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      Tubular-specific CDK12 knockout causes a defect in urine concentration due to premature cleavage of the slc12a1 gene

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          Abstract

          Cyclin-dependent kinase 12 (CDK12) plays a critical role in regulating gene transcription. CDK12 inhibition is a potential anticancer therapeutic strategy. However, several clinical trials have shown that CDK inhibitors might cause renal dysfunction and electrolyte disorders. CDK12 is abundant in renal tubular epithelial cells (RTECs), but the exact role of CDK12 in renal physiology remains unclear. Genetic knockout of CDK12 in mouse RTECs causes polydipsia, polyuria, and hydronephrosis. This phenotype is caused by defects in water reabsorption that are the result of reduced Na-K-2Cl cotransporter 2 (NKCC2) levels in the kidney. In addition, CKD12 knockout causes an increase in Slc12a1 (which encodes NKCC2) intronic polyadenylation events, which results in Slc12a1 truncated transcript production and NKCC2 downregulation. These findings provide novel insight into CDK12 being necessary for maintaining renal homeostasis by regulating NKCC2 transcription, which explains the critical water and electrolyte disturbance that occurs during the application of CDK12 inhibitors for cancer treatment. Therefore, there are safety concerns about the clinical use of these new anticancer drugs.

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          Abstract

          Renal-tubular-epithelial-cell-specific CDK12 knockout mice presented with polydipsia and polyuria due to renal concentrating defects. The mechanism of polyuria is that CKD12 knockout causes an increase in Slc12a1 (which encodes NKCC2) intronic polyadenylation events, resulting in Slc12a1 truncated transcript production and NKCC2 downregulation.

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          A survey of best practices for RNA-seq data analysis

          RNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data analysis, including experimental design, quality control, read alignment, quantification of gene and transcript levels, visualization, differential gene expression, alternative splicing, functional analysis, gene fusion detection and eQTL mapping. We highlight the challenges associated with each step. We discuss the analysis of small RNAs and the integration of RNA-seq with other functional genomics techniques. Finally, we discuss the outlook for novel technologies that are changing the state of the art in transcriptomics. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-0881-8) contains supplementary material, which is available to authorized users.
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            Absolute quantification of somatic DNA alterations in human cancer

            We developed a computational method (ABSOLUTE) that infers tumor purity and malignant cell ploidy directly from analysis of somatic DNA alterations. ABSOLUTE can detect subclonal heterogeneity, somatic homozygosity, and calculate statistical sensitivity to detect specific aberrations. We used ABSOLUTE to analyze ovarian cancer data and identified pervasive subclonal somatic point mutations. In contrast, mutations occurring in key tumor suppressor genes, TP53 and NF1 were predominantly clonal and homozygous, as were mutations in a candidate tumor suppressor gene, CDK12. Analysis of absolute allelic copy-number profiles from 3,155 cancer specimens revealed that genome-doubling events are common in human cancer, and likely occur in already aneuploid cells. By correlating genome-doubling status with mutation data, we found that homozygous mutations in NF1 occurred predominantly in non-doubled samples. This finding suggests that genome doubling influences the pathways of tumor progression, with recessive inactivation being less common after genome doubling.
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              Renal tubule injury: a driving force toward chronic kidney disease.

              Renal tubules are the major component of the kidney and are vulnerable to a variety of injuries including hypoxia, proteinuria, toxins, metabolic disorders, and senescence. It has long been believed that tubules are the victim of injury. In this review, we shift this concept to renal tubules as a driving force in the progression of kidney diseases. In response to injury, tubular epithelial cells undergo changes and function as inflammatory and fibrogenic cells, with the consequent production of various bioactive molecules that drive interstitial inflammation and fibrosis. Innate immune-sensing receptors on the tubular epithelium also aggravate immune responses. Necroinflammation, an autoamplification loop between tubular cell death and interstitial inflammation, leads to the exacerbation of renal injury. Furthermore, tubular cells also play an active role in progressive renal injury via emerging mechanisms associated with a partial epithelial-mesenchymal transition, cell-cycle arrest at both G1/S and G2/M check points, and metabolic disorder. Thus, a better understanding the mechanisms by which tubular injury drives inflammation and fibrosis is necessary for the development of therapeutics to halt the progression of chronic kidney disease.
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                Author and article information

                Contributors
                Journal
                Mol Ther
                Mol Ther
                Molecular Therapy
                American Society of Gene & Cell Therapy
                1525-0016
                1525-0024
                05 October 2022
                16 May 2022
                : 30
                : 10
                : 3300-3312
                Affiliations
                [1 ]Institute of Nephrology, Zhong da Hospital, Southeast University School of Medicine, No. 87, Dingjiaqiao Road, Gulou District, Nanjing, Jiangsu Province, China
                [2 ]Nanjing Medical University, Nanjing, Jiangsu, China
                [3 ]Department of Nephrology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu, China
                Author notes
                []Corresponding author: Yi Wen, MD, PhD, Institute of Nephrology, Zhongda Hospital, Southeast University School of Medicine, No. 87, Dingjiaqiao Road, Gulou District, Nanjing, Jiangsu Province, China. wy3511362@ 123456126.com
                [∗∗ ]Corresponding author: Bi-Cheng Liu, MD, PhD, Institute of Nephrology, Zhongda Hospital, Southeast University School of Medicine, No. 87, Dingjiaqiao Road, Gulou District, Nanjing, Jiangsu Province, China. liubc64@ 123456163.com
                [4]

                These authors contributed equally

                Article
                S1525-0016(22)00310-0
                10.1016/j.ymthe.2022.05.012
                9552909
                35581939
                db752c88-3aa7-4a5f-b4bf-84b05665163f
                © 2022 The Authors

                This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

                History
                : 3 December 2021
                : 11 May 2022
                Categories
                Original Article

                Molecular medicine
                cyclin-dependent kinase 12,na-k-2cl cotransporter 2,urine concentration,cdk12 inhibitor,rna polymerase ii

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