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Research article
Baoan Chen
Department of Hematology and Oncology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, People’s Republic of China
Corresponding Author
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: Multiple myeloma (MM) is an incurable hematological tumor, which is closely related to hypoxic bone marrow microenvironment. We took integrated bioinformatics analysis with expression profile GSE110113 downloaded from National Center for Biotechnology Information-Gene Expression Omnibus (NCBI-GEO) database, and screened out major histocompatibility complex, class II, DP alpha 1 (HLA-DPA1) as a hub gene related to hypoxia in MM.
Methods: Differentially expressed genes (DEGs) were filtrated with R package “limma”. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were performed using “clusterProfiler” package in R. Then, protein-protein interaction (PPI) network was established. Hub genes were screened out according to Maximal Clique Centrality (MCC). PrognoScan evaluated all the significant hub genes for survival analysis. ScanGEO was used for visualization of gene expression in different clinical studies.
Results: HLA-DPA1 was finally picked out as a hub gene in MM related to hypoxia. MM patients with down-regulated expression of HLA-DPA1 has statistically significantly shorter disease specific survival (DSS) (COX p =0.005411). Based on the clinical data of GSE47552 dataset, HLA-DPA1 expression showed significantly lower in MM patients than that in healthy donors (HDs) (p=0.017).
Conclusion: We identified HLA-DPA1 as a hub gene in MM related to hypoxia. HLA-DPA1 down-regulated expression was associated with MM patients’ poor outcome. Further function and mechanism studies are need to investigate HLA-DPA1 as potential therapeutic target.
Keywords
multiple myeloma, hypoxia, prognosis, bioinformatics analysis
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CURRENT STATUS: Published
View the published article at BMC Cancer.
No community comments so far
Editorial decision: Accept
On 09 Sep, 2020
Editor assigned
On 08 Sep, 2020
Reviewers invited
Invitations sent on 08 Sep, 2020
Reviewer #1 agreed
On 08 Sep, 2020
Reviewer #2 agreed
On 08 Sep, 2020
Review #1 received
Received 08 Sep, 2020
Review #2 received
Received 08 Sep, 2020
Submission checks complete
On 07 Sep, 2020
Editor invited
On 07 Sep, 2020
Version 1
Posted 01 Jul, 2020
No comments provided
Editorial decision: Major revision
On 24 Aug, 2020
Review #2 received
Received 20 Aug, 2020
Reviewer #2 agreed
On 31 Jul, 2020
Review #1 received
Received 30 Jul, 2020
Reviewer #1 agreed
On 28 Jul, 2020
Reviewers invited
Invitations sent on 15 Jul, 2020
Editor assigned
On 21 Jun, 2020
Submission checks complete
On 20 Jun, 2020
Editor invited
On 20 Jun, 2020
First submitted
On 19 Jun, 2020
Metrics
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Subject Areas
Cancer Biology
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A new preprint design is coming!
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See the published version of this preprint at BMC Cancer.
This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Baoan Chen
Department of Hematology and Oncology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, People’s Republic of China
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
View the published article at BMC Cancer.
No community comments so far
Editorial decision: Accept
On 09 Sep, 2020
Editor assigned
On 08 Sep, 2020
Reviewers invited
Invitations sent on 08 Sep, 2020
Reviewer #1 agreed
On 08 Sep, 2020
Reviewer #2 agreed
On 08 Sep, 2020
Review #1 received
Received 08 Sep, 2020
Review #2 received
Received 08 Sep, 2020
Submission checks complete
On 07 Sep, 2020
Editor invited
On 07 Sep, 2020
Version 1
Posted 01 Jul, 2020
No comments provided
Editorial decision: Major revision
On 24 Aug, 2020
Review #2 received
Received 20 Aug, 2020
Reviewer #2 agreed
On 31 Jul, 2020
Review #1 received
Received 30 Jul, 2020
Reviewer #1 agreed
On 28 Jul, 2020
Reviewers invited
Invitations sent on 15 Jul, 2020
Editor assigned
On 21 Jun, 2020
Submission checks complete
On 20 Jun, 2020
Editor invited
On 20 Jun, 2020
First submitted
On 19 Jun, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Cancer Biology
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published article at BMC Cancer.
Background: Multiple myeloma (MM) is an incurable hematological tumor, which is closely related to hypoxic bone marrow microenvironment. We took integrated bioinformatics analysis with expression profile GSE110113 downloaded from National Center for Biotechnology Information-Gene Expression Omnibus (NCBI-GEO) database, and screened out major histocompatibility complex, class II, DP alpha 1 (HLA-DPA1) as a hub gene related to hypoxia in MM.
Methods: Differentially expressed genes (DEGs) were filtrated with R package “limma”. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were performed using “clusterProfiler” package in R. Then, protein-protein interaction (PPI) network was established. Hub genes were screened out according to Maximal Clique Centrality (MCC). PrognoScan evaluated all the significant hub genes for survival analysis. ScanGEO was used for visualization of gene expression in different clinical studies.
Results: HLA-DPA1 was finally picked out as a hub gene in MM related to hypoxia. MM patients with down-regulated expression of HLA-DPA1 has statistically significantly shorter disease specific survival (DSS) (COX p =0.005411). Based on the clinical data of GSE47552 dataset, HLA-DPA1 expression showed significantly lower in MM patients than that in healthy donors (HDs) (p=0.017).
Conclusion: We identified HLA-DPA1 as a hub gene in MM related to hypoxia. HLA-DPA1 down-regulated expression was associated with MM patients’ poor outcome. Further function and mechanism studies are need to investigate HLA-DPA1 as potential therapeutic target.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
This is a list of supplementary files associated with this preprint. Click to download.
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