A Nextflow pipeline for T-cell receptor repertoire reconstruction and analysis from RNA sequencing data
T-cell receptor (TCR) analysis is relevant for the study of immune system diseases. The expression of TCRs is usually measured with targeted sequencing approaches where TCR genes are selectively amplified. However, many non-targeted RNA-seq experiments also contain reads of TCR genes, which could be...
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Elsevier
2022-06-01
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| Series: | ImmunoInformatics |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2667119022000040 |
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| author | Teresa Rubio Maria Chernigovskaya Susanna Marquez Cristina Marti Paula Izquierdo-Altarejos Amparo Urios Carmina Montoliu Vicente Felipo Ana Conesa Victor Greiff Sonia Tarazona |
| author_facet | Teresa Rubio Maria Chernigovskaya Susanna Marquez Cristina Marti Paula Izquierdo-Altarejos Amparo Urios Carmina Montoliu Vicente Felipo Ana Conesa Victor Greiff Sonia Tarazona |
| author_sort | Teresa Rubio |
| collection | DOAJ |
| description | T-cell receptor (TCR) analysis is relevant for the study of immune system diseases. The expression of TCRs is usually measured with targeted sequencing approaches where TCR genes are selectively amplified. However, many non-targeted RNA-seq experiments also contain reads of TCR genes, which could be leveraged for TCR expression analysis while reducing sample requirements and costs. Moreover, a step-by-step pipeline for the processing of transcriptome RNA-seq reads to deliver immune repertoire data is missing, and these types of analyses are usually not included in RNA-seq studies of immunological conditions. This represents a missed opportunity for complementing them with the analysis of the immune repertoire.We present a Nextflow pipeline for T-cell receptor repertoire reconstruction and analysis from RNA sequencing data. We used a case study where TCR repertoire profiles were recovered from bulk RNA-seq of isolated CD4 T cells from control patients, cirrhotic patients without and with Minimal Hepatic Encephalopathy (MHE). MHE is a neuropsychiatric syndrome, mediated by peripheral inflammation, that may affect cirrhotic patients. After the recovery of 498-1,114 distinct TCR beta chains per patient, repertoire analysis of patients resulted in few public clones, high diversity and elevated within-repertoire sequence similarity, independently of immune status. Additionally, TCRs associated with celiac disease and inflammatory bowel disease were significantly overrepresented in MHE patient repertoires. The provided computational pipeline functions as a resource to facilitate TCR profiling from RNA-seq data boosting immunophenotype analyses of immunological diseases. |
| format | Article |
| id | doaj-art-a9c87492a74c495fa73825fe5daae9e2 |
| institution | Kabale University |
| issn | 2667-1190 |
| language | English |
| publishDate | 2022-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | ImmunoInformatics |
| spelling | doaj-art-a9c87492a74c495fa73825fe5daae9e22025-01-10T04:38:19ZengElsevierImmunoInformatics2667-11902022-06-016100012A Nextflow pipeline for T-cell receptor repertoire reconstruction and analysis from RNA sequencing dataTeresa Rubio0Maria Chernigovskaya1Susanna Marquez2Cristina Marti3Paula Izquierdo-Altarejos4Amparo Urios5Carmina Montoliu6Vicente Felipo7Ana Conesa8Victor Greiff9Sonia Tarazona10Laboratory of Neurobiology, Centro Investigación Príncipe Felipe, Valencia, SpainDepartment of Immunology, University of Oslo and Oslo University Hospital, Oslo, NorwayDoctoral Program in Design, Manufacture, and Management of Industrial Projects, Universitat Politècnica de València, Valencia, SpainLaboratory of Biological Noise and Cell Plasticity, Centro Investigación Príncipe Felipe, Valencia, SpainLaboratory of Neurobiology, Centro Investigación Príncipe Felipe, Valencia, SpainLaboratory of Neurobiology, Centro Investigación Príncipe Felipe, Valencia, Spain; Neurological Impairment Laboratory. Fundación Investigación Hospital Clínico Universitario de Valencia, Instituto de Investigación Sanitaria-INCLIVA, Valencia, SpainNeurological Impairment Laboratory. Fundación Investigación Hospital Clínico Universitario de Valencia, Instituto de Investigación Sanitaria-INCLIVA, Valencia, Spain; Department of Pathology, Facultad de Medicina, Universidad de Valencia, SpainLaboratory of Neurobiology, Centro Investigación Príncipe Felipe, Valencia, SpainGenomics of Gene Expression Laboratory, Institute for Integrative Systems Biology, Spanish National Research Council, Valencia, SpainDepartment of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway; Corresponding author.Departamento de Estadística e Investigación Operativa Aplicadas y Calidad, Universitat Politècnica de València, Valencia, SpainT-cell receptor (TCR) analysis is relevant for the study of immune system diseases. The expression of TCRs is usually measured with targeted sequencing approaches where TCR genes are selectively amplified. However, many non-targeted RNA-seq experiments also contain reads of TCR genes, which could be leveraged for TCR expression analysis while reducing sample requirements and costs. Moreover, a step-by-step pipeline for the processing of transcriptome RNA-seq reads to deliver immune repertoire data is missing, and these types of analyses are usually not included in RNA-seq studies of immunological conditions. This represents a missed opportunity for complementing them with the analysis of the immune repertoire.We present a Nextflow pipeline for T-cell receptor repertoire reconstruction and analysis from RNA sequencing data. We used a case study where TCR repertoire profiles were recovered from bulk RNA-seq of isolated CD4 T cells from control patients, cirrhotic patients without and with Minimal Hepatic Encephalopathy (MHE). MHE is a neuropsychiatric syndrome, mediated by peripheral inflammation, that may affect cirrhotic patients. After the recovery of 498-1,114 distinct TCR beta chains per patient, repertoire analysis of patients resulted in few public clones, high diversity and elevated within-repertoire sequence similarity, independently of immune status. Additionally, TCRs associated with celiac disease and inflammatory bowel disease were significantly overrepresented in MHE patient repertoires. The provided computational pipeline functions as a resource to facilitate TCR profiling from RNA-seq data boosting immunophenotype analyses of immunological diseases.http://www.sciencedirect.com/science/article/pii/S2667119022000040T-cell receptorCD4 isolationRNA sequencingImmune repertoire analysisMinimal Hepatic Encephalopathy |
| spellingShingle | Teresa Rubio Maria Chernigovskaya Susanna Marquez Cristina Marti Paula Izquierdo-Altarejos Amparo Urios Carmina Montoliu Vicente Felipo Ana Conesa Victor Greiff Sonia Tarazona A Nextflow pipeline for T-cell receptor repertoire reconstruction and analysis from RNA sequencing data ImmunoInformatics T-cell receptor CD4 isolation RNA sequencing Immune repertoire analysis Minimal Hepatic Encephalopathy |
| title | A Nextflow pipeline for T-cell receptor repertoire reconstruction and analysis from RNA sequencing data |
| title_full | A Nextflow pipeline for T-cell receptor repertoire reconstruction and analysis from RNA sequencing data |
| title_fullStr | A Nextflow pipeline for T-cell receptor repertoire reconstruction and analysis from RNA sequencing data |
| title_full_unstemmed | A Nextflow pipeline for T-cell receptor repertoire reconstruction and analysis from RNA sequencing data |
| title_short | A Nextflow pipeline for T-cell receptor repertoire reconstruction and analysis from RNA sequencing data |
| title_sort | nextflow pipeline for t cell receptor repertoire reconstruction and analysis from rna sequencing data |
| topic | T-cell receptor CD4 isolation RNA sequencing Immune repertoire analysis Minimal Hepatic Encephalopathy |
| url | http://www.sciencedirect.com/science/article/pii/S2667119022000040 |
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