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Leonard AS, Mapel XM, Pausch H. RNA-DNA differences in variant calls from cattle tissues result in erroneous eQTLs. BMC Genomics 2024; 25:750. [PMID: 39090567 PMCID: PMC11295900 DOI: 10.1186/s12864-024-10645-z] [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: 05/16/2024] [Accepted: 07/22/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND Association testing between molecular phenotypes and genomic variants can help to understand how genotype affects phenotype. RNA sequencing provides access to molecular phenotypes such as gene expression and alternative splicing while DNA sequencing or microarray genotyping are the prevailing options to obtain genomic variants. RESULTS We genotype variants for 74 male Braunvieh cattle from both DNA (~ 13-fold coverage) and deep total RNA sequencing from testis, vas deferens, and epididymis tissue (~ 250 million reads per tissue). We show that RNA sequencing can be used to identify approximately 40% of variants (7-10 million) called from DNA sequencing, with over 80% precision. Within highly expressed coding regions, over 92% of expected variants were called with nearly 98% precision. Allele-specific expression and putative post-transcriptional modifications negatively impact variant genotyping accuracy from RNA sequencing and contribute to RNA-DNA differences. Variants called from RNA sequencing detect roughly 75% of eGenes identified using variants called from DNA sequencing, demonstrating a nearly 2-fold enrichment of eQTL variants. We observe a moderate-to-strong correlation in nominal association p-values (Spearman ρ2 ~ 0.6), although only 9% of eGenes have the same top associated variant. CONCLUSIONS We find hundreds of thousands of RNA-DNA differences in variants called from RNA and DNA sequencing on the same individuals. We identify several highly significant eQTL when using RNA sequencing variant genotypes which are not found with DNA sequencing variant genotypes, suggesting that using RNA sequencing variant genotypes for association testing results in an increased number of false positives. Our findings demonstrate that caution must be exercised beyond filtering for variant quality or imputation accuracy when analysing or imputing variants called from RNA sequencing.
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Affiliation(s)
- Alexander S Leonard
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, Zurich, 8092, Switzerland.
| | - Xena M Mapel
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, Zurich, 8092, Switzerland
| | - Hubert Pausch
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, Zurich, 8092, Switzerland.
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2
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Rossi S, Barresi S, Colafati GS, Genovese S, Tancredi C, Costabile V, Patrizi S, Giovannoni I, Asioli S, Poliani PL, Gardiman MP, Cardoni A, Del Baldo G, Antonelli M, Gianno F, Piccirilli E, Catino G, Martucci L, Quacquarini D, Toni F, Melchionda F, Viscardi E, Zucchelli M, Dal Pos S, Gatti E, Liserre R, Schiavello E, Diomedi-Camassei F, Carai A, Mastronuzzi A, Gessi M, Giannini C, Novelli A, Onetti Muda A, Miele E, Alesi V, Alaggio R. PATZ1-Rearranged Tumors of the Central Nervous System: Characterization of a Pediatric Series of Seven Cases. Mod Pathol 2024; 37:100387. [PMID: 38007157 DOI: 10.1016/j.modpat.2023.100387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/28/2023] [Accepted: 11/06/2023] [Indexed: 11/27/2023]
Abstract
PATZ1-rearranged sarcomas are well-recognized tumors as part of the family of round cell sarcoma with EWSR1-non-ETS fusions. Whether PATZ1-rearranged central nervous system (CNS) tumors are a distinct tumor type is debatable. We thoroughly characterized a pediatric series of PATZ1-rearranged CNS tumors by chromosome microarray analysis (CMA), DNA methylation analysis, gene expression profiling and, when frozen tissue is available, optical genome mapping (OGM). The series consisted of 7 cases (M:F=1.3:1, 1-17 years, median 12). On MRI, the tumors were supratentorial in close relation to the lateral ventricles (intraventricular or iuxtaventricular), preferentially located in the occipital lobe. Two major histologic groups were identified: one (4 cases) with an overall glial appearance, indicated as "neuroepithelial" (NET) by analogy with the corresponding methylation class (MC); the other (3 cases) with a predominant spindle cell sarcoma morphology, indicated as "sarcomatous" (SM). A single distinct methylation cluster encompassing both groups was identified by multidimensional scaling analysis. Despite the epigenetic homogeneity, unsupervised clustering analysis of gene expression profiles revealed 2 distinct transcriptional subgroups correlating with the histologic phenotypes. Interestingly, genes implicated in epithelial-mesenchymal transition and extracellular matrix composition were enriched in the subgroup associated to the SM phenotype. The combined use of CMA and OGM enabled the identification of chromosome 22 chromothripsis in all cases suitable for the analyses, explaining the physical association of PATZ1 to EWSR1 or MN1. Six patients are currently disease-free (median follow-up 30 months, range 12-92). One patient of the SM group developed spinal metastases at 26 months from diagnosis and is currently receiving multimodal therapy (42 months). Our data suggest that PATZ1-CNS tumors are defined by chromosome 22 chromothripsis as causative of PATZ1 fusion, show peculiar MRI features (eg, relation to lateral ventricles, supratentorial frequently posterior site), and, although epigenetically homogenous, encompass 2 distinct histologic and transcriptional subgroups.
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Affiliation(s)
- Sabrina Rossi
- Pathology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
| | - Sabina Barresi
- Pathology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Giovanna Stefania Colafati
- Imaging Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy; Department of Neuroscience, Imaging and Clinical Sciences (DNISC), University "Gabriele D'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Silvia Genovese
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Chantal Tancredi
- Pathology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Valentino Costabile
- Multimodal Research Area, Unit of Microbiology and Diagnostics in Immunology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Sara Patrizi
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Isabella Giovannoni
- Pathology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Sofia Asioli
- Department of Biomedical and Neuromotor Sciences (DIBINEM)-Surgical Pathology Section-Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Pietro Luigi Poliani
- Pathology Unit, San Raffaele Hospital Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy
| | - Marina Paola Gardiman
- Surgical Pathology and Cytopathology Unit, Department of Medicine, University Hospital of Padua, Padua, Italy
| | - Antonello Cardoni
- Pathology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Giada Del Baldo
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Manila Antonelli
- Department of Radiology, Oncology and Anatomic Pathology, University La Sapienza, Rome, Italy
| | - Francesca Gianno
- Department of Radiology, Oncology and Anatomic Pathology, University La Sapienza, Rome, Italy; IRCCS Neuromed, Pozzilli, Isernia, Italy
| | - Eleonora Piccirilli
- Imaging Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy; Department of Neuroscience, Imaging and Clinical Sciences (DNISC), University "Gabriele D'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Giorgia Catino
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Licia Martucci
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Denise Quacquarini
- Pathology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Francesco Toni
- Neuroradiology Unit, IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Fraia Melchionda
- SSD Oncoematologia Pediatrica, IRCCS AOU Policlinico S.Orsola, Bologna, Italy
| | - Elisabetta Viscardi
- Department of Pediatrics, Azienda Ospedale-Università di Padova, Padova, Italy
| | - Mino Zucchelli
- Paediatric Neurosurgery, IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Sandro Dal Pos
- Department of Radiology, Azienda Ospedale-Università di Padova, Padova, Italy
| | - Enza Gatti
- Department of Radiology, Neuroradiology Unit, ASST Spedali Civili University Hospital, Brescia, Italy
| | - Roberto Liserre
- Department of Radiology, Neuroradiology Unit, ASST Spedali Civili University Hospital, Brescia, Italy
| | - Elisabetta Schiavello
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Andrea Carai
- Neurosurgery Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Angela Mastronuzzi
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Marco Gessi
- Neuropathology Unit, Pathology Division, Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica S.Cuore, Rome, Italy
| | - Caterina Giannini
- Department of Biomedical and Neuromotor Sciences (DIBINEM)-Surgical Pathology Section-Alma Mater Studiorum - University of Bologna, Bologna, Italy; Department of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Evelina Miele
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
| | - Viola Alesi
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Rita Alaggio
- Pathology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy; Department of Medico-surgical Sciences and Biotechnologies, Sapienza University, Rome, Italy
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3
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Grosch M, Schraft L, Chan A, Küchenhoff L, Rapti K, Ferreira AM, Kornienko J, Li S, Radke MH, Krämer C, Clauder-Münster S, Perlas E, Backs J, Gotthardt M, Dieterich C, van den Hoogenhof MMG, Grimm D, Steinmetz LM. Striated muscle-specific base editing enables correction of mutations causing dilated cardiomyopathy. Nat Commun 2023; 14:3714. [PMID: 37349314 PMCID: PMC10287752 DOI: 10.1038/s41467-023-39352-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 06/08/2023] [Indexed: 06/24/2023] Open
Abstract
Dilated cardiomyopathy is the second most common cause for heart failure with no cure except a high-risk heart transplantation. Approximately 30% of patients harbor heritable mutations which are amenable to CRISPR-based gene therapy. However, challenges related to delivery of the editing complex and off-target concerns hamper the broad applicability of CRISPR agents in the heart. We employ a combination of the viral vector AAVMYO with superior targeting specificity of heart muscle tissue and CRISPR base editors to repair patient mutations in the cardiac splice factor Rbm20, which cause aggressive dilated cardiomyopathy. Using optimized conditions, we repair >70% of cardiomyocytes in two Rbm20 knock-in mouse models that we have generated to serve as an in vivo platform of our editing strategy. Treatment of juvenile mice restores the localization defect of RBM20 in 75% of cells and splicing of RBM20 targets including TTN. Three months after injection, cardiac dilation and ejection fraction reach wild-type levels. Single-nuclei RNA sequencing uncovers restoration of the transcriptional profile across all major cardiac cell types and whole-genome sequencing reveals no evidence for aberrant off-target editing. Our study highlights the potential of base editors combined with AAVMYO to achieve gene repair for treatment of hereditary cardiac diseases.
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Affiliation(s)
- Markus Grosch
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Laura Schraft
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Adrian Chan
- Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Heidelberg, Germany
| | - Leonie Küchenhoff
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Kleopatra Rapti
- Department of Infectious Diseases/Virology, Section Viral Vector Technologies, Medical Faculty, BioQuant, University of Heidelberg, Heidelberg, Germany
| | - Anne-Maud Ferreira
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia Kornienko
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Shengdi Li
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Michael H Radke
- Translational Cardiology and Functional Genomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
| | - Chiara Krämer
- Department of Infectious Diseases/Virology, Section Viral Vector Technologies, Medical Faculty, BioQuant, University of Heidelberg, Heidelberg, Germany
| | | | - Emerald Perlas
- Epigenetics and Neurobiology Unit, EMBL Rome, Monterotondo, Italy
| | - Johannes Backs
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
- Institute of Experimental Cardiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Michael Gotthardt
- Translational Cardiology and Functional Genomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
- Department of Cardiology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Christoph Dieterich
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
- Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Heidelberg, Germany
| | - Maarten M G van den Hoogenhof
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
- Institute of Experimental Cardiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Dirk Grimm
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
- Department of Infectious Diseases/Virology, Section Viral Vector Technologies, Medical Faculty, BioQuant, University of Heidelberg, Heidelberg, Germany
- German Center for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
| | - Lars M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany.
- Stanford Genome Technology Center, Palo Alto, CA, USA.
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4
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Cook DE, Venkat A, Yelizarov D, Pouliot Y, Chang PC, Carroll A, De La Vega FM. A deep-learning-based RNA-seq germline variant caller. BIOINFORMATICS ADVANCES 2023; 3:vbad062. [PMID: 37416509 PMCID: PMC10320079 DOI: 10.1093/bioadv/vbad062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/31/2023] [Accepted: 05/30/2023] [Indexed: 07/08/2023]
Abstract
Summary RNA sequencing (RNA-seq) can be applied to diverse tasks including quantifying gene expression, discovering quantitative trait loci and identifying gene fusion events. Although RNA-seq can detect germline variants, the complexities of variable transcript abundance, target capture and amplification introduce challenging sources of error. Here, we extend DeepVariant, a deep-learning-based variant caller, to learn and account for the unique challenges presented by RNA-seq data. Our DeepVariant RNA-seq model produces highly accurate variant calls from RNA-sequencing data, and outperforms existing approaches such as Platypus and GATK. We examine factors that influence accuracy, how our model addresses RNA editing events and how additional thresholding can be used to facilitate our models' use in a production pipeline. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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5
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Nagi SC, Oruni A, Weetman D, Donnelly MJ. RNA-Seq-Pop: Exploiting the sequence in RNA sequencing-A Snakemake workflow reveals patterns of insecticide resistance in the malaria vector Anopheles gambiae. Mol Ecol Resour 2023; 23:946-961. [PMID: 36695302 PMCID: PMC10568660 DOI: 10.1111/1755-0998.13759] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/12/2022] [Accepted: 01/06/2023] [Indexed: 01/26/2023]
Abstract
We provide a reproducible and scalable Snakemake workflow, called RNA-Seq-Pop, which provides end-to-end analysis of RNA sequencing data sets. The workflow allows the user to perform quality control, perform differential expression analyses and call genomic variants. Additional options include the calculation of allele frequencies of variants of interest, summaries of genetic variation and population structure, and genome-wide selection scans, together with clear visualizations. RNA-Seq-Pop is applicable to any organism, and we demonstrate the utility of the workflow by investigating pyrethroid resistance in selected strains of the major malaria mosquito, Anopheles gambiae. The workflow provides additional modules specifically for An. gambiae, including estimating recent ancestry and determining the karyotype of common chromosomal inversions. The Busia laboratory colony used for selections was collected in Busia, Uganda, in November 2018. We performed a comparative analysis of three groups: a parental G24 Busia strain; its deltamethrin-selected G28 offspring; and the susceptible reference strain Kisumu. Measures of genetic diversity reveal patterns consistent with that of laboratory colonization and selection, with the parental Busia strain exhibiting the highest nucleotide diversity, followed by the selected Busia offspring, and finally, Kisumu. Differential expression and variant analyses reveal that the selected Busia colony exhibits a number of distinct mechanisms of pyrethroid resistance, including the Vgsc-995S target-site mutation, upregulation of SAP genes, P450s and a cluster of carboxylesterases. During deltamethrin selections, the 2La chromosomal inversion rose in frequency (from 33% to 86%), supporting a previous link with pyrethroid resistance. RNA-Seq-Pop is hosted at: github.com/sanjaynagi/rna-seq-pop. We anticipate that the workflow will provide a useful tool to facilitate reproducible, transcriptomic studies in An. gambiae and other taxa.
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Affiliation(s)
- Sanjay C. Nagi
- Department of Vector BiologyLiverpool School of Tropical MedicineLiverpoolUK
| | | | - David Weetman
- Department of Vector BiologyLiverpool School of Tropical MedicineLiverpoolUK
| | - Martin J. Donnelly
- Department of Vector BiologyLiverpool School of Tropical MedicineLiverpoolUK
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6
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Camp FA, Brunetti TM, Williams MM, Christenson JL, Sreekanth V, Costello JC, Hay ZLZ, Kedl RM, Richer JK, Slansky JE. Antigens Expressed by Breast Cancer Cells Undergoing EMT Stimulate Cytotoxic CD8 + T Cell Immunity. Cancers (Basel) 2022; 14:cancers14184397. [PMID: 36139558 PMCID: PMC9496737 DOI: 10.3390/cancers14184397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 11/26/2022] Open
Abstract
Simple Summary The transition of cells with epithelial characteristics to those with mesenchymal characteristics (termed EMT) facilitates breast cancer invasive capacity. The EMT program can also contribute to immunosuppressive and immunoevasive properties, altering susceptibility to immune cell recognition and killing. The goal of our study was to manipulate EMT to reveal potential neoantigens that might affect the ability of tumor cells to circumvent immune escape and/or be utilized as an anticancer vaccine to kill cancer cells exhibiting the cellular plasticity that permits therapy resistance and metastatic progression. We identified potential neoantigens resulting from EMT-associated altered gene expression and alternative splicing events and observed increased immunogenicity and susceptibility to killing of the more epithelial-like cancer cells. Although the tested peptides did not protect from tumor growth, a limited number of predicted neoantigens derived from intron retention events were tested. In the future, refined prediction programs may facilitate exciting antigen discoveries. Abstract Antigenic differences formed by alterations in gene expression and alternative splicing are predicted in breast cancer cells undergoing epithelial to mesenchymal transition (EMT) and the reverse plasticity known as MET. How these antigenic differences impact immune interactions and the degree to which they can be exploited to enhance immune responses against mesenchymal cells is not fully understood. We utilized a master microRNA regulator of EMT to alter mesenchymal-like EO771 mammary carcinoma cells to a more epithelial phenotype. A computational approach was used to identify neoantigens derived from the resultant differentially expressed somatic variants (SNV) and alternative splicing events (neojunctions). Using whole cell vaccines and peptide-based vaccines, we find superior cytotoxicity against the more-epithelial cells and explore the potential of neojunction-derived antigens to elicit T cell responses through experiments designed to validate the computationally predicted neoantigens. Overall, results identify EMT-associated splicing factors common to both mouse and human breast cancer cells as well as immunogenic SNV- and neojunction-derived neoantigens in mammary carcinoma cells.
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Affiliation(s)
- Faye A. Camp
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Tonya M. Brunetti
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Michelle M. Williams
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Jessica L. Christenson
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Varsha Sreekanth
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - James C. Costello
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Zachary L. Z. Hay
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Ross M. Kedl
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Jennifer K. Richer
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Jill E. Slansky
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Correspondence:
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7
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Escudero-Martinez C, Coulter M, Alegria Terrazas R, Foito A, Kapadia R, Pietrangelo L, Maver M, Sharma R, Aprile A, Morris J, Hedley PE, Maurer A, Pillen K, Naclerio G, Mimmo T, Barton GJ, Waugh R, Abbott J, Bulgarelli D. Identifying plant genes shaping microbiota composition in the barley rhizosphere. Nat Commun 2022; 13:3443. [PMID: 35710760 PMCID: PMC9203816 DOI: 10.1038/s41467-022-31022-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/30/2022] [Indexed: 12/13/2022] Open
Abstract
A prerequisite to exploiting soil microbes for sustainable crop production is the identification of the plant genes shaping microbiota composition in the rhizosphere, the interface between roots and soil. Here, we use metagenomics information as an external quantitative phenotype to map the host genetic determinants of the rhizosphere microbiota in wild and domesticated genotypes of barley, the fourth most cultivated cereal globally. We identify a small number of loci with a major effect on the composition of rhizosphere communities. One of those, designated the QRMC-3HS, emerges as a major determinant of microbiota composition. We subject soil-grown sibling lines harbouring contrasting alleles at QRMC-3HS and hosting contrasting microbiotas to comparative root RNA-seq profiling. This allows us to identify three primary candidate genes, including a Nucleotide-Binding-Leucine-Rich-Repeat (NLR) gene in a region of structural variation of the barley genome. Our results provide insights into the footprint of crop improvement on the plant's capacity of shaping rhizosphere microbes.
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Affiliation(s)
| | - Max Coulter
- University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK
- University of Dundee, Computational Biology, School of Life Sciences, Dundee, UK
| | - Rodrigo Alegria Terrazas
- University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK
- Mohammed VI Polytechnic University, Agrobiosciences Program, Plant & Soil Microbiome Subprogram, Bengurir, Morocco
| | | | - Rumana Kapadia
- University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK
| | - Laura Pietrangelo
- University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK
- Department of Biosciences and Territory, University of Molise, Campobasso, Italy
| | - Mauro Maver
- University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Bolzano, Italy
- Competence Centre for Plant Health, Free University of Bozen-Bolzano, Bolzano, Italy
| | | | - Alessio Aprile
- University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | | | | | - Andreas Maurer
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University, Halle-Wittenberg, Germany
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University, Halle-Wittenberg, Germany
| | - Gino Naclerio
- Department of Biosciences and Territory, University of Molise, Campobasso, Italy
| | - Tanja Mimmo
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Bolzano, Italy
- Competence Centre for Plant Health, Free University of Bozen-Bolzano, Bolzano, Italy
| | - Geoffrey J Barton
- University of Dundee, Computational Biology, School of Life Sciences, Dundee, UK
| | - Robbie Waugh
- University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK
- The James Hutton Institute, Invergowrie, UK
| | - James Abbott
- University of Dundee, Computational Biology, School of Life Sciences, Dundee, UK
| | - Davide Bulgarelli
- University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK.
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8
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Guo D, Daman K, Chen JJC, Shi MJ, Yan J, Matijasevic Z, Rickard AM, Bennett MH, Kiselyov A, Zhou H, Bang AG, Wagner KR, Maehr R, King OD, Hayward LJ, Emerson CP. iMyoblasts for ex vivo and in vivo investigations of human myogenesis and disease modeling. eLife 2022; 11:e70341. [PMID: 35076017 PMCID: PMC8789283 DOI: 10.7554/elife.70341] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 12/10/2021] [Indexed: 12/13/2022] Open
Abstract
Skeletal muscle myoblasts (iMyoblasts) were generated from human induced pluripotent stem cells (iPSCs) using an efficient and reliable transgene-free induction and stem cell selection protocol. Immunofluorescence, flow cytometry, qPCR, digital RNA expression profiling, and scRNA-Seq studies identify iMyoblasts as a PAX3+/MYOD1+ skeletal myogenic lineage with a fetal-like transcriptome signature, distinct from adult muscle biopsy myoblasts (bMyoblasts) and iPSC-induced muscle progenitors. iMyoblasts can be stably propagated for >12 passages or 30 population doublings while retaining their dual commitment for myotube differentiation and regeneration of reserve cells. iMyoblasts also efficiently xenoengrafted into irradiated and injured mouse muscle where they undergo differentiation and fetal-adult MYH isoform switching, demonstrating their regulatory plasticity for adult muscle maturation in response to signals in the host muscle. Xenograft muscle retains PAX3+ muscle progenitors and can regenerate human muscle in response to secondary injury. As models of disease, iMyoblasts from individuals with Facioscapulohumeral Muscular Dystrophy revealed a previously unknown epigenetic regulatory mechanism controlling developmental expression of the pathological DUX4 gene. iMyoblasts from Limb-Girdle Muscular Dystrophy R7 and R9 and Walker Warburg Syndrome patients modeled their molecular disease pathologies and were responsive to small molecule and gene editing therapeutics. These findings establish the utility of iMyoblasts for ex vivo and in vivo investigations of human myogenesis and disease pathogenesis and for the development of muscle stem cell therapeutics.
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Affiliation(s)
- Dongsheng Guo
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
- Li Weibo Institute for Rare Disease Research, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Katelyn Daman
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
- Li Weibo Institute for Rare Disease Research, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Jennifer JC Chen
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Meng-Jiao Shi
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Jing Yan
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Zdenka Matijasevic
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
- Transgenic Animal Modeling Core, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | | | | | | | - Haowen Zhou
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | - Anne G Bang
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | - Kathryn R Wagner
- Center for Genetic Muscle Disorders, Kennedy Krieger InstituteBaltimoreUnited States
| | - René Maehr
- Program in Molecular Medicine, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Oliver D King
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Lawrence J Hayward
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
- Li Weibo Institute for Rare Disease Research, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Charles P Emerson
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
- Li Weibo Institute for Rare Disease Research, University of Massachusetts Chan Medical SchoolWorcesterUnited States
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9
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Deragon E, Schuler M, Aiese Cigliano R, Dellero Y, Si Larbi G, Falconet D, Jouhet J, Maréchal E, Michaud M, Amato A, Rébeillé F. An Oil Hyper-Accumulator Mutant Highlights Peroxisomal ATP Import as a Regulatory Step for Fatty Acid Metabolism in Aurantiochytrium limacinum. Cells 2021; 10:2680. [PMID: 34685660 PMCID: PMC8534400 DOI: 10.3390/cells10102680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/24/2021] [Accepted: 09/24/2021] [Indexed: 11/17/2022] Open
Abstract
Thraustochytrids are marine protists that naturally accumulate triacylglycerol with long chains of polyunsaturated fatty acids, such as ω3-docosahexaenoic acid (DHA). They represent a sustainable response to the increasing demand for these "essential" fatty acids (FAs). Following an attempt to transform a strain of Aurantiochytrium limacinum, we serendipitously isolated a clone that did not incorporate any recombinant DNA but contained two to three times more DHA than the original strain. Metabolic analyses indicated a deficit in FA catabolism. However, whole transcriptome analysis did not show down-regulation of genes involved in FA catabolism. Genome sequencing revealed extensive DNA deletion in one allele encoding a putative peroxisomal adenylate transporter. Phylogenetic analyses and yeast complementation experiments confirmed the gene as a peroxisomal adenylate nucleotide transporter (AlANT1), homologous to yeast ScANT1 and plant peroxisomal adenylate nucleotide carrier AtPNC genes. In yeast and plants, a deletion of the peroxisomal adenylate transporter inhibits FA breakdown and induces FA accumulation, a phenotype similar to that described here. In response to this metabolic event, several compensatory mechanisms were observed. In particular, genes involved in FA biosynthesis were upregulated, also contributing to the high FA accumulation. These results support AlANT1 as a promising target for enhancing DHA production in Thraustochytrids.
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Affiliation(s)
- Etienne Deragon
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, CEDEX 9, 38054 Grenoble, France; (E.D.); (M.S.); (Y.D.); (G.S.L.); (D.F.); (J.J.); (E.M.); (M.M.)
| | - Martin Schuler
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, CEDEX 9, 38054 Grenoble, France; (E.D.); (M.S.); (Y.D.); (G.S.L.); (D.F.); (J.J.); (E.M.); (M.M.)
| | | | - Younès Dellero
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, CEDEX 9, 38054 Grenoble, France; (E.D.); (M.S.); (Y.D.); (G.S.L.); (D.F.); (J.J.); (E.M.); (M.M.)
- Institute of Genetic, Environment and Plant Protection, UMR 1349 IGEPP INRA, Agrocampus Ouest Rennes, Université Rennes 1, Domaine de la Motte BP35327, CEDEX, 35653 Le Rheu, France
| | - Gregory Si Larbi
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, CEDEX 9, 38054 Grenoble, France; (E.D.); (M.S.); (Y.D.); (G.S.L.); (D.F.); (J.J.); (E.M.); (M.M.)
| | - Denis Falconet
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, CEDEX 9, 38054 Grenoble, France; (E.D.); (M.S.); (Y.D.); (G.S.L.); (D.F.); (J.J.); (E.M.); (M.M.)
| | - Juliette Jouhet
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, CEDEX 9, 38054 Grenoble, France; (E.D.); (M.S.); (Y.D.); (G.S.L.); (D.F.); (J.J.); (E.M.); (M.M.)
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, CEDEX 9, 38054 Grenoble, France; (E.D.); (M.S.); (Y.D.); (G.S.L.); (D.F.); (J.J.); (E.M.); (M.M.)
| | - Morgane Michaud
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, CEDEX 9, 38054 Grenoble, France; (E.D.); (M.S.); (Y.D.); (G.S.L.); (D.F.); (J.J.); (E.M.); (M.M.)
| | - Alberto Amato
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, CEDEX 9, 38054 Grenoble, France; (E.D.); (M.S.); (Y.D.); (G.S.L.); (D.F.); (J.J.); (E.M.); (M.M.)
| | - Fabrice Rébeillé
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, CEDEX 9, 38054 Grenoble, France; (E.D.); (M.S.); (Y.D.); (G.S.L.); (D.F.); (J.J.); (E.M.); (M.M.)
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10
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Thind AS, Monga I, Thakur PK, Kumari P, Dindhoria K, Krzak M, Ranson M, Ashford B. Demystifying emerging bulk RNA-Seq applications: the application and utility of bioinformatic methodology. Brief Bioinform 2021; 22:6330938. [PMID: 34329375 DOI: 10.1093/bib/bbab259] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 06/14/2021] [Accepted: 06/18/2021] [Indexed: 12/13/2022] Open
Abstract
Significant innovations in next-generation sequencing techniques and bioinformatics tools have impacted our appreciation and understanding of RNA. Practical RNA sequencing (RNA-Seq) applications have evolved in conjunction with sequence technology and bioinformatic tools advances. In most projects, bulk RNA-Seq data is used to measure gene expression patterns, isoform expression, alternative splicing and single-nucleotide polymorphisms. However, RNA-Seq holds far more hidden biological information including details of copy number alteration, microbial contamination, transposable elements, cell type (deconvolution) and the presence of neoantigens. Recent novel and advanced bioinformatic algorithms developed the capacity to retrieve this information from bulk RNA-Seq data, thus broadening its scope. The focus of this review is to comprehend the emerging bulk RNA-Seq-based analyses, emphasizing less familiar and underused applications. In doing so, we highlight the power of bulk RNA-Seq in providing biological insights.
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Affiliation(s)
- Amarinder Singh Thind
- University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Isha Monga
- Columbia University, New York City, NY, USA
| | | | - Pallawi Kumari
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Kiran Dindhoria
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | | | - Marie Ranson
- University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Bruce Ashford
- University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
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11
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Jehl F, Degalez F, Bernard M, Lecerf F, Lagoutte L, Désert C, Coulée M, Bouchez O, Leroux S, Abasht B, Tixier-Boichard M, Bed'hom B, Burlot T, Gourichon D, Bardou P, Acloque H, Foissac S, Djebali S, Giuffra E, Zerjal T, Pitel F, Klopp C, Lagarrigue S. RNA-Seq Data for Reliable SNP Detection and Genotype Calling: Interest for Coding Variant Characterization and Cis-Regulation Analysis by Allele-Specific Expression in Livestock Species. Front Genet 2021; 12:655707. [PMID: 34262593 PMCID: PMC8273700 DOI: 10.3389/fgene.2021.655707] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 06/01/2021] [Indexed: 12/19/2022] Open
Abstract
In addition to their common usages to study gene expression, RNA-seq data accumulated over the last 10 years are a yet-unexploited resource of SNPs in numerous individuals from different populations. SNP detection by RNA-seq is particularly interesting for livestock species since whole genome sequencing is expensive and exome sequencing tools are unavailable. These SNPs detected in expressed regions can be used to characterize variants affecting protein functions, and to study cis-regulated genes by analyzing allele-specific expression (ASE) in the tissue of interest. However, gene expression can be highly variable, and filters for SNP detection using the popular GATK toolkit are not yet standardized, making SNP detection and genotype calling by RNA-seq a challenging endeavor. We compared SNP calling results using GATK suggested filters, on two chicken populations for which both RNA-seq and DNA-seq data were available for the same samples of the same tissue. We showed, in expressed regions, a RNA-seq precision of 91% (SNPs detected by RNA-seq and shared by DNA-seq) and we characterized the remaining 9% of SNPs. We then studied the genotype (GT) obtained by RNA-seq and the impact of two factors (GT call-rate and read number per GT) on the concordance of GT with DNA-seq; we proposed thresholds for them leading to a 95% concordance. Applying these thresholds to 767 multi-tissue RNA-seq of 382 birds of 11 chicken populations, we found 9.5 M SNPs in total, of which ∼550,000 SNPs per tissue and population with a reliable GT (call rate ≥ 50%) and among them, ∼340,000 with a MAF ≥ 10%. We showed that such RNA-seq data from one tissue can be used to (i) detect SNPs with a strong predicted impact on proteins, despite their scarcity in each population (16,307 SIFT deleterious missenses and 590 stop-gained), (ii) study, on a large scale, cis-regulations of gene expression, with ∼81% of protein-coding and 68% of long non-coding genes (TPM ≥ 1) that can be analyzed for ASE, and with ∼29% of them that were cis-regulated, and (iii) analyze population genetic using such SNPs located in expressed regions. This work shows that RNA-seq data can be used with good confidence to detect SNPs and associated GT within various populations and used them for different analyses as GTEx studies.
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Affiliation(s)
- Frédéric Jehl
- INRAE, INSTITUT AGRO, PEGASE UMR 1348, Saint-Gilles, France
| | - Fabien Degalez
- INRAE, INSTITUT AGRO, PEGASE UMR 1348, Saint-Gilles, France
| | - Maria Bernard
- INRAE, SIGENAE, Genotoul Bioinfo MIAT, Castanet-Tolosan, France.,INRAE, AgroParisTech, Université Paris-Saclay, GABI UMR 1313, Jouy-en-Josas, France
| | | | | | - Colette Désert
- INRAE, INSTITUT AGRO, PEGASE UMR 1348, Saint-Gilles, France
| | - Manon Coulée
- INRAE, INSTITUT AGRO, PEGASE UMR 1348, Saint-Gilles, France
| | - Olivier Bouchez
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Sophie Leroux
- INRAE, INPT, ENVT, Université de Toulouse, GenPhySE UMR 1388, Castanet-Tolosan, France
| | - Behnam Abasht
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, United States
| | | | - Bertrand Bed'hom
- INRAE, AgroParisTech, Université Paris-Saclay, GABI UMR 1313, Jouy-en-Josas, France
| | | | | | - Philippe Bardou
- INRAE, SIGENAE, Genotoul Bioinfo MIAT, Castanet-Tolosan, France
| | - Hervé Acloque
- INRAE, AgroParisTech, Université Paris-Saclay, GABI UMR 1313, Jouy-en-Josas, France
| | - Sylvain Foissac
- INRAE, INPT, ENVT, Université de Toulouse, GenPhySE UMR 1388, Castanet-Tolosan, France
| | - Sarah Djebali
- INRAE, INPT, ENVT, Université de Toulouse, GenPhySE UMR 1388, Castanet-Tolosan, France
| | - Elisabetta Giuffra
- INRAE, AgroParisTech, Université Paris-Saclay, GABI UMR 1313, Jouy-en-Josas, France
| | - Tatiana Zerjal
- INRAE, AgroParisTech, Université Paris-Saclay, GABI UMR 1313, Jouy-en-Josas, France
| | - Frédérique Pitel
- INRAE, INPT, ENVT, Université de Toulouse, GenPhySE UMR 1388, Castanet-Tolosan, France
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12
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Li L, Halpert G, Lerner MG, Hu H, Dimitrion P, Weiss MJ, He J, Philosophe B, Burkhart R, Burns WR, Wesson RN, MacGregor Cameron A, Wolfgang CL, Georgiades C, Kawamoto S, Azad NS, Yarchoan M, Meltzer SJ, Oshima K, Ensign LM, Bader JS, Selaru FM. Protein synthesis inhibitor omacetaxine is effective against hepatocellular carcinoma. JCI Insight 2021; 6:138197. [PMID: 34003798 PMCID: PMC8262474 DOI: 10.1172/jci.insight.138197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/12/2021] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the sixth most common and the fourth most deadly cancer worldwide. The development cost of new therapeutics is a major limitation in patient outcomes. Importantly, there is a paucity of preclinical HCC models in which to test new small molecules. Herein, we implemented potentially novel patient-derived organoid (PDO) and patient-derived xenografts (PDX) strategies for high-throughput drug screening. Omacetaxine, an FDA-approved drug for chronic myelogenous leukemia (CML), was found to be a top effective small molecule in HCC PDOs. Next, omacetaxine was tested against a larger cohort of 40 human HCC PDOs. Serial dilution experiments demonstrated that omacetaxine is effective at low (nanomolar) concentrations. Mechanistic studies established that omacetaxine inhibits global protein synthesis, with a disproportionate effect on short–half-life proteins. High-throughput expression screening identified molecular targets for omacetaxine, including key oncogenes, such as PLK1. In conclusion, by using an innovative strategy, we report — for the first time to our knowledge — the effectiveness of omacetaxine in HCC. In addition, we elucidate key mechanisms of omacetaxine action. Finally, we provide a proof-of-principle basis for future studies applying drug screening PDOs sequenced with candidate validation in PDX models. Clinical trials could be considered to evaluate omacetaxine in patients with HCC.
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Affiliation(s)
- Ling Li
- Division of Gastroenterology and Hepatology and
| | - Gilad Halpert
- Center for Nanomedicine at the Wilmer Eye Institute, Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael G Lerner
- Department of Physics and Astronomy, Earlham College, Richmond, Indiana, USA
| | - Haijie Hu
- Division of Gastroenterology and Hepatology and
| | - Peter Dimitrion
- Center for Nanomedicine at the Wilmer Eye Institute, Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Matthew J Weiss
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jin He
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Benjamin Philosophe
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Richard Burkhart
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - William R Burns
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Russell N Wesson
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | | | | | - Nilofer S Azad
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mark Yarchoan
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Stephen J Meltzer
- Division of Gastroenterology and Hepatology and.,Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Laura M Ensign
- Center for Nanomedicine at the Wilmer Eye Institute, Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Joel S Bader
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Florin M Selaru
- Division of Gastroenterology and Hepatology and.,Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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13
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Li J, West JB, Hart A, Wegrzyn JL, Smith MA, Domec JC, Loopstra CA, Casola C. Extensive Variation in Drought-Induced Gene Expression Changes Between Loblolly Pine Genotypes. Front Genet 2021; 12:661440. [PMID: 34140968 PMCID: PMC8203665 DOI: 10.3389/fgene.2021.661440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/07/2021] [Indexed: 01/22/2023] Open
Abstract
Drought response is coordinated through expression changes in a large suite of genes. Interspecific variation in this response is common and associated with drought-tolerant and -sensitive genotypes. The extent to which different genetic networks orchestrate the adjustments to water deficit in tolerant and sensitive genotypes has not been fully elucidated, particularly in non-model or woody plants. Differential expression analysis via RNA-seq was evaluated in root tissue exposed to simulated drought conditions in two loblolly pine (Pinus taeda L.) clones with contrasting tolerance to drought. Loblolly pine is the prevalent conifer in southeastern U.S. and a major commercial forestry species worldwide. Significant changes in gene expression levels were found in more than 4,000 transcripts [drought-related transcripts (DRTs)]. Genotype by environment (GxE) interactions were prevalent, suggesting that different cohorts of genes are influenced by drought conditions in the tolerant vs. sensitive genotypes. Functional annotation categories and metabolic pathways associated with DRTs showed higher levels of overlap between clones, with the notable exception of GO categories in upregulated DRTs. Conversely, both differentially expressed transcription factors (TFs) and TF families were largely different between clones. Our results indicate that the response of a drought-tolerant loblolly pine genotype vs. a sensitive genotype to water limitation is remarkably different on a gene-by-gene level, although it involves similar genetic networks. Upregulated transcripts under drought conditions represent the most diverging component between genotypes, which might depend on the activation and repression of substantially different groups of TFs.
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Affiliation(s)
- Jingjia Li
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, United States
| | - Jason B West
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, United States
| | - Alexander Hart
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Matthew A Smith
- Department of Biological Sciences, Florida International University, Miami, FL, United States
| | - Jean-Christophe Domec
- Bordeaux Sciences Agro, UMR 1391 INRA ISPA, Gradignan, France.,Nicholas School of the Environment, Duke University, Durham, NC, United States
| | - Carol A Loopstra
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, United States
| | - Claudio Casola
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, United States
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14
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Tarlinton RE, Fabijan J, Hemmatzadeh F, Meers J, Owen H, Sarker N, Seddon JM, Simmons G, Speight N, Trott DJ, Woolford L, Emes RD. Transcriptomic and genomic variants between koala populations reveals underlying genetic components to disorders in a bottlenecked population. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01340-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
AbstractHistorical hunting pressures on koalas in the southern part of their range in Australia have led to a marked genetic bottleneck when compared with their northern counterparts. There are a range of suspected genetic disorders such as testicular abnormalities, oxalate nephrosis and microcephaly reported at higher prevalence in these genetically restricted southern animals. This paper reports analysis of differential expression of genes from RNAseq of lymph nodes, SNPs present in genes and the fixation index (population differentiation due to genetic structure) of these SNPs from two populations, one in south east Queensland, representative of the northern genotype and one in the Mount Lofty Ranges South Australia, representative of the southern genotype. SNPs that differ between these two populations were significantly enriched in genes associated with brain diseases. Genes which were differentially expressed between the two populations included many associated with brain development or disease, and in addition a number associated with testicular development, including the androgen receptor. Finally, one of the 8 genes both differentially expressed and with a statistical difference in SNP frequency between populations was SLC26A6 (solute carrier family 26 member 6), an anion transporter that was upregulated in SA koalas and is associated with oxalate transport and calcium oxalate uroliths in humans. Together the differences in SNPs and gene expression described in this paper suggest an underlying genetic basis for several disorders commonly seen in southern Australian koalas, supporting the need for further research into the genetic basis of these conditions, and highlighting that genetic selection in managed populations may need to be considered in the future.
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15
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Das T, Deb A, Parida S, Mondal S, Khatua S, Ghosh Z. LncRBase V.2: an updated resource for multispecies lncRNAs and ClinicLSNP hosting genetic variants in lncRNAs for cancer patients. RNA Biol 2020; 18:1136-1151. [PMID: 33112702 DOI: 10.1080/15476286.2020.1833529] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The recent discovery of long non-coding RNA as a regulatory molecule in the cellular system has altered the concept of the functional aptitude of the genome. Since our publication of the first version of LncRBase in 2014, there has been an enormous increase in the number of annotated lncRNAs of multiple species other than Human and Mouse. LncRBase V.2 hosts information of 549,648 lncRNAs corresponding to six additional species besides Human and Mouse, viz. Rat, Fruitfly, Zebrafish, Chicken, Cow and C.elegans. It provides additional distinct features such as (i) Transcription Factor Binding Site (TFBS) in the lncRNA promoter region, (ii) sub-cellular localization pattern of lncRNAs (iii) lnc-pri-miRNAs (iv) Possible small open reading frames (sORFs) within lncRNA. (v) Manually curated information of interacting target molecules and disease association of lncRNA genes (vi) Distribution of lncRNAs across multiple tissues of all species. Moreover, we have hosted ClinicLSNP within LncRBase V.2. ClinicLSNP has a comprehensive catalogue of lncRNA variants present within breast, ovarian, and cervical cancer inferred from 561 RNA-Seq data corresponding to these cancers. Further, we have checked whether these lncRNA variants overlap with (i)Repeat elements,(ii)CGI, (iii)TFBS within lncRNA loci (iv)SNP localization in trait-associated Linkage Disequilibrium(LD) region, (v)predicted the potentially pathogenic variants and (vi)effect of SNP on lncRNA secondary structure. Overall, LncRBaseV.2 is a user-friendly database to survey, search and retrieve information about multi-species lncRNAs. Further, ClinicLSNP will serve as a useful resource for cancer specific lncRNA variants and their related information. The database is freely accessible and available at http://dibresources.jcbose.ac.in/zhumur/lncrbase2/.
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Affiliation(s)
- Troyee Das
- Division of Bioinformatics, Bose Institute, Kolkata, India
| | - Aritra Deb
- Division of Bioinformatics, Bose Institute, Kolkata, India
| | - Sibun Parida
- Division of Bioinformatics, Bose Institute, Kolkata, India
| | - Sudip Mondal
- Department of Computer Science and Engineering, University of Calcutta, Kolkata, India
| | - Sunirmal Khatua
- Department of Computer Science and Engineering, University of Calcutta, Kolkata, India
| | - Zhumur Ghosh
- Division of Bioinformatics, Bose Institute, Kolkata, India
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Tsering T, Laskaris A, Abdouh M, Bustamante P, Parent S, Jin E, Ferrier ST, Arena G, Burnier JV. Uveal Melanoma-Derived Extracellular Vesicles Display Transforming Potential and Carry Protein Cargo Involved in Metastatic Niche Preparation. Cancers (Basel) 2020; 12:cancers12102923. [PMID: 33050649 PMCID: PMC7600758 DOI: 10.3390/cancers12102923] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/05/2020] [Accepted: 10/07/2020] [Indexed: 12/13/2022] Open
Abstract
Extracellular vesicles (EVs) carry molecules derived from donor cells and are able to alter the properties of recipient cells. They are important players during the genesis and progression of tumors. Uveal melanoma (UM) is the most common primary intraocular tumor in adults and is associated with a high rate of metastasis, primarily to the liver. However, the mechanisms underlying this process are poorly understood. In the present study, we analyzed the oncogenic potential of UM-derived EVs and their protein signature. We isolated and characterized EVs from five UM cell lines and from normal choroidal melanocytes (NCMs). BRCA1-deficient fibroblasts (Fibro-BKO) were exposed to the EVs and analyzed for their growth in vitro and their reprograming potential in vivo following inoculation into NOD-SCID mice. Mass spectrometry of proteins from UM-EVs and NCM-EVs was performed to determine a protein signature that could elucidate potential key players in UM progression. In-depth analyses showed the presence of exosomal markers, and proteins involved in cell-cell and focal adhesion, endocytosis, and PI3K-Akt signaling pathway. Notably, we observed high expression levels of HSP90, HSP70 and integrin V in UM-EVs. Our data bring new evidence on the involvement of UM-EVs in cancer progression and metastasis.
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Affiliation(s)
- Thupten Tsering
- Cancer Research Program, Research Institute of the McGill University Health Centre, 1001 Decarie Blvd, Montreal, QC H4A 3J1, Canada; (T.T.); (A.L.); (M.A.); (P.B.); (S.P.); (E.J.); (S.T.F.); (G.A.)
| | - Alexander Laskaris
- Cancer Research Program, Research Institute of the McGill University Health Centre, 1001 Decarie Blvd, Montreal, QC H4A 3J1, Canada; (T.T.); (A.L.); (M.A.); (P.B.); (S.P.); (E.J.); (S.T.F.); (G.A.)
| | - Mohamed Abdouh
- Cancer Research Program, Research Institute of the McGill University Health Centre, 1001 Decarie Blvd, Montreal, QC H4A 3J1, Canada; (T.T.); (A.L.); (M.A.); (P.B.); (S.P.); (E.J.); (S.T.F.); (G.A.)
| | - Prisca Bustamante
- Cancer Research Program, Research Institute of the McGill University Health Centre, 1001 Decarie Blvd, Montreal, QC H4A 3J1, Canada; (T.T.); (A.L.); (M.A.); (P.B.); (S.P.); (E.J.); (S.T.F.); (G.A.)
| | - Sabrina Parent
- Cancer Research Program, Research Institute of the McGill University Health Centre, 1001 Decarie Blvd, Montreal, QC H4A 3J1, Canada; (T.T.); (A.L.); (M.A.); (P.B.); (S.P.); (E.J.); (S.T.F.); (G.A.)
| | - Eva Jin
- Cancer Research Program, Research Institute of the McGill University Health Centre, 1001 Decarie Blvd, Montreal, QC H4A 3J1, Canada; (T.T.); (A.L.); (M.A.); (P.B.); (S.P.); (E.J.); (S.T.F.); (G.A.)
| | - Sarah Tadhg Ferrier
- Cancer Research Program, Research Institute of the McGill University Health Centre, 1001 Decarie Blvd, Montreal, QC H4A 3J1, Canada; (T.T.); (A.L.); (M.A.); (P.B.); (S.P.); (E.J.); (S.T.F.); (G.A.)
| | - Goffredo Arena
- Cancer Research Program, Research Institute of the McGill University Health Centre, 1001 Decarie Blvd, Montreal, QC H4A 3J1, Canada; (T.T.); (A.L.); (M.A.); (P.B.); (S.P.); (E.J.); (S.T.F.); (G.A.)
- Ospedale Giuseppe Giglio Fondazione San Raffaele Cefalu Sicily, 90015 Cefalu, Italy
- Mediterranean Institute of Oncology, 95029 Viagrande, Italy
| | - Julia V. Burnier
- Cancer Research Program, Research Institute of the McGill University Health Centre, 1001 Decarie Blvd, Montreal, QC H4A 3J1, Canada; (T.T.); (A.L.); (M.A.); (P.B.); (S.P.); (E.J.); (S.T.F.); (G.A.)
- Experimental Pathology Unit, Department of Pathology, McGill University, QC H3A 2B4, Canada
- Correspondence: ; Tel.: +1-514-934-1934 (ext. 76307)
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17
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Lam S, Zeidan J, Miglior F, Suárez-Vega A, Gómez-Redondo I, Fonseca PAS, Guan LL, Waters S, Cánovas A. Development and comparison of RNA-sequencing pipelines for more accurate SNP identification: practical example of functional SNP detection associated with feed efficiency in Nellore beef cattle. BMC Genomics 2020; 21:703. [PMID: 33032519 PMCID: PMC7545862 DOI: 10.1186/s12864-020-07107-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 09/28/2020] [Indexed: 12/14/2022] Open
Abstract
Background Optimization of an RNA-Sequencing (RNA-Seq) pipeline is critical to maximize power and accuracy to identify genetic variants, including SNPs, which may serve as genetic markers to select for feed efficiency, leading to economic benefits for beef production. This study used RNA-Seq data (GEO Accession ID: PRJEB7696 and PRJEB15314) from muscle and liver tissue, respectively, from 12 Nellore beef steers selected from 585 steers with residual feed intake measures (RFI; n = 6 low-RFI, n = 6 high-RFI). Three RNA-Seq pipelines were compared including multi-sample calling from i) non-merged samples; ii) merged samples by RFI group, iii) merged samples by RFI and tissue group. The RNA-Seq reads were aligned against the UMD3.1 bovine reference genome (release 94) assembly using STAR aligner. Variants were called using BCFtools and variant effect prediction (VeP) and functional annotation (ToppGene) analyses were performed. Results On average, total reads detected for Approach i) non-merged samples for liver and muscle, were 18,362,086.3 and 35,645,898.7, respectively. For Approach ii), merging samples by RFI group, total reads detected for each merged group was 162,030,705, and for Approach iii), merging samples by RFI group and tissues, was 324,061,410, revealing the highest read depth for Approach iii). Additionally, Approach iii) merging samples by RFI group and tissues, revealed the highest read depth per variant coverage (572.59 ± 3993.11) and encompassed the majority of localized positional genes detected by each approach. This suggests Approach iii) had optimized detection power, read depth, and accuracy of SNP calling, therefore increasing confidence of variant detection and reducing false positive detection. Approach iii) was then used to detect unique SNPs fixed within low- (12,145) and high-RFI (14,663) groups. Functional annotation of SNPs revealed positional candidate genes, for each RFI group (2886 for low-RFI, 3075 for high-RFI), which were significantly (P < 0.05) associated with immune and metabolic pathways. Conclusion The most optimized RNA-Seq pipeline allowed for more accurate identification of SNPs, associated positional candidate genes, and significantly associated metabolic pathways in muscle and liver tissues, providing insight on the underlying genetic architecture of feed efficiency in beef cattle.
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Affiliation(s)
- S Lam
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road E, Guelph, Ontario, N1G2W1, Canada
| | - J Zeidan
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road E, Guelph, Ontario, N1G2W1, Canada
| | - F Miglior
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road E, Guelph, Ontario, N1G2W1, Canada
| | - A Suárez-Vega
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road E, Guelph, Ontario, N1G2W1, Canada
| | - I Gómez-Redondo
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road E, Guelph, Ontario, N1G2W1, Canada.,Spanish National Institute for Agriculture and Food Research and Technology, Carretera de La Coruña, 28040, Madrid, Spain
| | - P A S Fonseca
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road E, Guelph, Ontario, N1G2W1, Canada
| | - L L Guan
- Department of Agriculture, Food & Nutritional Science, University of Alberta, Edmonton, Alberta, T6H 2P5, Canada
| | - S Waters
- Teagasc, Animal & Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, C15 PW93, Ireland
| | - A Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road E, Guelph, Ontario, N1G2W1, Canada.
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18
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Genome-Wide Development and Validation of Cost-Effective KASP Marker Assays for Genetic Dissection of Heat Stress Tolerance in Maize. Int J Mol Sci 2020; 21:ijms21197386. [PMID: 33036291 PMCID: PMC7582619 DOI: 10.3390/ijms21197386] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/24/2020] [Accepted: 08/28/2020] [Indexed: 02/06/2023] Open
Abstract
Maize is the third most important cereal crop worldwide. However, its production is vulnerable to heat stress, which is expected to become more and more severe in coming years. Germplasm resilient to heat stress has been identified, but its underlying genetic basis remains poorly understood. Genomic mapping technologies can fill the void, provided robust markers are available to tease apart the genotype-phenotype relationship. In the present investigation, we used data from an RNA-seq experiment to identify single nucleotide polymorphisms (SNPs) between two contrasting lines, LM11 and CML25, sensitive and tolerant to heat stress, respectively. The libraries for RNA-seq were made following heat stress treatment from three separate tissues/organs, comprising the top leaf, ovule, and pollen, all of which are highly vulnerable to damage by heat stress. The single nucleotide variants (SNVs) calling used STAR mapper and GATK caller pipelines in a combined approach to identify highly accurate SNPs between the two lines. A total of 554,423, 410,698, and 596,868 SNVs were discovered between LM11 and CML25 after comparing the transcript sequence reads from the leaf, pollen, and ovule libraries, respectively. Hundreds of these SNPs were then selected to develop into genome-wide Kompetitive Allele-Specific PCR (KASP) markers, which were validated to be robust with a successful SNP conversion rate of 71%. Subsequently, these KASP markers were used to effectively genotype an F2 mapping population derived from a cross of LM11 and CML25. Being highly cost-effective, these KASP markers provide a reliable molecular marker toolkit to not only facilitate the genetic dissection of the trait of heat stress tolerance but also to accelerate the breeding of heat-resilient maize by marker-assisted selection (MAS).
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19
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Hagiwara K, Ding L, Edmonson MN, Rice SV, Newman S, Easton J, Dai J, Meshinchi S, Ries RE, Rusch M, Zhang J. RNAIndel: discovering somatic coding indels from tumor RNA-Seq data. Bioinformatics 2020; 36:1382-1390. [PMID: 31593214 DOI: 10.1093/bioinformatics/btz753] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 08/29/2019] [Accepted: 10/01/2019] [Indexed: 12/23/2022] Open
Abstract
MOTIVATION Reliable identification of expressed somatic insertions/deletions (indels) is an unmet need due to artifacts generated in PCR-based RNA-Seq library preparation and the lack of normal RNA-Seq data, presenting analytical challenges for discovery of somatic indels in tumor transcriptome. RESULTS We present RNAIndel, a tool for predicting somatic, germline and artifact indels from tumor RNA-Seq data. RNAIndel leverages features derived from indel sequence context and biological effect in a machine-learning framework. Except for tumor samples with microsatellite instability, RNAIndel robustly predicts 88-100% of somatic indels in five diverse test datasets of pediatric and adult cancers, even recovering subclonal (VAF range 0.01-0.15) driver indels missed by targeted deep-sequencing, outperforming the current best-practice for RNA-Seq variant calling which had 57% sensitivity but with 14 times more false positives. AVAILABILITY AND IMPLEMENTATION RNAIndel is freely available at https://github.com/stjude/RNAIndel. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Kohei Hagiwara
- Computational Biology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Liang Ding
- Computational Biology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Michael N Edmonson
- Computational Biology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Stephen V Rice
- Computational Biology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Scott Newman
- Computational Biology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - John Easton
- Computational Biology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Juncheng Dai
- Department of Epidemiology, Nanjing Medical University School of Public Health, Jiangning District, Nanjing, 211166, People's Republic of China
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Rhonda E Ries
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Michael Rusch
- Computational Biology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jinghui Zhang
- Computational Biology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
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20
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Genomic Dissection of a Wild Region in a Superior Solanum pennellii Introgression Sub-Line with High Ascorbic Acid Accumulation in Tomato Fruit. Genes (Basel) 2020; 11:genes11080847. [PMID: 32722275 PMCID: PMC7466095 DOI: 10.3390/genes11080847] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/20/2020] [Accepted: 07/22/2020] [Indexed: 11/16/2022] Open
Abstract
The Solanum pennellii introgression lines (ILs) have been exploited to map quantitative trait loci (QTLs) and identify favorable alleles that could improve fruit quality traits in tomato varieties. Over the past few years, ILs exhibiting increased content of ascorbic acid in the fruit have been selected, among which the sub-line R182. The aims of this work were to identify the genes of the wild donor S. pennellii harbored by the sub-line and to detect genes controlling ascorbic acid accumulation by using genomics tools. A Genotyping-By-Sequencing (GBS) approach confirmed that no wild introgressions were present in the sub-line besides one region on chromosome 7. By using a dense single nucleotide polymorphism (SNP) map obtained by RNA sequencing (RNA-Seq), the wild region of the sub-line was finely identified; thus, defining 39 wild genes that replaced 33 genes of the ILs genetic background (cv. M82). The differentially expressed genes mapping in the region and the variants detected among the cultivated and the wild alleles evidenced the potential role of the novel genes present in the wild region. Interestingly, one upregulated gene, annotated as a major facilitator superfamily protein, showed a novel structure in R182, with respect to the parental lines. These genes will be further investigated using gene editing strategies.
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21
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Cheung PPH, Jiang B, Booth GT, Chong TH, Unarta IC, Wang Y, Suarez GD, Wang J, Lis JT, Huang X. Identifying Transcription Error-Enriched Genomic Loci Using Nuclear Run-on Circular-Sequencing Coupled with Background Error Modeling. J Mol Biol 2020; 432:3933-3949. [PMID: 32325070 DOI: 10.1016/j.jmb.2020.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 04/08/2020] [Accepted: 04/08/2020] [Indexed: 01/30/2023]
Abstract
RNA polymerase transcribes certain genomic loci with higher errors rates. These transcription error-enriched genomic loci (TEELs) have implications in disease. Current deep-sequencing methods cannot distinguish TEELs from post-transcriptional modifications, stochastic transcription errors, and technical noise, impeding efforts to elucidate the mechanisms linking TEELs to disease. Here, we describe background error model-coupled precision nuclear run-on circular-sequencing (EmPC-seq) to discern genomic regions enriched for transcription misincorporations. EmPC-seq innovatively combines a nuclear run-on assay for capturing nascent RNA before post-transcriptional modifications, a circular-sequencing step that sequences the same nascent RNA molecules multiple times to improve accuracy, and a statistical model for distinguishing error-enriched regions among stochastic polymerase errors. Applying EmPC-seq to the ribosomal RNA transcriptome, we show that TEELs of RNA polymerase I are not randomly distributed but clustered together, with higher error frequencies at nascent transcript 3' ends. Our study establishes a reliable method of identifying TEELs with nucleotide precision, which can help elucidate their molecular origins.
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Affiliation(s)
- Peter Pak-Hang Cheung
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China; Department of Chemistry, Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Biaobin Jiang
- Division of Life Science, Department of Chemical and Biological Engineering, Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong; The HKUST Jockey Club Institute for Advanced Study (IAS), The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Gregory T Booth
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Tin Hang Chong
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China
| | - Ilona Christy Unarta
- Bioengineering Graduate Program, Department of Biological and Chemical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Yuqing Wang
- Bioengineering Graduate Program, Department of Biological and Chemical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Gianmarco D Suarez
- Bioengineering Graduate Program, Department of Biological and Chemical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Jiguang Wang
- Division of Life Science, Department of Chemical and Biological Engineering, Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; The HKUST Jockey Club Institute for Advanced Study (IAS), The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
| | - Xuhui Huang
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China; Department of Chemistry, Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong; Bioengineering Graduate Program, Department of Biological and Chemical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
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22
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Wagle MC, Castillo J, Srinivasan S, Holcomb T, Yuen KC, Kadel EE, Mariathasan S, Halligan DL, Carr AR, Bylesjo M, McAdam PR, Lynagh S, Marien KM, Kockx M, Waumans Y, Huang SMA, Lackner MR, Mounir Z. Tumor Fusion Burden as a Hallmark of Immune Infiltration in Prostate Cancer. Cancer Immunol Res 2020; 8:844-850. [PMID: 32321776 DOI: 10.1158/2326-6066.cir-19-0568] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 11/01/2019] [Accepted: 04/17/2020] [Indexed: 11/16/2022]
Abstract
Prostate cancer is the second leading cause of cancer-related death in men. Despite having a relatively lower tumor mutational burden than most tumor types, multiple gene fusions such as TMPRSS2:ERG have been characterized and linked to more aggressive disease. Individual tumor samples have been found to contain multiple fusions, and it remains unknown whether these fusions increase tumor immunogenicity. Here, we investigated the role of fusion burden on the prevalence and expression of key molecular and immune effectors in prostate cancer tissue specimens that represented the different stages of disease progression and androgen sensitivity, including hormone-sensitive and castration-resistant prostate cancer. We found that tumor fusion burden was inversely correlated with tumor mutational burden and not associated with disease stage. High fusion burden correlated with high immune infiltration, PD-L1 expression on immune cells, and immune signatures, representing activation of T cells and M1 macrophages. High fusion burden inversely correlated with immune-suppressive signatures. Our findings suggest that high tumor fusion burden may be a more appropriate biomarker than tumor mutational burden in prostate cancer, as it more closely associates with immunogenicity, and suggests that tumors with high fusion burden could be potential candidates for immunotherapeutic agents.
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Affiliation(s)
- Marie-Claire Wagle
- Oncology Biomarker Development, Genentech, Inc., South San Francisco, California.
| | - Joseph Castillo
- Oncology Biomarker Development, Genentech, Inc., South San Francisco, California
| | | | - Thomas Holcomb
- Oncology Biomarker Development, Genentech, Inc., South San Francisco, California
| | - Kobe C Yuen
- Oncology Biomarker Development, Genentech, Inc., South San Francisco, California
| | - Edward E Kadel
- Oncology Biomarker Development, Genentech, Inc., South San Francisco, California
| | - Sanjeev Mariathasan
- Oncology Biomarker Development, Genentech, Inc., South San Francisco, California
| | | | - Adrian R Carr
- Fios Genomics, Nine Edinburgh Bioquarter, Edinburgh, United Kingdom
| | - Max Bylesjo
- Fios Genomics, Nine Edinburgh Bioquarter, Edinburgh, United Kingdom
| | - Paul R McAdam
- Fios Genomics, Nine Edinburgh Bioquarter, Edinburgh, United Kingdom
| | - Sarah Lynagh
- Fios Genomics, Nine Edinburgh Bioquarter, Edinburgh, United Kingdom
| | | | | | | | - Shih-Min A Huang
- Oncology Biomarker Development, Genentech, Inc., South San Francisco, California
| | - Mark R Lackner
- Oncology Biomarker Development, Genentech, Inc., South San Francisco, California
| | - Zineb Mounir
- Oncology Biomarker Development, Genentech, Inc., South San Francisco, California.
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23
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Intraspecific Diversity in the Cold Stress Response of Transposable Elements in the Diatom Leptocylindrus aporus. Genes (Basel) 2019; 11:genes11010009. [PMID: 31861932 PMCID: PMC7017206 DOI: 10.3390/genes11010009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 12/19/2019] [Indexed: 01/18/2023] Open
Abstract
Transposable elements (TEs), activated as a response to unfavorable conditions, have been proposed to contribute to the generation of genetic and phenotypic diversity in diatoms. Here we explore the transcriptome of three warm water strains of the diatom Leptocylindrus aporus, and the possible involvement of TEs in their response to changing temperature conditions. At low temperature (13 °C) several stress response proteins were overexpressed, confirming low temperature to be unfavorable for L. aporus, while TE-related transcripts of the LTR retrotransposon superfamily were the most enriched transcripts. Their expression levels, as well as most of the stress-related proteins, were found to vary significantly among strains, and even within the same strains analysed at different times. The lack of overexpression after many months of culturing suggests a possible role of physiological plasticity in response to growth under controlled laboratory conditions. While further investigation on the possible central role of TEs in the diatom stress response is warranted, the strain-specific responses and possible role of in-culture evolution draw attention to the interplay between the high intraspecific variability and the physiological plasticity of diatoms, which can both contribute to the adaptation of a species to a wide range of conditions in the marine environment.
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24
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Adetunji MO, Lamont SJ, Abasht B, Schmidt CJ. Variant analysis pipeline for accurate detection of genomic variants from transcriptome sequencing data. PLoS One 2019; 14:e0216838. [PMID: 31545812 PMCID: PMC6756534 DOI: 10.1371/journal.pone.0216838] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/10/2019] [Indexed: 12/27/2022] Open
Abstract
The wealth of information deliverable from transcriptome sequencing (RNA-seq) is significant, however current applications for variant detection still remain a challenge due to the complexity of the transcriptome. Given the ability of RNA-seq to reveal active regions of the genome, detection of RNA-seq SNPs can prove valuable in understanding the phenotypic diversity between populations. Thus, we present a novel computational workflow named VAP (Variant Analysis Pipeline) that takes advantage of multiple RNA-seq splice aware aligners to call SNPs in non-human models using RNA-seq data only. We applied VAP to RNA-seq from a highly inbred chicken line and achieved high accuracy when compared with the matching whole genome sequencing (WGS) data. Over 65% of WGS coding variants were identified from RNA-seq. Further, our results discovered SNPs resulting from post transcriptional modifications, such as RNA editing, which may reveal potentially functional variation that would have otherwise been missed in genomic data. Even with the limitation in detecting variants in expressed regions only, our method proves to be a reliable alternative for SNP identification using RNA-seq data. The source code and user manuals are available at https://modupeore.github.io/VAP/.
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Affiliation(s)
- Modupeore O. Adetunji
- Department of Animal and Food Sciences, University of Delaware, Newark, Delaware, United States of America
- * E-mail:
| | - Susan J. Lamont
- Department of Animal Science, Iowa State University, Ames, Iowa, United States of America
| | - Behnam Abasht
- Department of Animal and Food Sciences, University of Delaware, Newark, Delaware, United States of America
| | - Carl J. Schmidt
- Department of Animal and Food Sciences, University of Delaware, Newark, Delaware, United States of America
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25
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Abdouh M, Floris M, Gao ZH, Arena V, Arena M, Arena GO. Colorectal cancer-derived extracellular vesicles induce transformation of fibroblasts into colon carcinoma cells. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:257. [PMID: 31200749 PMCID: PMC6567673 DOI: 10.1186/s13046-019-1248-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 05/27/2019] [Indexed: 12/21/2022]
Abstract
BACKGROUND We reported that horizontal transfer of malignant traits to target cells is a potential pathway to explain cancer dissemination. Although these results were encouraging, they were never corroborated by data showing the molecular mechanisms responsible for the observed phenomenon. METHODS In the present study, we exposed BRCA1-KO fibroblasts to extracellular vesicles (EVs) isolated from a colon cancer cell line (HT29) and from sera of patients with colorectal cancer. Three weeks after exposure, fibroblasts were injected subcutaneously into NOD-SCID mice. Whole genome sequencing, transcriptome analysis and RNA sequencing of cancer EVs and fibroblasts prior and after exposure to cancer EVs were performed. RESULTS Phenotypical transformation of the fibroblasts into colon cancer cells was confirmed by histopathological study of the xenotransplants. We observed that EV-mediated transfer of cancer microRNAs was responsible for the transition from a mesenchymal to an epithelial phenotype (MET) in the treated fibroblasts as well as activation of cell cycle progression and cell survival pathways. DNA and RNA sequencing suggested that cancer DNA was transferred and possibly transcribed in target cells. Furthermore, injection of colon cancer EVs in the tail vein of NOD-SCID mice determined neoplastic transformation and metastases in the lungs of the mice confirming for the first time the hypothesis that transfer of malignant epithelial cancer traits to distant target cells is a concept applicable to in vivo models. CONCLUSIONS These discoveries shed new light into the molecular mechanisms behind the horizontal transfer of malignant traits and confirm the notion that metastatic disease might be reproduced through transfer of circulating genetic material.
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Affiliation(s)
- Mohamed Abdouh
- Cancer Research Program, McGill University Health Centre-Research Institute, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3J1, Canada
| | - Matteo Floris
- Department of Biomedical Sciences, Sassari University, Piazza Universita 11, Sassari, Italy
| | - Zu-Hua Gao
- Department of Pathology, McGill University Health Centre-Research Institute, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3J1, Canada
| | - Vincenzo Arena
- Department of Obstetrics and Gynecology, Santo Bambino Hospital, via Torre del Vescovo 4, Catania, Italy
| | - Manuel Arena
- Department of Surgical Sciences, Organ Transplantation and Advances Technologies, University of Catania, via Santa Sofia 84, Catania, Italy
| | - Goffredo Orazio Arena
- Cancer Research Program, McGill University Health Centre-Research Institute, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3J1, Canada. .,Department of Surgery, McGill University, St. Mary Hospital, 3830 Lacombe Avenue, Montreal, Quebec, H3T 1M5, Canada.
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Kulkarni N, Alessandrì L, Panero R, Arigoni M, Olivero M, Ferrero G, Cordero F, Beccuti M, Calogero RA. Reproducible bioinformatics project: a community for reproducible bioinformatics analysis pipelines. BMC Bioinformatics 2018; 19:349. [PMID: 30367595 PMCID: PMC6191970 DOI: 10.1186/s12859-018-2296-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Background Reproducibility of a research is a key element in the modern science and it is mandatory for any industrial application. It represents the ability of replicating an experiment independently by the location and the operator. Therefore, a study can be considered reproducible only if all used data are available and the exploited computational analysis workflow is clearly described. However, today for reproducing a complex bioinformatics analysis, the raw data and the list of tools used in the workflow could be not enough to guarantee the reproducibility of the results obtained. Indeed, different releases of the same tools and/or of the system libraries (exploited by such tools) might lead to sneaky reproducibility issues. Results To address this challenge, we established the Reproducible Bioinformatics Project (RBP), which is a non-profit and open-source project, whose aim is to provide a schema and an infrastructure, based on docker images and R package, to provide reproducible results in Bioinformatics. One or more Docker images are then defined for a workflow (typically one for each task), while the workflow implementation is handled via R-functions embedded in a package available at github repository. Thus, a bioinformatician participating to the project has firstly to integrate her/his workflow modules into Docker image(s) exploiting an Ubuntu docker image developed ad hoc by RPB to make easier this task. Secondly, the workflow implementation must be realized in R according to an R-skeleton function made available by RPB to guarantee homogeneity and reusability among different RPB functions. Moreover she/he has to provide the R vignette explaining the package functionality together with an example dataset which can be used to improve the user confidence in the workflow utilization. Conclusions Reproducible Bioinformatics Project provides a general schema and an infrastructure to distribute robust and reproducible workflows. Thus, it guarantees to final users the ability to repeat consistently any analysis independently by the used UNIX-like architecture.
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Affiliation(s)
- Neha Kulkarni
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Luca Alessandrì
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Riccardo Panero
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Maddalena Arigoni
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Martina Olivero
- Department of Oncology, University of Torino, Candiolo, Italy
| | - Giulio Ferrero
- Department of Computer Sciences, University of Torino, Torino, Italy
| | - Francesca Cordero
- Department of Computer Sciences, University of Torino, Torino, Italy.
| | - Marco Beccuti
- Department of Computer Sciences, University of Torino, Torino, Italy
| | - Raffaele A Calogero
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy.
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Prodduturi N, Bhagwate A, Kocher JPA, Sun Z. Indel sensitive and comprehensive variant/mutation detection from RNA sequencing data for precision medicine. BMC Med Genomics 2018; 11:67. [PMID: 30255803 PMCID: PMC6157028 DOI: 10.1186/s12920-018-0391-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Background RNA-seq is the most commonly used sequencing application. Not only does it measure gene expression but it is also an excellent media to detect important structural variants such as single nucleotide variants (SNVs), insertion/deletion (Indels) or fusion transcripts. However, detection of these variants is challenging and complex from RNA-seq. Here we describe a sensitive and accurate analytical pipeline which detects various mutations at once for translational precision medicine. Methods The pipeline incorporates most sensitive aligners for Indels in RNA-Seq, the best practice for data preprocessing and variant calling, and STAR-fusion is for chimeric transcripts. Variants/mutations are annotated, and key genes can be extracted for further investigation and clinical actions. Three datasets were used to evaluate the performance of the pipeline for SNVs, indels and fusion transcripts. Results For the well-defined variants from NA12878 by GIAB project, about 95% and 80% of sensitivities were obtained for SNVs and indels, respectively, in matching RNA-seq. Comparison with other variant specific tools showed good performance of the pipeline. For the lung cancer dataset with 41 known and oncogenic mutations, 39 were detected by the pipeline with STAR aligner and all by the GSNAP aligner. An actionable EML4 and ALK fusion was also detected in one of the tumors, which also demonstrated outlier ALK expression. For 9 fusions spiked-into RNA-seq libraries with different concentrations, the pipeline was able to detect all in unfiltered results although some at very low concentrations may be missed when filtering was applied. Conclusions The new RNA-seq workflow is an accurate and comprehensive mutation profiler from RNA-seq. Key or actionable mutations are reliably detected from RNA-seq, which makes it a practical alternative source for personalized medicine. Electronic supplementary material The online version of this article (10.1186/s12920-018-0391-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Naresh Prodduturi
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, 200 First St SW, Rochester, MN, 55905, USA
| | - Aditya Bhagwate
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, 200 First St SW, Rochester, MN, 55905, USA
| | - Jean-Pierre A Kocher
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, 200 First St SW, Rochester, MN, 55905, USA
| | - Zhifu Sun
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, 200 First St SW, Rochester, MN, 55905, USA.
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A 2-transcript host cell signature distinguishes viral from bacterial diarrhea and it is influenced by the severity of symptoms. Sci Rep 2018; 8:8043. [PMID: 29795312 PMCID: PMC5966427 DOI: 10.1038/s41598-018-26239-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 05/08/2018] [Indexed: 02/03/2023] Open
Abstract
Recently, a biomarker signature consisting of 2-transcript host RNAs was proposed for discriminating bacterial from viral infections in febrile children. We evaluated the performance of this signature in a different disease scenario, namely a cohort of Mexican children (n = 174) suffering from acute diarrhea of different infectious etiologies. We first examined the admixed background of the patients, indicating that most of them have a predominantly Native American genetic ancestry with a variable amount of European background (ranging from 0% to 57%). The results confirm that the RNA test can discriminate between viral and bacterial causes of infection (t-test; P-value = 6.94×10−11; AUC = 80%; sensitivity: 68% [95% CI: 55%–79%]; specificity: 84% [95% CI: 78%–90%]), but the strength of the signal differs substantially depending on the causal pathogen, with the stronger signal being that of Shigella (P-value = 3.14 × 10−12; AUC = 89; sensitivity: 70% [95% CI: 57%–83%]; specificity: 100% [95% CI: 100%–100%]). The accuracy of this test improves significantly when excluding mild cases (P-value = 2.13 × 10−6; AUC = 85%; sensitivity: 79% [95% CI: 58%–95%]; specificity: 78% [95% CI: 65%–88%]). The results broaden the scope of previous studies by incorporating different pathogens, variable levels of disease severity, and different ancestral background of patients, and add confirmatory support to the clinical utility of these 2-transcript biomarkers.
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