Table6_Integrating genomics and AI to uncover molecular targets for mRNA vaccine development in lupus nephritis.xlsx
<p>Lupus nephritis (LN), a complex complication of systemic lupus erythematosus, requires in-depth cellular and molecular analysis for advanced treatment strategies, including mRNA vaccine development. In this study, we analyzed single-cell RNA sequencing data from 24 LN patients and 10 health...
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2024
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| _version_ | 1852026158749581312 |
|---|---|
| author | Lisha Mou (151003) |
| author2 | Ying Lu (66401) Zijing Wu (3391769) Zuhui Pu (10931751) Meiying Wang (1309134) |
| author2_role | author author author author |
| author_facet | Lisha Mou (151003) Ying Lu (66401) Zijing Wu (3391769) Zuhui Pu (10931751) Meiying Wang (1309134) |
| author_role | author |
| dc.creator.none.fl_str_mv | Lisha Mou (151003) Ying Lu (66401) Zijing Wu (3391769) Zuhui Pu (10931751) Meiying Wang (1309134) |
| dc.date.none.fl_str_mv | 2024-10-04T04:03:42Z |
| dc.identifier.none.fl_str_mv | 10.3389/fimmu.2024.1381445.s017 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/dataset/Table6_Integrating_genomics_and_AI_to_uncover_molecular_targets_for_mRNA_vaccine_development_in_lupus_nephritis_xlsx/27166926 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Immunology Applied Immunology (incl. Antibody Engineering, Xenotransplantation and T-cell Therapies) Autoimmunity Cellular Immunology Humoural Immunology and Immunochemistry Immunogenetics (incl. Genetic Immunology) Innate Immunity Transplantation Immunology Tumour Immunology Immunology not elsewhere classified Genetic Immunology Animal Immunology Veterinary Immunology systemic lupus erythematosus lupus nephritis genomics single cell single-cell RNA sequencing non-negative matrix factorization (NMF) machine learning functional network analysis |
| dc.title.none.fl_str_mv | Table6_Integrating genomics and AI to uncover molecular targets for mRNA vaccine development in lupus nephritis.xlsx |
| dc.type.none.fl_str_mv | Dataset info:eu-repo/semantics/publishedVersion dataset |
| description | <p>Lupus nephritis (LN), a complex complication of systemic lupus erythematosus, requires in-depth cellular and molecular analysis for advanced treatment strategies, including mRNA vaccine development. In this study, we analyzed single-cell RNA sequencing data from 24 LN patients and 10 healthy controls, supplemented by bulk RNA-seq data from additional LN patients and controls. By applying non-negative matrix factorization (NMF), we identified four distinct leukocyte meta-programs in LN, highlighting diverse immune functions and potential mRNA vaccine targets. Utilizing 12 machine learning algorithms, we developed 417 predictive models incorporating gene sets linked to key biological pathways, such as MTOR signaling, autophagy, Toll-like receptor, and adaptive immunity pathways. These models were instrumental in identifying potential targets for mRNA vaccine development. Our functional network analysis further revealed intricate gene interactions, providing novel insights into the molecular basis of LN. Additionally, we validated the mRNA expression levels of potential vaccine targets across multiple cohorts and correlated them with clinical parameters such as the glomerular filtration rate (GFR) and pathological stage. This study represents a significant advance in LN research by merging single-cell genomics with the precision of NMF and machine learning, broadening our understanding of LN at the cellular and molecular levels. More importantly, our findings shed light on the development of targeted mRNA vaccines, offering new possibilities for diagnostics and therapeutics for this complex autoimmune disease.</p> |
| eu_rights_str_mv | openAccess |
| id | Manara_b6fcafa57e5c4b2bb8a264caacf64df1 |
| identifier_str_mv | 10.3389/fimmu.2024.1381445.s017 |
| network_acronym_str | Manara |
| network_name_str | ManaraRepo |
| oai_identifier_str | oai:figshare.com:article/27166926 |
| publishDate | 2024 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | Table6_Integrating genomics and AI to uncover molecular targets for mRNA vaccine development in lupus nephritis.xlsxLisha Mou (151003)Ying Lu (66401)Zijing Wu (3391769)Zuhui Pu (10931751)Meiying Wang (1309134)ImmunologyApplied Immunology (incl. Antibody Engineering, Xenotransplantation and T-cell Therapies)AutoimmunityCellular ImmunologyHumoural Immunology and ImmunochemistryImmunogenetics (incl. Genetic Immunology)Innate ImmunityTransplantation ImmunologyTumour ImmunologyImmunology not elsewhere classifiedGenetic ImmunologyAnimal ImmunologyVeterinary Immunologysystemic lupus erythematosuslupus nephritisgenomicssingle cellsingle-cell RNA sequencingnon-negative matrix factorization (NMF)machine learningfunctional network analysis<p>Lupus nephritis (LN), a complex complication of systemic lupus erythematosus, requires in-depth cellular and molecular analysis for advanced treatment strategies, including mRNA vaccine development. In this study, we analyzed single-cell RNA sequencing data from 24 LN patients and 10 healthy controls, supplemented by bulk RNA-seq data from additional LN patients and controls. By applying non-negative matrix factorization (NMF), we identified four distinct leukocyte meta-programs in LN, highlighting diverse immune functions and potential mRNA vaccine targets. Utilizing 12 machine learning algorithms, we developed 417 predictive models incorporating gene sets linked to key biological pathways, such as MTOR signaling, autophagy, Toll-like receptor, and adaptive immunity pathways. These models were instrumental in identifying potential targets for mRNA vaccine development. Our functional network analysis further revealed intricate gene interactions, providing novel insights into the molecular basis of LN. Additionally, we validated the mRNA expression levels of potential vaccine targets across multiple cohorts and correlated them with clinical parameters such as the glomerular filtration rate (GFR) and pathological stage. This study represents a significant advance in LN research by merging single-cell genomics with the precision of NMF and machine learning, broadening our understanding of LN at the cellular and molecular levels. More importantly, our findings shed light on the development of targeted mRNA vaccines, offering new possibilities for diagnostics and therapeutics for this complex autoimmune disease.</p>2024-10-04T04:03:42ZDatasetinfo:eu-repo/semantics/publishedVersiondataset10.3389/fimmu.2024.1381445.s017https://figshare.com/articles/dataset/Table6_Integrating_genomics_and_AI_to_uncover_molecular_targets_for_mRNA_vaccine_development_in_lupus_nephritis_xlsx/27166926CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/271669262024-10-04T04:03:42Z |
| spellingShingle | Table6_Integrating genomics and AI to uncover molecular targets for mRNA vaccine development in lupus nephritis.xlsx Lisha Mou (151003) Immunology Applied Immunology (incl. Antibody Engineering, Xenotransplantation and T-cell Therapies) Autoimmunity Cellular Immunology Humoural Immunology and Immunochemistry Immunogenetics (incl. Genetic Immunology) Innate Immunity Transplantation Immunology Tumour Immunology Immunology not elsewhere classified Genetic Immunology Animal Immunology Veterinary Immunology systemic lupus erythematosus lupus nephritis genomics single cell single-cell RNA sequencing non-negative matrix factorization (NMF) machine learning functional network analysis |
| status_str | publishedVersion |
| title | Table6_Integrating genomics and AI to uncover molecular targets for mRNA vaccine development in lupus nephritis.xlsx |
| title_full | Table6_Integrating genomics and AI to uncover molecular targets for mRNA vaccine development in lupus nephritis.xlsx |
| title_fullStr | Table6_Integrating genomics and AI to uncover molecular targets for mRNA vaccine development in lupus nephritis.xlsx |
| title_full_unstemmed | Table6_Integrating genomics and AI to uncover molecular targets for mRNA vaccine development in lupus nephritis.xlsx |
| title_short | Table6_Integrating genomics and AI to uncover molecular targets for mRNA vaccine development in lupus nephritis.xlsx |
| title_sort | Table6_Integrating genomics and AI to uncover molecular targets for mRNA vaccine development in lupus nephritis.xlsx |
| topic | Immunology Applied Immunology (incl. Antibody Engineering, Xenotransplantation and T-cell Therapies) Autoimmunity Cellular Immunology Humoural Immunology and Immunochemistry Immunogenetics (incl. Genetic Immunology) Innate Immunity Transplantation Immunology Tumour Immunology Immunology not elsewhere classified Genetic Immunology Animal Immunology Veterinary Immunology systemic lupus erythematosus lupus nephritis genomics single cell single-cell RNA sequencing non-negative matrix factorization (NMF) machine learning functional network analysis |