scholarly journals AEBP1 is Upregulated in Diabetic Nephropathy Biopsies

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Benjamin Freije ◽  
Ricardo Melo Ferreira ◽  
Ying-Hua Cheng ◽  
Samir Parikh ◽  
Michael Eadon
Keyword(s):  
Diabetic Nephropathy ◽  
Kidney Disease ◽  
Interstitial Fibrosis ◽  
Treatment Strategies ◽  
Human Kidney ◽  
Sequencing Data ◽  
Specific Expression ◽  
Enhancer Binding Protein ◽  
Organ Specific ◽  
Matrix Organization

Background: Worldwide, one in eleven adults have diabetes mellitus and 30% to 40% will develop diabetic kidney disease (DKD). A mechanistic understanding of DKD is crucial to develop treatment strategies. To unravel DKD’s pathogenesis, single cell (scRNA) sequencing has proven a powerful tool, but is limited by a lack of localization. Spatial transcriptomics allows the mapping of scRNA sequencing data back to histology. Methods: Frozen human nephrectomy and biopsy samples were processed according to Visium spatial gene expression protocols, stained with H&E, and imaged. Samples were permeabilized for RNA capture, reverse transcribed and sequenced on an Illumina NovaSeq 6000. Mapping and counting were completed in Space Ranger and data was processed in Seurat. Samples were laser microdissected, protein was isolated, and protein was quantified by HPLC-MS. Results: Clusters from scRNAseq were mapped upon reference and DKD spatial transcriptomic images (N=4 reference, 2 DKD). Differentially expressed genes were identified in diabetic kidneys, including the upregulation of Adipocyte Enhancer Binding Protein (AEBP1).  Pathway analysis revealed enrichment of extracellular matrix organization and immune process pathways. To increase the confidence of these findings, glomeruli and the tubulointerstitium were laser microdissected (N=7 diseased, 4 reference) for proteomic analysis. AEBP1 was upregulated in the tubular interstitium of diseased kidneys and selectively upregulated in the glomeruli of Diabetic Nephropathy samples (N=2). AEBP1 localized to the interstitium by spatial transcriptomics and was expressed in highly fibrotic regions. Glomerular expression was not observed due to glomerulosclerosis. Conclusion: AEBP1 upregulation is a marker of interstitial fibrosis, with specific expression in the glomeruli of diabetic nephropathy specimens with glomerulosclerosis. Impact: This is the first study utilizing spatial transcriptomics to define and localize markers of human kidney disease. Confirmatory studies are required in larger sample sizes. AEBP1 is a previously unidentified marker of DKD previously associated with fibrosis in other organ-specific diseases.

Expression of Lactate Dehydrogenase A and B isoforms in the mouse kidney

2021 ◽  
Author(s):  
Gunars Osis ◽  
Amie M. Traylor ◽  
Laurence M Black ◽  
Daryll Spangler ◽  
James F George ◽  
...  
Keyword(s):  
Chronic Kidney Disease ◽  
Lactate Dehydrogenase ◽  
Kidney Disease ◽  
Rna Sequencing ◽  
Cellular Localization ◽  
Ischemia Reperfusion Injury ◽  
Ischemia Reperfusion ◽  
Sequencing Data ◽  
Post Injury ◽  
Specific Expression

Cellular metabolic rates in the kidney are critical for maintaining renal function. In a hypoxic milieu, cells rely on glycolysis to meet energy needs, resulting in the generation of pyruvate and NADH. In the absence of oxidative phosphorylation, the continuation of glycolysis is dependent on the regeneration of NAD+ from NADH accompanied by the fermentation of pyruvate to lactate. This reaction is catalyzed by lactate dehydrogenase (LDH) isoform A (LDHA), while isoform B (LDHB) catalyzes the opposite reaction. LDH is widely used as a potential injury marker, yet the precise isoform-specific cellular localization of the enzyme along the nephron has not been characterized. By combining immunohistochemistry and single-cell RNA sequencing data on healthy mouse kidneys we identified that LDHA is primarily expressed in proximal segments while LDHB is expressed in the distal parts of the nephron. In vitro studies in mouse and human renal proximal tubule cells show an increase in LDHA following hypoxia with no change in LDHB. We observed that the overall expression of both LDHA and LDHB decreased following renal ischemia-reperfusion injury (IRI) as well as in the adenine-diet induced model of chronic kidney disease. Single-nucleus RNA sequencing analyses of kidneys following IRI revealed a significant decline in the number of cells expressing Ldha and Ldhb, however, cells that were positive showed increased average expression post-injury which subsided during the recovery phase. These data provide information on the cell-specific expression of LDHA and LDHB in the normal kidney as well as following acute and chronic kidney disease.

scholarly journals Endoglin Promotes Myofibroblast Differentiation and Extracellular Matrix Production in Diabetic Nephropathy

2020 ◽  
Vol 21 (20) ◽  
pp. 7713
Author(s):  
Tessa Gerrits ◽  
Malu Zandbergen ◽  
Ron Wolterbeek ◽  
Jan A. Bruijn ◽  
Hans J. Baelde ◽  
...  
Keyword(s):  
Diabetic Nephropathy ◽  
Cell Function ◽  
Interstitial Fibrosis ◽  
Human Kidney ◽  
Fibroblast Cell ◽  
Diabetic Patients ◽  
Endothelial Cell Function ◽  
Intestinal Fibrosis ◽  
Kidney Fibroblast ◽  
Sirius Red

Diabetic nephropathy (DN) is a complication of diabetes mellitus that can lead to proteinuria and a progressive decline in renal function. Endoglin, a co-receptor of TGF-β, is known primarily for regulating endothelial cell function; however, endoglin is also associated with hepatic, cardiac, and intestinal fibrosis. This study investigates whether endoglin contributes to the development of interstitial fibrosis in DN. Kidney autopsy material from 80 diabetic patients was stained for endoglin and Sirius Red and scored semi-quantitatively. Interstitial endoglin expression was increased in samples with DN and was correlated with Sirius Red staining (p < 0.001). Endoglin expression was also correlated with reduced eGFR (p = 0.001), increased creatinine (p < 0.01), increased systolic blood pressure (p < 0.05), hypertension (p < 0.05), and higher IFTA scores (p < 0.001). Biopsy samples from DN patients were also co-immunostained for endoglin together with CD31, CD68, vimentin, or α-SMA Endoglin co-localized with both the endothelial marker CD31 and the myofibroblast marker α-SMA. Finally, we used shRNA to knockdown endoglin expression in a human kidney fibroblast cell line. We found that TGF-β1 stimulation upregulated SERPINE1, CTGF, and ACTA2 mRNA and α-SMA protein, and that these effects were significantly reduced in fibroblasts after endoglin knockdown. Taken together, these data suggest that endoglin plays a role in the pathogenesis of interstitial fibrosis in DN.

scholarly journals High-protein diet accelerates diabetes and kidney disease in the BTBRob/ob mouse

2020 ◽  
Vol 318 (3) ◽  
pp. F763-F771 ◽  
Author(s):  
Anna Björnson Granqvist ◽  
Anette Ericsson ◽  
José Sanchez ◽  
Pernilla Tonelius ◽  
Lena William-Olsson ◽  
...  
Keyword(s):  
Kidney Disease ◽  
Mouse Model ◽  
Interstitial Fibrosis ◽  
High Protein Diet ◽  
Human Kidney ◽  
Fold Change ◽  
High Protein ◽  
Protein Diet ◽  
Standard Diet ◽  
Chronic Injury

There is a need for improved animal models that better translate to human kidney disease to predict outcome of pharmacological effects in the patient. The diabetic BTBR ob/ob mouse model mimics key features of early diabetic nephropathy in humans, but with chronic injury limited to glomeruli. To explore if we could induce an accelerated and more advanced disease phenotype that closer translates to human disease, we challenged BTBR ob/ob mice with a high-protein diet (HPD; 30%) and followed the progression of metabolic and renal changes up to 20 wk of age. Animals on the HPD showed enhanced metabolic derangements, evidenced by further increased levels of glucose, HbA1C, cholesterol, and alanine aminotransferase. The urinary albumin-to-creatinine ratio was markedly increased with a 53-fold change compared with lean controls, whereas BTBR ob/ob mice on the standard diet only presented an 8-fold change. HPD resulted in more advanced mesangial expansion already at 14 wk of age compared with BTBR ob/ob mice on the standard diet and also aggravated glomerular pathology as well as interstitial fibrosis. Gene expression analysis revealed that HPD triggered expression of markers of fibrosis and inflammation in the kidney and increased oxidative stress markers in urine. This study showed that HPD significantly aggravated renal injury in BTBR ob/ob mice by further advancing albuminuria, glomerular, and tubulointerstitial pathology by 20 wk of age. This mouse model offers closer translation to humans and enables exploration of new end points for pharmacological efficacy studies that also holds promise to shorten study length.

scholarly journals miRNA analysis with Prost! reveals evolutionary conservation of organ-enriched expression and post-transcriptional modifications in three-spined stickleback and zebrafish

2018 ◽  
Author(s):  
Thomas Desvignes ◽  
Peter Batzel ◽  
Jason Sydes ◽  
B. Frank Eames ◽  
John Postlethwait
Keyword(s):  
Gasterosteus Aculeatus ◽  
Mature Mirnas ◽  
Evolutionary Conservation ◽  
Small Rna Sequencing ◽  
Sequencing Data ◽  
Specific Expression ◽  
Tissue Specific ◽  
Mirna Genes ◽  
Evolutionarily Conserved ◽  
Organ Specific

AbstractMicroRNAs (miRNAs) can have tissue-specific expression and functions; they can originate from dedicated miRNA genes, from non-canonical miRNA genes, or from mirror-miRNA genes and can also experience post-transcriptional variations. It remains unclear, however, which mechanisms of miRNA production or modification are tissue-specific and the extent of their evolutionary conservation. To address these issues, we developed the software Prost! (PRocessing Of Short Transcripts), which, among other features, allows accurate quantification of mature miRNAs, takes into account post-transcriptional processing, such as nucleotide editing, and helps identify mirror-miRNAs. Here, we applied Prost! to annotate and analyze miRNAs in three-spined stickleback (Gasterosteus aculeatus), a model fish for evolutionary biology reported to have a miRNome larger than most teleost fish. Zebrafish (Danio rerio), a distantly related teleost with a well-known miRNome, served as comparator. Despite reports suggesting that stickleback had a large miRNome, results showed that stickleback has 277 evolutionary-conserved mir genes and 366 unique mature miRNAs (excluding mir430 gene replicates and the vaultRNA-derived mir733), similar to zebrafish. In addition, small RNA sequencing data from brain, heart, testis, and ovary in both stickleback and zebrafish identified suites of mature miRNAs that display organ-specific enrichment, which is, for many miRNAs, evolutionarily-conserved. These data also supported the hypothesis that evolutionarily-conserved, organ-specific mechanisms regulate miRNA post-transcriptional variations. In both stickleback and zebrafish, miR2188-5p was edited frequently with similar nucleotide editing patterns in the seed sequence in various tissues, and the editing rate was organ-specific with higher editing in the brain. In summary, Prost! is a critical new tool to identify and understand small RNAs and can help clarify a species’ miRNA biology, as shown here for an important fish model for the evolution of developmental mechanisms, and can provide insight into organ-specific expression and evolutionary-conserved miRNA post-transcriptional mechanisms.

scholarly journals Kidney disease genetic risk variants alter lysosomal beta-mannosidase (MANBA) expression and disease severity

2021 ◽  
Vol 13 (576) ◽  
pp. eaaz1458 ◽  
Author(s):  
Xiangchen Gu ◽  
Hongliu Yang ◽  
Xin Sheng ◽  
Yi-An Ko ◽  
Chengxiang Qiu ◽  
...  
Keyword(s):  
Kidney Disease ◽  
Kidney Function ◽  
Association Studies ◽  
Inflammasome Activation ◽  
Genome Wide Association Studies ◽  
Disease Development ◽  
Loss Of Function ◽  
Sequencing Data ◽  
Specific Expression ◽  
Coding Variants

More than 800 million people in the world suffer from chronic kidney disease (CKD). Genome-wide association studies (GWAS) have identified hundreds of loci where genetic variants are associated with kidney function; however, causal genes and pathways for CKD remain unknown. Here, we performed integration of kidney function GWAS and human kidney–specific expression quantitative trait analysis and identified that the expression of beta-mannosidase (MANBA) was lower in kidneys of subjects with CKD risk genotype. We also show an increased incidence of renal failure in subjects with rare heterozygous loss-of-function coding variants in MANBA using phenome-wide association analysis of 40,963 subjects with exome sequencing data. MANBA is a lysosomal gene highly expressed in kidney tubule cells. Deep phenotyping revealed structural and functional lysosomal alterations in human kidneys from subjects with CKD risk alleles and mice with genetic deletion of Manba. Manba heterozygous and knockout mice developed more severe kidney fibrosis when subjected to toxic injury induced by cisplatin or folic acid. Manba loss altered multiple pathways, including endocytosis and autophagy. In the absence of Manba, toxic acute tubule injury induced inflammasome activation and fibrosis. Together, these results illustrate the convergence of common noncoding and rare coding variants in MANBA in kidney disease development and demonstrate the role of the endolysosomal system in kidney disease development.

scholarly journals KidneyNetwork: Using kidney-derived gene expression data to predict and prioritize novel genes involved in kidney disease

2021 ◽  
Author(s):  
Floranne Boulogne ◽  
Laura R. Claus ◽  
Henry Wiersma ◽  
Roy Oelen ◽  
Floor Schukking ◽  
...  
Keyword(s):  
Genetic Testing ◽  
Kidney Disease ◽  
Candidate Gene ◽  
Specific Gene ◽  
Sequencing Data ◽  
Specific Expression ◽  
Disease Phenotypes ◽  
Exome Sequencing Data ◽  
Pathogenic Variants ◽  
Gene Functions

AbstractBackgroundGenetic testing in patients with suspected hereditary kidney disease may not reveal the genetic cause for the disorder as potentially pathogenic variants can reside in genes that are not yet known to be involved in kidney disease. To help identify these genes, we have developed KidneyNetwork, that utilizes tissue-specific expression to predict kidney-specific gene functions.MethodsKidneyNetwork is a co-expression network built upon a combination of 878 kidney RNA-sequencing samples and a multi-tissue dataset of 31,499 samples. It uses expression patterns to predict which genes have a kidney-related function and which (disease) phenotypes might result from variants in these genes. We applied KidneyNetwork to prioritize rare variants in exome sequencing data from 13 kidney disease patients without a genetic diagnosis.ResultsKidneyNetwork can accurately predict kidney-specific gene functions and (kidney disease) phenotypes for disease-associated genes. Applying it to exome sequencing data of kidney disease patients allowed us to identify a promising candidate gene for kidney and liver cysts: ALG6.ConclusionWe present KidneyNetwork, a kidney-specific co-expression network that accurately predicts which genes have kidney-specific functions and can result in kidney disease. We show the added value of KidneyNetwork by applying it to kidney disease patients without a molecular diagnosis and consequently, we propose ALG6 as candidate gene in one of these patients. KidneyNetwork can be applied to clinically unsolved kidney disease cases, but it can also be used by researchers to gain insight into individual genes in order to better understand kidney physiology and pathophysiology.Significance statementGenetic testing in patients with suspected hereditary kidney disease may not reveal the genetic cause for the patient’s disorder. Potentially pathogenic variants can reside in genes not yet known to be involved in kidney disease, making it difficult to interpret the relevance of these variants. This reveals a clear need for methods to predict the phenotypic consequences of genetic variation in an unbiased manner. Here we describe KidneyNetwork, a tool that utilizes tissue-specific expression to predict kidney-specific gene functions. Applying KidneyNetwork to a group of undiagnosed cases identified ALG6 as a candidate gene in cystic kidney and liver disease. In summary, KidneyNetwork can aid the interpretation of genetic variants and can therefore be of value in translational nephrogenetics and help improve the diagnostic yield in kidney disease patients.

scholarly journals Development of a Model of Chronic Kidney Disease in the C57BL/6 Mouse with Properties of Progressive Human CKD

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Zahraa Mohammed-Ali ◽  
Gaile L. Cruz ◽  
Chao Lu ◽  
Rachel E. Carlisle ◽  
Kaitlyn E. Werner ◽  
...  
Keyword(s):  
Chronic Kidney Disease ◽  
Animal Model ◽  
Kidney Disease ◽  
Interstitial Fibrosis ◽  
Treatment Strategies ◽  
Premenopausal Women ◽  
Cell Loss ◽  
Tubular Epithelial Cell ◽  
Common Features ◽  
Stage Renal Disease

Chronic kidney disease (CKD) is a major healthcare problem with increasing prevalence in the population. CKD leads to end stage renal disease and increases the risk of cardiovascular disease. As such, it is important to study the mechanisms underlying CKD progression. To this end, an animal model was developed to allow the testing of new treatment strategies or molecular targets for CKD prevention. Many underlying risk factors result in CKD but the disease itself has common features, including renal interstitial fibrosis, tubular epithelial cell loss through apoptosis, glomerular damage, and renal inflammation. Further, CKD shows differences in prevalence between the genders with premenopausal women being relatively resistant to CKD. We sought to develop and characterize an animal model with these common features of human CKD in the C57BL/6 mouse. Mice of this genetic background have been used to produce transgenic strains that are commercially available. Thus, a CKD model in this strain would allow the testing of the effects of numerous genes on the severity or progression of CKD with minimal cost. This paper describes such a mouse model of CKD utilizing angiotensin II and deoxycorticosterone acetate as inducers.

scholarly journals The proximal tubule is the primary target of injury and progression of kidney disease: role of the glomerulotubular junction

2016 ◽  
Vol 311 (1) ◽  
pp. F145-F161 ◽  
Author(s):  
Robert L. Chevalier
Keyword(s):  
Kidney Disease ◽  
Proximal Tubule ◽  
Interstitial Fibrosis ◽  
Treatment Options ◽  
Kidney Injury ◽  
Human Kidney ◽  
Functional Responses ◽  
Atubular Glomeruli ◽  
Progression Of Kidney Disease ◽  
End Stage

There is an alarming global increase in the incidence of end-stage kidney disease, for which early biomarkers and effective treatment options are lacking. Largely based on the histology of the end-stage kidney and on the model of unilateral ureteral obstruction, current investigation is focused on the pathogenesis of renal interstitial fibrosis as a central mechanism in the progression of chronic kidney disease (CKD). It is now recognized that cumulative episodes of acute kidney injury (AKI) can lead to CKD, and, conversely, CKD is a risk factor for AKI. Based on recent and historic studies, this review shifts attention from the glomerulus and interstitium to the proximal tubule as the primary sensor and effector in the progression of CKD as well as AKI. Packed with mitochondria and dependent on oxidative phosphorylation, the proximal tubule is particularly vulnerable to injury (obstructive, ischemic, hypoxic, oxidative, metabolic), resulting in cell death and ultimately in the formation of atubular glomeruli. Animal models of human glomerular and tubular disorders have provided evidence for a broad repertoire of morphological and functional responses of the proximal tubule, revealing processes of degeneration and repair that may lead to new therapeutic strategies. Most promising are studies that encompass the entire life cycle from fetus to senescence, recognizing epigenetic factors. The application of techniques in molecular characterization of tubule segments and the development of human kidney organoids may provide new insights into the mammalian kidney subjected to stress or injury, leading to biomarkers of early CKD and new therapies.

scholarly journals Twenty years after ACEIs and ARBs: emerging treatment strategies for diabetic nephropathy

2015 ◽  
Vol 309 (10) ◽  
pp. F807-F820 ◽  
Author(s):  
Stacy A. Johnson ◽  
Robert F. Spurney
Keyword(s):  
Diabetes Mellitus ◽  
Diabetic Nephropathy ◽  
Kidney Disease ◽  
Diabetic Kidney Disease ◽  
Angiotensin Receptor Blockers ◽  
Treatment Strategies ◽  
Renin Angiotensin System ◽  
Developed Countries ◽  
Converting Enzyme Inhibitors ◽  
Diabetic Kidney

Diabetic nephropathy (DN) is a serious complication of both type 1 and type 2 diabetes mellitus. The disease is now the most common cause of end-stage kidney disease (ESKD) in developed countries, and both the incidence and prevalence of diabetes mellitus is increasing worldwide. Current treatments are directed at controlling hyperglycemia and hypertension, as well as blockade of the renin angiotensin system with angiotensin-converting enzyme inhibitors (ACEIs), and angiotensin receptor blockers. Despite these therapies, DN progresses to ESKD in many patients. As a result, much interest is focused on developing new therapies. It has been over two decades since ACEIs were shown to have beneficial effects in DN independent of their blood pressure-lowering actions. Since that time, our understanding of disease mechanisms in DN has evolved. In this review, we summarize major cell signaling pathways implicated in the pathogenesis of diabetic kidney disease, as well as emerging treatment strategies. The goal is to identify promising targets that might be translated into therapies for the treatment of patients with diabetic kidney disease.

scholarly journals Upgrading the Repertoire of miRNAs in Gastric Adenocarcinoma to Provide a New Resource for Biomarker Discovery

2019 ◽  
Vol 20 (22) ◽  
pp. 5697 ◽  
Author(s):  
Michelle E. Pewarchuk ◽  
Mateus C. Barros-Filho ◽  
Brenda C. Minatel ◽  
David E. Cohn ◽  
Florian Guisier ◽  
...  
Keyword(s):  
Gastric Adenocarcinoma ◽  
Biomarker Discovery ◽  
The Cancer Genome Atlas ◽  
Small Rna Sequencing ◽  
Sequencing Data ◽  
Specific Expression ◽  
Novel Mirna ◽  
Cancer Genome Atlas ◽  
Context Specific ◽  
Independent Cohort

Recent studies have uncovered microRNAs (miRNAs) that have been overlooked in early genomic explorations, which show remarkable tissue- and context-specific expression. Here, we aim to identify and characterize previously unannotated miRNAs expressed in gastric adenocarcinoma (GA). Raw small RNA-sequencing data were analyzed using the miRMaster platform to predict and quantify previously unannotated miRNAs. A discovery cohort of 475 gastric samples (434 GA and 41 adjacent nonmalignant samples), collected by The Cancer Genome Atlas (TCGA), were evaluated. Candidate miRNAs were similarly assessed in an independent cohort of 25 gastric samples. We discovered 170 previously unannotated miRNA candidates expressed in gastric tissues. The expression of these novel miRNAs was highly specific to the gastric samples, 143 of which were significantly deregulated between tumor and nonmalignant contexts (p-adjusted < 0.05; fold change > 1.5). Multivariate survival analyses showed that the combined expression of one previously annotated miRNA and two novel miRNA candidates was significantly predictive of patient outcome. Further, the expression of these three miRNAs was able to stratify patients into three distinct prognostic groups (p = 0.00003). These novel miRNAs were also present in the independent cohort (43 sequences detected in both cohorts). Our findings uncover novel miRNA transcripts in gastric tissues that may have implications in the biology and management of gastric adenocarcinoma.

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