1
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Trogdon M, Abbott K, Arang N, Lande K, Kaur N, Tong M, Bakhoum M, Gutkind JS, Stites EC. Systems modeling of oncogenic G-protein and GPCR signaling reveals unexpected differences in downstream pathway activation. NPJ Syst Biol Appl 2024; 10:75. [PMID: 39013872 PMCID: PMC11252164 DOI: 10.1038/s41540-024-00400-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 06/27/2024] [Indexed: 07/18/2024] Open
Abstract
Mathematical models of biochemical reaction networks are an important and emerging tool for the study of cell signaling networks involved in disease processes. One promising potential application of such mathematical models is the study of how disease-causing mutations promote the signaling phenotype that contributes to the disease. It is commonly assumed that one must have a thorough characterization of the network readily available for mathematical modeling to be useful, but we hypothesized that mathematical modeling could be useful when there is incomplete knowledge and that it could be a tool for discovery that opens new areas for further exploration. In the present study, we first develop a mechanistic mathematical model of a G-protein coupled receptor signaling network that is mutated in almost all cases of uveal melanoma and use model-driven explorations to uncover and explore multiple new areas for investigating this disease. Modeling the two major, mutually-exclusive, oncogenic mutations (Gαq/11 and CysLT2R) revealed the potential for previously unknown qualitative differences between seemingly interchangeable disease-promoting mutations, and our experiments confirmed oncogenic CysLT2R was impaired at activating the FAK/YAP/TAZ pathway relative to Gαq/11. This led us to hypothesize that CYSLTR2 mutations in UM must co-occur with other mutations to activate FAK/YAP/TAZ signaling, and our bioinformatic analysis uncovers a role for co-occurring mutations involving the plexin/semaphorin pathway, which has been shown capable of activating this pathway. Overall, this work highlights the power of mechanism-based computational systems biology as a discovery tool that can leverage available information to open new research areas.
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Affiliation(s)
- Michael Trogdon
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Pfizer, La Jolla, CA, 92037, USA
| | - Kodye Abbott
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Nadia Arang
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, 92093, USA
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Kathryn Lande
- Razavi Newman Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Navneet Kaur
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Melinda Tong
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Mathieu Bakhoum
- Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, CT, 06520, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, 06520, USA
| | - J Silvio Gutkind
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Edward C Stites
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, 06520, USA.
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, 06520, USA.
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2
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Zheng R, Dunlap M, Bobkov GOM, Gonzalez-Figueroa C, Patel KJ, Lyu J, Harvey SE, Chan TW, Quinones-Valdez G, Choudhury M, Le Roux CA, Bartels MD, Vuong A, Flynn RA, Chang HY, Van Nostrand EL, Xiao X, Cheng C. hnRNPM protects against the dsRNA-mediated interferon response by repressing LINE-associated cryptic splicing. Mol Cell 2024; 84:2087-2103.e8. [PMID: 38815579 PMCID: PMC11204102 DOI: 10.1016/j.molcel.2024.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 01/09/2024] [Accepted: 05/07/2024] [Indexed: 06/01/2024]
Abstract
RNA splicing is pivotal in post-transcriptional gene regulation, yet the exponential expansion of intron length in humans poses a challenge for accurate splicing. Here, we identify hnRNPM as an essential RNA-binding protein that suppresses cryptic splicing through binding to deep introns, maintaining human transcriptome integrity. Long interspersed nuclear elements (LINEs) in introns harbor numerous pseudo splice sites. hnRNPM preferentially binds at intronic LINEs to repress pseudo splice site usage for cryptic splicing. Remarkably, cryptic exons can generate long dsRNAs through base-pairing of inverted ALU transposable elements interspersed among LINEs and consequently trigger an interferon response, a well-known antiviral defense mechanism. Significantly, hnRNPM-deficient tumors show upregulated interferon-associated pathways and elevated immune cell infiltration. These findings unveil hnRNPM as a guardian of transcriptome integrity by repressing cryptic splicing and suggest that targeting hnRNPM in tumors may be used to trigger an inflammatory immune response, thereby boosting cancer surveillance.
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Affiliation(s)
- Rong Zheng
- Lester & Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mikayla Dunlap
- Lester & Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Georg O M Bobkov
- Lester & Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Carlos Gonzalez-Figueroa
- Department of Integrative Biology and Physiology and the Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Khushali J Patel
- Lester & Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jingyi Lyu
- Lester & Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Samuel E Harvey
- Lester & Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tracey W Chan
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Giovanni Quinones-Valdez
- Department of Integrative Biology and Physiology and the Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Mudra Choudhury
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Charlotte A Le Roux
- Verna & Marrs McLean Department of Biochemistry & Molecular Pharmacology and Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mason D Bartels
- Verna & Marrs McLean Department of Biochemistry & Molecular Pharmacology and Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Amy Vuong
- Lester & Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ryan A Flynn
- Center for Personal Dynamic Regulome, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulome, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Eric L Van Nostrand
- Verna & Marrs McLean Department of Biochemistry & Molecular Pharmacology and Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xinshu Xiao
- Department of Integrative Biology and Physiology and the Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Chonghui Cheng
- Lester & Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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3
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Dasgupta A, Prensner JR. Upstream open reading frames: new players in the landscape of cancer gene regulation. NAR Cancer 2024; 6:zcae023. [PMID: 38774471 PMCID: PMC11106035 DOI: 10.1093/narcan/zcae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 05/24/2024] Open
Abstract
The translation of RNA by ribosomes represents a central biological process and one of the most dysregulated processes in cancer. While translation is traditionally thought to occur exclusively in the protein-coding regions of messenger RNAs (mRNAs), recent transcriptome-wide approaches have shown abundant ribosome activity across diverse stretches of RNA transcripts. The most common type of this kind of ribosome activity occurs in gene leader sequences, also known as 5' untranslated regions (UTRs) of the mRNA, that precede the main coding sequence. Translation of these upstream open reading frames (uORFs) is now known to occur in upwards of 25% of all protein-coding genes. With diverse functions from RNA regulation to microprotein generation, uORFs are rapidly igniting a new arena of cancer biology, where they are linked to cancer genetics, cancer signaling, and tumor-immune interactions. This review focuses on the contributions of uORFs and their associated 5'UTR sequences to cancer biology.
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Affiliation(s)
- Anwesha Dasgupta
- Chad Carr Pediatric Brain Tumor Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - John R Prensner
- Chad Carr Pediatric Brain Tumor Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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4
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Fu T, Amoah K, Chan TW, Bahn JH, Lee JH, Terrazas S, Chong R, Kosuri S, Xiao X. Massively parallel screen uncovers many rare 3' UTR variants regulating mRNA abundance of cancer driver genes. Nat Commun 2024; 15:3335. [PMID: 38637555 PMCID: PMC11026479 DOI: 10.1038/s41467-024-46795-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 03/06/2024] [Indexed: 04/20/2024] Open
Abstract
Understanding the function of rare non-coding variants represents a significant challenge. Using MapUTR, a screening method, we studied the function of rare 3' UTR variants affecting mRNA abundance post-transcriptionally. Among 17,301 rare gnomAD variants, an average of 24.5% were functional, with 70% in cancer-related genes, many in critical cancer pathways. This observation motivated an interrogation of 11,929 somatic mutations, uncovering 3928 (33%) functional mutations in 155 cancer driver genes. Functional MapUTR variants were enriched in microRNA- or protein-binding sites and may underlie outlier gene expression in tumors. Further, we introduce untranslated tumor mutational burden (uTMB), a metric reflecting the amount of somatic functional MapUTR variants of a tumor and show its potential in predicting patient survival. Through prime editing, we characterized three variants in cancer-relevant genes (MFN2, FOSL2, and IRAK1), demonstrating their cancer-driving potential. Our study elucidates the function of tens of thousands of non-coding variants, nominates non-coding cancer driver mutations, and demonstrates their potential contributions to cancer.
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Affiliation(s)
- Ting Fu
- Molecular, Cellular and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Kofi Amoah
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Tracey W Chan
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jae Hoon Bahn
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jae-Hyung Lee
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Life and Nanopharmaceutical Sciences & Oral Microbiology, School of Dentistry, Kyung Hee University, Seoul, South Korea
| | - Sari Terrazas
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Rockie Chong
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Sriram Kosuri
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Xinshu Xiao
- Molecular, Cellular and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
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5
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Choi T, Li Z, Song G, Chen HF. Comprehensive Comparison and Critical Assessment of RNA-Specific Force Fields. J Chem Theory Comput 2024; 20:2676-2688. [PMID: 38447040 DOI: 10.1021/acs.jctc.4c00066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Molecular dynamics simulations play a pivotal role in elucidating the dynamic behaviors of RNA structures, offering a valuable complement to traditional methods such as nuclear magnetic resonance or X-ray. Despite this, the current precision of RNA force fields lags behind that of protein force fields. In this work, we systematically compared the performance of four RNA force fields (ff99bsc0χOL3, AMBERDES, ff99OL3_CMAP1, AMBERMaxEnt) across diverse RNA structures. Our findings highlight significant challenges in maintaining stability, particularly with regard to cross-strand and cross-loop hydrogen bonds. Furthermore, we observed the limitations in accurately describing the conformations of nonhelical structural motif, terminal nucleotides, and also base pairing and base stacking interactions by the tested RNA force fields. The identified deficiencies in existing RNA force fields provide valuable insights for subsequent force field development. Concurrently, these findings offer recommendations for selecting appropriate force fields in RNA simulations.
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Affiliation(s)
- Taeyoung Choi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhengxin Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ge Song
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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6
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Lynn N, Tuller T. Detecting and understanding meaningful cancerous mutations based on computational models of mRNA splicing. NPJ Syst Biol Appl 2024; 10:25. [PMID: 38453965 PMCID: PMC10920900 DOI: 10.1038/s41540-024-00351-7] [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: 03/10/2023] [Accepted: 02/22/2024] [Indexed: 03/09/2024] Open
Abstract
Cancer research has long relied on non-silent mutations. Yet, it has become overwhelmingly clear that silent mutations can affect gene expression and cancer cell fitness. One fundamental mechanism that apparently silent mutations can severely disrupt is alternative splicing. Here we introduce Oncosplice, a tool that scores mutations based on models of proteomes generated using aberrant splicing predictions. Oncosplice leverages a highly accurate neural network that predicts splice sites within arbitrary mRNA sequences, a greedy transcript constructor that considers alternate arrangements of splicing blueprints, and an algorithm that grades the functional divergence between proteins based on evolutionary conservation. By applying this tool to 12M somatic mutations we identify 8K deleterious variants that are significantly depleted within the healthy population; we demonstrate the tool's ability to identify clinically validated pathogenic variants with a positive predictive value of 94%; we show strong enrichment of predicted deleterious mutations across pan-cancer drivers. We also achieve improved patient survival estimation using a proposed set of novel cancer-involved genes. Ultimately, this pipeline enables accelerated insight-gathering of sequence-specific consequences for a class of understudied mutations and provides an efficient way of filtering through massive variant datasets - functionalities with immediate experimental and clinical applications.
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Affiliation(s)
- Nicolas Lynn
- Department of Biomedical Engineering, the Engineering Faculty, Tel Aviv University, Tel-Aviv, 69978, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, the Engineering Faculty, Tel Aviv University, Tel-Aviv, 69978, Israel.
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7
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Mello AC, Leao D, Dias L, Colombelli F, Recamonde-Mendoza M, Turchetto-Zolet AC, Matte U. Broken silence: 22,841 predicted deleterious synonymous variants identified in the human exome through computational analysis. Genet Mol Biol 2024; 46:e20230125. [PMID: 38259032 PMCID: PMC10804382 DOI: 10.1590/1678-4685-gmb-2023-0125] [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: 05/03/2023] [Accepted: 12/10/2023] [Indexed: 01/24/2024] Open
Abstract
Synonymous single nucleotide variants (sSNVs) do not alter the primary structure of a protein, thus it was previously accepted that they were neutral. Recently, several studies demonstrated their significance to a range of diseases. Still, variant prioritization strategies lack focus on sSNVs. Here, we identified 22,841 deleterious synonymous variants in 125,748 human exomes using two in silico predictors (SilVA and CADD). While 98.2% of synonymous variants are classified as neutral, 1.8% are predicted to be deleterious, yielding an average of 9.82 neutral and 0.18 deleterious sSNVs per exome. Further investigation of prediction features via Heterogeneous Ensemble Feature Selection revealed that impact on amino acid sequence and conservation carry the most weight for a deleterious prediction. Thirty nine detrimental sSNVs are not rare and are located on disease associated genes. Ten distinct putatively non-deleterious sSNVs are likely to be under positive selection in the North-Western European and East Asian populations. Taken together our analysis gives voice to the so-called silent mutations as we propose a robust framework for evaluating the deleteriousness of sSNVs in variant prioritization studies.
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Affiliation(s)
- Ana Carolina Mello
- Hospital de Clínicas de Porto Alegre, Núcleo de Bioinformática,
Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa
Experimental, Laboratório de Células, Tecidos e Genes, Porto Alegre, RS,
Brazil
- Universidade Federal do Rio Grande do Sul, Programa de
Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Delva Leao
- Universidade Federal do Rio Grande do Sul, Programa de
Pós-Graduação em Ciências Biológicas: Bioquímica, Porto Alegre, RS, Brazil
| | - Luis Dias
- Hospital de Clínicas de Porto Alegre, Núcleo de Bioinformática,
Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa
Experimental, Laboratório de Células, Tecidos e Genes, Porto Alegre, RS,
Brazil
| | - Felipe Colombelli
- Hospital de Clínicas de Porto Alegre, Núcleo de Bioinformática,
Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de
Informática, Porto Alegre, RS, Brazil
| | - Mariana Recamonde-Mendoza
- Hospital de Clínicas de Porto Alegre, Núcleo de Bioinformática,
Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de
Informática, Porto Alegre, RS, Brazil
| | - Andreia Carina Turchetto-Zolet
- Universidade Federal do Rio Grande do Sul, Programa de
Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de
Genética, Porto Alegre, RS, Brazil
| | - Ursula Matte
- Hospital de Clínicas de Porto Alegre, Núcleo de Bioinformática,
Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa
Experimental, Laboratório de Células, Tecidos e Genes, Porto Alegre, RS,
Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de
Genética, Porto Alegre, RS, Brazil
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8
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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.
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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
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9
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Sanoguera-Miralles L, Valenzuela-Palomo A, Bueno-Martínez E, Esteban-Sánchez A, Lorca V, Llinares-Burguet I, García-Álvarez A, Pérez-Segura P, Infante M, Easton DF, Devilee P, Vreeswijk MPG, de la Hoya M, Velasco-Sampedro EA. Systematic Minigene-Based Splicing Analysis and Tentative Clinical Classification of 52 CHEK2 Splice-Site Variants. Clin Chem 2024; 70:319-338. [PMID: 37725924 DOI: 10.1093/clinchem/hvad125] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 07/07/2023] [Indexed: 09/21/2023]
Abstract
BACKGROUND Disrupted pre-mRNA splicing is a frequent deleterious mechanism in hereditary cancer. We aimed to functionally analyze candidate spliceogenic variants of the breast cancer susceptibility gene CHEK2 by splicing reporter minigenes. METHODS A total of 128 CHEK2 splice-site variants identified in the Breast Cancer After Diagnostic Gene Sequencing (BRIDGES) project (https://cordis.europa.eu/project/id/634935) were analyzed with MaxEntScan and subsetted to 52 variants predicted to impact splicing. Three CHEK2 minigenes, which span all 15 exons, were constructed and validated. The 52 selected variants were then genetically engineered into the minigenes and assayed in MCF-7 (human breast adenocarcinoma) cells. RESULTS Of 52 variants, 46 (88.5%) impaired splicing. Some of them led to complex splicing patterns with up to 11 different transcripts. Thirty-four variants induced splicing anomalies without any trace or negligible amounts of the full-length transcript. A total of 89 different transcripts were annotated, which derived from different events: single- or multi-exon skipping, alternative site-usage, mutually exclusive exon inclusion, intron retention or combinations of the abovementioned events. Fifty-nine transcripts were predicted to introduce premature termination codons, 7 kept the original open-reading frame, 5 removed the translation start codon, 6 affected the 5'UTR (Untranslated Region), and 2 included missense variations. Analysis of variant c.684-2A > G revealed the activation of a non-canonical TG-acceptor site and exon 6 sequences critical for its recognition. CONCLUSIONS Incorporation of minigene read-outs into an ACMG/AMP (American College of Medical Genetics and Genomics/Association for Molecular Pathology)-based classification scheme allowed us to classify 32 CHEK2 variants (27 pathogenic/likely pathogenic and 5 likely benign). However, 20 variants (38%) remained of uncertain significance, reflecting in part the complex splicing patterns of this gene.
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Affiliation(s)
- Lara Sanoguera-Miralles
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas-Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
| | - Alberto Valenzuela-Palomo
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas-Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
| | - Elena Bueno-Martínez
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas-Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
| | - Ada Esteban-Sánchez
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Víctor Lorca
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Inés Llinares-Burguet
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas-Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
| | - Alicia García-Álvarez
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas-Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
| | - Pedro Pérez-Segura
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Mar Infante
- Cancer Genetics, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, CB1 8RN, Cambridge, United Kingdom
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Maaike P G Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Miguel de la Hoya
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Eladio A Velasco-Sampedro
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas-Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
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10
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Kafita D, Nkhoma P, Dzobo K, Sinkala M. Shedding light on the dark genome: Insights into the genetic, CRISPR-based, and pharmacological dependencies of human cancers and disease aggressiveness. PLoS One 2023; 18:e0296029. [PMID: 38117798 PMCID: PMC10732413 DOI: 10.1371/journal.pone.0296029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/05/2023] [Indexed: 12/22/2023] Open
Abstract
Investigating the human genome is vital for identifying risk factors and devising effective therapies to combat genetic disorders and cancer. Despite the extensive knowledge of the "light genome", the poorly understood "dark genome" remains understudied. In this study, we integrated data from 20,412 protein-coding genes in Pharos and 8,395 patient-derived tumours from The Cancer Genome Atlas (TCGA) to examine the genetic and pharmacological dependencies in human cancers and their treatment implications. We discovered that dark genes exhibited high mutation rates in certain cancers, similar to light genes. By combining the drug response profiles of cancer cells with cell fitness post-CRISPR-mediated gene knockout, we identified the crucial vulnerabilities associated with both dark and light genes. Our analysis also revealed that tumours harbouring dark gene mutations displayed worse overall and disease-free survival rates than those without such mutations. Furthermore, dark gene expression levels significantly influenced patient survival outcomes. Our findings demonstrated a similar distribution of genetic and pharmacological dependencies across the light and dark genomes, suggesting that targeting the dark genome holds promise for cancer treatment. This study underscores the need for ongoing research on the dark genome to better comprehend the underlying mechanisms of cancer and develop more effective therapies.
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Affiliation(s)
- Doris Kafita
- Department of Biomedical Sciences, University of Zambia, School of Health Sciences, Lusaka, Zambia
| | - Panji Nkhoma
- Department of Biomedical Sciences, University of Zambia, School of Health Sciences, Lusaka, Zambia
| | - Kevin Dzobo
- Department of Medicine, Division of Dermatology, Hair and Skin Research Laboratory, Wound and Keloid Scarring Research Unit, The South African Medical Research Council, University of Cape Town, Cape Town, South Africa
| | - Musalula Sinkala
- Department of Biomedical Sciences, University of Zambia, School of Health Sciences, Lusaka, Zambia
- Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine and Department of Integrative Biomedical Sciences, University of Cape Town, Computational Biology Division, Cape Town, South Africa
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11
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Chamchoy K, Sudsumrit S, Wongwigkan J, Petmitr S, Songdej D, Adams ER, Edwards T, Leartsakulpanich U, Boonyuen U. Molecular characterization of G6PD mutations identifies new mutations and a high frequency of intronic variants in Thai females. PLoS One 2023; 18:e0294200. [PMID: 37967096 PMCID: PMC10651042 DOI: 10.1371/journal.pone.0294200] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 10/26/2023] [Indexed: 11/17/2023] Open
Abstract
Glucose-6-phosphate dehydrogenase (G6PD) deficiency is an X-linked enzymopathy caused by mutations in the G6PD gene. A medical concern associated with G6PD deficiency is acute hemolytic anemia induced by certain foods, drugs, and infections. Although phenotypic tests can correctly identify hemizygous males, as well as homozygous and compound heterozygous females, heterozygous females with a wide range of G6PD activity may be misclassified as normal. This study aimed to develop multiplex high-resolution melting (HRM) analyses to enable the accurate detection of G6PD mutations, especially among females with heterozygous deficiency. Multiplex HRM assays were developed to detect six G6PD variants, i.e., G6PD Gaohe (c.95A>G), G6PD Chinese-4 (c.392G>T), G6PD Mahidol (c.487G>A), G6PD Viangchan (c.871G>A), G6PD Chinese-5 (c.1024C>T), and G6PD Union (c.1360C>T) in two reactions. The assays were validated and then applied to genotype G6PD mutations in 248 Thai females. The sensitivity of the HRM assays developed was 100% [95% confidence interval (CI): 94.40%-100%] with a specificity of 100% (95% CI: 88.78%-100%) for detecting these six mutations. The prevalence of G6PD deficiency was estimated as 3.63% (9/248) for G6PD deficiency and 31.05% (77/248) for intermediate deficiency by phenotypic assay. The developed HRM assays identified three participants with normal enzyme activity as heterozygous for G6PD Viangchan. Interestingly, a deletion in intron 5 nucleotide position 637/638 (c.486-34delT) was also detected by the developed HRM assays. G6PD genotyping revealed a total of 12 G6PD genotypes, with a high prevalence of intronic variants. Our results suggested that HRM analysis-based genotyping is a simple and reliable approach for detecting G6PD mutations, and could be used to prevent the misdiagnosis of heterozygous females by phenotypic assay. This study also sheds light on the possibility of overlooking intronic variants, which could affect G6PD expression and contribute to enzyme deficiency.
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Affiliation(s)
- Kamonwan Chamchoy
- Princess Srisavangavadhana College of Medicine, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Sirapapha Sudsumrit
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Jutamas Wongwigkan
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Songsak Petmitr
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Duantida Songdej
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Emily R. Adams
- Centre for Drugs and Diagnostics Research, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Thomas Edwards
- Centre for Drugs and Diagnostics Research, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Ubolsree Leartsakulpanich
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Usa Boonyuen
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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12
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Zhang M, Lang X, Chen X, Lv Y. Prospective Identification of Prognostic Hot-Spot Mutant Gene Signatures for Leukemia: A Computational Study Based on Integrative Analysis of TCGA and cBioPortal Data. Mol Biotechnol 2023; 65:1898-1912. [PMID: 36879146 DOI: 10.1007/s12033-023-00704-3] [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: 09/15/2022] [Accepted: 02/14/2023] [Indexed: 03/08/2023]
Abstract
The advantage of an increasing amount of bioinformatics data on leukemias intrigued us to explore the hot-spot mutation profiles and investigate the implications of those hot-spot mutations in patient survival. We retrieved somatic mutations and their distribution in protein domains through data analysis of The Cancer Genome Atlas and cBioPortal databases. After determining differentially expressed mutant genes related to leukemia, we further conducted principal component analysis and single-factor Cox regression analyses. Moreover, survival analysis was performed for the obtained candidate genes, followed by a multi-factor Cox proportional hazard model method for the impacts of the candidate genes on the survival and prognosis of patients with leukemia. At last, the signaling pathways involved in leukemia were investigated by gene set enrichment analysis. There were 223 somatic missense mutation hot-spots identified with pertinence to leukemia, which were distributed in 41 genes. Differential expression in leukemia was witnessed in 39 genes. We found a close correlation between seven genes and the prognosis of leukemia patients, among which, three genes could significantly influence the survival rate. In addition, among these three genes, CD74 and P2RY8 were highlighted due to close pertinence with survival conditions of leukemia patients. Finally, data suggested that B cell receptor, Hedgehog, and TGF-beta signaling pathways were enriched in low-hazard patients. In conclusion, these data underline the involvement of hot-spot mutations of CD74 and P2RY8 genes in survival status of leukemia patients, highlighting their as novel therapeutic targets or prognostic indicators for leukemia patients. Summary of Graphical Abstract: We identified 223 leukemia-associated somatic missense mutation hotspots concentrated in 41 different genes from 2297 leukemia patients in the TCGA database. Differential analysis of leukemic and normal samples from the TCGA and GTEx databases revealed that 39 of these 41 genes showed significant differential expression in leukemia. These 39 genes were subjected to PCA analysis, univariate Cox analysis, survival analysis, multivariate Cox regression analysis, GSEA pathway enrichment analysis, and then the association with leukemia survival prognosis and related pathways were investigated.
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Affiliation(s)
- Min Zhang
- Department of Hematology, The First People's Hospital of Yongkang, Affiliated to Hangzhou Medical College, No. 599, Jinshan West Road, Yongkang, Jinhua City, Zhejiang Province, 321300, People's Republic of China.
| | - Xianghua Lang
- Department of Hematology, The First People's Hospital of Yongkang, Affiliated to Hangzhou Medical College, No. 599, Jinshan West Road, Yongkang, Jinhua City, Zhejiang Province, 321300, People's Republic of China
| | - Xinyi Chen
- Department of Hematology, The First People's Hospital of Yongkang, Affiliated to Hangzhou Medical College, No. 599, Jinshan West Road, Yongkang, Jinhua City, Zhejiang Province, 321300, People's Republic of China
| | - Yuke Lv
- Department of Hematology, The First People's Hospital of Yongkang, Affiliated to Hangzhou Medical College, No. 599, Jinshan West Road, Yongkang, Jinhua City, Zhejiang Province, 321300, People's Republic of China
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13
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Wang J, Zhang X, Wang X, Li F, Zhang D, Li X, Zhang Y, Zhao Y, Song Q, Zhao L, Xu D, Cheng J, Li W, Zhou B, Lin C, Wang W. Polymorphism and expression of the HMGA1 gene and association with tail fat deposition in Hu sheep. Anim Biotechnol 2023; 34:1626-1634. [PMID: 34775926 DOI: 10.1080/10495398.2021.1998093] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Hu sheep is an excellent short fat-tailed breed in China. Fat deposition in Hu sheep tail affects carcass quality and consumes a lot of energy, leading to an increase in feed cost. The objective of this study was to analyze the effects of HMGA1 polymorphism on tail fat weight in Hu sheep. Partial coding and non-coding sequences of HMGA1 were amplified with PCR and single nucleotide polymorphisms (SNP) of HMGA1 in 1163 Hu sheep were detected using DNA sequencing and KASPar technology. RT-qPCR analysis was performed to test HMGA1 expression in different tissues. The results showed that the expression of HMGA1 was higher in the duodenum, liver, spleen, kidney, and lung than in the heart, muscle, rumen, tail fat, and lymph. A mutation, g.5312 C > T, was detected in HMGA1; g.5312 C > T was significantly associated with tail fat weight, relative weight of tail fat (body weight), and relative weight of tail fat (carcass) (p < 0.05). The tail fat weight of the TT genotype was remarkably higher than that of the CC and TC genotypes. Therefore, HMGA1 can be used as a genetic marker for marker-assisted selection of tail fat weight in Hu sheep.
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Affiliation(s)
- Jianghui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Xiaojuan Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Fadi Li
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu, China
- Engineering Laboratory of Sheep Breeding and Reproduction Biotechnology in Gansu Province, Minqin, China
| | - Deyin Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Yukun Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Yuan Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Qizhi Song
- Linze County Animal Disease Prevention and Control Center of Gansu Province, Linze, China
| | - Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Jiangbo Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Wenxin Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Bubo Zhou
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Changchun Lin
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Weimin Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
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14
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Di Fusco D, Segreto MT, Di Maggio G, Iannucci A, Maresca C, Di Grazia A, Colella M, Stolfi C, Monteleone G, Monteleone I. Insulin-like Growth Factor II mRNA-Binding Protein 1 Regulates Pancreatic Cancer Cell Growth through the Surveillance of CDC25A mRNA. Cancers (Basel) 2023; 15:4983. [PMID: 37894350 PMCID: PMC10605367 DOI: 10.3390/cancers15204983] [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: 07/26/2023] [Revised: 09/27/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
A number of data indicate that the sources of different kinds of PDAC may be discovered at the transcription/transduction stage. RNA metabolism is manipulated at various steps by different RNA-binding proteins (RBPs), and the deregulation or irregular activity of RBPs is known to contribute to tumor promotion and progression. The insulin-like growth factor 2 mRNA-binding protein family (IMPs), and IMP1 in particular, has been linked with a poor prognosis in PDAC patients; however, little is known about its contribution in PDAC carcinogenesis. In this study, we investigated the function of IMP1 in PDAC. To evaluate IMP1 expression and correlation with PDAC prognosis, we utilized several public databases. Using a specific siRNA IMP1, we analyzed cell death and cell cycle progression in PDAC cell lines and 3D spheroids. The role of IMP1 was also evaluated in vivo in a Panc-1-derived tumor xenograft murine model. Public data suggest that PDAC patients with higher expression of IMP1 showed poor overall and progression-free survival. IMP1 silencing leads to reduced cell growth in PDAC cells and three-dimensional spheroids. Abrogation of IMP1 in PDAC cells showed lower levels of CDC25A, increased phosphorylation of the cyclin-dependent kinase (CDK)2, and accumulation of PDAC cells in the G1 phase. Immunoprecipitation experiments revealed that IMP1 binds CDC25A mRNA, thus controlling cell-cycle progression. Ultimately, we proved that suppression of IMP1 blocked in vivo growth of Panc-1 transferred into immunodeficient mice. Our results indicate that IMP1 drives the PDCA cell cycle and represents a novel strategy for overcoming PDCA cell proliferation.
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Affiliation(s)
- Davide Di Fusco
- Department of Systems Medicine, University of “Tor Vergata”, 00133 Rome, Italy; (D.D.F.); (M.T.S.); (G.D.M.); (C.M.); (A.D.G.); (M.C.); (C.S.); (G.M.)
| | - Maria Teresa Segreto
- Department of Systems Medicine, University of “Tor Vergata”, 00133 Rome, Italy; (D.D.F.); (M.T.S.); (G.D.M.); (C.M.); (A.D.G.); (M.C.); (C.S.); (G.M.)
| | - Giulia Di Maggio
- Department of Systems Medicine, University of “Tor Vergata”, 00133 Rome, Italy; (D.D.F.); (M.T.S.); (G.D.M.); (C.M.); (A.D.G.); (M.C.); (C.S.); (G.M.)
| | - Andrea Iannucci
- Department of Biomedicine and Prevention, University of “Tor Vergata”, 00133 Rome, Italy;
| | - Claudia Maresca
- Department of Systems Medicine, University of “Tor Vergata”, 00133 Rome, Italy; (D.D.F.); (M.T.S.); (G.D.M.); (C.M.); (A.D.G.); (M.C.); (C.S.); (G.M.)
| | - Antonio Di Grazia
- Department of Systems Medicine, University of “Tor Vergata”, 00133 Rome, Italy; (D.D.F.); (M.T.S.); (G.D.M.); (C.M.); (A.D.G.); (M.C.); (C.S.); (G.M.)
| | - Marco Colella
- Department of Systems Medicine, University of “Tor Vergata”, 00133 Rome, Italy; (D.D.F.); (M.T.S.); (G.D.M.); (C.M.); (A.D.G.); (M.C.); (C.S.); (G.M.)
| | - Carmine Stolfi
- Department of Systems Medicine, University of “Tor Vergata”, 00133 Rome, Italy; (D.D.F.); (M.T.S.); (G.D.M.); (C.M.); (A.D.G.); (M.C.); (C.S.); (G.M.)
| | - Giovanni Monteleone
- Department of Systems Medicine, University of “Tor Vergata”, 00133 Rome, Italy; (D.D.F.); (M.T.S.); (G.D.M.); (C.M.); (A.D.G.); (M.C.); (C.S.); (G.M.)
| | - Ivan Monteleone
- Department of Biomedicine and Prevention, University of “Tor Vergata”, 00133 Rome, Italy;
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15
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Srivastava A, Srivastava A, Singh RK. Insight into the Epigenetics of Kaposi's Sarcoma-Associated Herpesvirus. Int J Mol Sci 2023; 24:14955. [PMID: 37834404 PMCID: PMC10573522 DOI: 10.3390/ijms241914955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 10/15/2023] Open
Abstract
Epigenetic reprogramming represents a series of essential events during many cellular processes including oncogenesis. The genome of Kaposi's sarcoma-associated herpesvirus (KSHV), an oncogenic herpesvirus, is predetermined for a well-orchestrated epigenetic reprogramming once it enters into the host cell. The initial epigenetic reprogramming of the KSHV genome allows restricted expression of encoded genes and helps to hide from host immune recognition. Infection with KSHV is associated with Kaposi's sarcoma, multicentric Castleman's disease, KSHV inflammatory cytokine syndrome, and primary effusion lymphoma. The major epigenetic modifications associated with KSHV can be labeled under three broad categories: DNA methylation, histone modifications, and the role of noncoding RNAs. These epigenetic modifications significantly contribute toward the latent-lytic switch of the KSHV lifecycle. This review gives a brief account of the major epigenetic modifications affiliated with the KSHV genome in infected cells and their impact on pathogenesis.
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Affiliation(s)
- Anusha Srivastava
- Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Ankit Srivastava
- Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Rajnish Kumar Singh
- Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
- Faculty of Medical Sciences, Charotar University of Science and Technology, Changa 388421, Gujarat, India
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16
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Li J, Xiao Z, Wang D, Jia L, Nie S, Zeng X, Hu W. The screening, identification, design and clinical application of tumor-specific neoantigens for TCR-T cells. Mol Cancer 2023; 22:141. [PMID: 37649123 PMCID: PMC10466891 DOI: 10.1186/s12943-023-01844-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023] Open
Abstract
Recent advances in neoantigen research have accelerated the development of tumor immunotherapies, including adoptive cell therapies (ACTs), cancer vaccines and antibody-based therapies, particularly for solid tumors. With the development of next-generation sequencing and bioinformatics technology, the rapid identification and prediction of tumor-specific antigens (TSAs) has become possible. Compared with tumor-associated antigens (TAAs), highly immunogenic TSAs provide new targets for personalized tumor immunotherapy and can be used as prospective indicators for predicting tumor patient survival, prognosis, and immune checkpoint blockade response. Here, the identification and characterization of neoantigens and the clinical application of neoantigen-based TCR-T immunotherapy strategies are summarized, and the current status, inherent challenges, and clinical translational potential of these strategies are discussed.
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Affiliation(s)
- Jiangping Li
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China.
| | - Zhiwen Xiao
- Department of Otolaryngology Head and Neck Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, People's Republic of China
| | - Donghui Wang
- Department of Radiation Oncology, The Third Affiliated Hospital Sun Yat-Sen University, Guangzhou, 510630, People's Republic of China
| | - Lei Jia
- International Health Medicine Innovation Center, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Shihong Nie
- Department of Radiation Oncology, West China Hospital, Sichuan University, Cancer Center, Chengdu, 610041, People's Republic of China
| | - Xingda Zeng
- Department of Parasitology of Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Wei Hu
- Division of Vascular Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, People's Republic of China
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17
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Jaskiewicz K, Maleszka-Kurpiel M, Kabza M, Karolak JA, Gajecka M. Sequence variants contributing to dysregulated inflammatory responses across keratoconic cone surface in adolescent patients with keratoconus. Front Immunol 2023; 14:1197054. [PMID: 37483635 PMCID: PMC10359427 DOI: 10.3389/fimmu.2023.1197054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/09/2023] [Indexed: 07/25/2023] Open
Abstract
Background Keratoconus (KTCN) is the most common corneal ectasia resulting in a conical shape of the cornea. Here, genomic variation in the corneal epithelium (CE) across the keratoconic cone surface in patients with KTCN and its relevance in the functioning of the immune system were assessed. Methods Samples from four unrelated adolescent patients with KTCN and two control individuals were obtained during the CXL and PRK procedures, respectively. Three topographic regions, central, middle, and peripheral, were separated towards the whole-genome sequencing (WGS) study embracing a total of 18 experimental samples. The coding and non-coding sequence variation, including structural variation, was assessed and then evaluated together with the previously reported transcriptomic outcomes for the same CE samples and full-thickness corneas. Results First, pathway enrichment analysis of genes with identified coding variants pointed to "Antigen presentation" and "Interferon alpha/beta signaling" as the most overrepresented pathways, indicating the involvement of inflammatory responses in KTCN. Both coding and non-coding sequence variants were found in genes (or in their close proximity) linked to the previously revealed KTCN-specific cellular components, namely, "Actin cytoskeleton", "Extracellular matrix", "Collagen-containing extracellular matrix", "Focal adhesion", "Hippo signaling pathway", and "Wnt signaling" pathways. No genomic heterogeneity across the corneal surface was found comparing the assessed topographic regions. Thirty-five chromosomal regions enriched in both coding and non-coding KTCN-specific sequence variants were revealed, with a most representative 5q locus previously recognized as involved in KTCN. Conclusion The identified genomic features indicate the involvement of innate and adaptive immune system responses in KTCN pathogenesis.
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Affiliation(s)
| | - Magdalena Maleszka-Kurpiel
- Optegra Eye Health Care Clinic in Poznan, Poznan, Poland
- Chair of Ophthalmology and Optometry, Poznan University of Medical Sciences, Poznan, Poland
| | - Michał Kabza
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Justyna A. Karolak
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Marzena Gajecka
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
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18
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Dabiri H, Safarzadeh Kozani P, Habibi Anbouhi M, Mirzaee Godarzee M, Haddadi MH, Basiri M, Ziaei V, Sadeghizadeh M, Hajizadeh Saffar E. Site-specific transgene integration in chimeric antigen receptor (CAR) T cell therapies. Biomark Res 2023; 11:67. [PMID: 37403182 DOI: 10.1186/s40364-023-00509-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 06/09/2023] [Indexed: 07/06/2023] Open
Abstract
Chimeric antigen receptor (CAR) T cells and natural killer (NK) cells are genetically engineered immune cells that can detect target antigens on the surface of target cells and eliminate them following adoptive transfer. Recent progress in CAR-based therapies has led to outstanding clinical success in certain patients with leukemias and lymphomas and offered therapeutic benefits to those resistant to conventional therapies. The universal approach to stable CAR transgene delivery into the T/NK cells is the use of viral particles. Such approaches mediate semi-random transgene insertions spanning the entire genome with a high preference for integration into sites surrounding highly-expressed genes and active loci. Regardless of the variable CAR expression level based on the integration site of the CAR transgene, foreign integrated DNA fragments may affect the neighboring endogenous genes and chromatin structure and potentially change a transduced T/NK cell behavior and function or even favor cellular transformation. In contrast, site-specific integration of CAR constructs using recent genome-editing technologies could overcome the limitations and disadvantages of universal random gene integration. Herein, we explain random and site-specific integration of CAR transgenes in CAR-T/NK cell therapies. Also, we tend to summarize the methods for site-specific integration as well as the clinical outcomes of certain gene disruptions or enhancements due to CAR transgene integration. Also, the advantages and limitations of using site-specific integration methods are discussed in this review. Ultimately, we will introduce the genomic safe harbor (GSH) standards and suggest some appropriate safety prospects for CAR integration in CAR-T/NK cell therapies.
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Affiliation(s)
- Hamed Dabiri
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Pooria Safarzadeh Kozani
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | | | - Mohadeseh Mirzaee Godarzee
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | | | - Mohsen Basiri
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Vahab Ziaei
- National Cell Bank of Iran, Pasteur Institute of Iran, Tehran, Iran
| | - Majid Sadeghizadeh
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ensiyeh Hajizadeh Saffar
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
- Advanced Therapy Medicinal Product Technology Development Center (ATMP-TDC), Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
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19
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Dabiri H, Safarzadeh Kozani P, Habibi Anbouhi M, Mirzaee Godarzee M, Haddadi MH, Basiri M, Ziaei V, Sadeghizadeh M, Hajizadeh Saffar E. Site-specific transgene integration in chimeric antigen receptor (CAR) T cell therapies. Biomark Res 2023; 11:67. [DOI: https:/doi.org/10.1186/s40364-023-00509-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 06/09/2023] [Indexed: 09/15/2023] Open
Abstract
AbstractChimeric antigen receptor (CAR) T cells and natural killer (NK) cells are genetically engineered immune cells that can detect target antigens on the surface of target cells and eliminate them following adoptive transfer. Recent progress in CAR-based therapies has led to outstanding clinical success in certain patients with leukemias and lymphomas and offered therapeutic benefits to those resistant to conventional therapies. The universal approach to stable CAR transgene delivery into the T/NK cells is the use of viral particles. Such approaches mediate semi-random transgene insertions spanning the entire genome with a high preference for integration into sites surrounding highly-expressed genes and active loci. Regardless of the variable CAR expression level based on the integration site of the CAR transgene, foreign integrated DNA fragments may affect the neighboring endogenous genes and chromatin structure and potentially change a transduced T/NK cell behavior and function or even favor cellular transformation. In contrast, site-specific integration of CAR constructs using recent genome-editing technologies could overcome the limitations and disadvantages of universal random gene integration. Herein, we explain random and site-specific integration of CAR transgenes in CAR-T/NK cell therapies. Also, we tend to summarize the methods for site-specific integration as well as the clinical outcomes of certain gene disruptions or enhancements due to CAR transgene integration. Also, the advantages and limitations of using site-specific integration methods are discussed in this review. Ultimately, we will introduce the genomic safe harbor (GSH) standards and suggest some appropriate safety prospects for CAR integration in CAR-T/NK cell therapies.
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20
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Geissler M, Jia W, Kiraz EN, Kulacz I, Liu X, Rombach A, Prinz V, Jussen D, Kokkaliaris KD, Medyouf H, Sevenich L, Czabanka M, Broggini T. The Brain Pre-Metastatic Niche: Biological and Technical Advancements. Int J Mol Sci 2023; 24:10055. [PMID: 37373202 DOI: 10.3390/ijms241210055] [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: 02/28/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Metastasis, particularly brain metastasis, continues to puzzle researchers to this day, and exploring its molecular basis promises to break ground in developing new strategies for combatting this deadly cancer. In recent years, the research focus has shifted toward the earliest steps in the formation of metastasis. In this regard, significant progress has been achieved in understanding how the primary tumor affects distant organ sites before the arrival of tumor cells. The term pre-metastatic niche was introduced for this concept and encompasses all influences on sites of future metastases, ranging from immunological modulation and ECM remodeling to the softening of the blood-brain barrier. The mechanisms governing the spread of metastasis to the brain remain elusive. However, we begin to understand these processes by looking at the earliest steps in the formation of metastasis. This review aims to present recent findings on the brain pre-metastatic niche and to discuss existing and emerging methods to further explore the field. We begin by giving an overview of the pre-metastatic and metastatic niches in general before focusing on their manifestations in the brain. To conclude, we reflect on the methods usually employed in this field of research and discuss novel approaches in imaging and sequencing.
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Affiliation(s)
- Maximilian Geissler
- Department of Neurosurgery, University Hospital, Goethe-University, 60528 Frankfurt am Main, Germany
| | - Weiyi Jia
- Department of Neurosurgery, University Hospital, Goethe-University, 60528 Frankfurt am Main, Germany
| | - Emine Nisanur Kiraz
- Department of Neurosurgery, University Hospital, Goethe-University, 60528 Frankfurt am Main, Germany
| | - Ida Kulacz
- Department of Neurosurgery, University Hospital, Goethe-University, 60528 Frankfurt am Main, Germany
| | - Xiao Liu
- Department of Neurosurgery, University Hospital, Goethe-University, 60528 Frankfurt am Main, Germany
| | - Adrian Rombach
- Department of Neurosurgery, University Hospital, Goethe-University, 60528 Frankfurt am Main, Germany
| | - Vincent Prinz
- Department of Neurosurgery, University Hospital, Goethe-University, 60528 Frankfurt am Main, Germany
| | - Daniel Jussen
- Department of Neurosurgery, University Hospital, Goethe-University, 60528 Frankfurt am Main, Germany
| | - Konstantinos D Kokkaliaris
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, 60528 Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, 60528 Frankfurt am Main, Germany
- Frankfurt Cancer Institute (FCI), Goethe University Frankfurt, 60528 Frankfurt am Main, Germany
| | - Hind Medyouf
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, 60528 Frankfurt am Main, Germany
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, 60528 Frankfurt am Main, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Lisa Sevenich
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, 60528 Frankfurt am Main, Germany
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, 60528 Frankfurt am Main, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Marcus Czabanka
- Department of Neurosurgery, University Hospital, Goethe-University, 60528 Frankfurt am Main, Germany
- Frankfurt Cancer Institute (FCI), Goethe University Frankfurt, 60528 Frankfurt am Main, Germany
| | - Thomas Broggini
- Department of Neurosurgery, University Hospital, Goethe-University, 60528 Frankfurt am Main, Germany
- Frankfurt Cancer Institute (FCI), Goethe University Frankfurt, 60528 Frankfurt am Main, Germany
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21
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Stachelek K, Harutyunyan N, Lee S, Beck A, Kim J, Xu L, Berry JL, Nagiel A, Reynolds CP, Murphree AL, Lee TC, Aparicio JG, Cobrinik D. Non-synonymous, synonymous, and non-coding nucleotide variants contribute to recurrently altered biological processes during retinoblastoma progression. Genes Chromosomes Cancer 2023; 62:275-289. [PMID: 36550020 PMCID: PMC10006380 DOI: 10.1002/gcc.23120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Retinoblastomas form in response to biallelic RB1 mutations or MYCN amplification and progress to more aggressive and therapy-resistant phenotypes through accumulation of secondary genomic changes. Progression-related changes include recurrent somatic copy number alterations and typically non-recurrent nucleotide variants, including synonymous and non-coding variants, whose significance has been unclear. To determine if nucleotide variants recurrently affect specific biological processes, we identified altered genes and over-represented variant gene ontologies in 168 exome or whole-genome-sequenced retinoblastomas and 12 tumor-matched cell lines. In addition to RB1 mutations, MYCN amplification, and established retinoblastoma somatic copy number alterations, the analyses revealed enrichment of variant genes related to diverse biological processes including histone monoubiquitination, mRNA processing (P) body assembly, and mitotic sister chromatid segregation and cytokinesis. Importantly, non-coding and synonymous variants increased the enrichment significance of each over-represented biological process term. To assess the effects of such mutations, we examined the consequences of a 3' UTR variant of PCGF3 (a BCOR-binding component of Polycomb repressive complex I), dual 3' UTR variants of CDC14B (a regulator of sister chromatid segregation), and a synonymous variant of DYNC1H1 (a regulator of P-body assembly). One PCGF3 and one of two CDC14B 3' UTR variants impaired gene expression whereas a base-edited DYNC1H1 synonymous variant altered protease sensitivity and stability. Retinoblastoma cell lines retained only ~50% of variants detected in tumors and enriched for new variants affecting p53 signaling. These findings reveal potentially important differences in retinoblastoma cell lines and tumors and implicate synonymous and non-coding variants, along with non-synonymous variants, in retinoblastoma oncogenesis.
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Affiliation(s)
- Kevin Stachelek
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
- Cancer Biology and Genomics Program, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Narine Harutyunyan
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
| | - Susan Lee
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
| | - Assaf Beck
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
| | - Jonathan Kim
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
- Department of Ophthalmology and Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Liya Xu
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
- Department of Ophthalmology and Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Jesse L. Berry
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
- Department of Ophthalmology and Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Aaron Nagiel
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
- Department of Ophthalmology and Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - C. Patrick Reynolds
- Department of Pediatrics and Cancer Center, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, TX
| | - A. Linn Murphree
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
- Department of Ophthalmology and Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Thomas C. Lee
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
- Department of Ophthalmology and Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Jennifer G. Aparicio
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
| | - David Cobrinik
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
- Department of Ophthalmology and Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
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22
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Di Fusco D, Di Grazia A, Di Maggio G, Segreto MT, Iannucci A, Maresca C, De Stefano A, Sica G, Stolfi C, Monteleone G, Monteleone I. A novel tumour enhancer function of Insulin-like growth factor II mRNA-binding protein 3 in colorectal cancer. Cell Death Dis 2023; 14:243. [PMID: 37024466 PMCID: PMC10079693 DOI: 10.1038/s41419-023-05772-6] [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: 08/01/2022] [Revised: 03/17/2023] [Accepted: 03/23/2023] [Indexed: 04/08/2023]
Abstract
CRC cells evolve a variety of strategies to limit or circumvent apoptosis cell death. RNA binding proteins (RBPs) regulate many of the molecular mechanisms that underlie the development of cancer. The insulin-like growth factor II mRNA-binding proteins (IMP) family are oncofoetal RBPs, consisting of IMP1, IMP2 and IMP3, which have an important role in RNA metabolism. IMP3 is highly expressed in colorectal cancer (CRC) tissue, where its expression often correlates with poor prognosis. However, the role of IMP3 in CRC is not fully understood. IMP3 expression was analysed using a public database and by Western blotting and immunohistochemistry in human colon samples derived from patients with sporadic CRC and healthy subjects. To address whether IMP3 controls cancer cell survival, we analysed cell death pathways in in vitro and in vivo experiments after IMP3 downregulation by siRNA or an antisense oligonucleotide. IMP3 was highly expressed in CRC samples compared to normal control tissues. The knockdown of IMP3 enhanced a caspase-independent cell death in CRC cell lines. Furthermore, the treatment of CRC cells with IMP3 siRNA did not alter the expression of GSDMD, GPX-4 and the activated form of RIP3, three key molecules that govern pyroptosis, ferroptosis and necroptosis, respectively. Abrogation of IMP3 in CRC significantly reduced Bcl-2 and Bcl-xL mRNA and was associated with an altered mitochondrial membrane potential that allowed the nuclear migration of the apoptosis-inducing factor (AIF). Moreover, specific immunoprecipitation experiments on CRC human cell lines indicated that IMP3 binds Bcl-2 and Bcl-xL mRNA, suggesting that IMP3 acts as a regulator of the intrinsic apoptotic pathway through the surveillance of anti-apoptotic Bcl mRNA metabolism. Finally, we showed that IMP3 block inhibited the growth of CRC cell lines in vivo after transplantation into immunodeficient mice. Altogether, these data support a novel role for IMP3 in controlling the intrinsic caspase-independent apoptotic pathway in CRC.
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Affiliation(s)
- Davide Di Fusco
- Department of Systems Medicine, University of 'Tor Vergata', Rome, Italy
| | - Antonio Di Grazia
- Department of Systems Medicine, University of 'Tor Vergata', Rome, Italy
| | - Giulia Di Maggio
- Department of Systems Medicine, University of 'Tor Vergata', Rome, Italy
| | | | - Andrea Iannucci
- Department of Biomedicine and Prevention, University of 'Tor Vergata', Rome, Italy
| | - Claudia Maresca
- Department of Systems Medicine, University of 'Tor Vergata', Rome, Italy
| | | | - Giuseppe Sica
- Department of Surgery, University of 'Tor Vergata', Rome, Italy
| | - Carmine Stolfi
- Department of Systems Medicine, University of 'Tor Vergata', Rome, Italy
| | | | - Ivan Monteleone
- Department of Biomedicine and Prevention, University of 'Tor Vergata', Rome, Italy.
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23
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Yan Y, Liu X, Li Y, Yan J, Zhao P, Yang L. EPB41L4A-AS1 and UNC5B-AS1 have diagnostic and prognostic significance in osteosarcoma. J Orthop Surg Res 2023; 18:261. [PMID: 36998043 PMCID: PMC10064547 DOI: 10.1186/s13018-023-03754-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 03/24/2023] [Indexed: 04/01/2023] Open
Abstract
BACKGROUND Deregulation of lncRNAs has been observed in human osteosarcoma. This study explored the diagnostic and prognostic significance of EPB41L4A-AS1 and UNC5B-AS1 in osteosarcoma. METHODS Relative levels of EPB41L4A-AS1 and UNC5B-AS1 were detected in osteosarcoma tissue samples and cells. The ability to distinguish osteosarcoma from health was assessed by receiver operating characteristic (ROC) curve construction. Kaplan-Meier (K-M) and Cox proportional-hazards analyses were performed for prognosis factors. The bioinformatics approach was used to identify targeting miRNA for EPB41L4A-AS1 and UNC5B-AS1. Kaplan-Meier survival curves and Whitney Mann U tests were conducted for validating the statistical significance. In cell culture experiments, the influence of EPB41L4A-AS1 and UNC5B-AS1 on proliferation, migration, and invasion of the osteosarcoma cell line was examined by CCK-8 and Transwell assays. RESULTS Levels of EPB41L4A-AS1 and UNC5B-AS1 were upregulated in osteosarcoma patients and cells compared with the healthy participants and normal cell lines. EPB41L4A-AS1 and UNC5B-AS1 have a potent ability to distinguish the patients with osteosarcoma from the health. EPB41L4A-AS1 and UNC5B-AS1 levels correlated with SSS stage. Patients with high levels of EPB41L4A-AS1 and UNC5B-AS1 had significantly shorter survival times. EPB41L4A-AS1 and UNC5B-AS1 were independent prognostic indexes for overall survival. miR-1306-5p was a common target for EPB41L4A-AS1 and UNC5B-AS1. A propulsive impact on cell proliferation, migration, and invasion by EPB41L4A-AS1 and UNC5B-AS1 was observed, but can be rescued by miR-1306-5p. CONCLUSIONS It was concluded that upregulations of EPB41L4A-AS1 and UNC5B-AS1 expression were diagnostic and prognostic biomarkers for human osteosarcoma. EPB41L4A-AS1 and UNC5B-AS1 contribute to the biological behavior of osteosarcoma via miR-1306-5p.
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Affiliation(s)
- Ying Yan
- Shanghai Baoshan Center for Disease Control and Prevention, Shanghai, 201901, China
| | - Xiaochuan Liu
- Clinical Research Center, Shanghai Baoshan Luodian Hospital, No. 121 Luoxi Road, Baoshan District, Shanghai, 201908, China
| | - Yamei Li
- Clinical Research Center, Shanghai Baoshan Luodian Hospital, No. 121 Luoxi Road, Baoshan District, Shanghai, 201908, China
| | - Jingyi Yan
- Juquan New Town Community Health Service Center, Gucun Town, Baoshan District, Shanghai, 201907, China
| | - Ping Zhao
- Clinical Research Center, Shanghai Baoshan Luodian Hospital, No. 121 Luoxi Road, Baoshan District, Shanghai, 201908, China.
| | - Lu Yang
- Clinical Research Center, Shanghai Baoshan Luodian Hospital, No. 121 Luoxi Road, Baoshan District, Shanghai, 201908, China.
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24
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Rasheed S, Bouley RA, Yoder RJ, Petreaca RC. Protein Arginine Methyltransferase 5 (PRMT5) Mutations in Cancer Cells. Int J Mol Sci 2023; 24:6042. [PMID: 37047013 PMCID: PMC10094674 DOI: 10.3390/ijms24076042] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/15/2023] [Accepted: 03/20/2023] [Indexed: 04/14/2023] Open
Abstract
Arginine methylation is a form of posttranslational modification that regulates many cellular functions such as development, DNA damage repair, inflammatory response, splicing, and signal transduction, among others. Protein arginine methyltransferase 5 (PRMT5) is one of nine identified methyltransferases, and it can methylate both histone and non-histone targets. It has pleiotropic functions, including recruitment of repair machinery to a chromosomal DNA double strand break (DSB) and coordinating the interplay between repair and checkpoint activation. Thus, PRMT5 has been actively studied as a cancer treatment target, and small molecule inhibitors of its enzymatic activity have already been developed. In this report, we analyzed all reported PRMT5 mutations appearing in cancer cells using data from the Catalogue of Somatic Mutations in Cancers (COSMIC). Our goal is to classify mutations as either drivers or passengers to understand which ones are likely to promote cellular transformation. Using gold standard artificial intelligence algorithms, we uncovered several key driver mutations in the active site of the enzyme (D306H, L315P, and N318K). In silico protein modeling shows that these mutations may affect the affinity of PRMT5 for S-adenosylmethionine (SAM), which is required as a methyl donor. Electrostatic analysis of the enzyme active site shows that one of these mutations creates a tunnel in the vicinity of the SAM binding site, which may allow interfering molecules to enter the enzyme active site and decrease its activity. We also identified several non-coding mutations that appear to affect PRMT5 splicing. Our analyses provide insights into the role of PRMT5 mutations in cancer cells. Additionally, since PRMT5 single molecule inhibitors have already been developed, this work may uncover future directions in how mutations can affect targeted inhibition.
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Affiliation(s)
- Shayaan Rasheed
- James Comprehensive Cancer Center, The Ohio State University Columbus, Columbus, OH 43210, USA
- Biology Program, The Ohio State University, Columbus, OH 43210, USA
| | - Renee A. Bouley
- Department of Chemistry and Biochemistry, The Ohio State University, Marion, OH 43302, USA
| | - Ryan J. Yoder
- Department of Chemistry and Biochemistry, The Ohio State University, Marion, OH 43302, USA
| | - Ruben C. Petreaca
- James Comprehensive Cancer Center, The Ohio State University Columbus, Columbus, OH 43210, USA
- Department of Molecular Genetics, The Ohio State University, Marion, OH 43302, USA
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25
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Fackenthal JD. Alternative mRNA Splicing and Promising Therapies in Cancer. Biomolecules 2023; 13:biom13030561. [PMID: 36979496 PMCID: PMC10046298 DOI: 10.3390/biom13030561] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/09/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Cancer is among the leading causes of mortality worldwide. While considerable attention has been given to genetic and epigenetic sources of cancer-specific cellular activities, the role of alternative mRNA splicing has only recently received attention as a major contributor to cancer initiation and progression. The distribution of alternate mRNA splicing variants in cancer cells is different from their non-cancer counterparts, and cancer cells are more sensitive than non-cancer cells to drugs that target components of the splicing regulatory network. While many of the alternatively spliced mRNAs in cancer cells may represent "noise" from splicing dysregulation, certain recurring splicing variants have been shown to contribute to tumor progression. Some pathogenic splicing disruption events result from mutations in cis-acting splicing regulatory sequences in disease-associated genes, while others may result from shifts in balance among naturally occurring alternate splicing variants among mRNAs that participate in cell cycle progression and the regulation of apoptosis. This review provides examples of cancer-related alternate splicing events resulting from each step of mRNA processing and the promising therapies that may be used to address them.
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Affiliation(s)
- James D Fackenthal
- Department of Biological Sciences, College of Science and Health, Benedictine University, Lisle, IL 60532, USA
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Abbes S, Baldi S, Sellami H, Amedei A, Keskes L. Molecular methods for colorectal cancer screening: Progress with next-generation sequencing evolution. World J Gastrointest Oncol 2023; 15:425-442. [PMID: 37009313 PMCID: PMC10052664 DOI: 10.4251/wjgo.v15.i3.425] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/02/2023] [Accepted: 02/15/2023] [Indexed: 03/14/2023] Open
Abstract
Currently, colorectal cancer (CRC) represents the third most common malignancy and the second most deadly cancer worldwide, with a higher incidence in developed countries. Like other solid tumors, CRC is a heterogeneous genomic disease in which various alterations, such as point mutations, genomic rearrangements, gene fusions or chromosomal copy number alterations, can contribute to the disease development. However, because of its orderly natural history, easily accessible onset location and high lifetime incidence, CRC is ideally suited for preventive intervention, but the many screening efforts of the last decades have been compromised by performance limitations and low penetrance of the standard screening tools. The advent of next-generation sequencing (NGS) has both facilitated the identification of previously unrecognized CRC features such as its relationship with gut microbial pathogens and revolutionized the speed and throughput of cataloguing CRC-related genomic alterations. Hence, in this review, we summarized the several diagnostic tools used for CRC screening in the past and the present, focusing on recent NGS approaches and their revolutionary role in the identification of novel genomic CRC characteristics, the advancement of understanding the CRC carcinogenesis and the screening of clinically actionable targets for personalized medicine.
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Affiliation(s)
- Salma Abbes
- Laboratory of Parasitic and Fungal Molecular Biology, University of Sfax, Sfax 3029, Tunisia
| | - Simone Baldi
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50134, Italy
| | - Hayet Sellami
- Drosophila Research Unit-Parasitology and Mycologie Laboratory, University of Sfax, Sfax 3029, Tunisia
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50134, Italy
- SOD of Interdisciplinary Internal Medicine, Careggi University Hospital, Florence 50134, Italy
| | - Leila Keskes
- Laboratory of Human Molecular Genetic, University of Sfax, Sfax 3029, Tunisia
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Identification and in silico characterization of CSRP3 synonymous variants in dilated cardiomyopathy. Mol Biol Rep 2023; 50:4105-4117. [PMID: 36877346 DOI: 10.1007/s11033-023-08314-7] [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: 10/12/2021] [Accepted: 01/31/2023] [Indexed: 03/07/2023]
Abstract
BACKGROUND Synonymous variations have always been ignored while studying the underlying genetic mechanisms for most of the human diseases. However, recent studies have suggested that these silent changes in the genome can alter the protein expression and folding. METHODS AND RESULTS CSRP3, which is a well-known candidate gene associated with dilated cardiomyopathy (DCM) and hypertrophic cardiomyopathy (HCM), was screened for 100 idiopathic DCM cases and 100 controls. Three synonymous variations were identified viz., c.96G > A, p.K32=; c.336G > A, p.A112=; c.354G > A, p.E118=. A comprehensive in silico analysis was performed using various web based widely accepted tools, Mfold, Codon Usage, HSF3.1 and RNA22. Mfold predicted structural changes in all the variants except c.96 G > A (p.K32=), however it predicted changes in the stability of mRNA due to all the synonymous variants. Codon bias was observed as evident by the Relative Synonymous Codon Usage and Log Ratio of Codon Usage Frequencies. The Human Splicing Finder also predicted remarkable changes in the regulatory elements in the variants c.336G > A and c.354 G > A. The miRNA target prediction using varied modes available in RNA22 revealed that 70.6% of the target sites of miRNAs in CSRP3 were altered due to variant c.336G > A while 29.41% sites were completely lost. CONCLUSION Findings of the present study suggest that synonymous variants revealed striking deviations in the structural conformation of mRNA, stability of mRNA, relative synonymous codon usage, splicing and miRNA binding sites from the wild type suggesting their possible role in the pathogenesis of DCM, either by destabilizing the mRNA structure, or codon usage bias or else altering the cis-acting regulatory elements during splicing.
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Khan A, Waqas M, Tufail M, Halim SA, Murad W, Ahmad SU, Faheem M, Uddin J, Khalid A, Abdalla AN, Khan A, Al-Harrasi A. In silico scanning of structural and functional deleterious nsSNPs in Arabidopsis thaliana's SOG1 protein, using molecular dynamic simulation approaches. J Biomol Struct Dyn 2023; 41:11629-11646. [PMID: 36734218 DOI: 10.1080/07391102.2023.2174187] [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: 07/28/2022] [Accepted: 01/02/2023] [Indexed: 02/04/2023]
Abstract
Suppressor of gamma response 1 (SOG1) is a member of the NAC domain family transcription factors of the DNA damage response (DDR) signaling in the plant's genome. SOG1 is directly involved in transcriptional response to DNA damage, cell cycle checkpoints and ATR or ATM-mediated activation of the DNA damage responses and repair functioning in programmed cell death and regulation of end reduplication. Different mutations in the SOG1 protein lead to severe diseases and, ultimately, cell death. Single nucleotide polymorphisms (SNPs) are an important type of genetic alteration that cause different diseases or programmed cell death. The current study applied different computational approaches to Arabidopsis thaliana L. SOG1 protein to identify the potential deleterious nsSNPs and monitor their impact on the structure, function and protein stability. Various bioinformatics tools were applied to analyze the retrieved 34 nsSNPs and interestingly extracted four deleterious nsSNPs, that is, ensvath13968004 (Q166L), tmp18998388 (P159L), ensvath01103049 (K199N) and tmp18998295 (Y190F). For example, homology modeling, conservation and conformational analysis of the mutant's models were considered to scrutinize the deviations of these variants from the native SOG1 structure. All atoms molecular dynamic simulation confirmed the significance of these mutations on the protein stability, residual and structural conformation, compactness, surface conformation, dominant motion, Gibbs free energy distribution and dynamic effects. Similarly, protein-protein interaction revealed that SOG1 operates as a hub-linking cluster of various proteins, and any changes in the SOG1 might result in the disassociation of several signal transduction cascades.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Asif Khan
- Laboratory of Phytochemistry, Department of Botany, University of São Paulo, São Paulo, Brazil
| | - Muhammad Waqas
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Sultanate of Oman
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Dhodial, Pakistan
| | - Muhammad Tufail
- Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Sultanate of Oman
| | - Waheed Murad
- Department of Botany, Abdul Wali Khan University Mardan, Pakistan
| | - Syed Umair Ahmad
- Department of Bioinformatics, Hazara University, Mansehra, Dhodial, Pakistan
| | - Muhammad Faheem
- Department of Biological Sciences, National University of Medical Sciences, The Mall, Rawalpindi, Pakistan
| | - Jalal Uddin
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Abha, Kingdom of Saudi Arabia
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Center, Jazan University, Jazan, Saudi Arabia
- Medicinal and Aromatic Plants and Traditional Medicine Research Institute, National Center for Research, Khartoum, Sudan
| | - Ashraf N Abdalla
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Sultanate of Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Sultanate of Oman
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A Group of Tumor-Suppressive micro-RNAs Changes Expression Coordinately in Colon Cancer. Curr Issues Mol Biol 2023; 45:975-989. [PMID: 36826008 PMCID: PMC9955927 DOI: 10.3390/cimb45020063] [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: 12/16/2022] [Revised: 01/12/2023] [Accepted: 01/17/2023] [Indexed: 01/22/2023] Open
Abstract
MicroRNAs (miRNAs) are molecules with a role in the post-transcriptional regulation of messenger RNA, being involved in a wide range of biological and pathological processes. In the present study, we aim to characterize the behavior of a few miRNAs with roles in the cell cycle and differentiation of colon cancer (CC) cells. The present work considers miRNAs as reflections of the complex cellular processes in which they are generated, their observed variations being used to characterize the molecular networks in which they are part and through which cell proliferation is achieved. Tumoral and adjacent normal tissue samples were obtained from 40 CC patients, and the expression of miR-29a, miR-146a, miR-215 and miR-449 were determined by qRT-PCR analysis. Subsequent bioinformatic analysis was performed to highlight the transcription factors (TFs) network that regulate the miRNAs and functionally characterizes this network. There was a significant decrease in the expression of all miRNAs in tumor tissue. All miRNAs were positively correlated with each other. The analysis of the TF network showed tightly connected functional modules related to the cell cycle and associated processes. The four miRNAs are downregulated in CC; they are strongly correlated, showing coherence within the cellular network that regulates them and highlighting possible approach strategies.
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Huang S, Jing D, Xu L, Luo G, Hu Y, Wu T, Hu Y, Li F, He K, Qin W, Sun Y, Liu H. Genome-wide identification and functional analysis of long non-coding RNAs in Chilo suppressalis reveal their potential roles in chlorantraniliprole resistance. Front Physiol 2023; 13:1091232. [PMID: 36699669 PMCID: PMC9868556 DOI: 10.3389/fphys.2022.1091232] [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: 11/06/2022] [Accepted: 12/16/2022] [Indexed: 01/11/2023] Open
Abstract
Long non-coding RNAs, referred to as lncRNAs, perform essential functions in some biological processes, including reproduction, metamorphosis, and other critical life functions. Yet, lncRNAs are poorly understood in pesticide resistance, and no reports to date have characterized which lncRNAs are associated with chlorantraniliprole resistance in Chilo suppressalis. Here, RNA-seq was performed on two strains of C. suppressalis exposed to chlorantraniliprole: one is a susceptible strain (S), and the other is a resistant strain (R). In total, 3,470 lncRNAs were identified from 40,573 merged transcripts in six libraries, including 1,879 lincRNAs, 245 intronic lncRNAs, 853 sense lncRNAs, and 493 antisense lncRNAs. Moreover, differential expression analysis revealed 297 and 335 lncRNAs upregulated in S and R strains, respectively. Differentially expressed (DE) lncRNAs are usually assumed to be involved in the chlorantraniliprole resistance in C. suppressalis. As potential targets, adjacent protein-coding genes (within <1000 kb range upstream or downstream of DE lncRNAs), especially detoxification enzyme genes (cytochrome P450s, carboxyl/cholinesterases/esterases, and ATP-binding cassette transporter), were analyzed. Furthermore, the strand-specific RT-PCR was conducted to confirm the transcript orientation of randomly selected 20 DE lincRNAs, and qRT-PCR was carried out to verify the expression status of 8 out of them. MSTRG.25315.3, MSTRG.25315.6, and MSTRG.7482.1 were upregulated in the R strain. Lastly, RNA interference and bioassay analyses indicated overexpressed lincRNA MSTRG.7482.1 was involved in chlorantraniliprole resistance. In conclusion, we represent, for the first time, the genome-wide identification of chlorantraniliprole-resistance-related lncRNAs in C. suppressalis. It elaborates the views underlying the mechanism conferring chlorantraniliprole resistance in lncRNAs.
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Affiliation(s)
- Shuijin Huang
- Institute of Plant Protection, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Dong Jing
- Institute of Insect Sciences/Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Lu Xu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
| | - Guanghua Luo
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
| | - Yanyue Hu
- Institute of Plant Protection, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Ting Wu
- Institute of Plant Protection, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Yao Hu
- Institute of Animal Husbandry and Veterinary Medicine, Jiangxi Academy of Agricultural Sciences, Nanchang City, China
| | - Fei Li
- Institute of Insect Sciences/Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Kang He
- Institute of Insect Sciences/Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Wenjing Qin
- Institute of Soil Fertilizer and Environmental Resource, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Yang Sun
- Institute of Plant Protection, Jiangxi Academy of Agricultural Sciences, Nanchang, China,*Correspondence: Yang Sun, ; Hui Liu,
| | - Hui Liu
- Institute of Red Soil and Germplasm Resources in Jiangxi, Nanchang, China,*Correspondence: Yang Sun, ; Hui Liu,
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Voss G, Ceder Y. Two-Tailed RT-qPCR for the Quantification of A-to-I-Edited microRNA Isoforms. Curr Protoc 2023; 3:e645. [PMID: 36688607 DOI: 10.1002/cpz1.645] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
MicroRNAs are short non-coding RNAs with important functions in the regulation of gene expression in healthy and diseased tissues. To optimally utilize the biological and clinical information that is contained in microRNA expression levels, tools for their accurate and cost-effective quantification are needed. While the standard method, qPCR, allows for quick and cheap microRNA quantification, specificity is limited due to the short lengths of microRNAs and the high similarity between closely related microRNA family members. A-to-I editing can further diversify the microRNA pool by altering individual nucleotides. There is currently a lack of protocols for the accurate quantification of A-to-I-edited microRNA isoforms using qPCR. Here, we describe a protocol to quantify microRNA editing isoforms using two-tailed RT-qPCR, with either SYBR Green or hydrolysis probes. The user will perform reverse transcription of RNA samples, generate standard curves, and quantify the resulting cDNA in the following qPCR step. We also give guidelines for primer design and for the evaluation of assays using synthetic oligonucleotides. These tools are expected to be transferable to any A-to-I-edited microRNA and its isoforms. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Two-tailed reverse transcription of A-to-I-edited microRNAs Basic Protocol 2: SYBR Green-based qPCR for A-to-I-edited microRNAs Alternate Protocol: Hydrolysis probe-based qPCR for A-to-I-edited microRNAs Support Protocol: Preparation of standard curves using synthetic RNA oligonucleotides.
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Affiliation(s)
- Gjendine Voss
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Current address: Eugene Bell Center, Marine Biological Laboratory, Woods Hole, Massachusetts
| | - Yvonne Ceder
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
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Ma T, Chen Y, Yi ZG, Liu J, Li YH, Bai J, Tie WT, Huang M, Zhu XF, Wang J, Du J, Zuo XQ, Li Q, Lin FL, Tang L, Guo J, Xiao HW, Lei Q, Ma XL, Li LJ, Zhang LS. NORAD promotes multiple myeloma cell progression via BMP6/P-ERK1/2 axis. Cell Signal 2022; 100:110474. [PMID: 36126794 DOI: 10.1016/j.cellsig.2022.110474] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/01/2022] [Accepted: 09/14/2022] [Indexed: 11/03/2022]
Abstract
Multiple myeloma (MM) is one of the most common tumors of the hematological system and remains incurable. Recent studies have shown that long noncoding RNA NORAD is a potential oncogene in a variety of tumors. However, the general biological role and clinical value of NORAD in MM remains unknown. In this study, we measured NORAD expression in bone marrow of 60 newly diagnosed MM, 30 post treatment MM and 17 healthy donors by real-time quantitative polymerase chain reaction (qPCR). The NORAD gene was knockdown by lentiviral transfection in MM cell lines, and the effects of NORAD on apoptosis, cell cycle and cell proliferation in MM cells were examined by flow cytometry, CCK8 assay, EDU assay and Western blot, and the differential genes after knockdown of NORAD were screened by mRNA sequencing, followed by in vivo experiments and immunohistochemical assays. We found that knockdown of NORAD promoted MM cell apoptosis, induced cell cycle G1 phase arrest, and inhibited MM cell apoptosis in in vivo and in vitro experiments. Mechanistically, NORAD plays these roles through the BMP6/P-ERK1/2 axis. We discuss a novel mechanism by which NORAD acts pro-tumorigenically in MM via the BMP6/P-ERK1/2 axis.
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Affiliation(s)
- Tao Ma
- Department of Hematology, Lanzhou University Second Hospital, Lanzhou 730000, China; Department of Hematology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
| | - Yan Chen
- Department of Hematology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
| | - Zhi-Gang Yi
- Department of Hematology, Lanzhou University Second Hospital, Lanzhou 730000, China
| | - Jia Liu
- Department of Hematology, Lanzhou University Second Hospital, Lanzhou 730000, China
| | - Yan-Hong Li
- Department of Hematology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
| | - Jun Bai
- Department of Hematology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
| | - Wen-Ting Tie
- Department of Hematology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
| | - Mei Huang
- Department of Hematology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
| | - Xiao-Feng Zhu
- Department of Hematology, Lanzhou University Second Hospital, Lanzhou 730000, China; Department of Hematology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
| | - Ji Wang
- Department of Hematology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
| | - Juan Du
- Department of Hematology, Lanzhou University Second Hospital, Lanzhou 730000, China
| | - Xiu-Qin Zuo
- Department of Hematology, Lanzhou University Second Hospital, Lanzhou 730000, China
| | - Qin Li
- Department of Hematology, Lanzhou University Second Hospital, Lanzhou 730000, China
| | - Fan-Li Lin
- Department of Hematology, Lanzhou University Second Hospital, Lanzhou 730000, China
| | - Liu Tang
- Department of Hematology, Lanzhou University Second Hospital, Lanzhou 730000, China
| | - Jing Guo
- Department of Hematology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
| | - Hong-Wen Xiao
- Department of Hematology, Lanzhou University Second Hospital, Lanzhou 730000, China
| | - Qian Lei
- Department of Hematology, Lanzhou University Second Hospital, Lanzhou 730000, China
| | - Xiao-Li Ma
- Department of Hematology, Lanzhou University Second Hospital, Lanzhou 730000, China
| | - Li-Juan Li
- Department of Hematology, Lanzhou University Second Hospital, Lanzhou 730000, China.
| | - Lian-Sheng Zhang
- Department of Hematology, Lanzhou University Second Hospital, Lanzhou 730000, China.
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Takahashi H, Sovadinova I, Yasuhara K, Vemparala S, Caputo GA, Kuroda K. Biomimetic antimicrobial polymers—Design, characterization, antimicrobial, and novel applications. WIRES NANOMEDICINE AND NANOBIOTECHNOLOGY 2022; 15:e1866. [PMID: 36300561 DOI: 10.1002/wnan.1866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 09/15/2022] [Accepted: 09/27/2022] [Indexed: 11/05/2022]
Abstract
Biomimetic antimicrobial polymers have been an area of great interest as the need for novel antimicrobial compounds grows due to the development of resistance. These polymers were designed and developed to mimic naturally occurring antimicrobial peptides in both physicochemical composition and mechanism of action. These antimicrobial peptide mimetic polymers have been extensively investigated using chemical, biophysical, microbiological, and computational approaches to gain a deeper understanding of the molecular interactions that drive function. These studies have helped inform SARs, mechanism of action, and general physicochemical factors that influence the activity and properties of antimicrobial polymers. However, there are still lingering questions in this field regarding 3D structural patterning, bioavailability, and applicability to alternative targets. In this review, we present a perspective on the development and characterization of several antimicrobial polymers and discuss novel applications of these molecules emerging in the field. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Therapeutic Approaches and Drug Discovery > Nanomedicine for Infectious Disease.
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Affiliation(s)
- Haruko Takahashi
- Graduate School of Integrated Sciences for Life Hiroshima University Higashi‐Hiroshima Hiroshima Japan
| | - Iva Sovadinova
- RECETOX, Faculty of Science Masaryk University Brno Czech Republic
| | - Kazuma Yasuhara
- Division of Materials Science, Graduate School of Science and Technology Nara Institute of Science and Technology Nara Japan
- Center for Digital Green‐Innovation Nara Institute of Science and Technology Nara Japan
| | - Satyavani Vemparala
- The Institute of Mathematical Sciences CIT Campus Chennai India
- Homi Bhabha National Institute Training School Complex Mumbai India
| | - Gregory A. Caputo
- Department of Chemistry & Biochemistry Rowan University Glassboro New Jersey USA
| | - Kenichi Kuroda
- Department of Biologic and Materials Sciences & Prosthodontics, School of Dentistry University of Michigan Ann Arbor Michigan USA
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Khan N, Umar MS, Haq M, Rauf T, Zubair S, Owais M. Exosome-encapsulated ncRNAs: Emerging yin and yang of tumor hallmarks. Front Genet 2022; 13:1022734. [PMID: 36338993 PMCID: PMC9632295 DOI: 10.3389/fgene.2022.1022734] [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: 08/18/2022] [Accepted: 09/30/2022] [Indexed: 11/21/2022] Open
Abstract
Tumorigenesis is a multifaceted process, where multiple physiological traits serving as cancer’s distinctive characteristics are acquired. “Hallmarks of cancer” is a set of cognitive abilities acquired by human cells that are pivotal to their tumor-forming potential. With limited or no protein-coding ability, non-coding RNAs (ncRNAs) interact with their target molecules and yield significant regulatory effects on several cell cycle processes. They play a “yin” and “yang” role, thereby functioning both as oncogenic and tumor suppressor and considered important in the management of various types of cancer entities. ncRNAs serve as important post-transcriptional and translational regulators of not only unrestricted expansion and metastasis of tumor cells but also of various biological processes, such as genomic mutation, DNA damage, immune escape, and metabolic disorder. Dynamical attributes such as increased proliferative signaling, migration, invasion, and epithelial–mesenchymal transition are considered to be significant determinants of tumor malignancy, metastatic dissemination, and therapeutic resistance. Furthermore, these biological attributes engage tumor cells with immune cells within the tumor microenvironment to promote tumor formation. We elaborate the interaction of ncRNAs with various factors in order to regulate cancer intra/intercellular signaling in a specific tumor microenvironment, which facilitates the cancer cells in acquiring malignant hallmarks. Exosomes represent a means of intercellular communication and participate in the maintenance of the tumor hallmarks, adding depth to the intricate, multifactorial character of malignant neoplasia. To summarize, ncRNAs have a profound impact on tumors, affecting their microcirculation, invasiveness, altered metabolism, microenvironment, and the capacity to modify the host immunological environment. Though the significance of ncRNAs in crosstalk between the tumor and its microenvironment is being extensively explored, we intend to review the hallmarks in the light of exosome-derived non-coding RNAs and their impact on the tumor microenvironment.
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Affiliation(s)
- Nazoora Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Mohd Saad Umar
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Mohamed Haq
- University of Houston, Houston, TX, United States
| | - Talha Rauf
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Swaleha Zubair
- Department of Computer Science, Faculty of Science, Aligarh Muslim University, Aligarh, India
| | - Mohammad Owais
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
- *Correspondence: Mohammad Owais,
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Competing Endogenous RNA (ceRNA) Networks and Splicing Switches in Cervical Cancer: HPV Oncogenesis, Clinical Significance and Therapeutic Opportunities. Microorganisms 2022; 10:microorganisms10091852. [PMID: 36144454 PMCID: PMC9501168 DOI: 10.3390/microorganisms10091852] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/25/2022] [Accepted: 09/09/2022] [Indexed: 12/20/2022] Open
Abstract
Cervical cancer (CC) is the primary cause of female cancer fatalities in low-middle-income countries (LMICs). Persistent infections from the human papillomavirus (HPV) can result in cervical cancer. However, numerous different factors influence the development and progression of cervical cancer. Transcriptomic knowledge of the mechanisms with which HPV causes cervical cancer pathogenesis is growing. Nonetheless, there is an existing gap hindering the development of therapeutic approaches and the improvement of patient outcomes. Alternative splicing allows for the production of numerous RNA transcripts and protein isoforms from a single gene, increasing the transcriptome and protein diversity in eukaryotes. Cancer cells exhibit astounding transcriptome modifications by expressing cancer-specific splicing isoforms. High-risk HPV uses cellular alternative splicing events to produce viral and host splice variants and proteins that drive cancer progression or contribute to distinct cancer hallmarks. Understanding how viruses utilize alternative splicing to drive pathogenesis and tumorigenesis is essential. Although research into the role of miRNAs in tumorigenesis is advancing, the function of other non-coding RNAs, including lncRNA and circRNA, has been understudied. Through their interaction with mRNA, non-coding RNAs form a network of competing endogenous RNAs (ceRNAs), which regulate gene expression and promote cervical cancer development and advancement. The dysregulated expression of non-coding RNAs is an understudied and tangled process that promotes cervical cancer development. This review will present the role of aberrant alternative splicing and immunosuppression events in HPV-mediated cervical tumorigenesis, and ceRNA network regulation in cervical cancer pathogenesis will also be discussed. Furthermore, the therapeutic potential of splicing disruptor drugs in cervical cancer will be deliberated.
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Nisar A, Kayani MA, Nasir W, Mehmood A, Ahmed MW, Parvez A, Mahjabeen I. Fyn and Lyn gene polymorphisms impact the risk of thyroid cancer. Mol Genet Genomics 2022; 297:1649-1659. [PMID: 36058999 DOI: 10.1007/s00438-022-01946-7] [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: 06/27/2021] [Accepted: 08/11/2022] [Indexed: 10/14/2022]
Abstract
Thyroid cancer is the most common malignancy of the endocrine glands, and during last couple of decades, its incidence has risen alarmingly, across the globe. Etiology of thyroid cancer is still debatable. There are a few worth mentioning risk factors which contribute to initiation of abnormalities in thyroid gland leading to cancer. Genetic instability is major risk factors in thyroid carcinogenesis. Among the genetic factors, the Src family of genes (Src, Yes1, Fyn and Lyn) have been implicated in many cancers but there is little data regarding the association of these (Src, Yes1, Fyn and Lyn) genes with thyroid carcinogenesis. Fyn and Lyn genes of Src family found engaged in proliferation, migration, invasion, angiogenesis, and metastasis in different cancers. This study was planned to examine the effect of Fyn and Lyn SNPs on thyroid cancer risk in Pakistani population in 500 patients and 500 controls. Three polymorphisms of Fyn gene (rs6916861, rs2182644 and rs12910) and three polymorphisms of Lyn gene (rs2668011, rs45587541 and rs45489500) were analyzed using Tetra-primer ARMS-PCR followed by DNA sequencing. SNP rs6916861 of Fyn gene mutant genotype (CC) showed statistically significant threefold increased risk of thyroid cancer (P < 0.0001). In case of rs2182644 of Fyn gene, mutant genotype (AA) indicated statistically significant 17-fold increased risk of thyroid cancer (P < 0.0001). Statistically significant threefold increased risk of thyroid cancer was observed in genotype AC (P < 0.0001) of Fyn gene polymorphism rs12910. In SNP rs2668011 of Lyn gene, TT genotype showed statistically significant threefold increased risk of thyroid cancer (P < 0.0001). In case of rs45587541 of Lyn gene, GA genotypes showed statistically significant 11-fold increased risk in thyroid cancer (P < 0.0001). Haplotype analysis revealed that AAATAG*, AGACAG*, AGCCAA*, AGCCAG*, CAATAG*, CGCCAG* and CGCCGA* haplotypes of Fyn and Lyn polymorphisms are associated with increased thyroid cancer risk. These results showed that genotypes and allele distribution of Fyn and Lyn are significantly linked with increased thyroid cancer risk and could be genetic adjuster for said disease.
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Affiliation(s)
- Asif Nisar
- Cancer Genetics and Epigenetics Lab, Department of Biosciences, COMSATS University Islamabad, Park Road Tarlai Kalan, Islamabad, Pakistan
| | - Mahmood Akhtar Kayani
- Cancer Genetics and Epigenetics Lab, Department of Biosciences, COMSATS University Islamabad, Park Road Tarlai Kalan, Islamabad, Pakistan
| | - Wajiha Nasir
- Department of Radiation, Nuclear Oncology Radiation Institute, Islamabad, Pakistan
| | - Azhar Mehmood
- Cancer Genetics and Epigenetics Lab, Department of Biosciences, COMSATS University Islamabad, Park Road Tarlai Kalan, Islamabad, Pakistan
| | - Malik Waqar Ahmed
- Cancer Genetics and Epigenetics Lab, Department of Biosciences, COMSATS University Islamabad, Park Road Tarlai Kalan, Islamabad, Pakistan.,Pakistan Institute of Rehabilitation Sciences (PIRS), Isra University Islamabad Campus, Islamabad, Pakistan
| | - Aamir Parvez
- Cancer Genetics and Epigenetics Lab, Department of Biosciences, COMSATS University Islamabad, Park Road Tarlai Kalan, Islamabad, Pakistan
| | - Ishrat Mahjabeen
- Cancer Genetics and Epigenetics Lab, Department of Biosciences, COMSATS University Islamabad, Park Road Tarlai Kalan, Islamabad, Pakistan.
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Molecular Characterization, Expression Profiles of SMAD4, SMAD5 and SMAD7 Genes and Lack of Association with Litter Size in Tibetan Sheep. Animals (Basel) 2022; 12:ani12172232. [PMID: 36077952 PMCID: PMC9455033 DOI: 10.3390/ani12172232] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/23/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
SMAD4, SMAD5 and SMAD7 belonging to the transforming growth factor β (TGF-β) superfamily are indispensable for oocyte formation and development, ovarian organogenesis and folliculogenesis. However, only a few studies have investigated the characteristics of SMAD4, SMAD5 and SMAD7 in Tibetan sheep and the effect of their polymorphism on litter size. In this study, we examined the expression of SMAD4, SMAD5 and SMAD7 in 13 tissues of Tibetan sheep by reverse transcription-quantitative polymerase chain reaction. Further, cDNA of these genes was cloned, sequenced and subjected to bioinformatics analysis. DNA sequencing was also used to detect single nucleotide polymorphisms (SNPs). However, iM-LDRTM technology was used for SNP genotyping. Associations between polymorphisms and litter size were analyzed using data from genotyping of 433 Tibetan sheep. The results showed that the expression of SMAD4, SMAD5 and SMAD7 genes was ubiquitous in the tissues of Tibetan sheep, such as the ovary, uterus and oviduct, hypothalamus, hypophysis, heart, liver, spleen, lung, kidney, rumen, duodenum and longissimus dorsi. However, the expression was unbalanced and upregulated in the spleen, lung, ovary and uterus and downregulated in the longissimus dorsi. The bioinformatics analysis showed that SMAD4, SMAD5 and SMAD7 in Tibetan sheep encoded proteins of 533, 465 and 427 amino acids, respectively. Sequence homology analysis of the three proteins among other animals showed that the sequences of SMAD4, SMAD5 and SMAD7 of Tibetan sheep were similar to those in sheep, yak, cattle, dog, human, pig, chimpanzee, rhesus monkey and house mouse. Two synonymous mutations, g.51537A>G and g.319C>T, were detected in SMAD5 and SMAD7, respectively. The associations of these SNPs and litter size were determined, and it was found that both g.51537A>G and g.319C>T have no significant effect on the litter size of Tibetan sheep. The results provided novel insights into the molecular characterization, expression profiles and polymorphisms of SMAD4, SMAD5 and SMAD7 in Tibetan sheep, but our results do not support associations between these genes and the litter size of Tibetan sheep.
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Ghareyazi A, Kazemi A, Hamidieh K, Dashti H, Tahaei MS, Rabiee HR, Alinejad-Rokny H, Dehzangi I. Pan-cancer integrative analysis of whole-genome De novo somatic point mutations reveals 17 cancer types. BMC Bioinformatics 2022; 23:298. [PMID: 35879674 PMCID: PMC9316662 DOI: 10.1186/s12859-022-04840-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 07/14/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The advent of high throughput sequencing has enabled researchers to systematically evaluate the genetic variations in cancer, identifying many cancer-associated genes. Although cancers in the same tissue are widely categorized in the same group, they demonstrate many differences concerning their mutational profiles. Hence, there is no definitive treatment for most cancer types. This reveals the importance of developing new pipelines to identify cancer-associated genes accurately and re-classify patients with similar mutational profiles. Classification of cancer patients with similar mutational profiles may help discover subtypes of cancer patients who might benefit from specific treatment types. RESULTS In this study, we propose a new machine learning pipeline to identify protein-coding genes mutated in many samples to identify cancer subtypes. We apply our pipeline to 12,270 samples collected from the international cancer genome consortium, covering 19 cancer types. As a result, we identify 17 different cancer subtypes. Comprehensive phenotypic and genotypic analysis indicates distinguishable properties, including unique cancer-related signaling pathways. CONCLUSIONS This new subtyping approach offers a novel opportunity for cancer drug development based on the mutational profile of patients. Additionally, we analyze the mutational signatures for samples in each subtype, which provides important insight into their active molecular mechanisms. Some of the pathways we identified in most subtypes, including the cell cycle and the Axon guidance pathways, are frequently observed in cancer disease. Interestingly, we also identified several mutated genes and different rates of mutation in multiple cancer subtypes. In addition, our study on "gene-motif" suggests the importance of considering both the context of the mutations and mutational processes in identifying cancer-associated genes. The source codes for our proposed clustering pipeline and analysis are publicly available at: https://github.com/bcb-sut/Pan-Cancer .
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Affiliation(s)
- Amin Ghareyazi
- Bioinformatics and Computational Biology Lab, Department of Computer Engineering, Sharif University of Technology, Tehran, 11365, Iran
| | - Amirreza Kazemi
- Bioinformatics and Computational Biology Lab, Department of Computer Engineering, Sharif University of Technology, Tehran, 11365, Iran.,Department of Computer Engineering, Simon Fraser University, Burnaby, BC, 1S6, Canada
| | - Kimia Hamidieh
- Department of Computer Science, University of Toronto, Toronto, ON, M5S 3H2, Canada
| | - Hamed Dashti
- Bioinformatics and Computational Biology Lab, Department of Computer Engineering, Sharif University of Technology, Tehran, 11365, Iran
| | - Maedeh Sadat Tahaei
- Bioinformatics and Computational Biology Lab, Department of Computer Engineering, Sharif University of Technology, Tehran, 11365, Iran
| | - Hamid R Rabiee
- Bioinformatics and Computational Biology Lab, Department of Computer Engineering, Sharif University of Technology, Tehran, 11365, Iran.
| | - Hamid Alinejad-Rokny
- BioMedical Machine Learning Lab (BML), The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW, 2052, Australia.,UNSW Data Science Hub, The University of New South Wales (UNSW Sydney), Sydney, NSW, 2052, Australia.,AI-Enabled Processes (AIP) Research Centre, Macquarie University, Sydney, 2109, Australia
| | - Iman Dehzangi
- Department of Computer Science, Rutgers University, Camden, NJ, 08102, USA. .,Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, 08102, USA.
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Boldyreva LV, Andreyeva EN, Pindyurin AV. Position Effect Variegation: Role of the Local Chromatin Context in Gene Expression Regulation. Mol Biol 2022. [DOI: 10.1134/s0026893322030049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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40
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Genetic Polymorphisms of IGF1 and IGF1R Genes and Their Effects on Growth Traits in Hulun Buir Sheep. Genes (Basel) 2022; 13:genes13040666. [PMID: 35456472 PMCID: PMC9031115 DOI: 10.3390/genes13040666] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/25/2022] [Accepted: 04/07/2022] [Indexed: 01/08/2023] Open
Abstract
The identification of candidate genes and genetic variations associated with growth traits is important for sheep breeding. Insulin like growth factor 1 (IGF1) and insulin like growth factor 1 receptor (IGF1R) are well-accepted candidate genes that affect animal growth and development. The current study attempted to assess the association between IGF1 and IGF1R genetic polymorphisms and growth traits in Hulun Buir sheep. To achieve this goal, we first identified three and ten single nucleotide polymorphisms (SNPs) in exons of IGF1 and IGF1R in Hulun Buir sheep and then constructed six haplotypes of IGF1R based on linkage disequilibrium, respectively. Association studies were performed between SNPs and haplotypes of IGF1 and IGF1R with twelve growth traits in a population encompassing 229 Hulun Buir sheep using a general linear model. Our result indicated three SNPs in IGF1 were significantly associated with four growth traits (p < 0.05). In IGF1R, three SNPs and two haplotype blocks were significantly associated with twelve growth traits (p < 0.05). The combined haplotype H5H5 and H5H6 in IGF1R showed the strong association with 12 superior growth traits in Hulun Buir sheep (p < 0.05). In conclusion, we identified SNPs and haplotype combinations associated with the growth traits, which provided genetic resources for marker-assisted selection (MAS) in Hulun Buir sheep breeding.
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Disciglio V, Sanese P, Fasano C, Lotesoriere C, Valentini AM, Forte G, Lepore Signorile M, De Marco K, Grossi V, Lolli I, Cariola F, Simone C. Identification and Somatic Characterization of the Germline PTEN Promoter Variant rs34149102 in a Family with Gastrointestinal and Breast Tumors. Genes (Basel) 2022; 13:644. [PMID: 35456450 PMCID: PMC9025445 DOI: 10.3390/genes13040644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/31/2022] [Accepted: 04/02/2022] [Indexed: 02/04/2023] Open
Abstract
Genetic variants located in non-coding regions can affect processes that regulate protein expression, functionally contributing to human disease. Germline heterozygous mutations in the non-coding region of the PTEN gene have been previously identified in patients with PTEN hamartoma tumor syndrome (PHTS) diagnosed with breast, thyroid, and/or endometrial cancer. In this study, we report a PTEN promoter variant (rs34149102 A allele) that was identified by direct sequencing in an Italian family with a history of gastroesophageal junction (GEJ) adenocarcinoma and breast cancer. In order to investigate the putative functional role of the rs34149102 A allele variant, we evaluated the status of PTEN alterations at the somatic level. We found that PTEN protein expression was absent in the GEJ adenocarcinoma tissue of the index case. Moreover, we detected the occurrence of copy number loss involving the PTEN rs34149102 major C allele in tumor tissue, revealing that the second allele was somatically inactivated. This variant is located within an active regulatory region of the PTEN core promoter, and in silico analysis suggests that it may affect the binding of the nuclear transcription factor MAZ and hence PTEN expression. Overall, these results reveal the functional role of the PTEN promoter rs34149102 A allele variant in the modulation of PTEN protein expression and highlight its contribution to hereditary cancer risk.
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Affiliation(s)
- Vittoria Disciglio
- Medical Genetics, National Institute of Gastroenterology—IRCCS “S. de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (V.D.); (P.S.); (C.F.); (G.F.); (M.L.S.); (K.D.M.); (V.G.); (F.C.)
| | - Paola Sanese
- Medical Genetics, National Institute of Gastroenterology—IRCCS “S. de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (V.D.); (P.S.); (C.F.); (G.F.); (M.L.S.); (K.D.M.); (V.G.); (F.C.)
| | - Candida Fasano
- Medical Genetics, National Institute of Gastroenterology—IRCCS “S. de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (V.D.); (P.S.); (C.F.); (G.F.); (M.L.S.); (K.D.M.); (V.G.); (F.C.)
| | - Claudio Lotesoriere
- Oncology Unit, National Institute of Gastroenterology—IRCCS “S. de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (C.L.); (I.L.)
| | - Anna Maria Valentini
- Department of Pathology, National Institute of Gastroenterology—IRCCS “S. de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy;
| | - Giovanna Forte
- Medical Genetics, National Institute of Gastroenterology—IRCCS “S. de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (V.D.); (P.S.); (C.F.); (G.F.); (M.L.S.); (K.D.M.); (V.G.); (F.C.)
| | - Martina Lepore Signorile
- Medical Genetics, National Institute of Gastroenterology—IRCCS “S. de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (V.D.); (P.S.); (C.F.); (G.F.); (M.L.S.); (K.D.M.); (V.G.); (F.C.)
| | - Katia De Marco
- Medical Genetics, National Institute of Gastroenterology—IRCCS “S. de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (V.D.); (P.S.); (C.F.); (G.F.); (M.L.S.); (K.D.M.); (V.G.); (F.C.)
| | - Valentina Grossi
- Medical Genetics, National Institute of Gastroenterology—IRCCS “S. de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (V.D.); (P.S.); (C.F.); (G.F.); (M.L.S.); (K.D.M.); (V.G.); (F.C.)
| | - Ivan Lolli
- Oncology Unit, National Institute of Gastroenterology—IRCCS “S. de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (C.L.); (I.L.)
| | - Filomena Cariola
- Medical Genetics, National Institute of Gastroenterology—IRCCS “S. de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (V.D.); (P.S.); (C.F.); (G.F.); (M.L.S.); (K.D.M.); (V.G.); (F.C.)
| | - Cristiano Simone
- Medical Genetics, National Institute of Gastroenterology—IRCCS “S. de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (V.D.); (P.S.); (C.F.); (G.F.); (M.L.S.); (K.D.M.); (V.G.); (F.C.)
- Medical Genetics, Department of Biomedical Sciences and Human Oncology (DIMO), University of Bari Aldo Moro, 70124 Bari, Italy
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Gogleva A, Polychronopoulos D, Pfeifer M, Poroshin V, Ughetto M, Martin MJ, Thorpe H, Bornot A, Smith PD, Sidders B, Dry JR, Ahdesmäki M, McDermott U, Papa E, Bulusu KC. Knowledge graph-based recommendation framework identifies drivers of resistance in EGFR mutant non-small cell lung cancer. Nat Commun 2022; 13:1667. [PMID: 35351890 PMCID: PMC8964738 DOI: 10.1038/s41467-022-29292-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 03/09/2022] [Indexed: 12/25/2022] Open
Abstract
Resistance to EGFR inhibitors (EGFRi) presents a major obstacle in treating non-small cell lung cancer (NSCLC). One of the most exciting new ways to find potential resistance markers involves running functional genetic screens, such as CRISPR, followed by manual triage of significantly enriched genes. This triage process to identify ‘high value’ hits resulting from the CRISPR screen involves manual curation that requires specialized knowledge and can take even experts several months to comprehensively complete. To find key drivers of resistance faster we build a recommendation system on top of a heterogeneous biomedical knowledge graph integrating pre-clinical, clinical, and literature evidence. The recommender system ranks genes based on trade-offs between diverse types of evidence linking them to potential mechanisms of EGFRi resistance. This unbiased approach identifies 57 resistance markers from >3,000 genes, reducing hit identification time from months to minutes. In addition to reproducing known resistance markers, our method identifies previously unexplored resistance mechanisms that we prospectively validate. Resistance to EGFR inhibitors presents a major obstacle in treating non-small cell lung cancer. Here, the authors develop a recommender system ranking genes based on trade-offs between diverse types of evidence linking them to potential mechanisms of EGFRi resistance.
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Kobayashi Y, Chhoeu C, Li J, Price KS, Kiedrowski LA, Hutchins JL, Hardin AI, Wei Z, Hong F, Bahcall M, Gokhale PC, Jänne PA. Silent mutations reveal therapeutic vulnerability in RAS Q61 cancers. Nature 2022; 603:335-342. [PMID: 35236983 DOI: 10.1038/s41586-022-04451-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/20/2022] [Indexed: 12/26/2022]
Abstract
RAS family members are the most frequently mutated oncogenes in human cancers. Although KRAS(G12C)-specific inhibitors show clinical activity in patients with cancer1-3, there are no direct inhibitors of NRAS, HRAS or non-G12C KRAS variants. Here we uncover the requirement of the silent KRASG60G mutation for cells to produce a functional KRAS(Q61K). In the absence of this G60G mutation in KRASQ61K, a cryptic splice donor site is formed, promoting alternative splicing and premature protein termination. A G60G silent mutation eliminates the splice donor site, yielding a functional KRAS(Q61K) variant. We detected a concordance of KRASQ61K and a G60G/A59A silent mutation in three independent pan-cancer cohorts. The region around RAS Q61 is enriched in exonic splicing enhancer (ESE) motifs and we designed mutant-specific oligonucleotides to interfere with ESE-mediated splicing, rendering the RAS(Q61) protein non-functional in a mutant-selective manner. The induction of aberrant splicing by antisense oligonucleotides demonstrated therapeutic effects in vitro and in vivo. By studying the splicing necessary for a functional KRAS(Q61K), we uncover a mutant-selective treatment strategy for RASQ61 cancer and expose a mutant-specific vulnerability, which could potentially be exploited for therapy in other genetic contexts.
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Affiliation(s)
- Yoshihisa Kobayashi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Medicine, Harvard Medical School, Boston, MA, USA. .,Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan.
| | - Chhayheng Chhoeu
- Experimental Therapeutics Core, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jiaqi Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kristin S Price
- Department of Medical Affairs, Guardant Health, Redwood City, CA, USA
| | | | - Jamie L Hutchins
- Department of Medical Affairs, Guardant Health, Redwood City, CA, USA
| | - Aaron I Hardin
- Department of Medical Affairs, Guardant Health, Redwood City, CA, USA
| | - Zihan Wei
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Fangxin Hong
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.,Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Magda Bahcall
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Prafulla C Gokhale
- Experimental Therapeutics Core, Dana-Farber Cancer Institute, Boston, MA, USA.,Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Pasi A Jänne
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Medicine, Harvard Medical School, Boston, MA, USA. .,Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA. .,Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
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44
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Chen J, Liu H, Cui X, Li Z, Chen HF. RNA-Specific Force Field Optimization with CMAP and Reweighting. J Chem Inf Model 2022; 62:372-385. [PMID: 35021622 DOI: 10.1021/acs.jcim.1c01148] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
RNA plays a key role in a variety of cell activities. However, it is difficult to capture its structure dynamics by the traditional experimental methods because of the inherent limitations. Molecular dynamics simulation has become a valuable complement to the experimental methods. Previous studies have indicated that the current force fields cannot accurately reproduce the conformations and structural dynamics of RNA. Therefore, an RNA-specific force field was developed to improve the conformation sampling of RNA. The distribution of ζ/α dihedrals of tetranucleotides was optimized by a reweighting method, and the grid-based energy correction map (CMAP) term was first introduced into the Amber RNA force field of ff99bsc0χOL3, named ff99OL3_CMAP1. Extensive validations of tetranucleotides and tetraloops show that ff99OL3_CMAP1 can significantly decrease the population of an incorrect structure, increase the consistency between the simulation results and experimental values for tetranucleotides, and improve the stability of tetraloops. ff99OL3_CMAP1 can also precisely reproduce the conformation of a duplex and riboswitches. These findings confirm that the newly developed force field ff99OL3_CMAP1 can improve the conformer sampling of RNA.
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Affiliation(s)
- Jun Chen
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 20024 Shanghai, China
| | - Hao Liu
- Institute of Natural Sciences, Shanghai Jiao Tong University, 200240 Shanghai, China
| | - Xiaochen Cui
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 20024 Shanghai, China
| | - Zhengxin Li
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 20024 Shanghai, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 20024 Shanghai, China.,Shanghai Center for Bioinformation Technology, 200240 Shanghai, China
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45
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Vannini I, Ferracin M, Fabbri F, Fabbri M. Overexpression of ultraconserved region 83- induces lung cancer tumorigenesis. PLoS One 2022; 17:e0261464. [PMID: 35015757 PMCID: PMC8752010 DOI: 10.1371/journal.pone.0261464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 12/02/2021] [Indexed: 01/12/2023] Open
Abstract
The expression of non-coding RNAs (ncRNAs) is dysregulated in human cancers. The transcribed ultraconserved regions (T-UCRs) express long ncRNAs involved in human carcinogenesis. T-UCRs are non-coding genomic sequence that are 100% conserved across humans, rats and mice. Conservation of genomic sequences across species intrinsically implies an essential functional role and so we considered the expression of T-UCRs in lung cancer. Using a custom microarray we analyzed the global expression of T-UCRs. Among these T-UCRs, the greatest variation was observed for antisense ultraconserved element 83 (uc.83-), which was upregulated in human lung cancer tissues compared with adjacent non cancerous tissues. Even though uc.83- is located within the long intergenic non-protein coding RNA 1876 (LINC01876) gene, we found that the transcribed uc.83- is expressed independently of LINC01876 and was cloned as a 1143-bp RNA gene. In this study, functional analysis confirmed important effects of uc.83- on genes involved in cell growth of human cells. siRNA against uc.83- decreased the growth of lung cancer cells while the upregulation through a vector overexpressing the uc.83- RNA increased cell proliferation. We also show the oncogenic function of uc.83- is mediated by the phosphorylation of AKT and ERK 1/2, two important biomarkers of lung cancer cell proliferation. Based on our findings, inhibition against uc.83- could be a future therapeutic treatment for NSCLC to achieve simultaneous blockade of pathways involved in lung carcinogenesis.
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Affiliation(s)
- Ivan Vannini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Manuela Ferracin
- Department of Experimental, Diagnostic and Specialty Medicine—DIMES, University of Bologna, Bologna, Italy
| | - Francesco Fabbri
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Muller Fabbri
- Center for Cancer and Immunology Research, Children’s National Hospital, Washington, DC, United States of America
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Impact of Alternative Splicing Variants on Liver Cancer Biology. Cancers (Basel) 2021; 14:cancers14010018. [PMID: 35008179 PMCID: PMC8750444 DOI: 10.3390/cancers14010018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Among the top ten deadly solid tumors are the two most frequent liver cancers, hepatocellular carcinoma, and intrahepatic cholangiocarcinoma, whose development and malignancy are favored by multifactorial conditions, which include aberrant maturation of pre-mRNA due to abnormalities in either the machinery involved in the splicing, i.e., the spliceosome and associated factors, or the nucleotide sequences of essential sites for the exon recognition process. As a consequence of cancer-associated aberrant splicing in hepatocytes- and cholangiocytes-derived cancer cells, abnormal proteins are synthesized. They contribute to the dysregulated proliferation and eventually transformation of these cells to phenotypes with enhanced invasiveness, migration, and multidrug resistance, which contributes to the poor prognosis that characterizes these liver cancers. Abstract The two most frequent primary cancers affecting the liver, whose incidence is growing worldwide, are hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA), which are among the five most lethal solid tumors with meager 5-year survival rates. The common difficulty in most cases to reach an early diagnosis, the aggressive invasiveness of both tumors, and the lack of favorable response to pharmacotherapy, either classical chemotherapy or modern targeted therapy, account for the poor outcome of these patients. Alternative splicing (AS) during pre-mRNA maturation results in changes that might affect proteins involved in different aspects of cancer biology, such as cell cycle dysregulation, cytoskeleton disorganization, migration, and adhesion, which favors carcinogenesis, tumor promotion, and progression, allowing cancer cells to escape from pharmacological treatments. Reasons accounting for cancer-associated aberrant splicing include mutations that create or disrupt splicing sites or splicing enhancers or silencers, abnormal expression of splicing factors, and impaired signaling pathways affecting the activity of the splicing machinery. Here we have reviewed the available information regarding the impact of AS on liver carcinogenesis and the development of malignant characteristics of HCC and iCCA, whose understanding is required to develop novel therapeutical approaches aimed at manipulating the phenotype of cancer cells.
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Lin C, Li F, Zhang X, Zhang D, Li X, Zhang Y, Zhao Y, Song Q, Wang J, Zhou B, Cheng J, Xu D, Li W, Zhao L, Wang W. Expression and polymorphisms of CD8B gene and its associations with body weight and size traits in sheep. Anim Biotechnol 2021:1-9. [PMID: 34928779 DOI: 10.1080/10495398.2021.2016432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The growth traits are economically important traits in sheep. Improving growth rates will increase the profitability of producers. The aim of this study was to identify alleles of CD8B (encoding T-cell surface glycoprotein CD8 beta chain) that are aberrantly expressed in different tissues and to assess the effects and associations of its different genotypes on weight and size traits in sheep. Using quantitative real-time reverse transcription PCR arrays, expression profiling of CD8B was performed in various organs and tissues. CD8B was ubiquitously expressed, with very high expression in the lung, spleen, lymph, duodenum, and liver. One intronic mutation (chr3:62,718,030 (Oar_rambouillet_v1.0, same below) G > A) was identified using pooled DNA sequencing. Subsequently, the variants (AA, AG, and GG) were genotyped using the KASPar® PCR single nucleotide polymorphism (SNP) genotyping system. The results of association analysis with body weight and body size traits in 1304 sheep showed that increases in multiple phenotypic traits correlated with the AA genotype (body weight, p < 0.05; body length, p < 0.05). Thus, SNP chr3:62,718,030 G > A is a promising molecular marker for marker-assisted selection in sheep breeding.
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Affiliation(s)
- Changchun Lin
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Fadi Li
- Engineering Laboratory of Sheep Breeding and Reproduction Biotechnology in Gansu Province, Minqin, China.,The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Deyin Zhang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yukun Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yuan Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Qizhi Song
- Linze County Animal Disease Prevention and Control Center of Gansu Province, Linze, China
| | - Jianghui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Bubo Zhou
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiangbo Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Wenxin Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Weimin Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
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Nawrocka PM, Galka-Marciniak P, Urbanek-Trzeciak MO, M-Thirusenthilarasan I, Szostak N, Philips A, Susok L, Sand M, Kozlowski P. Profile of Basal Cell Carcinoma Mutations and Copy Number Alterations - Focus on Gene-Associated Noncoding Variants. Front Oncol 2021; 11:752579. [PMID: 34900699 PMCID: PMC8656283 DOI: 10.3389/fonc.2021.752579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/08/2021] [Indexed: 11/13/2022] Open
Abstract
Basal cell carcinoma (BCC) of the skin is the most common cancer in humans, characterized by the highest mutation rate among cancers, and is mostly driven by mutations in genes involved in the hedgehog pathway. To date, almost all BCC genetic studies have focused exclusively on protein-coding sequences; therefore, the impact of noncoding variants on the BCC genome is unrecognized. In this study, with the use of whole-exome sequencing of 27 tumor/normal pairs of BCC samples, we performed an analysis of somatic mutations in both protein-coding sequences and gene-associated noncoding regions, including 5'UTRs, 3'UTRs, and exon-adjacent intron sequences. Separately, in each region, we performed hotspot identification, mutation enrichment analysis, and cancer driver identification with OncodriveFML. Additionally, we performed a whole-genome copy number alteration analysis with GISTIC2. Of the >80,000 identified mutations, ~50% were localized in noncoding regions. The results of the analysis generally corroborated the previous findings regarding genes mutated in coding sequences, including PTCH1, TP53, and MYCN, but more importantly showed that mutations were also clustered in specific noncoding regions, including hotspots. Some of the genes specifically mutated in noncoding regions were identified as highly potent cancer drivers, of which BAD had a mutation hotspot in the 3'UTR, DHODH had a mutation hotspot in the Kozak sequence in the 5'UTR, and CHCHD2 frequently showed mutations in the 5'UTR. All of these genes are functionally implicated in cancer-related processes (e.g., apoptosis, mitochondrial metabolism, and de novo pyrimidine synthesis) or the pathogenesis of UV radiation-induced cancers. We also found that the identified BAD and CHCHD2 mutations frequently occur in melanoma but not in other cancers via The Cancer Genome Atlas analysis. Finally, we identified a frequent deletion of chr9q, encompassing PTCH1, and unreported frequent copy number gain of chr9p, encompassing the genes encoding the immune checkpoint ligands PD-L1 and PD-L2. In conclusion, this study is the first systematic analysis of coding and noncoding mutations in BCC and provides a strong basis for further analyses of the variants in BCC and cancer in general.
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Affiliation(s)
- Paulina Maria Nawrocka
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Paulina Galka-Marciniak
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | | | | | - Natalia Szostak
- Laboratory of Bioinformatics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Anna Philips
- Laboratory of Bioinformatics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Laura Susok
- Department of Dermatology, Venereology and Allergology, St. Josef Hospital, Ruhr-University Bochum, Bochum, Germany
| | - Michael Sand
- Department of Dermatology, Venereology and Allergology, St. Josef Hospital, Ruhr-University Bochum, Bochum, Germany.,Department of Plastic Surgery, St. Josef Hospital, Catholic Clinics of the Ruhr Peninsula, Essen, Germany Department of Plastic, Reconstructive and Aesthetic Surgery, St. Josef Hospital, Essen, Germany
| | - Piotr Kozlowski
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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Xu D, Wang X, Zhang X, Li F, Zhang D, Li X, Zhang Y, Zhao Y, Song Q, Cheng J, Zhao L, Wang J, Li W, Zhou B, Lin C, Wang W. Polymorphisms in the ovine GP5 gene associated with blood physiological indices. Anim Biotechnol 2021:1-11. [PMID: 34904532 DOI: 10.1080/10495398.2021.2013859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
This study aimed to analyze the effects of polymorphisms in GP5 on blood physiological indices of 1065 sheep. The coefficients of variation of the red blood cell count (RBC), hemoglobin concentration (HGB), mean platelet volume (MPV), mean erythrocyte hemoglobin content (MCH), and red blood cell distribution-coefficient of variation (RDW-CV) were greater than 10%, and there was a very significant correlation between the main indices such as RBC, white blood cell, and platelet count (PLT) and most other indices (p < 0.01). qRT-PCR showed that GP5 was expressed in the heart, liver, spleen, lung, kidney, rumen, duodenum, muscle, tail fat, and lymph tissue, with significantly higher expression in the lymph. Subsequently, we detected single nucleotide polymorphisms (SNPs) in GP5 from group, which identified synonymous mutation g.657 T > C in the first exon of GP5. Association analysis showed significant correlations between the SNP and the physiological traits (p < 0.05), in which the RBC, neutrophilic granulocyte (NEUT) and RDW-CV values in sheep with the TC genotype and TT genotype were markedly lower than those in the CC genotype (p < 0.05). Thus, GP5 polymorphisms could be candidate biomarkers to screen blood physiological indices.
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Affiliation(s)
- Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaojuan Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Fadi Li
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Deyin Zhang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yukun Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yuan Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Qizhi Song
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiangbo Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jianghui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Wenxin Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Bubo Zhou
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Changchun Lin
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Weimin Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
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Macias A, Fichna JP, Topolewska M, Rȩdowicz MJ, Kaminska AM, Kostera-Pruszczyk A. Targeted Next-Generation Sequencing Reveals Mutations in Non-coding Regions and Potential Regulatory Sequences of Calpain-3 Gene in Polish Limb-Girdle Muscular Dystrophy Patients. Front Neurosci 2021; 15:692482. [PMID: 34720847 PMCID: PMC8551377 DOI: 10.3389/fnins.2021.692482] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 09/17/2021] [Indexed: 01/22/2023] Open
Abstract
Limb–girdle muscular dystrophy type R1 (LGMDR1) is caused by mutations in CAPN3 and is the most common type of recessive LGMD. Even with the use of whole-exome sequencing (WES), only one mutant allele of CAPN3 is found in a significant number of LGMDR patients. This points to a role of non-coding, intronic or regulatory, sequence variants in the disease pathogenesis. Targeted sequencing of the whole CAPN3 gene including not only intronic, 3′ and 5′ UTRs but also potential regulatory regions was performed in 27 patients suspected with LGMDR1. This group included 13 patients with only one mutated CAPN3 allele detected previously with exome sequencing. A second rare variant in the non-coding part of CAPN3 was found in 11 of 13 patients with previously identified single mutation. Intronic mutations were found in 10 cases, with c.1746-20C>G variant present in seven patients. In addition, a large deletion of exons 2–8 was found in one patient. In the patients with no causative mutation previously found, we detected rare CAPN3 variants in 5 out of 10 patients and in two of them in a compound heterozygous state. Rare variants within putative regulatory sequences distant from the CAPN3 gene were found in 15 patients, although in 11 of these cases, other variants are deemed causative. The results indicate that intronic mutations are common in Polish LGMDR patients, and testing for non-coding mutations in CAPN3 should be performed in apparently single heterozygous patients.
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Affiliation(s)
- Anna Macias
- Department of Neurology, Medical University of Warsaw, Warsaw, Poland
| | - Jakub Piotr Fichna
- Laboratory of Neurogenetics, Department of Neurodegenerative Disorders, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | - Malgorzata Topolewska
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Maria J Rȩdowicz
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Anna M Kaminska
- Department of Neurology, Medical University of Warsaw, Warsaw, Poland
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