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Sanjuan-Sanjuan A, Alors-Perez E, Sanchez-Frías M, Monserrat-Barbudo JA, Falguera Uceda M, Heredero-Jung S, Luque RM. Splicing Machinery Is Impaired in Oral Squamous Cell Carcinomas and Linked to Key Pathophysiological Features. Int J Mol Sci 2024; 25:6929. [PMID: 39000035 PMCID: PMC11240936 DOI: 10.3390/ijms25136929] [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: 05/30/2024] [Revised: 06/19/2024] [Accepted: 06/20/2024] [Indexed: 07/14/2024] Open
Abstract
Alternative splicing dysregulation is an emerging cancer hallmark, potentially serving as a source of novel diagnostic, prognostic, or therapeutic tools. Inhibitors of the activity of the splicing machinery can exert antitumoral effects in cancer cells. We aimed to characterize the splicing machinery (SM) components in oral squamous cell carcinoma (OSCC) and to evaluate the direct impact of the inhibition of SM-activity on OSCC-cells. The expression of 59 SM-components was assessed using a prospective case-control study of tumor and healthy samples from 37 OSCC patients, and the relationship with clinical and histopathological features was assessed. The direct effect of pladienolide-B (SM-inhibitor) on the proliferation rate of primary OSCC cell cultures was evaluated. A significant dysregulation in several SM components was found in OSCC vs. adjacent-healthy tissues [i.e., 12 out of 59 (20%)], and their expression was associated with clinical and histopathological features of less aggressiveness and overall survival. Pladienolide-B treatment significantly decreased OSCC-cell proliferation. Our data reveal a significantly altered expression of several SM-components and link it to pathophysiological features, reinforcing a potential clinical and pathophysiological relevance of the SM dysregulation in OSCC. The inhibition of SM-activity might be a therapeutic avenue in OSCC, offering a clinically relevant opportunity to be explored.
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Affiliation(s)
- Alba Sanjuan-Sanjuan
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain
- Oral and Maxillofacial Surgery Department, HURS, 14004 Cordoba, Spain
- Oral and Maxillofacial Surgery Department, CAMC Hospital, Charleston, WV 25301, USA
| | - Emilia Alors-Perez
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Cordoba, 14014 Cordoba, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain
| | - Marina Sanchez-Frías
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain
- Anatomical Pathology Service, IMIBIC/HURS, 14004 Cordoba, Spain
| | - José A Monserrat-Barbudo
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain
- Oral and Maxillofacial Surgery Department, HURS, 14004 Cordoba, Spain
| | - Mabel Falguera Uceda
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain
- Oral and Maxillofacial Surgery Department, HURS, 14004 Cordoba, Spain
| | - Susana Heredero-Jung
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain
- Oral and Maxillofacial Surgery Department, HURS, 14004 Cordoba, Spain
| | - Raúl M Luque
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Cordoba, 14014 Cordoba, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain
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Jayaram S, Balakrishnan L, Singh M, Zabihi A, Ganesh RA, Mangalaparthi KK, Sonpatki P, Gupta MK, Amaresha CB, Prasad K, Mariswamappa K, Pillai S, Lakshmikantha A, Shah N, Sirdeshmukh R. Identification of a Novel Splice Variant of Neural Cell Adhesion Molecule in Glioblastoma Through Proteogenomics Analysis. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2019; 22:437-448. [PMID: 29927716 DOI: 10.1089/omi.2017.0220] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Splice variants are known to be important in the pathophysiology of tumors, including the brain cancers. We applied a proteogenomics pipeline to identify splice variants in glioblastoma (GBM, grade IV glioma), a highly malignant brain tumor, using in-house generated mass spectrometric proteomic data and public domain RNASeq dataset. Our analysis led to the identification of a novel exon that maps to the long isoform of Neural cell adhesion molecule 1 (NCAM1), expressed on the surface of glial cells and neurons, important for cell adhesion and cell signaling. The presence of the novel exon is supported with the identification of five peptides spanning it. Additional peptides were also detected in sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) gel separated proteins from GBM patient tissue, underscoring the presence of the novel peptides in the intact brain protein. The novel exon was detected in the RNASeq dataset in 18 of 25 GBM samples and separately validated in additional 10 GBM tumor tissues using quantitative real-time-polymerase chain reaction (qRT-PCR). Both transcriptomic and proteomic data indicate downregulation of NCAM1, including the novel variant, in GBM. Domain analysis of the novel NCAM1 sequence indicates that the insertion of the novel exon contributes extra low-complexity region in the protein that may be important for protein-protein interactions and hence for cell signaling associated with tumor development. Taken together, the novel NCAM1 variant reported in this study exemplifies the importance of future multiomics research and systems biology applications in GBM.
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Affiliation(s)
- Savita Jayaram
- 1 Institute of Bioinformatics , International Tech Park, Bangalore, India .,2 Manipal Academy of Higher Education , Manipal, India
| | - Lavanya Balakrishnan
- 3 Mazumdar Shaw Center for Translational Research , Narayana Hrudayalaya Health City, Bangalore, India
| | - Manika Singh
- 1 Institute of Bioinformatics , International Tech Park, Bangalore, India .,4 Amrita School of Biotechnology , Amrita Vishwa Vidyapeetham, Kollam, India
| | - Azin Zabihi
- 3 Mazumdar Shaw Center for Translational Research , Narayana Hrudayalaya Health City, Bangalore, India
| | - Raksha A Ganesh
- 3 Mazumdar Shaw Center for Translational Research , Narayana Hrudayalaya Health City, Bangalore, India
| | - Kiran K Mangalaparthi
- 1 Institute of Bioinformatics , International Tech Park, Bangalore, India .,4 Amrita School of Biotechnology , Amrita Vishwa Vidyapeetham, Kollam, India
| | - Pranali Sonpatki
- 3 Mazumdar Shaw Center for Translational Research , Narayana Hrudayalaya Health City, Bangalore, India
| | - Manoj Kumar Gupta
- 1 Institute of Bioinformatics , International Tech Park, Bangalore, India .,2 Manipal Academy of Higher Education , Manipal, India
| | - Chaitra B Amaresha
- 3 Mazumdar Shaw Center for Translational Research , Narayana Hrudayalaya Health City, Bangalore, India
| | - Komal Prasad
- 5 Mazumdar Shaw Medical Center , Narayana Health City, Bangalore, India
| | | | - Shibu Pillai
- 5 Mazumdar Shaw Medical Center , Narayana Health City, Bangalore, India
| | | | - Nameeta Shah
- 3 Mazumdar Shaw Center for Translational Research , Narayana Hrudayalaya Health City, Bangalore, India
| | - Ravi Sirdeshmukh
- 1 Institute of Bioinformatics , International Tech Park, Bangalore, India .,2 Manipal Academy of Higher Education , Manipal, India .,3 Mazumdar Shaw Center for Translational Research , Narayana Hrudayalaya Health City, Bangalore, India
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3
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Lu M, Han J, Zhu B, Jia H, Yang T, Wang R, Deng WW, Zhang ZZ. Significantly increased amino acid accumulation in a novel albino branch of the tea plant (Camellia sinensis). PLANTA 2019; 249:363-376. [PMID: 30209617 DOI: 10.1007/s00425-018-3007-6] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 09/05/2018] [Indexed: 05/08/2023]
Abstract
A normal tea plant with one albino branch was discovered. RNA sequencing, albinism phenotype and ultrastructural observations provided a valuable understanding of the albino mechanism in tea plants. Tea plants with a specific color (white or yellow) have been studied extensively. A normal tea plant (Camellia sinensis cv. quntizhong) with one albino branch was discovered in a local tea plantation in Huangshan, Anhui, China. The pure albino leaves on this special branch had accumulated a fairly high content of amino acids, especially theanine (45.31 mg/g DW), and had a low concentration of polyphenols and an extremely low chlorophyll (Chl) content compared with control leaves. Ultrastructural observation of an albino leaf revealed no chloroplasts, whereas it was viable in the control leaf. RNA sequencing and differentially expressed gene (DEG) analysis were performed on the albino leaves and on control leaves from a normal green branch. The related genes involved in theanine and polyphenol biosynthesis were also investigated in this study. DEG expression patterns in Chl biosynthesis or degradation, carotenoid biosynthesis or degradation, chloroplast development, and biosynthesis were influenced in the albino leaves. Chloroplast deletion in albino leaves had probably destroyed the balance of carbon and nitrogen metabolism, leading to a high accumulation of free amino acids and a low concentration of polyphenols in the albino leaves. The obtained results can provide insight into the mechanism underlying this special albino branch phenotype, and are a valuable contribution toward understanding the albino mechanism in tea plants.
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Affiliation(s)
- Mengqian Lu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui, China
| | - Jieyun Han
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui, China
| | - Biying Zhu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui, China
| | - Huiyan Jia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui, China
| | - Tianyuan Yang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui, China
| | - Rangjian Wang
- Tea Research Institute, Fujian Academy of Agricultural Science, Hutouyang, Shekou, Fuan, 355015, Fujian, China
| | - Wei-Wei Deng
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui, China.
| | - Zheng-Zhu Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui, China.
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Zhuhong H, Zhenyu B, Xiangyuan C, Tingzhen X, Libin S. Genome-wide isoform-level analysis reveals tumor-specific isoforms for lung adenocarcinoma diagnosis and prognosis. Cancer Genet 2018; 230:58-65. [PMID: 30470588 DOI: 10.1016/j.cancergen.2018.11.004] [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: 06/25/2018] [Revised: 10/09/2018] [Accepted: 11/07/2018] [Indexed: 11/28/2022]
Abstract
Last decades have witnessed the great progress in exploration of tumor transcriptome. However, most researches were restricted in gene-level expression. mRNA isoforms, especially tumor-specific isoforms have not been fully explored in tumor. Here, by analyzing RNA-seq data derived from hundreds of samples in TCGA projects, we comprehensively characterized the expression variations of mRNA isoforms in adenocarcinoma of lung (LUAD), which is one of leading causes of cancer-related death. Our analysis found that a variety of mRNA isoforms showed differential expression in LUAD tumor samples. Some of them even showed distinct variations compared to their host genes. Further analysis of functional enrichment revealed that up- and down-regulated mRNA isoforms took part in different types of biological process. In addition, we also identified hundreds of isoforms that expressed exclusively in LUAD tumor samples. Furthermore, the expression level of several isoforms, such as uc001kuk.3 and uc003yls.2, could separate tumor patients by overall survival periods. Our study provided new candidates for the diagnosis and prognosis of lung cancer.
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Affiliation(s)
- Hu Zhuhong
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Zhejiang, China
| | - Bai Zhenyu
- Department of Laboratory, General Hospital of Pingmei Shenma Medical Group, Henan, China
| | - Chen Xiangyuan
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xu Tingzhen
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Song Libin
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
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Zhang T, Huang J, Tian H, Ma Y, Chen Z, Wang J, Shi H, Luo J. trans-10,cis-12 conjugated linoleic acid alters lipid metabolism of goat mammary epithelial cells by regulation of de novo synthesis and the AMPK signaling pathway. J Dairy Sci 2018. [DOI: 10.3168/jds.2017-12822] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Yang Q, Guo B, Sun H, Zhang J, Liu S, Hexige S, Yu X, Wang X. Identification of the key genes implicated in the transformation of OLP to OSCC using RNA-sequencing. Oncol Rep 2017; 37:2355-2365. [PMID: 28259920 DOI: 10.3892/or.2017.5487] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 01/02/2017] [Indexed: 11/06/2022] Open
Abstract
Oral lichen planus (OLP) is a chronic inflammatory disease that may transform to oral squamous cell carcinoma (OSCC), while its carcinogenesis mechanisms are not entirely clear. This study was designed to identify the important genes involved in the malignant transformation of OLP to OSCC. After RNA-sequencing, the differently expressed genes (DEGs) in OLP vs. normal and OSCC vs. normal groups, respectively, were identified by limma package in R language, and then clustering analysis were conducted by Pheatmap package in R language. Weighed gene co-expression network analysis (WGCNA) was performed for the DEGs to screen disease-associated modules. Using Cytoscape software, co-expression networks were constructed for the genes involved in the modules. Enrichment analysis was conducted for the genes involved in the co-expression networks using GOstat package in R language. Finally, quantitative real-time PCR (qRT-PCR) experiments were conducted to validate the key genes. There were, respectively, 223 and 548 DEGs in OLP vs. normal and OSCC vs. normal groups. WGCNA identified the blue modules for the DEGs in the two groups as disease-associated modules. Moreover, 19 common DEGs (including upregulated BCL9L, PER2 and TSPAN33, and downregulated GMPS and HES1) associated with both OLP and OSCC were identified. In the co-expression networks, BCL9L, HES1, PER2 and TSPAN33 might function in OLP via interactions (such as BCL9L-TSPAN33 and HES1-PER2). qRT-PCR analysis showed that BCL9L, PER2 and TSPAN33 were significantly upregulated, and GMP and HES1 were downregulated. These findings indicated that BCL9L, GMPS, HES1, PER2 and TSPAN33 affected the transformation of OLP to OSCC.
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Affiliation(s)
- Qiaozhen Yang
- Department of Stomatology, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Bin Guo
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, P.R. China
| | - Hongying Sun
- Department of Stomatology, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Jie Zhang
- Department of Stomatology, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Shangfeng Liu
- Department of Stomatology, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Saiyin Hexige
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, P.R. China
| | - Xuedi Yu
- Department of Stomatology, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Xiaxia Wang
- Department of Stomatology, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
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7
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Identification and quantification of novel RNA isoforms in horn cancer of Bos indicus by comprehensive RNA-Seq. 3 Biotech 2016; 6:259. [PMID: 28330331 PMCID: PMC5143338 DOI: 10.1007/s13205-016-0577-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 11/26/2016] [Indexed: 02/07/2023] Open
Abstract
Horn cancer (HC) is a squamous cell carcinoma of horn, commonly observed in Bos indicus of the Asian countries. To elucidate the complexity of alternative splicing present in the HC, high-throughput sequencing and analysis of HC and matching horn normal (HN) tissue were carried out. A total of 535,067 and 849,077 reads were analysed after stringent quality filtering for HN and HC, respectively. Cufflinks pipeline for transcriptome analysis revealed 4786 novel splice isoforms comprising 2432 exclusively in HC, 2055 exclusively in HN and 298 in both the conditions. Based on pathway clustering and in silico verification, 102 novel splice isoforms were selected and further analysed with respect to change in protein sequence using Blastp. Finally, fourteen novel splicing events supported both by Cufflinks and UCSC genome browser were selected and confirmed expression by RT-qPCR. Future studies targeted at in-depth characterization of these potential candidate splice isoforms might be helpful in the development of relevant biomarkers for early diagnosis of HC. The results reported in this study refine the available information on transcriptome repertoire of bovine species and boost the research in the line of development of relevant biomarkers for early diagnosis of HC.
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Wu Q, Chen Z, Sun W, Deng T, Chen M. De novo Sequencing of the Leaf Transcriptome Reveals Complex Light-Responsive Regulatory Networks in Camellia sinensis cv. Baijiguan. FRONTIERS IN PLANT SCIENCE 2016; 7:332. [PMID: 27047513 PMCID: PMC4801010 DOI: 10.3389/fpls.2016.00332] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 03/04/2016] [Indexed: 05/08/2023]
Abstract
Tea plants (Camellia sinensis L.) possess high genetic diversity that is important for breeding. One cultivar, Baijiguan, exhibits a yellow leaf phenotype, reduced chlorophyll (Chl) content, and aberrant chloroplast structures under high light intensity. In contrast, under low light intensity, the flush shoot from Baijiguan becomes green, the Chl content increases significantly, and the chloroplasts exhibit normal structures. To understand the underlying molecular mechanisms for these observations, we performed de novo transcriptome sequencing and digital gene expression (DGE) profiling using Illumina sequencing technology. De novo transcriptome assembly identified 88,788 unigenes, including 1652 transcription factors from 25 families. In total, 1993 and 2576 differentially expressed genes (DEGs) were identified in Baijiguan plants treated with 3 and 6 days of shade, respectively. Gene Ontology (GO) and pathway enrichment analyses indicated that the DEGs are predominantly involved in the ROS scavenging system, chloroplast development, photosynthetic pigment synthesis, secondary metabolism, and circadian systems. The light-responsive gene POR (protochlorophyllide oxidoreductase) and transcription factor HY5 were identified. Quantitative real-time PCR (qRT-PCR) analysis of 20 selected DEGs confirmed the RNA-sequencing (RNA-Seq) results. Overall, these findings suggest that high light intensity inhibits the expression of photosystem II 10-kDa protein (PsbR) in Baijiguan, thus affecting PSII stability, chloroplast development and chlorophyll biosynthesis.
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Affiliation(s)
- Quanjin Wu
- Department of Tea Science, College of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Zhidan Chen
- Department of Tea Science, Anxi College of Tea Science, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Weijiang Sun
- Department of Tea Science, College of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
- Department of Tea Science, Anxi College of Tea Science, Fujian Agriculture and Forestry UniversityFuzhou, China
- *Correspondence: Weijiang Sun
| | - Tingting Deng
- Department of Tea Science, College of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Mingjie Chen
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry UniversityFuzhou, China
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Ropka-Molik K, Zukowski K, Eckert R, Gurgul A, Piórkowska K, Oczkowicz M. Comprehensive analysis of the whole transcriptomes from two different pig breeds using RNA-Seq method. Anim Genet 2014; 45:674-84. [PMID: 24961663 DOI: 10.1111/age.12184] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2014] [Indexed: 02/03/2023]
Abstract
Next-generation sequencing RNA-Seq technology is a powerful tool that creates new possibilities for whole-transcriptome analysis. In our study, the RNA-Seq method was applied to analyze global changes in transcriptome from muscle tissue (m. semimembranosus) in two pig breeds (Pietrain and Polish Landrace, PL). The breeds differ in terms of muscularity, growth rate and reproduction traits. Using three different approaches (deseq, cufflinks and edger) and taking into account the most restrictive criteria, 35 genes differentially expressed between Pietrain and PL pigs were identified. In both breeds, the most abundant were transcripts encoding ribosomal and cytoskeletal proteins (TPM3, TCAP, TMOD4, TPM2, TNNC1) and calcium-binding proteins involved in muscle contraction, calcium-mediated signaling or cation transport (CASQ1, MLC2V, SLC25A4, MYL3). In PL pigs, we identified up-regulation of several genes that play crucial roles in reproduction: female gamete generation (BDP1, PTPN21, USP9X), fertilization (EGFR) and embryonic development (CPEB4). In the Pietrain breed, only seven genes were over-expressed (CISH, SPP1, TUBA8, ATP6V1C2, IGKC, predicted LOC100510960 and LOC100626400), and they play important roles in, for example, negative regulation of apoptosis, immune response, cell-cell signaling, cell growth and migration as well as the metabolic process. The functions of the majority of selected genes were consistent with phenotypic variation in investigated breeds; thus, we proposed a new panel of candidate genes that can be associated with economically important pig traits.
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Affiliation(s)
- Katarzyna Ropka-Molik
- Laboratory of Genomics, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland
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McHale CM, Zhang L, Thomas R, Smith MT. Analysis of the transcriptome in molecular epidemiology studies. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2013; 54:500-517. [PMID: 23907930 PMCID: PMC5142298 DOI: 10.1002/em.21798] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 06/07/2013] [Accepted: 06/08/2013] [Indexed: 05/29/2023]
Abstract
The human transcriptome is complex, comprising multiple transcript types, mostly in the form of non-coding RNA (ncRNA). The majority of ncRNA is of the long form (lncRNA, ≥ 200 bp), which plays an important role in gene regulation through multiple mechanisms including epigenetics, chromatin modification, control of transcription factor binding, and regulation of alternative splicing. Both mRNA and ncRNA exhibit additional variability in the form of alternative splicing and RNA editing. All aspects of the human transcriptome can potentially be dysregulated by environmental exposures. Next-generation RNA sequencing (RNA-Seq) is the best available methodology to measure this although it has limitations, including experimental bias. The third phase of the MicroArray Quality Control Consortium project (MAQC-III), also called Sequencing Quality Control (SeQC), aims to address these limitations through standardization of experimental and bioinformatic methodologies. A limited number of toxicogenomic studies have been conducted to date using RNA-Seq. This review describes the complexity of the human transcriptome, the application of transcriptomics by RNA-Seq or microarray in molecular epidemiology studies, and limitations of these approaches including the type of cell or tissue analyzed, experimental variation, and confounding. By using good study designs with precise, individual exposure measurements, sufficient power and incorporation of phenotypic anchors, studies in human populations can identify biomarkers of exposure and/or early effect and elucidate mechanisms of action underlying associated diseases, even at low doses. Analysis of datasets at the pathway level can compensate for some of the limitations of RNA-Seq and, as more datasets become available, will increasingly elucidate the exposure-disease continuum.
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Affiliation(s)
- Cliona M McHale
- Division of Environmental Health Sciences, Genes and Environment Laboratory, School of Public Health, University of California, Berkeley, California 94720, USA.
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