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Audet S, Triassi V, Gelinas M, Legault-Cadieux N, Ferraro V, Duquette A, Tetreault M. Integration of multi-omics technologies for molecular diagnosis in ataxia patients. Front Genet 2024; 14:1304711. [PMID: 38239855 PMCID: PMC10794629 DOI: 10.3389/fgene.2023.1304711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 11/27/2023] [Indexed: 01/22/2024] Open
Abstract
Background: Episodic ataxias are rare neurological disorders characterized by recurring episodes of imbalance and coordination difficulties. Obtaining definitive molecular diagnoses poses challenges, as clinical presentation is highly heterogeneous, and literature on the underlying genetics is limited. While the advent of high-throughput sequencing technologies has significantly contributed to Mendelian disorders genetics, interpretation of variants of uncertain significance and other limitations inherent to individual methods still leaves many patients undiagnosed. This study aimed to investigate the utility of multi-omics for the identification and validation of molecular candidates in a cohort of complex cases of ataxia with episodic presentation. Methods: Eight patients lacking molecular diagnosis despite extensive clinical examination were recruited following standard genetic testing. Whole genome and RNA sequencing were performed on samples isolated from peripheral blood mononuclear cells. Integration of expression and splicing data facilitated genomic variants prioritization. Subsequently, long-read sequencing played a crucial role in the validation of those candidate variants. Results: Whole genome sequencing uncovered pathogenic variants in four genes (SPG7, ATXN2, ELOVL4, PMPCB). A missense and a nonsense variant, both previously reported as likely pathogenic, configured in trans in individual #1 (SPG7: c.2228T>C/p.I743T, c.1861C>T/p.Q621*). An ATXN2 microsatellite expansion (CAG32) in another late-onset case. In two separate individuals, intronic variants near splice sites (ELOVL4: c.541 + 5G>A; PMPCB: c.1154 + 5G>C) were predicted to induce loss-of-function splicing, but had never been reported as disease-causing. Long-read sequencing confirmed the compound heterozygous variants configuration, repeat expansion length, as well as splicing landscape for those pathogenic variants. A potential genetic modifier of the ATXN2 expansion was discovered in ZFYVE26 (c.3022C>T/p.R1008*). Conclusion: Despite failure to identify pathogenic variants through clinical genetic testing, the multi-omics approach enabled the molecular diagnosis in 50% of patients, also giving valuable insights for variant prioritization in remaining cases. The findings demonstrate the value of long-read sequencing for the validation of candidate variants in various scenarios. Our study demonstrates the effectiveness of leveraging complementary omics technologies to unravel the underlying genetics in patients with unresolved rare diseases such as ataxia. Molecular diagnoses not only hold significant promise in improving patient care management, but also alleviates the burden of diagnostic odysseys, more broadly enhancing quality of life.
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Affiliation(s)
- Sebastien Audet
- University of Montreal Hospital Research Center (CRCHUM), Montreal, QC, Canada
- Department of Neurosciences, University of Montreal, Montreal, QC, Canada
| | - Valerie Triassi
- University of Montreal Hospital Research Center (CRCHUM), Montreal, QC, Canada
| | - Myriam Gelinas
- Department of Medicine, University of Montreal Hospital Centre (CHUM), Montreal, QC, Canada
| | - Nab Legault-Cadieux
- University of Montreal Hospital Research Center (CRCHUM), Montreal, QC, Canada
- Department of Neurosciences, University of Montreal, Montreal, QC, Canada
| | - Vincent Ferraro
- Department of Medicine, University of Montreal Hospital Centre (CHUM), Montreal, QC, Canada
| | - Antoine Duquette
- University of Montreal Hospital Research Center (CRCHUM), Montreal, QC, Canada
- Department of Neurosciences, University of Montreal, Montreal, QC, Canada
- Neurology Service, Department of Medicine, André-Barbeau Movement Disorders Unit, University of Montreal Hospital (CHUM), Montreal, QC, Canada
- Genetic Service, Department of Medicine, University of Montreal Hospital (CHUM), Montreal, QC, Canada
| | - Martine Tetreault
- University of Montreal Hospital Research Center (CRCHUM), Montreal, QC, Canada
- Department of Neurosciences, University of Montreal, Montreal, QC, Canada
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Nguyen BQT, Tran TPD, Nguyen HT, Nguyen TN, Pham TMQ, Nguyen HTP, Tran DH, Nguyen V, Tran TS, Pham TVN, Le MT, Phan MD, Giang H, Nguyen HN, Tran LS. Improvement in neoantigen prediction via integration of RNA sequencing data for variant calling. Front Immunol 2023; 14:1251603. [PMID: 37731488 PMCID: PMC10507271 DOI: 10.3389/fimmu.2023.1251603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 08/17/2023] [Indexed: 09/22/2023] Open
Abstract
Introduction Neoantigen-based immunotherapy has emerged as a promising strategy for improving the life expectancy of cancer patients. This therapeutic approach heavily relies on accurate identification of cancer mutations using DNA sequencing (DNAseq) data. However, current workflows tend to provide a large number of neoantigen candidates, of which only a limited number elicit efficient and immunogenic T-cell responses suitable for downstream clinical evaluation. To overcome this limitation and increase the number of high-quality immunogenic neoantigens, we propose integrating RNA sequencing (RNAseq) data into the mutation identification step in the neoantigen prediction workflow. Methods In this study, we characterize the mutation profiles identified from DNAseq and/or RNAseq data in tumor tissues of 25 patients with colorectal cancer (CRC). Immunogenicity was then validated by ELISpot assay using long synthesis peptides (sLP). Results We detected only 22.4% of variants shared between the two methods. In contrast, RNAseq-derived variants displayed unique features of affinity and immunogenicity. We further established that neoantigen candidates identified by RNAseq data significantly increased the number of highly immunogenic neoantigens (confirmed by ELISpot) that would otherwise be overlooked if relying solely on DNAseq data. Discussion This integrative approach holds great potential for improving the selection of neoantigens for personalized cancer immunotherapy, ultimately leading to enhanced treatment outcomes and improved survival rates for cancer patients.
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Affiliation(s)
| | | | - Huu Thinh Nguyen
- University Medical Center Ho Chi Minh City, Ho Chi Minh, Vietnam
| | | | | | | | - Duc Huy Tran
- University Medical Center Ho Chi Minh City, Ho Chi Minh, Vietnam
| | - Vy Nguyen
- Medical Genetics Institute, Ho Chi Minh, Vietnam
| | - Thanh Sang Tran
- University Medical Center Ho Chi Minh City, Ho Chi Minh, Vietnam
| | | | - Minh-Triet Le
- University Medical Center Ho Chi Minh City, Ho Chi Minh, Vietnam
| | | | - Hoa Giang
- Medical Genetics Institute, Ho Chi Minh, Vietnam
| | | | - Le Son Tran
- Medical Genetics Institute, Ho Chi Minh, Vietnam
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Wright ML, Goin DE, Smed MK, Jewell NP, Nelson JL, Olsen J, Hetland ML, Zoffmann V, Jawaheer D. Pregnancy-associated systemic gene expression compared to a pre-pregnancy baseline, among healthy women with term pregnancies. Front Immunol 2023; 14:1161084. [PMID: 37342349 PMCID: PMC10277629 DOI: 10.3389/fimmu.2023.1161084] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/09/2023] [Indexed: 06/22/2023] Open
Abstract
Background Pregnancy is known to induce extensive biological changes in the healthy mother. Little is known, however, about what these changes are at the molecular level. We have examined systemic expression changes in protein-coding genes and long non-coding (lnc) RNAs during and after pregnancy, compared to before pregnancy, among healthy women with term pregnancies. Methods Blood samples were collected from 14 healthy women enrolled in our prospective pregnancy cohort at 7 time-points (before, during and after pregnancy). Total RNA from frozen whole blood was used for RNA sequencing. Following raw read alignment and assembly, gene-level counts were obtained for protein-coding genes and long non-coding RNAs. At each time-point, cell type proportions were estimated using deconvolution. To examine associations between pregnancy status and gene expression over time, Generalized Estimating Equation (GEE) models were fitted, adjusting for age at conception, and with and without adjusting for changes in cell type proportions. Fold-changes in expression at each trimester were examined relative to the pre-pregnancy baseline. Results Numerous immune-related genes demonstrated pregnancy-associated expression, in a time-dependent manner. The genes that demonstrated the largest changes in expression included several that were neutrophil-related (over-expressed) and numerous immunoglobulin genes (under-expressed). Estimated cell proportions revealed a marked increase in neutrophils, and less so of activated CD4 memory T cells, during pregnancy, while most other cell type proportions decreased or remained unchanged. Adjusting for cell type proportions in our model revealed that although most of the expression changes were due to changes in cell type proportions in the bloodstream, transcriptional regulation was also involved, especially in down-regulating expression of type I interferon inducible genes. Conclusion Compared to a pre-pregnancy baseline, there were extensive systemic changes in cell type proportions, gene expression and biological pathways associated with different stages of pregnancy and postpartum among healthy women. Some were due to changes in cell type proportions and some due to gene regulation. In addition to providing insight into term pregnancy among healthy women, these findings also provide a "normal" reference for abnormal pregnancies and for autoimmune diseases that improve or worsen during pregnancy, to assess deviations from normal.
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Affiliation(s)
- Matthew L. Wright
- Children’s Hospital Oakland Research Institute, Oakland, CA, United States
- Northwestern University, Feinberg School of Medicine, Chicago, IL, United States
| | - Dana E. Goin
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, San Francisco, CA, United States
| | | | - Nicholas P. Jewell
- Department of Medical Statistics, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - J. Lee Nelson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Jørn Olsen
- Department of Epidemiology, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Clinical Epidemiology, Aarhus University Hospital, Aarhus, Denmark
| | - Merete Lund Hetland
- DANBIO Registry and Copenhagen Centre for Arthritis Research, Centre for Rheumatology and Spine Diseases, Rigshospitalet, Glostrup, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Vibeke Zoffmann
- Juliane Marie Centeret, Rigshospitalet, Copenhagen, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Damini Jawaheer
- Children’s Hospital Oakland Research Institute, Oakland, CA, United States
- Northwestern University, Feinberg School of Medicine, Chicago, IL, United States
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Gui J, Liu J, Han Z, Yang X, Ding R, Yang J, Luo H, Huang D, Chen H, Cheng L, Jiang L. The dysfunctionality of hippocampal synapses may be directly related to PM-induced impairments in spatial learning and memory in juvenile rats. Ecotoxicol Environ Saf 2023; 254:114729. [PMID: 36889211 DOI: 10.1016/j.ecoenv.2023.114729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 02/28/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
Epidemiological studies have demonstrated that exposure to air particulate matter (PM) increases the incidence of cardiovascular and respiratory diseases and exerts a significant neurotoxic effect on the nervous system, especially on the immature nervous system. Here, we selected PND28 rats to simulate the immature nervous system of young children and used neurobehavioral methods to examine how exposure to PM affected spatial learning and memory, as well as electrophysiology, molecular biology, and bioinformatics to study the morphology of hippocampus and the function of hippocampal synapses. We discovered that spatial learning and memory were impaired in rats exposed to PM. The morphology and structure of the hippocampus were altered in the PM group. In addition, after exposure to PM, the relative expression of synaptophysin (SYP) and postsynaptic density 95 (PSD95) proteins decreased dramatically in rats. Furthermore, PM exposure impaired long-term potentiation (LTP) in the hippocampal Schaffer-CA1 pathway. Interestingly, RNA sequencing and bioinformatics analysis revealed that the differentially expressed genes (DEGs) were rich in terms associated with synaptic function. Five hub genes (Agt, Camk2a, Grin2a, Snca, and Syngap1) that may play a significant role in the dysfunctionality of hippocampal synapses were identified. Our findings implied that exposure to PM impaired spatial learning and memory via exerting impacts on the dysfunctionality of hippocampal synapses in juvenile rats and that Agt, Camk2a, Grin2a, Snca, and Syngap1 may drive PM-caused synaptic dysfunction.
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Affiliation(s)
- Jianxiong Gui
- Department of Neurology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing 400014, China
| | - Jie Liu
- Department of Neurology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing 400014, China
| | - Ziyao Han
- Department of Neurology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing 400014, China
| | - Xiaoyue Yang
- Department of Neurology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing 400014, China
| | - Ran Ding
- Department of Neurology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing 400014, China
| | - Jiaxin Yang
- Department of Neurology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing 400014, China
| | - Hanyu Luo
- Department of Neurology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing 400014, China
| | - Dishu Huang
- Department of Neurology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing 400014, China
| | - Hengsheng Chen
- Department of Neurology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing 400014, China
| | - Li Cheng
- Department of Neurology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing 400014, China
| | - Li Jiang
- Department of Neurology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing 400014, China.
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Kelley DP, Albrechet-Souza L, Cruise S, Maiya R, Destouni A, Sakamuri SSVP, Duplooy A, Hibicke M, Nichols C, Katakam PVG, Gilpin NW, Francis J. Conditioned place avoidance is associated with a distinct hippocampal phenotype, partly preserved pattern separation, and reduced reactive oxygen species production after stress. Genes Brain Behav 2023; 22:e12840. [PMID: 36807494 PMCID: PMC10067435 DOI: 10.1111/gbb.12840] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 02/20/2023]
Abstract
Stress is associated with contextual memory deficits, which may mediate avoidance of trauma-associated contexts in posttraumatic stress disorder. These deficits may emerge from impaired pattern separation, the independent representation of similar experiences by the dentate gyrus-Cornu Ammonis 3 (DG-CA3) circuit of the dorsal hippocampus, which allows for appropriate behavioral responses to specific environmental stimuli. Neurogenesis in the DG is controlled by mitochondrial reactive oxygen species (ROS) production, and may contribute to pattern separation. In Experiment 1, we performed RNA sequencing of the dorsal hippocampus 16 days after stress in rats that either develop conditioned place avoidance to a predator urine-associated context (Avoiders), or do not (Non-Avoiders). Weighted genome correlational network analysis showed that increased expression of oxidative phosphorylation-associated gene transcripts and decreased expression of gene transcripts for axon guidance and insulin signaling were associated with avoidance behavior. Based on these data, in Experiment 2, we hypothesized that Avoiders would exhibit elevated hippocampal (HPC) ROS production and degraded object pattern separation (OPS) compared with Nonavoiders. Stress impaired pattern separation performance in Non-Avoider and Avoider rats compared with nonstressed Controls, but surprisingly, Avoiders exhibited partly preserved pattern separation performance and significantly lower ROS production compared with Non-Avoiders. Lower ROS production was associated with better OPS performance in Stressed rats, but ROS production was not associated with OPS performance in Controls. These results suggest a strong negative association between HPC ROS production and pattern separation after stress, and that stress effects on these outcome variables may be associated with avoidance of a stress-paired context.
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Affiliation(s)
- D Parker Kelley
- Comparative Biomedical Sciences, Louisiana State University School of Veterinary Medicine, Baton Rouge, Louisiana, USA.,Department of Physiology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Lucas Albrechet-Souza
- Department of Cell Biology & Anatomy, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA.,Alcohol & Drug Abuse Center of Excellence, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Shealan Cruise
- Department of Physiology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Rajani Maiya
- Department of Physiology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Aspasia Destouni
- Comparative Biomedical Sciences, Louisiana State University School of Veterinary Medicine, Baton Rouge, Louisiana, USA
| | - Siva S V P Sakamuri
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Alexander Duplooy
- Comparative Biomedical Sciences, Louisiana State University School of Veterinary Medicine, Baton Rouge, Louisiana, USA
| | - Meghan Hibicke
- Department of Pharmacology and Experimental Therapeutics, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Charles Nichols
- Alcohol & Drug Abuse Center of Excellence, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA.,Department of Pharmacology and Experimental Therapeutics, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Prasad V G Katakam
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Nicholas W Gilpin
- Department of Physiology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA.,Alcohol & Drug Abuse Center of Excellence, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA.,Neuroscience Center of Excellence, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA.,Southeast Louisiana VA Healthcare System (SLVHCS), New Orleans, Louisiana, USA
| | - Joseph Francis
- Comparative Biomedical Sciences, Louisiana State University School of Veterinary Medicine, Baton Rouge, Louisiana, USA
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Rohbeck E, Niersmann C, Köhrer K, Wachtmeister T, Roden M, Eckel J, Romacho T. Positive allosteric GABA A receptor modulation counteracts lipotoxicity-induced gene expression changes in hepatocytes in vitro. Front Physiol 2023; 14:1106075. [PMID: 36860523 PMCID: PMC9968943 DOI: 10.3389/fphys.2023.1106075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/31/2023] [Indexed: 02/16/2023] Open
Abstract
Introduction: We have previously shown that the novel positive allosteric modulator of the GABAA receptor, HK4, exerts hepatoprotective effects against lipotoxicity-induced apoptosis, DNA damage, inflammation and ER stress in vitro. This might be mediated by downregulated phosphorylation of the transcription factors NF-κB and STAT3. The current study aimed to investigate the effect of HK4 on lipotoxicity-induced hepatocyte injury at the transcriptional level. Methods: HepG2 cells were treated with palmitate (200 μM) in the presence or absence of HK4 (10 μM) for 7 h. Total RNA was isolated and the expression profiles of mRNAs were assessed. Differentially expressed genes were identified and subjected to the DAVID database and Ingenuity Pathway Analysis software for functional and pathway analysis, all under appropriate statistical testing. Results: Transcriptomic analysis showed substantial modifications in gene expression in response to palmitate as lipotoxic stimulus with 1,457 differentially expressed genes affecting lipid metabolism, oxidative phosphorylation, apoptosis, oxidative and ER stress among others. HK4 preincubation resulted in the prevention of palmitate-induced dysregulation by restoring initial gene expression pattern of untreated hepatocytes comprising 456 genes. Out of the 456 genes, 342 genes were upregulated and 114 downregulated by HK4. Enriched pathways analysis of those genes by Ingenuity Pathway Analysis, pointed towards oxidative phosphorylation, mitochondrial dysregulation, protein ubiquitination, apoptosis, and cell cycle regulation as affected pathways. These pathways are regulated by the key upstream regulators TP53, KDM5B, DDX5, CAB39 L and SYVN1, which orchestrate the metabolic and oxidative stress responses including modulation of DNA repair and degradation of ER stress-induced misfolded proteins in the presence or absence of HK4. Discussion: We conclude that HK4 specifically targets mitochondrial respiration, protein ubiquitination, apoptosis and cell cycle. This not only helps to counteract lipotoxic hepatocellular injury through modification of gene expression, but - by targeting transcription factors responsible for DNA repair, cell cycle progression and ER stress - might even prevent lipotoxic mechanisms. These findings suggest that HK4 has a great potential for the treatment of non-alcoholic fatty liver disease (NAFLD).
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Affiliation(s)
- Elisabeth Rohbeck
- German Diabetes Center, Institute for Clinical Diabetology, Leibniz Center for Diabetes Research at Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany,German Center for Diabetes Research (DZD), Partner Düsseldorf, München-Neuherberg, Germany,CureDiab Metabolic Research GmbH, Düsseldorf, Germany
| | - Corinna Niersmann
- German Diabetes Center, Institute for Clinical Diabetology, Leibniz Center for Diabetes Research at Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany,German Center for Diabetes Research (DZD), Partner Düsseldorf, München-Neuherberg, Germany,CureDiab Metabolic Research GmbH, Düsseldorf, Germany
| | - Karl Köhrer
- Biological and Medical Research Centre (BMFZ), Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Thorsten Wachtmeister
- Biological and Medical Research Centre (BMFZ), Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Michael Roden
- German Diabetes Center, Institute for Clinical Diabetology, Leibniz Center for Diabetes Research at Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany,German Center for Diabetes Research (DZD), Partner Düsseldorf, München-Neuherberg, Germany,Department of Endocrinology and Diabetology, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Jürgen Eckel
- German Diabetes Center, Institute for Clinical Diabetology, Leibniz Center for Diabetes Research at Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany,CureDiab Metabolic Research GmbH, Düsseldorf, Germany
| | - Tania Romacho
- German Diabetes Center, Institute for Clinical Diabetology, Leibniz Center for Diabetes Research at Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany,Chronic Complications of Diabetes Lab (ChroCoDiL), Department of Nursing Sciences, Physiotherapy and Medicine, Faculty of Health Sciences, University of Almería, Almería, Spain,*Correspondence: Tania Romacho,
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Iwahashi N, Umakoshi H, Ogata M, Fukumoto T, Kaneko H, Terada E, Katsuhara S, Uchida N, Sasaki K, Yokomoto-Umakoshi M, Matsuda Y, Sakamoto R, Ogawa Y. Whole Transcriptome Profiling of Adrenocortical Tumors Using Formalin-Fixed Paraffin-Embedded Samples. Front Endocrinol (Lausanne) 2022; 13:808331. [PMID: 35185794 PMCID: PMC8850780 DOI: 10.3389/fendo.2022.808331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/11/2022] [Indexed: 11/24/2022] Open
Abstract
Whole transcriptome profiling is a promising technique in adrenal studies; however, whole transcriptome profiling of adrenal disease using formalin-fixed paraffin-embedded (FFPE) samples has to be further explored. The aim of this study was to evaluate the utility of transcriptome data from FFPE samples of adrenocortical tumors. We performed whole transcriptome profiling of FFPE and fresh frozen samples of adrenocortical carcinoma (ACC, n = 3), aldosterone-producing adenoma (APA, n = 3), and cortisol-producing adenoma (CPA, n = 3), and examined the similarity between the transcriptome data. We further examined whether the transcriptome data of FFPE samples could be used to distinguish tumor types and detect marker genes. The number of read counts was smaller in FFPE samples than in fresh frozen samples (P < 0.01), while the number of genes detected was similar (P = 0.39). The gene expression profiles of FFPE and fresh frozen samples were highly correlated (r = 0.93, P < 0.01). Tumor types could be distinguished by consensus clustering and principal component analysis using transcriptome data from FFPE samples. In the differential expression analysis between ACC and APA-CPA, known marker genes of ACC (e.g., CCNB2, TOP2A, and MAD2L1) were detected in FFPE samples of ACC. In the differential expression analysis between APA and CPA, known marker genes of APA (e.g., CYP11B2, VSNL1, and KCNJ5) were detected in the APA of FFPE samples. The results suggest that FFPE samples may be a reliable alternative to fresh frozen samples for whole transcriptome profiling of adrenocortical tumors.
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Affiliation(s)
- Norifusa Iwahashi
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hironobu Umakoshi
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- *Correspondence: Hironobu Umakoshi, ; Yoshihiro Ogawa,
| | - Masatoshi Ogata
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tazuru Fukumoto
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroki Kaneko
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Eriko Terada
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shunsuke Katsuhara
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Naohiro Uchida
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Katsuhiko Sasaki
- Clinical Laboratory Department, Kyushu Pro Search Limited Liability Partnership, Fukuoka, Japan
| | - Maki Yokomoto-Umakoshi
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yayoi Matsuda
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Ryuichi Sakamoto
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshihiro Ogawa
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- *Correspondence: Hironobu Umakoshi, ; Yoshihiro Ogawa,
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8
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Fang W, Wu CH, Sun QL, Gu ZT, Zhu L, Mao T, Zhang XF, Xu N, Lu TP, Tsai MH, Chen LH, Lai LC, Chuang EY. Novel Tumor-Specific Antigens for Immunotherapy Identified From Multi-omics Profiling in Thymic Carcinomas. Front Immunol 2021; 12:748820. [PMID: 34867976 PMCID: PMC8635231 DOI: 10.3389/fimmu.2021.748820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/28/2021] [Indexed: 12/30/2022] Open
Abstract
Thymic carcinoma (TC) is the most aggressive thymic epithelial neoplasm. TC patients with microsatellite instability, whole-genome doubling, or alternative tumor-specific antigens from gene fusion are most likely to benefit from immunotherapies. However, due to the rarity of this disease, how to prioritize the putative biomarkers and what constitutes an optimal treatment regimen remains largely unknown. Therefore, we integrated genomic and transcriptomic analyses from TC patients and revealed that frameshift indels in KMT2C and CYLD frequently produce neoantigens. Moreover, a median of 3 fusion-derived neoantigens was predicted across affected patients, especially the CATSPERB-TC2N neoantigens that were recurrently predicted in TC patients. Lastly, potentially actionable alterations with early levels of evidence were uncovered and could be used for designing clinical trials. In summary, this study shed light on our understanding of tumorigenesis and presented new avenues for molecular characterization and immunotherapy in TC.
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Affiliation(s)
- Wentao Fang
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai JiaoTong University, Shanghai, China
| | - Chia-Hsin Wu
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - Qiang-Ling Sun
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai JiaoTong University, Shanghai, China.,Thoracic Cancer institute, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Zhi-Tao Gu
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai JiaoTong University, Shanghai, China
| | - Lei Zhu
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Teng Mao
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai JiaoTong University, Shanghai, China
| | - Xue-Fei Zhang
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai JiaoTong University, Shanghai, China
| | - Ning Xu
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai JiaoTong University, Shanghai, China
| | - Tzu-Pin Lu
- Bioinformatics and Biostatistics Core, Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan.,Department of Public Health, National Taiwan University, Taipei, Taiwan
| | - Mong-Hsun Tsai
- Bioinformatics and Biostatistics Core, Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan.,Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Li-Han Chen
- Institute of Fisheries Science, National Taiwan University, Taipei, Taiwan
| | - Liang-Chuan Lai
- Bioinformatics and Biostatistics Core, Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan.,Graduate Institute of Physiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Eric Y Chuang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan.,Bioinformatics and Biostatistics Core, Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan.,Department of Electrical Engineering, National Taiwan University, Taipei, Taiwan.,Master Program for Biomedical Engineering, China Medical University, Taichung, Taiwan
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9
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Dai SD, Wang S, Qin YN, Zhu JC. Multiomics Landscape Uncovers the Molecular Mechanism of the Malignant Evolution of Lung Adenocarcinoma Cells to Chronic Low Dose Cadmium Exposure. Front Oncol 2021; 11:654687. [PMID: 34858801 PMCID: PMC8631903 DOI: 10.3389/fonc.2021.654687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 10/26/2021] [Indexed: 11/23/2022] Open
Abstract
Cadmium (Cd) from cigarette smoke and polluted air can lead to lung adenocarcinoma after long-term inhalation. However, most studies are based on short-term exposure to this toxic metal at high concentrations. Here, we investigate the effects of long-term exposure of A549 cells (lung adenocarcinoma) to cadmium at low concentrations using morphological and multiomics analyses. First, we treated A549 cells continuously with CdCl2 at 1μM for 8 months and found that CdCl2 promoted cellular migration and invasion. After that, we applied transmission electron and fluorescence microscopies and did not observe significant morphological changes in Golgi apparatus, endoplasmic reticulum, lysosomes, or mitochondria on Cd treated cells; microfilaments, in contrast, accumulated in lamellipodium and adhesion plaques, which suggested that Cd enhanced cellular activity. Second, by using whole-exome sequencing (WES) we detected 4222 unique SNPs in Cd-treated cells, which included 382 unique non-synonymous mutation sites. The corresponding mutated genes, after GO and KEGG enrichments, were involved mainly in cell adhesion, movement, and metabolic pathways. Third, by RNA-seq analysis, we showed that 1250 genes (784 up and 466 down), 1623 mRNAs (1023 up and 591 down), and 679 lncRNAs (375 up and 304 down) were expressed differently. Furthermore, GO enrichment of these RNA-seq results suggested that most differentially expressed genes were related to cell adhesion and organization of the extracellular matrix in biological process terms; KEGG enrichment revealed that the differentially expressed genes took part in 26 pathways, among which the metabolic pathway was the most significant. These findings could be important for unveiling mechanisms of Cd-related cancers and for developing cancer therapies in the future.
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Affiliation(s)
- Shun-Dong Dai
- Department of Pathology, Shanghai Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Shuang Wang
- Department of Pathology, Shenyang Red Cross Hospital, Shenyang, China
| | - Ya-Nan Qin
- Department of Pathology, Shanghai Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Jin-Chao Zhu
- Department of Pathology, Shanghai Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
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10
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Di Mauro I, Dadone-Montaudie B, Sibony M, Ambrosetti D, Molinie V, Decaussin-Petrucci M, Bland V, Arbaud C, Cenciu B, Arbib F, Just PA, Derman J, Rioux-Leclercq N, Pedeutour F. RBM10-TFE3 fusions: A FISH-concealed anomaly in adult renal cell carcinomas displaying a variety of morphological and genomic features: Comprehensive study of six novel cases. Genes Chromosomes Cancer 2021; 60:772-784. [PMID: 34358382 DOI: 10.1002/gcc.22985] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/05/2021] [Accepted: 07/16/2021] [Indexed: 11/07/2022] Open
Abstract
The accurate diagnosis of Xp11-translocation renal cell carcinoma (RCC) in adults is challenging. TFE3 (located on chromosome X) fuses with a partner gene generally located on another chromosome. In rare cases TFE3 may fuse with a neighboring gene: RBM10. Because TFE3 false-positive immunostaining is a common pitfall in many laboratories, demonstration of the chromosomal rearrangement is required in order to ascertain the diagnosis. Fluorescence in situ hybridization (FISH)-that has been considered as the gold standard method-reaches its limits for detecting small Xp11 paracentric inversions. We performed a comprehensive clinical, histological and genomic study of six novel cases of RCC with RBM10-TFE3 fusion. Using FISH, TFE3 rearrangement was equivocal in one case and negative in others. RBM10-TFE3 fusion was discovered using targeted RNA sequencing (RNASeq). As all the previously reported cases (mean age: 50), the six patients were adults (mean age: 42), suggesting an epidemiologic difference between RBM10-TFE3 RCC and tumors harboring some other partner genes, such as ASPSCR1 that rather occur in children. Array-comparative genomic hybridization showed several alterations, notably a gain of 17q in four cases with papillary features and loss of 3p in one case with clear cells. Our study demonstrates that, though rare among adult cases of RCC, RBM10-TFE3 fusion is not exceptional and warrants appropriate molecular detection. Notably, it would be worthy to systemically investigate by RNASeq challenging RCC with type-2 papillary features and 17q gain.
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Affiliation(s)
- Ilaria Di Mauro
- Laboratory of Solid Tumor Genetics, University Hospital of Nice-Côte d'Azur University, Nice, France.,Laboratory of Solid Tumor Genetics, Institute for Research on Cancer and Aging of Nice (IRCAN), CNRS UMR 7284/INSERM U1081, Nice, France
| | - Bérengère Dadone-Montaudie
- Laboratory of Solid Tumor Genetics, University Hospital of Nice-Côte d'Azur University, Nice, France.,Laboratory of Solid Tumor Genetics, Institute for Research on Cancer and Aging of Nice (IRCAN), CNRS UMR 7284/INSERM U1081, Nice, France
| | - Mathilde Sibony
- Department of Pathology, Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpitaux Universitaires Paris-Centre, Hôpital Cochin, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Damien Ambrosetti
- Central Laboratory of Pathology, University Hospital of Nice-Côte d'Azur University, Nice, France
| | - Vincent Molinie
- Pathology Department, Aix en Provence Hospital, Aix en Provence, France
| | | | | | - Claire Arbaud
- Pathology Department, Métropole Savoie Hospital, Chambéry, France
| | - Béatrice Cenciu
- Oncology Department, Andrée Rosemon Hospital, Cayenne, France
| | | | - Pierre-Alexandre Just
- Department of Pathology, Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpitaux Universitaires Paris-Centre, Hôpital Cochin, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Jonathan Derman
- Department of Pathology, Henri-Mondor Hospital, Créteil, France
| | | | - Florence Pedeutour
- Laboratory of Solid Tumor Genetics, University Hospital of Nice-Côte d'Azur University, Nice, France.,Laboratory of Solid Tumor Genetics, Institute for Research on Cancer and Aging of Nice (IRCAN), CNRS UMR 7284/INSERM U1081, Nice, France
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- CARARE French Network (CAncers RAres du Rein: Rare Renal Cancers Network of the National Institute of Cancer, INCa), France
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11
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Samson J, Derlipanska M, Zaheed O, Dean K. Molecular and cellular characterization of two patient-derived ductal carcinoma in situ (DCIS) cell lines, ETCC-006 and ETCC-010. BMC Cancer 2021; 21:790. [PMID: 34238275 PMCID: PMC8268371 DOI: 10.1186/s12885-021-08511-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 06/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Currently it is unclear how in situ breast cancer progresses to invasive disease; therefore, a better understanding of the events that occur during the transition to invasive carcinoma is warranted. Here we have conducted a detailed molecular and cellular characterization of two, patient-derived, ductal carcinoma in situ (DCIS) cell lines, ETCC-006 and ETCC-010. METHODS Human DCIS cell lines, ETCC-006 and ETCC-010, were compared against a panel of cell lines including the immortalized, breast epithelial cell line, MCF10A, breast cancer cell lines, MCF7 and MDA-MB-231, and another DCIS line, MCF10DCIS.com. Cell morphology, hormone and HER2/ERBB2 receptor status, cell proliferation, survival, migration, anchorage-independent growth, indicators of EMT, cell signalling pathways and cell cycle proteins were examined using immunostaining, immunoblots, and quantitative, reverse transcriptase PCR (qRT-PCR), along with clonogenic, wound-closure and soft agar assays. RNA sequencing (RNAseq) was used to provide a transcriptomic profile. RESULTS ETCC-006 and ETCC-010 cells displayed notable differences to another DCIS cell line, MCF10DCIS.com, in terms of morphology, steroid-receptor/HER status and markers of EMT. The ETCC cell lines lack ER/PR and HER, form colonies in clonogenic assays, have migratory capacity and are capable of anchorage-independent growth. Despite being isogenic, less than 30% of differentially expressed transcripts overlapped between the two lines, with enrichment in pathways involving receptor tyrosine kinases and DNA replication/cell cycle programs and in gene sets responsible for extracellular matrix organisation and ion transport. CONCLUSIONS For the first time, we provide a molecular and cellular characterization of two, patient-derived DCIS cell lines, ETCC-006 and ETCC-010, facilitating future investigations into the molecular basis of DCIS to invasive ductal carcinoma transition.
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Affiliation(s)
- Julia Samson
- School of Biochemistry and Cell Biology, Western Gateway Building, University College Cork, Cork, T12XF62 Ireland
- Present address: EFOR, 25-29 Rue Anatole France, 92300 Levallois-Perret, France
| | - Magdalina Derlipanska
- School of Biochemistry and Cell Biology, Western Gateway Building, University College Cork, Cork, T12XF62 Ireland
| | - Oza Zaheed
- School of Biochemistry and Cell Biology, Western Gateway Building, University College Cork, Cork, T12XF62 Ireland
| | - Kellie Dean
- School of Biochemistry and Cell Biology, Western Gateway Building, University College Cork, Cork, T12XF62 Ireland
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12
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Abstract
The diagnostic rate of comprehensive genomic sequencing remains only 25% to 30% due to the difficulty in interpreting variants of uncertain significance and noncoding mutations and in elucidating downstream effects of these and other genetic changes. Unlike DNA sequencing, RNA sequencing (RNAseq) reveals the functional consequence of genetic variation through the detection of abnormal gene expression levels, differences in gene splicing, and allele-specific expression. RNAseq can provide nearly 40% improvement in diagnostic rates depending on disease and tissue source. In this burgeoning era of precision medicine, RNAseq offers a powerful tool to improve diagnostic rates and understand disease mechanisms.
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Affiliation(s)
- David R Murdock
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, BCM225, Houston, TX 77030, USA.
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13
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Ferreira JGG, Gava SG, Oliveira ES, Batista ICA, Fernandes GDR, Mourão MM, Calzavara-Silva CE. Gene Expression Signatures in AML-12 Hepatocyte Cells upon Dengue virus Infection and Acetaminophen Treatment. Viruses 2020; 12:E1284. [PMID: 33182673 DOI: 10.3390/v12111284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 12/21/2022] Open
Abstract
Dengue is an acute viral disease caused by Dengue virus (DENV) and is considered to be the most common arbovirus worldwide. The clinical characteristics of dengue may vary from asymptomatic to severe complications and severe organ impairment, particularly affecting the liver. Dengue treatment is palliative with acetaminophen (APAP), usually known as Paracetamol, being the most used drug aiming to relieve the mild symptoms of dengue. APAP is a safe and effective drug but, like dengue, can trigger the development of liver disorders. Given this scenario, it is necessary to investigate the effects of combining these two factors on hepatocyte homeostasis. Therefore, this study aimed to evaluate the molecular changes in hepatocytes resulting from the association between DENV infection and treatment with sub-toxic APAP concentrations. Using an in vitro experimental model of DENV-2 infected hepatocytes (AML-12 cells) treated with APAP, we evaluated the influence of the virus and drug association on the transcriptome of these hepatocytes by RNA sequencing (RNAseq). The virus-drug association was able to induce changes in the gene expression profile of AML-12 cells and here we highlight and explore these changes and its putative influence on biological processes for cellular homeostasis.
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14
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Walters D, Vogel KR, Brown M, Shi X, Roullet JB, Gibson KM. Transcriptome analysis in mice treated with vigabatrin identifies dysregulation of genes associated with retinal signaling circuitry. Epilepsy Res 2020; 166:106395. [PMID: 32679486 DOI: 10.1016/j.eplepsyres.2020.106395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/02/2020] [Accepted: 06/09/2020] [Indexed: 10/24/2022]
Abstract
Vigabatrin (VGB; γ-vinyl-GABA) is an antiepileptic drug that elevates CNS GABA via irreversible inactivation of the GABA catabolic enzyme GABA-transaminase. VGB's clinical utility, however, can be curtailed by peripheral visual field constriction (pVFC) and thinning of the retinal nerve fiber layer (RNFL). Earlier studies from our laboratory revealed disruptions of autophagy by VGB. Here, we tested the hypothesis that VGB administration to animals would reveal alterations of gene expression in VGB-treated retina that associated with autophagy. VGB (140 mg/kg/d; subcutaneous minipump) was continuously administered to mice (n = 6 each VGB/vehicle) for 12 days, after which animals were euthanized. Retina was isolated for transcriptome (RNAseq) analysis and further validation using qRT-PCR and immunohistochemistry (IHC). For 112 differentially expressed retinal genes (RNAseq), two databases (Gene Ontology; Kyoto Encyclopedia of Genes and Genomes) were used to identify genes associated with visual function. Twenty four genes were subjected to qRT-PCR validation, and five (Gb5, Bdnf, Cplx9, Crh, Sox9) revealed significant dysregulation. IHC of fixed retinas verified significant down-regulation of Gb5 in photoreceptor cells. All of these genes have been previously shown to play a role in retinal function/circuitry signaling. Minimal impact of VGB on retinal autophagic gene expression was observed. This is the first transcriptome analysis of retinal gene expression associated with VGB intake, highlighting potential novel molecular targets potentially related to VGB's well known ocular toxicity.
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Affiliation(s)
- Dana Walters
- Department of Pharmacotherapy, Washington State University College of Pharmacy and Pharmaceutical Sciences, Spokane, WA, USA.
| | - Kara R Vogel
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA.
| | - Madalyn Brown
- Department of Pharmacotherapy, Washington State University College of Pharmacy and Pharmaceutical Sciences, Spokane, WA, USA.
| | - Xutong Shi
- Department of Pharmacotherapy, Washington State University College of Pharmacy and Pharmaceutical Sciences, Spokane, WA, USA.
| | - Jean-Baptiste Roullet
- Department of Pharmacotherapy, Washington State University College of Pharmacy and Pharmaceutical Sciences, Spokane, WA, USA.
| | - K Michael Gibson
- Department of Pharmacotherapy, Washington State University College of Pharmacy and Pharmaceutical Sciences, Spokane, WA, USA.
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15
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Song WP, Zheng S, Yao HJ, Zhou XF, Li R, Zhang CY, Zhao JY, Wang LW, Shao RG, Li L. Different transcriptome profiles between human retinoblastoma Y79 cells and an etoposide-resistant subline reveal a chemoresistance mechanism. BMC Ophthalmol 2020; 20:92. [PMID: 32143590 PMCID: PMC7060629 DOI: 10.1186/s12886-020-01348-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 02/18/2020] [Indexed: 02/18/2023] Open
Abstract
Background Retinoblastoma (RB) is the most frequent pediatric retinal tumor. In the present study, to elucidate chemoresistance mechanisms and identify potential biomarkers in RB, we utilized RNA sequencing (RNAseq) technological platforms to reveal transcriptome profiles and identify any differentially expressed genes (DEGs) between an etoposide drug-resistant subline (Y79/EDR) and parental Y79 cells. Methods To test whether Y79/EDR cells showed resistance to antineoplastic agents for RB, we treated the cells with etoposide, carboplatin and vincristine and analyzed them with a Cell Counting Kit-8 (CCK-8). Y79/EDR and parental Y79 cells were used for RNAseq and bioinformatics analysis to enable a genome-wide review of DEGs between the two lines using the DESeq R package (1.10.1). Then, DEG enrichment in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways was analyzed with KOBAS software. Next, real-time quantitative reverse transcription polymerase chain reaction (real time QRT-PCR) and cytotoxicity assays were performed to experimentally and functionally validate the identified candidate biomarkers. Results Y79/EDR cells showed resistance to etoposide, carboplatin and vincristine at different concentrations. In total, 524 transcripts were differentially expressed in Y79/EDR cells based on analysis of fragments per kilobase of transcript per million fragments mapped (FPKM); among these, 57 genes were downregulated and 467 genes were upregulated in Y79/EDR cells compared to parental Y79 cells. We selected candidate DEGs, including ARHGAP9, HIST1H4H, RELN, DDIT4, HK2, STC1 and PFKFB4, for mRNA expression validation with real time QRT-PCR assays and found that the expression levels determined by real time QRT-PCR were consistent with the RNAseq data. Further studies involving downregulation of ARHGAP9 with a specific siRNA showed that ARHGAP9 altered the cellular sensitivity of Y79 cells to etoposide and carboplatin. Conclusion Our initial findings provided a genomic view of the transcription profiles of etoposide-induced acquired resistance in RB. Follow-up studies indicated that ARHGAP9 might be a chemoresistance biomarker in RB, providing insight into potential therapeutic targets for overcoming acquired chemoresistance in RB. These findings can aid in understanding and overcoming chemoresistance during treatment of RB in the clinic.
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Affiliation(s)
- Wen-Ping Song
- Department of Pharmacy, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, No.127 Dongming Road, Zhengzhou, 450008, China.,Key Laboratory of Antibiotic Bioengineering of National Health and Family Planning Commission (NHFPC), Institute of Medicinal Biotechnology (IMB), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), NO.1 Tiantan Xili, Beijing, 100050, China
| | - Si Zheng
- Institute of Medical Information (IMI) & Library, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), NO.3 Yabao Road, Beijing, 100020, China
| | - Hong-Juan Yao
- Key Laboratory of Antibiotic Bioengineering of National Health and Family Planning Commission (NHFPC), Institute of Medicinal Biotechnology (IMB), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), NO.1 Tiantan Xili, Beijing, 100050, China
| | - Xiao-Fei Zhou
- Key Laboratory of Antibiotic Bioengineering of National Health and Family Planning Commission (NHFPC), Institute of Medicinal Biotechnology (IMB), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), NO.1 Tiantan Xili, Beijing, 100050, China
| | - Rui Li
- Key Laboratory of Antibiotic Bioengineering of National Health and Family Planning Commission (NHFPC), Institute of Medicinal Biotechnology (IMB), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), NO.1 Tiantan Xili, Beijing, 100050, China
| | - Cheng-Yue Zhang
- Department of Ophthalmology, Beijing Children's Hospital, Capital Medical University, NO. 56 Nanlishi Road, Beijing, 100045, China
| | - Jun-Yang Zhao
- Department of Ophthalmology, Beijing Children's Hospital, Capital Medical University, NO. 56 Nanlishi Road, Beijing, 100045, China
| | - Lie-Wei Wang
- Division of Clinical Pharmacology, Department of Molecular Pharmocology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Rong-Guang Shao
- Key Laboratory of Antibiotic Bioengineering of National Health and Family Planning Commission (NHFPC), Institute of Medicinal Biotechnology (IMB), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), NO.1 Tiantan Xili, Beijing, 100050, China.
| | - Liang Li
- Key Laboratory of Antibiotic Bioengineering of National Health and Family Planning Commission (NHFPC), Institute of Medicinal Biotechnology (IMB), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), NO.1 Tiantan Xili, Beijing, 100050, China.
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16
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Huang W, Hamouche JE, Wang G, Smith M, Yin C, Dhand A, Dimitrova N, Fallon JT. Integrated Genome-Wide Analysis of an Isogenic Pair of Pseudomonas aeruginosa Clinical Isolates with Differential Antimicrobial Resistance to Ceftolozane/Tazobactam, Ceftazidime/Avibactam, and Piperacillin/Tazobactam. Int J Mol Sci 2020; 21:E1026. [PMID: 32033143 DOI: 10.3390/ijms21031026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/27/2020] [Accepted: 02/02/2020] [Indexed: 01/10/2023] Open
Abstract
Multidrug-resistant (MDR) Pseudomonas aeruginosa is one of the main causes of morbidity and mortality in hospitalized patients and the leading cause of nosocomial infections. We investigated, here, two MDR P. aeruginosa clinical isolates from a hospitalized patient with differential antimicrobial resistance to ceftazidime/avibactam (CZA), ceftolozane/tazobactam (C/T), and piperacillin/tazobactam (P/T). Their assembled complete genomes revealed they belonged to ST235, a widespread MDR clone; and were isogenic with only a single nucleotide variant, causing G183D mutation in AmpC β-lactamase, responsible for a phenotypic change from susceptible to resistant to CZA and C/T. Further epigenomic profiling uncovered two conserved DNA methylation motifs targeted by two distinct putative methyltransferase-containing restriction-modification systems, respectively; more intriguingly, there was a significant difference between the paired isolates in the pattern of genomic DNA methylation and modifications. Moreover, genome-wide gene expression profiling demonstrated the inheritable genomic methylation and modification induced 14 genes being differentially regulated, of which only toxR (downregulated), a regulatory transcription factor, had its promoter region differentially methylate and modified. Since highly expressed opdQ encodes an OprD porin family protein, therefore, we proposed an epigenetic regulation of opdQ expression pertinent to the phenotypic change of P. aeruginosa from resistant to susceptible to P/T. The disclosed epigenetic mechanism controlling phenotypic antimicrobial resistance deserves further experimental investigation.
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17
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Abstract
Identification of the unique features of human brain development and function can be critical towards the elucidation of intricate processes such as higher cognitive functions and human-specific pathologies like neuropsychiatric and behavioral disorders. The developing primate and human central nervous system (CNS) are distinguished by expanded progenitor zones and a protracted time course of neurogenesis, leading to the expansion in brain size, prominent gyral anatomy, distinctive synaptic properties, and complex neural circuits. Comparative genomic studies have revealed that adaptations of brain capacities may be partly explained by human-specific genetic changes that impact the function of proteins associated with neocortical expansion, synaptic function, and language development. However, the formation of complex gene networks may be most relevant for brain evolution. Indeed, recent studies identified distinct human-specific gene expression patterns across developmental time occurring in brain regions linked to cognition. Interestingly, such modules show species-specific divergence and are enriched in genes associated with neuronal development and synapse formation whilst also being implicated in neuropsychiatric diseases. microRNAs represent a powerful component of gene-regulatory networks by promoting spatiotemporal post-transcriptional control of gene expression in the human and primate brain. It has also been suggested that the divergence in miRNA expression plays an important role in shaping gene expression divergence among species. Primate-specific and human-specific miRNAs are principally involved in progenitor proliferation and neurogenic processes but also associate with human cognition, and neurological disorders. Human embryonic or induced pluripotent stem cells and brain organoids, permitting experimental access to neural cells and differentiation stages that are otherwise difficult or impossible to reach in humans, are an essential means for studying species-specific brain miRNAs. Single-cell sequencing approaches can further decode refined miRNA-mRNA interactions during developmental transitions. Elucidating species-specific miRNA regulation will shed new light into the mechanisms that control spatiotemporal events during human brain development and disease, an important step towards fostering novel, holistic and effective therapeutic approaches for neural disorders. In this review, we discuss species-specific regulation of miRNA function, its contribution to the evolving features of the human brain and in neurological disease, with respect also to future therapeutic approaches.
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Affiliation(s)
- Kanella Prodromidou
- Laboratory of Cellular and Molecular Neurobiology-Stem Cells, Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece
| | - Rebecca Matsas
- Laboratory of Cellular and Molecular Neurobiology-Stem Cells, Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece
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18
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Lanz TV, Pröbstel AK, Mildenberger I, Platten M, Schirmer L. Single-Cell High-Throughput Technologies in Cerebrospinal Fluid Research and Diagnostics. Front Immunol 2019; 10:1302. [PMID: 31244848 PMCID: PMC6579921 DOI: 10.3389/fimmu.2019.01302] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 05/22/2019] [Indexed: 01/08/2023] Open
Abstract
High-throughput single-cell technologies have recently emerged as essential tools in biomedical research with great potential for clinical pathology when studying liquid and solid biopsies. We provide an update on current single-cell methods in cerebrospinal fluid research and diagnostics, focusing on high-throughput cell-type specific proteomic and genomic technologies. Proteomic methods comprising flow cytometry and mass cytometry as well as genomic approaches including immune cell repertoire and single-cell transcriptomic studies are critically reviewed and future directions discussed.
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Affiliation(s)
- Tobias V. Lanz
- Department of Neurology, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Anne-Katrin Pröbstel
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
- Departments of Medicine and Biomedicine, Neurologic Clinic and Policlinic, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Iris Mildenberger
- Department of Neurology, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Michael Platten
- Department of Neurology, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
- DKTK Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lucas Schirmer
- Department of Neurology, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
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19
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Abstract
The circadian clock is an evolutionarily conserved mechanism that generates the rhythmic expression of downstream genes. The core circadian clock drives the expression of clock-controlled genes, which in turn play critical roles in carrying out many rhythmic physiological processes. Nevertheless, the molecular mechanisms by which clock output genes orchestrate rhythmic signals from the brain to peripheral tissues are largely unknown. Here we explored the role of one rhythmic gene, Achilles, in regulating the rhythmic transcriptome in the fly head. Achilles is a clock-controlled gene in Drosophila that encodes a putative RNA-binding protein. Achilles expression is found in neurons throughout the fly brain using fluorescence in situ hybridization (FISH), and legacy data suggest it is not expressed in core clock neurons. Together, these observations argue against a role for Achilles in regulating the core clock. To assess its impact on circadian mRNA rhythms, we performed RNA sequencing (RNAseq) to compare the rhythmic transcriptomes of control flies and those with diminished Achilles expression in all neurons. Consistent with previous studies, we observe dramatic upregulation of immune response genes upon knock-down of Achilles. Furthermore, many circadian mRNAs lose their rhythmicity in Achilles knock-down flies, suggesting that a subset of the rhythmic transcriptome is regulated either directly or indirectly by Achilles. These Achilles-mediated rhythms are observed in genes involved in immune function and in neuronal signaling, including Prosap, Nemy and Jhl-21. A comparison of RNAseq data from control flies reveals that only 42.7% of clock-controlled genes in the fly brain are rhythmic in both males and females. As mRNA rhythms of core clock genes are largely invariant between the sexes, this observation suggests that sex-specific mechanisms are an important, and heretofore under-appreciated, regulator of the rhythmic transcriptome.
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Affiliation(s)
- Jiajia Li
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Renee Yin Yu
- Centre for Research in Neuroscience, Research Institute of the McGill University Health Centre, Montreal General Hospital, Montréal, Québec, Canada
| | - Farida Emran
- Centre for Research in Neuroscience, Research Institute of the McGill University Health Centre, Montreal General Hospital, Montréal, Québec, Canada
| | - Brian E Chen
- Centre for Research in Neuroscience, Research Institute of the McGill University Health Centre, Montreal General Hospital, Montréal, Québec, Canada.,Departments of Medicine and Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada
| | - Michael E Hughes
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, MO, USA
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20
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Veltsos P, Cossard G, Beaudoing E, Beydon G, Savova Bianchi D, Roux C, C González-Martínez S, R Pannell J. Size and Content of the Sex-Determining Region of the Y Chromosome in Dioecious Mercurialis annua, a Plant with Homomorphic Sex Chromosomes. Genes (Basel) 2018; 9:E277. [PMID: 29844299 PMCID: PMC6027223 DOI: 10.3390/genes9060277] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/16/2018] [Accepted: 05/23/2018] [Indexed: 01/01/2023] Open
Abstract
Dioecious plants vary in whether their sex chromosomes are heteromorphic or homomorphic, but even homomorphic sex chromosomes may show divergence between homologues in the non-recombining, sex-determining region (SDR). Very little is known about the SDR of these species, which might represent particularly early stages of sex-chromosome evolution. Here, we assess the size and content of the SDR of the diploid dioecious herb Mercurialis annua, a species with homomorphic sex chromosomes and mild Y-chromosome degeneration. We used RNA sequencing (RNAseq) to identify new Y-linked markers for M. annua. Twelve of 24 transcripts showing male-specific expression in a previous experiment could be amplified by polymerase chain reaction (PCR) only from males, and are thus likely to be Y-linked. Analysis of genome-capture data from multiple populations of M. annua pointed to an additional six male-limited (and thus Y-linked) sequences. We used these markers to identify and sequence 17 sex-linked bacterial artificial chromosomes (BACs), which form 11 groups of non-overlapping sequences, covering a total sequence length of about 1.5 Mb. Content analysis of this region suggests that it is enriched for repeats, has low gene density, and contains few candidate sex-determining genes. The BACs map to a subset of the sex-linked region of the genetic map, which we estimate to be at least 14.5 Mb. This is substantially larger than estimates for other dioecious plants with homomorphic sex chromosomes, both in absolute terms and relative to their genome sizes. Our data provide a rare, high-resolution view of the homomorphic Y chromosome of a dioecious plant.
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Affiliation(s)
- Paris Veltsos
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
- Department of Biology, Jordan Hall, 1001 East Third Street, Indiana University, Bloomington, IN 47405, USA.
| | - Guillaume Cossard
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
| | - Emmanuel Beaudoing
- Faculty of Biology and Medicine, University of Lausanne, Bâtiment Génopode, 1014 Lausanne, Switzerland.
| | - Genséric Beydon
- National Centre for Genomic Resources (CNRGV), 24 Chemin de Borde Rouge-Auzeville-CS52627, 31326 Castanet Tolosan Cedex, France.
| | | | - Camille Roux
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
- CNRS, University of Lille, UMR 8198-Evo-Eco-Paleo, F-59000 Lille, France.
| | - Santiago C González-Martínez
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
- BIOGECO, INRA, University of Bordeaux, 33610 Cestas, France.
| | - John R Pannell
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
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21
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Majerczyk CD. Global Expression Analysis of Quorum Sensing-Controlled Genes by RNAseq. Methods Mol Biol 2018; 1673:177-192. [PMID: 29130173 DOI: 10.1007/978-1-4939-7309-5_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
RNA sequencing (RNAseq) enables transcriptional profiling of many organisms. This chapter describes the use of RNAseq in prokaryotes to identify quorum sensing (QS)-controlled transcripts by comparing samples from QS-induced and -uninduced conditions. Briefly, each RNA sample is converted to ds-cDNA in a method that limits amplification of ribosomal RNA species. The ds-cDNA contains adapters that enable sequencing and quantification by next-generation sequencing (NGS).
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22
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Lalaouna D, Prévost K, Eyraud A, Massé E. Identification of unknown RNA partners using MAPS. Methods 2016; 117:28-34. [PMID: 27876680 DOI: 10.1016/j.ymeth.2016.11.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 10/05/2016] [Accepted: 11/17/2016] [Indexed: 01/02/2023] Open
Abstract
Recent advances in high-throughput sequencing have led to an explosion in the rate of small regulatory RNAs (sRNAs) discovery among bacteria. However, only a handful of them are functionally characterized. Most of the time, little to no targets are known. In Lalaouna et al. (2015), we proposed a new technology to uncover sRNAs targetome, which is based on the MS2-affinity purification (MAPS). We were able to prove its efficiency by applying it on well-characterized sRNAs of Escherichia coli. Thereafter, we adapted the procedure to other kind of RNA (mRNAs and tRNA-derived RNA fragments) and bacteria (pathogenic or Gram-positive strains). Here, we clearly report all improvements and adjustments made to MAPS technology since it was originally reported.
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Affiliation(s)
- David Lalaouna
- Department of Biochemistry, RNA Group, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Karine Prévost
- Department of Biochemistry, RNA Group, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Alex Eyraud
- Department of Biochemistry, RNA Group, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Eric Massé
- Department of Biochemistry, RNA Group, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada.
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23
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Manzanares C, Barth S, Thorogood D, Byrne SL, Yates S, Czaban A, Asp T, Yang B, Studer B. A Gene Encoding a DUF247 Domain Protein Cosegregates with the S Self-Incompatibility Locus in Perennial Ryegrass. Mol Biol Evol 2015; 33:870-84. [PMID: 26659250 DOI: 10.1093/molbev/msv335] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The grass family (Poaceae), the fourth largest family of flowering plants, encompasses the most economically important cereal, forage, and energy crops, and exhibits a unique gametophytic self-incompatibility (SI) mechanism that is controlled by at least two multiallelic and independent loci, S and Z. Despite intense research efforts over the last six decades, the genes underlying S and Z remain uncharacterized. Here, we report a fine-mapping approach to identify the male component of the S-locus in perennial ryegrass (Lolium perenne L.) and provide multiple evidence that a domain of unknown function 247 (DUF247) gene is involved in its determination. Using a total of 10,177 individuals from seven different mapping populations segregating for S, we narrowed the S-locus to a genomic region containing eight genes, the closest recombinant marker mapping at a distance of 0.016 cM. Of the eight genes cosegregating with the S-locus, a highly polymorphic gene encoding for a protein containing a DUF247 was fully predictive of known S-locus genotypes at the amino acid level in the seven mapping populations. Strikingly, this gene showed a frameshift mutation in self-compatible darnel (Lolium temulentum L.), whereas all of the self-incompatible species of the Festuca-Lolium complex were predicted to encode functional proteins. Our results represent a major step forward toward understanding the gametophytic SI system in one of the most important plant families and will enable the identification of additional components interacting with the S-locus.
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Affiliation(s)
- Chloé Manzanares
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland Teagasc Crops, Environment and Land Use Programme, Oak Park Research Centre, Carlow, Ireland Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth, Ceredigion, United Kingdom
| | - Susanne Barth
- Teagasc Crops, Environment and Land Use Programme, Oak Park Research Centre, Carlow, Ireland
| | - Daniel Thorogood
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth, Ceredigion, United Kingdom
| | - Stephen L Byrne
- Department of Molecular Biology and Genetics, Research Centre Flakkebjerg, Aarhus University, Slagelse, Denmark
| | - Steven Yates
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Adrian Czaban
- Department of Molecular Biology and Genetics, Research Centre Flakkebjerg, Aarhus University, Slagelse, Denmark
| | - Torben Asp
- Department of Molecular Biology and Genetics, Research Centre Flakkebjerg, Aarhus University, Slagelse, Denmark
| | - Bicheng Yang
- BGI-Shenzhen, Building 1, Beishan Industrial Zone, Yantian District, Shenzhen, China
| | - Bruno Studer
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
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24
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Lalaouna D, Massé E. Identification of sRNA interacting with a transcript of interest using MS2-affinity purification coupled with RNA sequencing (MAPS) technology. Genom Data 2015; 5:136-8. [PMID: 26484242 DOI: 10.1016/j.gdata.2015.05.033] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 05/25/2015] [Indexed: 01/08/2023]
Abstract
RNA sequencing (RNAseq) technology recently allowed the identification of thousands of small RNAs (sRNAs) within the prokaryotic kingdom. However, drawing the comprehensive interaction map of a sRNA remains a challenging task. To address this problem, we recently developed a method called MAPS (MS2 affinity purification coupled with RNA sequencing) to characterize the full targetome of specific sRNAs. This method enabled the identification of target RNAs interacting with sRNAs, regardless of the type of regulation (positive or negative), type of targets (mRNA, tRNA, sRNA) or their abundance. We also demonstrated that we can use this technology to perform a reverse MAPS experiment, where an RNA fragment of interest is used as bait to identify interacting sRNAs. Here, we demonstrated that RybB and MicF sRNAs co-purified with internal transcribed spacers (ITS) of metZ–metW–metV tRNA transcript, confirming results obtained with MS2-RybB MAPS. Both raw and analyzed RNAseq data are available in GEO database (GSE66517).
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