Multimodal single cell sequencing implicates chromatin accessibility and genetic background in diabetic kidney disease progression

The proximal tubule is a key regulator of kidney function and glucose metabolism. Diabetic kidney disease leads to proximal tubule injury and changes in chromatin accessibility that modify the activity of transcription factors involved in glucose metabolism and inflammation. Here we use single nucleus RNA and ATAC sequencing to show that diabetic kidney disease leads to reduced accessibility of glucocorticoid receptor binding sites and an injury-associated expression signature in the proximal tubule. We hypothesize that chromatin accessibility is regulated by genetic background and closely-intertwined with metabolic memory, which pre-programs the proximal tubule to respond differently to external stimuli. Glucocorticoid excess has long been known to increase risk for type 2 diabetes, which raises the possibility that glucocorticoid receptor inhibition may mitigate the adverse metabolic effects of diabetic kidney disease

A single-cell multiomic analysis of kidney organoid differentiation

Kidney organoids differentiated from pluripotent stem cells are powerful models of kidney development and disease but are characterized by cell immaturity and off-target cell fates. Comparing the cell-specific gene regulatory landscape during organoid differentiation with human adult kidney can serve to benchmark progress in differentiation at the epigenome and transcriptome level for individual organoid cell types. Using single-cell multiome and histone modification analysis, we report more broadly open chromatin in organoid cell types compared to the human adult kidney. We infer enhancer dynamics by cis-coaccessibility analysis and validate an enhancer driving transcription o

Mapping the single-cell transcriptomic response of murine diabetic kidney disease to therapies

Diabetic kidney disease (DKD) occurs in ∼40% of patients with diabetes and causes kidney failure, cardiovascular disease, and premature death. We analyzed the response of a murine DKD model to five treatment regimens using single-cell RNA sequencing (scRNA-seq). Our atlas of ∼1 million cells revealed a heterogeneous response of all kidney cell types both to DKD and its treatment. Both monotherapy and combination therapies targeted differing cell types and induced distinct and non-overlapping transcriptional changes. The early effects of sodium-glucose cotransporter-2 inhibitors (SGLT2i) on the S1 segment of the proximal tubule suggest that this drug class induces fasting mimicry and hypoxia responses. Diabetes downregulated the spliceosome regulator serine/arginine-rich splicing factor 7 (Srsf7) in proximal tubule that was specifically rescued by SGLT2i. In vitro proximal tubule knockdown of Srsf7 induced a pro-inflammatory phenotype, implicating alternative splicing as a driver of DKD and suggesting SGLT2i regulation of proximal tubule alternative splicing as a potential mechanism of action for this drug class

Defining cellular complexity in human autosomal dominant polycystic kidney disease by multimodal single cell analysis

Autosomal dominant polycystic kidney disease (ADPKD) is the leading genetic cause of end stage renal disease characterized by progressive expansion of kidney cysts. To better understand the cell types and states driving ADPKD progression, we analyze eight ADPKD and five healthy human kidney samples, generating single cell multiomic atlas consisting of ~100,000 single nucleus transcriptomes and ~50,000 single nucleus epigenomes. Activation of proinflammatory, profibrotic signaling pathways are driven by proximal tubular cells with a failed repair transcriptomic signature, proinflammatory fibroblasts and collecting duct cells. We identify GPRC5A as a marker for cyst-lining collecting duct cells that exhibits increased transcription factor binding motif availability for NF-κB, TEAD, CREB and retinoic acid receptors. We identify and validate a distal enhancer regulating GPRC5A expression containing these motifs. This single cell multiomic analysis of human ADPKD reveals previously unrecognized cellular heterogeneity and provides a foundation to develop better diagnostic and therapeutic approaches

Predicting proximal tubule failed repair drivers through regularized regression analysis of single cell multiomic sequencing

Renal proximal tubule epithelial cells have considerable intrinsic repair capacity following injury. However, a fraction of injured proximal tubule cells fails to undergo normal repair and assumes a proinflammatory and profibrotic phenotype that may promote fibrosis and chronic kidney disease. The healthy to failed repair change is marked by cell state-specific transcriptomic and epigenomic changes. Single nucleus joint RNA- and ATAC-seq sequencing offers an opportunity to study the gene regulatory networks underpinning these changes in order to identify key regulatory drivers. We develop a regularized regression approach to construct genome-wide parametric gene regulatory networks using multiomic datasets. We generate a single nucleus multiomic dataset from seven adult human kidney samples and apply our method to study drivers of a failed injury response associated with kidney disease. We demonstrate that our approach is a highly effective tool for predicting key cis- and trans-regulatory elements underpinning the healthy to failed repair transition and use it to identify NFAT5 as a driver of the maladaptive proximal tubule state

Investigation on the Efficiency of Chinese Herbal Injections combined with Concurrent Chemoradiotherapy for Treating Nasopharyngeal Carcinoma based on Multidimensional Bayesian Network Meta-analysis

Introduction: Given the wide utilization of Chinese herbal injections in the treatment of nasopharyngeal carcinoma (NPC), this network meta-analysis (NMA) was devised to compare the clinical efficacy and safety of different Chinese herbal injections combined with concurrent chemoradiotherapy (CCRT) against NPC.Methods: Randomized controlled trials (RCTs) were retrieved from seven electronic databases from the date of database establishment to October 5, 2020. Study selection and data extraction conformed to a priori criteria. Focusing on clinical effective rate, performance status, grade ≥3 oral mucositis, nausea and vomiting, leukopenia, and thrombopenia, this NMA was performed with Review Manager 5.3.5, Stata 13.1, WinBUGS 1.4.3, and R 4.0.3 software.Results: Ten inventions from 37 RCTs involving 2,581 participants with NPC that evaluated the clinical effective rate, nausea and vomiting, leukopenia, thrombopenia, and grade ≥3 oral mucositis were included. Compared with CCRT alone, Elemene injection and Compound Kushen injection were associated with significantly improved clinical effective rates, and Elemene injection plus CCRT had the highest probability in terms of clinical effective rate (78.07%) compared with the other interventions. Shenqifuzheng injection, Xiaoaiping injection, and Shenmai injection ranked the best in terms of performance status (79.02%), nausea and vomiting (86.35%), and grade ≥3 oral mucositis (78.14%) when combined with CCRT. Kangai injection combined with CCRT ranked ahead of the other injections in terms of leukopenia (90.80%) and thrombopenia (91.04%), and had a better impact on improving performance status and reducing leukopenia, thrombopenia, grade ≥3 oral mucositis, and nausea and vomiting in the multidimensional cluster analysis.Conclusion: Current clinical evidence indicates that Elemene injection combined with CCRT has the best clinical effective rate and that Kangai injection might have a comprehensively better impact on improving performance status and reducing adverse reactions against NPC. Additionally, due to the limitations of this NMA, more multicenter, high-quality, and head-to-head RCTs are needed to properly support our findings