The expression of apoptosis related genes in HK-2 cells overexpressing PPM1K was determined by RNA-seq analysis

Li Zhang; Xiaohong Sang; Yuanyuan Han; Alpati Abulitibu; Mufunayi Elken; Zhijie Mao; Shaotao Kang; Wenjun Yang; Chen Lu

doi:10.3389/fgene.2022.1004610

The expression of apoptosis related genes in HK-2 cells overexpressing PPM1K was determined by RNA-seq analysis

Front Genet. 2022 Nov 1:13:1004610. doi: 10.3389/fgene.2022.1004610. eCollection 2022.

Authors

Li Zhang^{1

2

3

4

5}, Xiaohong Sang^{1

2

3

4

5}, Yuanyuan Han^{1

2

3

4

5}, Alpati Abulitibu^{1

2

3

4

5}, Mufunayi Elken^{1

2

3

4

5}, Zhijie Mao^{1

2

3

4

5}, Shaotao Kang^{1

2

3

4

5}, Wenjun Yang^{1

2

3

4

5}, Chen Lu^{1

2

3

4

5}

Affiliations

¹ Nephrology Center of the First Affiliated Hospital of Xinjiang Medical University, Urumqi, China.
² Xinjiang Clinical Research Center of Renal Replacement Therapy, Urumqi, China.
³ Xinjiang Branch of National Clinical Research Center for Kidney Disease, Urumqi, China.
⁴ Xinjiang Blood Purification Medical Quality Control Center, Urumqi, China.
⁵ Institute of Nephrology of Xinjiang, Urumqi, China.

Abstract

Chronic kidney disease (CKD) is a serious disease that endangers human health. It is reported that inhibiting renal cell apoptosis can delay the progress of CKD. Our previous study found that the mice with protein phosphatase Mg2+/Mn2+ dependent 1K (PPM1K) gene deletion had obvious symptoms of glomerular vascular and interstitial vascular dilatation, congestion and hemorrhage, glomerular hemorrhage and necrosis, interstitial fibrous tissue proliferation, decreased urinary creatinine clearance, and increased urinary protein level. In addition, studies have found that PPM1K is essential for cell survival, apoptosis and metabolism. However, no study has confirmed that PPM1K can inhibit renal cell apoptosis. In this study, PPM1K was overexpressed in human kidney-2 cells (HK-2), and the biological process of differentially expressed genes and its effect on apoptosis were comprehensively screened by RNA sequencing (RNA-seq). Through sequencing analysis, we found that there were 796 differentially expressed genes in human renal tubular epithelial cells transfected with PPM1K gene, of which 553 were down-regulated and 243 were up-regulated. Enrichment analysis found that differentially expressed genes may play an important role in amino acid metabolism and biosynthesis. In the GO analysis functional pathway list, we also found that multiple genes can be enriched in apoptosis related pathways, such as G0S2, GADD45A, TRIB3, VEGFA, NUPR1 and other up-regulated genes, and IL-6, MAGED1, CCL2, TP53INP1 and other down-regulated genes. Then we verified these differentially expressed genes by RT-PCR, and found that only the RT-PCR results of G0S2, VEGFA and NUPR1 were consistent with the transcriptome sequencing results. We believe that G0S2, VEGFA, NUPR1 and other genes may participate in the apoptosis process of HK-2 cells induced by PPM1K.In conclusion, these findings provide some data support for the study of HK-2 cell apoptosis mechanism, and also provide a scientific theoretical basis for further study of the effect of PPM1K on kidney disease.

Keywords: PPM1K; RNA-seq; apoptosis; enrichment analysis; human kidney-2 cell; transcriptome.