Integrated bioinformatics analysis reveals novel key biomarkers in diabetic nephropathy

Joshi, Harish; Vastrad, Basavaraj; Joshi, Nidhi; Vastrad, Chanabasayya

doi:10.1177/20503121221137005

Cited by 4 publications

(2 citation statements)

References 159 publications

(171 reference statements)

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“…3B ). ATP6V1G3 , which is a biomarker for diabetic nephropathy 118 , showed greater chromatin accessibility, particularly in the promoter, in Jamaican fruit bat type A and type B intercalated cells (Fig. 3C ).…”

Section: Resultsmentioning

confidence: 99%

Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas

Gordon,

Baek,

Nguyen

et al. 2024

Nat Commun

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Frugivory evolved multiple times in mammals, including bats. However, the cellular and molecular components driving it remain largely unknown. Here, we use integrative single-cell sequencing (scRNA-seq and scATAC-seq) on insectivorous (Eptesicus fuscus; big brown bat) and frugivorous (Artibeus jamaicensis; Jamaican fruit bat) bat kidneys and pancreases and identify key cell population, gene expression and regulatory differences associated with the Jamaican fruit bat that also relate to human disease, particularly diabetes. We find a decrease in loop of Henle and an increase in collecting duct cells, and differentially active genes and regulatory elements involved in fluid and electrolyte balance in the Jamaican fruit bat kidney. The Jamaican fruit bat pancreas shows an increase in endocrine and a decrease in exocrine cells, and differences in genes and regulatory elements involved in insulin regulation. We also find that these frugivorous bats share several molecular characteristics with human diabetes. Combined, our work provides insights from a frugivorous mammal that could be leveraged for therapeutic purposes.

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Section: Resultsmentioning

confidence: 99%

Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas

Gordon,

Baek,

Nguyen

et al. 2024

Nat Commun

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show abstract

“…3B). ATP6V1G3 , which is a biomarker for diabetic nephropathy ( 102 ), showed greater chromatin accessibility, particularly in the promoter, in fruit bat type A and type B intercalated cells (Fig. S4H).…”

Section: Resultsmentioning

confidence: 99%

Integrative single-cell characterization of frugivory adaptations in the bat kidney and pancreas

Gordon

Baek

Nguyen

et al. 2023

Preprint

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Frugivory evolved multiple times in mammals, including bats. However, the cellular and molecular components driving it remain largely unknown. Here, we used integrative single-cell sequencing on insectivorous and frugivorous bat kidneys and pancreases and identified key cell population, gene expression and regulatory element differences associated with frugivorous adaptation that also relate to human disease, particularly diabetes. We found an increase in collecting duct cells and differentially active genes and regulatory elements involved in fluid and electrolyte balance in the frugivore kidney. In the frugivorous pancreas, we observed an increase in endocrine and a decrease in exocrine cells and differences in genes and regulatory elements involved in insulin regulation. Combined, our work provides novel insights into frugivorous adaptation that also could be leveraged for therapeutic purposes.

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Screening and identification of key biomarkers in diabetic kidney disease and its complications: Evidence from bioinformatics and next generation sequencing data analysis

Vastrad¹,

Vastrad²

2023

Preprint

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Diabetic patients are prone to diabetic kidney disease (DKD), which may cause cardiovascular damage, hypertension and obesity, and reduce quality of life. As a result, the life quality of patients was seriously reduced. However, the pathogenesis of diabetic kidney disease (DKD) has not been fully elucidated, and current treatments remain inadequate. Therefore, it is essential to explore the molecular mechanism of DKD and its complications. Next Generation Sequancing (GSE217709) dataset was obtained from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were picked out by R software. Then Gene ontology (GO) and REACTOME pathway enrichment analysis were performed by g:Profiler database, protein-protein interaction (PPI) of DEGs was constructed by Human Integrated Protein-Protein Interaction rEference (HIPPIE) database . Module analysis was carried out by Cytoscape plug-in PEWCC. Subsequently, miRNA-hub gene regulatory network and TF- hub gene regulatory network were performed by miRNet database and NetworkAnalyst database. Finally, validation of hub genes was performed by receiver operating characteristic (ROC) curve analysis to predict the diagnostic effectiveness of the hub genes. In total, 958 DEGs, including 479 up regulated and 479 down regulated genes, were identified. The GO and pathway enrichment changes of DEGs were mainly enriched in biological regulation, multicellular organismal process, signaling by GPCR and extracellular matrix organization. Ten hub genes (HSPA8, HSP90AA1, HSPA5, SDCBP, HSP90B1, VCAM1, MYH9, FLNA, MDFI and PML) associated with DKD and its complications were identified. Bioinformatics analysis is a useful tool to explore the molecular mechanism and pathogenesis of DKD and its complications. The identified hub genes may participate in the onset and development of DKD and its complications and serve as therapeutic targets.

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Integrated bioinformatics analysis reveals novel key biomarkers in diabetic nephropathy

Cited by 4 publications

References 159 publications

Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas

Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas

Integrative single-cell characterization of frugivory adaptations in the bat kidney and pancreas

Screening and identification of key biomarkers in diabetic kidney disease and its complications: Evidence from bioinformatics and next generation sequencing data analysis

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