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The network structure of hematopoietic cancers

Hematopoietic cancers (HCs) are a heterogeneous group of malignancies that affect blood, bone marrow and lymphatic system. Here, by analyzing 1960 RNA-Seq samples from three independent datasets, we explored the co-expression landscape in HCs, by inferring gene co-expression networks (GCNs) with fou...

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Autores principales: Nakamura-García, Arturo Kenzuke, Espinal-Enríquez, Jesús
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10645882/
https://www.ncbi.nlm.nih.gov/pubmed/37963971
http://dx.doi.org/10.1038/s41598-023-46655-2
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author Nakamura-García, Arturo Kenzuke
Espinal-Enríquez, Jesús
author_facet Nakamura-García, Arturo Kenzuke
Espinal-Enríquez, Jesús
author_sort Nakamura-García, Arturo Kenzuke
collection PubMed
description Hematopoietic cancers (HCs) are a heterogeneous group of malignancies that affect blood, bone marrow and lymphatic system. Here, by analyzing 1960 RNA-Seq samples from three independent datasets, we explored the co-expression landscape in HCs, by inferring gene co-expression networks (GCNs) with four cancer phenotypes (B and T-cell acute leukemia -BALL, TALL-, acute myeloid leukemia -AML-, and multiple myeloma -MM-) as well as non-cancer bone marrow. We characterized their structure (topological features) and function (enrichment analyses). We found that, as in other types of cancer, the highest co-expression interactions are intra-chromosomal, which is not the case for control GCNs. We also detected a highly co-expressed group of overexpressed pseudogenes in HC networks. The four GCNs present only a small fraction of common interactions, related to canonical functions, like immune response or erythrocyte differentiation. With this approach, we were able to reveal cancer-specific features useful for detection of disease manifestations.
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spelling pubmed-106458822023-11-13 The network structure of hematopoietic cancers Nakamura-García, Arturo Kenzuke Espinal-Enríquez, Jesús Sci Rep Article Hematopoietic cancers (HCs) are a heterogeneous group of malignancies that affect blood, bone marrow and lymphatic system. Here, by analyzing 1960 RNA-Seq samples from three independent datasets, we explored the co-expression landscape in HCs, by inferring gene co-expression networks (GCNs) with four cancer phenotypes (B and T-cell acute leukemia -BALL, TALL-, acute myeloid leukemia -AML-, and multiple myeloma -MM-) as well as non-cancer bone marrow. We characterized their structure (topological features) and function (enrichment analyses). We found that, as in other types of cancer, the highest co-expression interactions are intra-chromosomal, which is not the case for control GCNs. We also detected a highly co-expressed group of overexpressed pseudogenes in HC networks. The four GCNs present only a small fraction of common interactions, related to canonical functions, like immune response or erythrocyte differentiation. With this approach, we were able to reveal cancer-specific features useful for detection of disease manifestations. Nature Publishing Group UK 2023-11-13 /pmc/articles/PMC10645882/ /pubmed/37963971 http://dx.doi.org/10.1038/s41598-023-46655-2 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Nakamura-García, Arturo Kenzuke
Espinal-Enríquez, Jesús
The network structure of hematopoietic cancers
title The network structure of hematopoietic cancers
title_full The network structure of hematopoietic cancers
title_fullStr The network structure of hematopoietic cancers
title_full_unstemmed The network structure of hematopoietic cancers
title_short The network structure of hematopoietic cancers
title_sort network structure of hematopoietic cancers
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10645882/
https://www.ncbi.nlm.nih.gov/pubmed/37963971
http://dx.doi.org/10.1038/s41598-023-46655-2
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