s)
| | - Nakyung Kim
- Cerebrovascular Haematology-Immunology Priority Research Center, Medical Science Research Institute, Dongguk University Ilsan Hospital, Goyang, 10326, Republic of Korea
| | - Ron Korstanje
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Seungbum Choi
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA. .,Cerebrovascular Haematology-Immunology Priority Research Center, Medical Science Research Institute, Dongguk University Ilsan Hospital, Goyang, 10326, Republic of Korea.
| |
Collapse
|
8
|
Erdem M, Ozgul İ, Dioken DN, Gurcuoglu I, Guntekin Ergun S, Cetin-Atalay R, Can T, Erson-Bensan AE. Identification of an mRNA isoform switch for HNRNPA1 in breast cancers. Sci Rep 2021; 11:24444. [PMID: 34961772 PMCID: PMC8712528 DOI: 10.1038/s41598-021-04007-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 12/06/2021] [Indexed: 12/02/2022] Open
Abstract
Roles of HNRNPA1 are beginning to emerge in cancers; however, mechanisms causing deregulation of HNRNPA1 function remain elusive. Here, we describe an isoform switch between the 3'-UTR isoforms of HNRNPA1 in breast cancers. We show that the dominantly expressed isoform in mammary tissue has a short half-life. In breast cancers, this isoform is downregulated in favor of a stable isoform. The stable isoform is expressed more in breast cancers, and more HNRNPA1 protein is synthesized from this isoform. High HNRNPA1 protein levels correlate with poor survival in patients. In support of this, silencing of HNRNPA1 causes a reversal in neoplastic phenotypes, including proliferation, clonogenic potential, migration, and invasion. In addition, silencing of HNRNPA1 results in the downregulation of microRNAs that map to intragenic regions. Among these miRNAs, miR-21 is known for its transcriptional upregulation in breast and numerous other cancers. Altogether, the cancer-specific isoform switch we describe here for HNRNPA1 emphasizes the need to study gene expression at the isoform level in cancers to identify novel cases of oncogene activation.
Collapse
Affiliation(s)
- Murat Erdem
- Department of Biological Sciences, Middle East Technical University (METU), Dumlupinar Blv No: 1 Universiteler Mah., Cankaya, Ankara, 06800, Turkey
| | - İbrahim Ozgul
- Department of Biological Sciences, Middle East Technical University (METU), Dumlupinar Blv No: 1 Universiteler Mah., Cankaya, Ankara, 06800, Turkey
| | - Didem Naz Dioken
- Department of Biological Sciences, Middle East Technical University (METU), Dumlupinar Blv No: 1 Universiteler Mah., Cankaya, Ankara, 06800, Turkey
| | - Irmak Gurcuoglu
- Department of Biological Sciences, Middle East Technical University (METU), Dumlupinar Blv No: 1 Universiteler Mah., Cankaya, Ankara, 06800, Turkey
| | - Sezen Guntekin Ergun
- Cancer Systems Biology Laboratory, CanSyL, Graduate School of Informatics, Middle East Technical University, 06800, Ankara, Turkey
- Department of Medical Biology, Hacettepe University, Ankara, Turkey
| | - Rengul Cetin-Atalay
- Cancer Systems Biology Laboratory, CanSyL, Graduate School of Informatics, Middle East Technical University, 06800, Ankara, Turkey
| | - Tolga Can
- Cancer Systems Biology Laboratory, CanSyL, Graduate School of Informatics, Middle East Technical University, 06800, Ankara, Turkey
- Department of Computer Engineering, Middle East Technical University (METU), Dumlupinar Blv No: 1 Universiteler Mah, Ankara, 06800, Turkey
| | - Ayse Elif Erson-Bensan
- Department of Biological Sciences, Middle East Technical University (METU), Dumlupinar Blv No: 1 Universiteler Mah., Cankaya, Ankara, 06800, Turkey.
- Cancer Systems Biology Laboratory, CanSyL, Graduate School of Informatics, Middle East Technical University, 06800, Ankara, Turkey.
| |
Collapse
|
9
|
Double-Stranded RNA Structural Elements Holding the Key to Translational Regulation in Cancer: The Case of Editing in RNA-Binding Motif Protein 8A. Cells 2021; 10:cells10123543. [PMID: 34944051 PMCID: PMC8699885 DOI: 10.3390/cells10123543] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/08/2021] [Accepted: 12/13/2021] [Indexed: 12/30/2022] Open
Abstract
Mesothelioma is an aggressive cancer associated with asbestos exposure. RNA-binding motif protein 8a (RBM8A) mRNA editing increases in mouse tissues upon asbestos exposure. The aim of this study was to further characterize the role of RBM8A in mesothelioma and the consequences of its mRNA editing. RBM8A protein expression was higher in mesothelioma compared to mesothelial cells. Silencing RBM8A changed splicing patterns in mesothelial and mesothelioma cells but drastically reduced viability only in mesothelioma cells. In the tissues of asbestos-exposed mice, editing of Rbm8a mRNA was associated with increased protein immunoreactivity, with no change in mRNA levels. Increased adenosine deaminase acting on dsRNA (ADAR)-dependent editing of Alu elements in the RBM8A 3′UTR was observed in mesothelioma cells compared to mesothelial cells. Editing stabilized protein expression. The unedited RBM8A 3′UTR had a stronger interaction with Musashi (MSI) compared to the edited form. The silencing of MSI2 in mesothelioma or overexpression of Adar2 in mesothelial cells resulted in increased RBM8A protein levels. Therefore, ADAR-dependent editing contributes to maintaining elevated RBM8A protein levels in mesothelioma by counteracting MSI2-driven downregulation. A wider implication of this mechanism for the translational control of protein expression is suggested by the editing of similarly structured Alu elements in several other transcripts.
Collapse
|
10
|
Circir A, Koksal Bicakci G, Savas B, Doken DN, Henden ŞO, Can T, Karaca E, Erson-Bensan AE. A C-term truncated EIF2Bγ protein encoded by an intronically polyadenylated isoform introduces unfavorable EIF2Bγ-EIF2γ interactions. Proteins 2021; 90:889-897. [PMID: 34796993 DOI: 10.1002/prot.26284] [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: 08/16/2021] [Revised: 11/01/2021] [Accepted: 11/15/2021] [Indexed: 11/11/2022]
Abstract
Eukaryotic translation initiates upon recruitment of the EIF2-GTP·Met-tRNAi ternary complex (TC) to the ribosomes. EIF2 (α, β, γ subunits) is a GTPase. The GDP to GTP exchange within EIF2 is facilitated by the guanine nucleotide exchange factor EIF2B (α-ε subunits). During stress-induced conditions, phosphorylation of the α-subunit of EIF2 turns EIF2 into an inhibitor of EIF2B. In turn, inhibition of EIF2B decreases TC formation and triggers the internal stress response (ISR), which determines the cell fate. Deregulated ISR has been linked to neurodegenerative disorders and cancer, positioning EIF2B as a promising therapeutic target. Hence, a better understanding of the mechanisms/factors that regulate EIF2B activity is required. Here, combining transcript and protein level analyses, we describe an intronically polyadenylated (IPA) transcript of EIF2B's γ-subunit. We show that the IPA mRNA isoform is translated into a C-terminus truncated protein. Using structural modeling, we predict that the truncated EIF2Bγ protein has unfavorable interactions with EIF2γ, leading to a potential decrease in the stability of the nonproductive EIF2:EIF2B complex. While we discovered and confirmed the IPA mRNA isoform in breast cancer cells, the expression of this isoform is not cancer-specific and is widely present in normal tissues. Overall, our data show that a truncated EIF2Bγ protein co-exists with the canonical protein and is an additional player to regulate the equilibrium between productive and nonproductive states of the EIF2:EIF2B complex. These results may have implications in stress-induced translation control in normal and disease states. Our combinatorial approach demonstrates the need to study noncanonical mRNA and protein isoforms to understand protein interactions and intricate molecular mechanisms.
Collapse
Affiliation(s)
- Ayca Circir
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Gozde Koksal Bicakci
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Busra Savas
- Izmir Biomedicine and Genome Center, Balcova, Izmir, Turkey.,Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Balcova, Izmir, Turkey
| | - Didem Naz Doken
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Şevki Onur Henden
- Department of Computer Engineering, Middle East Technical University (METU), Ankara, Turkey
| | - Tolga Can
- Department of Computer Engineering, Middle East Technical University (METU), Ankara, Turkey.,Cancer System Biology Laboratory (CanSyL), Graduate School of Informatics, Middle East Technical University (METU), Ankara, Turkey
| | - Ezgi Karaca
- Izmir Biomedicine and Genome Center, Balcova, Izmir, Turkey.,Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Balcova, Izmir, Turkey
| | - Ayse Elif Erson-Bensan
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey.,Cancer System Biology Laboratory (CanSyL), Graduate School of Informatics, Middle East Technical University (METU), Ankara, Turkey
| |
Collapse
|
11
|
Lange M, Begolli R, Giakountis A. Non-Coding Variants in Cancer: Mechanistic Insights and Clinical Potential for Personalized Medicine. Noncoding RNA 2021; 7:47. [PMID: 34449663 PMCID: PMC8395730 DOI: 10.3390/ncrna7030047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/26/2021] [Accepted: 08/01/2021] [Indexed: 12/11/2022] Open
Abstract
The cancer genome is characterized by extensive variability, in the form of Single Nucleotide Polymorphisms (SNPs) or structural variations such as Copy Number Alterations (CNAs) across wider genomic areas. At the molecular level, most SNPs and/or CNAs reside in non-coding sequences, ultimately affecting the regulation of oncogenes and/or tumor-suppressors in a cancer-specific manner. Notably, inherited non-coding variants can predispose for cancer decades prior to disease onset. Furthermore, accumulation of additional non-coding driver mutations during progression of the disease, gives rise to genomic instability, acting as the driving force of neoplastic development and malignant evolution. Therefore, detection and characterization of such mutations can improve risk assessment for healthy carriers and expand the diagnostic and therapeutic toolbox for the patient. This review focuses on functional variants that reside in transcribed or not transcribed non-coding regions of the cancer genome and presents a collection of appropriate state-of-the-art methodologies to study them.
Collapse
Affiliation(s)
- Marios Lange
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece; (M.L.); (R.B.)
| | - Rodiola Begolli
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece; (M.L.); (R.B.)
| | - Antonis Giakountis
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece; (M.L.); (R.B.)
- Institute for Fundamental Biomedical Research, B.S.R.C “Alexander Fleming”, 34 Fleming Str., 16672 Vari, Greece
| |
Collapse
|