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Analysis of Single Cell RNA-seq Data Revealed Interferon Gamma Signaling Alteration in Severe COVID patients
Background: SARS-COV2 virus detected in December 2019, and was considered a pandemic in March 2020 by the WHO. Symptoms range from asymptomatic to life threatening ones. Studying cell-cell interactions in patients' blood samples may lead to novel diagnosis and treatment approaches. Aim: This study a...
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2021
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| _version_ | 1867613419295735808 |
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| access_status_str | Open Access |
| author | Elbaz, Ahmed |
| author_browse | Elbaz, Ahmed |
| author_facet | Elbaz, Ahmed |
| author_sort | Elbaz, Ahmed |
| collection | Thesis |
| description | Background: SARS-COV2 virus detected in December 2019, and was considered a pandemic in March 2020 by the WHO. Symptoms range from asymptomatic to life threatening ones. Studying cell-cell interactions in patients' blood samples may lead to novel diagnosis and treatment approaches.
Aim: This study aims to analyze single-cell RNA sequencing data to identify differences in cell-cell communications between healthy and COVID patients and differentially expressed T-cells genes that contributed to immune system antiviral activity.
Materials and methods: Single-Cell RNA sequencing data from seven COVID patients and five healthy individuals were collected from (GEO accession GSE155673). Cell types were identified and cell-cell interactions were inferred for each condition (healthy, moderate and severe COVID patients). Additionally, T cells differentially expressed genes between the three conditions were identified and pathways enrichment were performed.
Results: Eight cell types were identified. Percentage of T cells decreased from 32.76% in healthy individuals to 16% in severe COVID cases. Cell-Cell interactions analysis revealed significant alterations among healthy, moderate, and severe conditions such as reduction of overall incoming signaling in T cells of severe cases. Additionally, SN signaling pathway was identified only in COVID cases, which in turn was found to be in IFN-γ reduction in distinct cell types. Pathways enrichment analysis identified IFN-γ signaling to be upregulated in moderate cases, and to be downregulated in severe ones. Protein interacting with IFN-γ also shows downregulation such as IRF1. However, the negative regulator of IFN-γ -SOCS3- was upregulated in COVID patients T cells.
Conclusion: Cell-cell interactions alteration in COVID patients might have resulted in eliciting improper immune response. Not only, did T cells percentage decreased in severe COVID cases, but also T cells overall incoming signaling was decreased. Additionally, cell-cell interaction alteration might have played a significant role in suppressing antiviral response through IFN-γ reduction which might contribute to the observed severity of COVID cases. |
| format | Thesis |
| id | oai:fount.aucegypt.edu:etds-2668 |
| institution | American University in Cairo (Egypt) |
| last_indexed | 2026-06-10T12:35:50.652Z |
| license_str | Not specified — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from AUC Knowledge Fountain — bepress |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | AUC Knowledge Fountain |
| publisherStr | AUC Knowledge Fountain |
| record_format | dspace |
| source_str | AUC Knowledge Fountain — bepress |
| spelling | oai:fount.aucegypt.edu:etds-2668 Analysis of Single Cell RNA-seq Data Revealed Interferon Gamma Signaling Alteration in Severe COVID patients Elbaz, Ahmed Background: SARS-COV2 virus detected in December 2019, and was considered a pandemic in March 2020 by the WHO. Symptoms range from asymptomatic to life threatening ones. Studying cell-cell interactions in patients' blood samples may lead to novel diagnosis and treatment approaches. Aim: This study aims to analyze single-cell RNA sequencing data to identify differences in cell-cell communications between healthy and COVID patients and differentially expressed T-cells genes that contributed to immune system antiviral activity. Materials and methods: Single-Cell RNA sequencing data from seven COVID patients and five healthy individuals were collected from (GEO accession GSE155673). Cell types were identified and cell-cell interactions were inferred for each condition (healthy, moderate and severe COVID patients). Additionally, T cells differentially expressed genes between the three conditions were identified and pathways enrichment were performed. Results: Eight cell types were identified. Percentage of T cells decreased from 32.76% in healthy individuals to 16% in severe COVID cases. Cell-Cell interactions analysis revealed significant alterations among healthy, moderate, and severe conditions such as reduction of overall incoming signaling in T cells of severe cases. Additionally, SN signaling pathway was identified only in COVID cases, which in turn was found to be in IFN-γ reduction in distinct cell types. Pathways enrichment analysis identified IFN-γ signaling to be upregulated in moderate cases, and to be downregulated in severe ones. Protein interacting with IFN-γ also shows downregulation such as IRF1. However, the negative regulator of IFN-γ -SOCS3- was upregulated in COVID patients T cells. Conclusion: Cell-cell interactions alteration in COVID patients might have resulted in eliciting improper immune response. Not only, did T cells percentage decreased in severe COVID cases, but also T cells overall incoming signaling was decreased. Additionally, cell-cell interaction alteration might have played a significant role in suppressing antiviral response through IFN-γ reduction which might contribute to the observed severity of COVID cases. 2021-05-25T07:00:00Z thesis application/pdf https://fount.aucegypt.edu/etds/1644 https://fount.aucegypt.edu/context/etds/article/2668/viewcontent/Thesis_Ahmed_ElBaz.pdf https://fount.aucegypt.edu/context/etds/article/2668/filename/3/type/additional/viewcontent/Supplementary_file_1.xlsx https://fount.aucegypt.edu/context/etds/article/2668/filename/4/type/additional/viewcontent/Supplementary_file_2.xlsx https://fount.aucegypt.edu/context/etds/article/2668/filename/5/type/additional/viewcontent/Supplementary_file_3.xlsx Theses and Dissertations AUC Knowledge Fountain COVID-19 SARS-CoV2 IFNG Interferon-Gamma scRNA-seq cell-cell interactions T-cells adaptive immunity Interferons Biological Phenomena, Cell Phenomena, and Immunity Virus Diseases Viruses |
| spellingShingle | COVID-19 SARS-CoV2 IFNG Interferon-Gamma scRNA-seq cell-cell interactions T-cells adaptive immunity Interferons Biological Phenomena, Cell Phenomena, and Immunity Virus Diseases Viruses Elbaz, Ahmed Analysis of Single Cell RNA-seq Data Revealed Interferon Gamma Signaling Alteration in Severe COVID patients |
| title | Analysis of Single Cell RNA-seq Data Revealed Interferon Gamma Signaling Alteration in Severe COVID patients |
| title_full | Analysis of Single Cell RNA-seq Data Revealed Interferon Gamma Signaling Alteration in Severe COVID patients |
| title_fullStr | Analysis of Single Cell RNA-seq Data Revealed Interferon Gamma Signaling Alteration in Severe COVID patients |
| title_full_unstemmed | Analysis of Single Cell RNA-seq Data Revealed Interferon Gamma Signaling Alteration in Severe COVID patients |
| title_short | Analysis of Single Cell RNA-seq Data Revealed Interferon Gamma Signaling Alteration in Severe COVID patients |
| title_sort | analysis of single cell rna seq data revealed interferon gamma signaling alteration in severe covid patients |
| topic | COVID-19 SARS-CoV2 IFNG Interferon-Gamma scRNA-seq cell-cell interactions T-cells adaptive immunity Interferons Biological Phenomena, Cell Phenomena, and Immunity Virus Diseases Viruses |
| url | https://fount.aucegypt.edu/etds/1644 https://fount.aucegypt.edu/context/etds/article/2668/viewcontent/Thesis_Ahmed_ElBaz.pdf https://fount.aucegypt.edu/context/etds/article/2668/filename/3/type/additional/viewcontent/Supplementary_file_1.xlsx https://fount.aucegypt.edu/context/etds/article/2668/filename/4/type/additional/viewcontent/Supplementary_file_2.xlsx https://fount.aucegypt.edu/context/etds/article/2668/filename/5/type/additional/viewcontent/Supplementary_file_3.xlsx |
| work_keys_str_mv | AT elbazahmed analysisofsinglecellrnaseqdatarevealedinterferongammasignalingalterationinseverecovidpatients |