Transcriptomic changes in human renal proximal tubular cells revealed under hypoxic conditions by RNA sequencing

Abstract

Chronic hypoxia often occurs among patients with chronic kidney disease (CKD). Renal proximal tubular cells may be the primary target of a hypoxic insult. However, the underlying transcriptional mechanisms remain undefined. In this study, we revealed the global changes in gene expression in HK‑2 human renal proximal tubular cells under hypoxic and normoxic conditions. We analyzed the transcriptome of HK‑2 cells exposed to hypoxia for 24 h using RNA sequencing. A total of 279 differentially expressed genes was examined, as these genes could potentially explain the differences in HK‑2 cells between hypoxic and normoxic conditions. Moreover, 17 genes were validated by qPCR, and the results were highly concordant with the RNA seqencing results. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to better understand the functions of these differentially expressed genes. The upregulated genes appeared to be significantly enriched in the pathyway of extracellular matrix (ECM)-receptor interaction, and in paticular, the pathway of renal cell carcinoma was upregulated under hypoxic conditions. The downregulated genes were enriched in the signaling pathway related to antigen processing and presentation; however, the pathway of glutathione metabolism was downregulated. Our analysis revealed numerous novel transcripts and alternative splicing events. Simultaneously, we also identified a large number of single nucleotide polymorphisms, which will be a rich resource for future marker development. On the whole, our data indicate that transcriptome analysis provides valuable information for a more in depth understanding of the molecular mechanisms in CKD and renal cell carcinoma.

Reduced O-GlcNAcylation and tubular hypoxia contribute to the antifibrotic effect of SGLT2 inhibitor dapagliflozin in the diabetic kidney

“…51). HIF-1␣ has also been reported to be elevated in 1% O 2 milieu, specifically in proximal tubular cells (10,31,58). In line with the literature, we found that hypoxia led to a robust HIF-1␣ increment and translocation to the nucleus of proximal tubular cells.…”

Role of hypoxia‐inducible factor 1α as a potential biomarker for renal diseases—A systematic review

“…The human kidney contains epithelial cells in the proximal tubules (HK‐2) that require high concentrations of O 2 to maintain their metabolic functions; therefore, in hypoxic conditions, the activation of antiregulatory mechanisms is initiated to adapt to decreased bioavailability of O 2 . Yu et al, aiming to elucidate the mechanisms involved in renal proximal tubule cells, performed a transcriptome analysis in this cell type. They identified an increased expression in 201 genes, all of which are associated with hypoxia and extracellular matrix deposition (ECM) such as TGF‐β1, VEGF, 6‐phosphofructo‐2‐kinase/fructose‐2,6‐bisphosphatase 4 enzyme (PFKFB4), GLUT1, HIF‐1α, and Collagen IV and found that a hypoxic environment induces increased HIF‐1α expression and exacerbates CKD, besides favouring tumorigenesis.…”

“…There are some divergences in literature on the relationship between HIF and other genes involved on the installation of renal dysfunction. VEGF, GLUT1, and TGF‐β1 have been described as coexpressed genes under renal failure conditions; according to these studies, these markers may interact directly with the expression of HIF …”

“…Therefore, HIF-1α regulates the activity of AMPK and contributes to the improvement of kidney function, which corroborates the study of Chen et al 68 Using the small interference RNA technique (SiRNA) for the HIF-1α gene, Chen et al 68 studies, these markers may interact directly with the expression of HIF. 52,68,69,74,76 Baumann et al 77 reported, in an animal experiment, that increased HIF-1α expression potentiates the damage caused by specific TGF-βmediated kidney diseases and found a strong correlation between the COL1A2 gene-regulating HIF-1α in response to TGF-β.…”

The kidney transcriptome, from single cells to whole organs and back

“…A critical limitation of transcriptomic analysis is that it cannot establish a causal relationship between expression of genes and disease development [16]. While some genes and pathways are involved in disease development, others are mostly just a consequence of the disease state [41,42]. As genotype assortment always occurs prior to disease development, genotype information can help to identify causal genetic pathways [43].…”