Biology subjects

Thimm, C.

Publications and source records attributed to Thimm, C..

8 recordsLinked to original sources

bioRxiv2026

Meta-analyses of the NEPTUNE dataset related to high and low risk FSGS and cellular APOL1 models identifies Calcium signalling, mTOR signaling and inflammation-associated pathways as operative in APOL1-mediated kidney disease.

BackgroundThe variants G1 and G2 within the APOL1 gene confer a higher risk of APOL1-mediated kidney disease (AMKD) whilst associated with an evolutionary advantage against trypanosome-mediated sleeping sickness. MethodsIn this study, we analysed transcriptome data of kidney biopsies from FSGS patients with the APOL1 high-risk (HR) and low-risk (LR) variants and compared it to cellular models based on patient-specific podocytes, HEK cells with engineered over-expressing HR variants and HR variant single-cell-RNA-seq data from kidney organoids. ResultsWe identified a signature of up- and down-regulated genes between biopsies from FSGS patients with APOL1 HR and LR variants. The up-regulated genes are functionally annotated to be associated with Calcium and mTOR signaling, whilst the down-regulated genes with inflammatory and immune response pathways. These pathways were confirmed by comparing with cellular models. Analysis of small molecules reverting the IFN-{gamma} stimulated gene expression to the non-stimulated gene expression in genome-edited APOL-G1 kidney organoids revealed several putative candidates such as the mTOR inhibitor AZD-2014. ConclusionWe have unveiled a signature of up- and down-regulated genes between APOL1 HR and LR kidney biopsies which could be assigned as associated with Calcium and mTOR signaling and down-regulated immune response.

molecular biology↗

bioRxiv2025

Urinary proteins from Sickle Cell patients induce inflammation and kidney injury via the TGFβ-p53 axis in a podocyte cell culture model.

BackgroundSickle cell disease (SCD) is an inherited blood disorder affecting the oxygen-carrying hemoglobin in red blood cells making them deform into a sickle shape. Hemolysis and vaso-occlusion associated with this process can lead to complications in many organs and frequently to renal complications. Numerous factors are considered to contribute towards the development of proteinuria (PU) in SCD including hyperfiltration, ischemia, oxidative stress and decreased nitric oxide (NO) bioavailability but the detailed pathophysiology still needs further elucidation. MethodsEmploying arrays, we investigated cytokines and kidney injury-associated markers in the urine of a cohort of SCD patients from Ghana carrying the SS and SC genotypes which were further sub-divided into groups with proteinuria (SCD_PU) and without proteinuria (SCD). ResultsWe identified up-and down-regulated proteins when comparing SCD with and without proteinuria. Amongst these is the well-established kidney injury marker-Clusterin which was up-regulated and could be validated in an ELISA-based assay. Refining the study to the SS and SC genotypes, we identified (and confirmed by ELISA) another established kidney injury marker-NGAL, as up-regulated in both genotypes and SCD with and without proteinuria. Metascape-based analysis of biological processes revealed "Cellular component disassembly" associated with proteins expressed in SCD but not regulated between PU and no PU and "leukocyte chemotaxis" down-regulated in SCD_PU vs. SCD. Interestingly, "Integrin-cell-surface interactions" was associated with proteins up-regulated between SCD_PU vs. SCD which is consistent with endothelial hyperplasia in the setting of glomerular hyperfiltration. To investigate the effect secreted urine proteins have on human podocytes in vitro, immortalized podocytes supplemented with SCD_PU urine showed elevated p53 levels in both immunofluorescence staining and RT-PCR compared to SCD. Additionally, RT-PCR revealed elevated levels of VEGF, NGAL and the pro-inflammatory proteins-TGF{beta}, IL6, IL8 and TNF. ConclusionWe hypothesize that the increased number of endothelial cells in hyperplasia and hyperfiltration leads to more Integrin-mediated links to podocyte foot processes at the glomerular basement membrane and to glomerular fibrosis. Severe inflammation and kidney injury in SCD_PU patients is induced by the TGF{beta}-p53 axis.

molecular biology↗

bioRxiv2025

Modelling APOL1-mediated kidney inflammation and fibrosis using a partially reprogrammed urine derived SIX2-positive renal progenitor cell line.

BackgroundCKD affects approximately 850 million people worldwide and is a leading cause of mortality. Podocytes, cells in the kidney are terminally differentiated and incapable of division in vivo making the establishment of primary cultures particularly challenging. The ability of cells to proliferate and avoid senescence is closely linked to telomere length. When telomere length becomes critically reduced, it results in cellular senescence. MethodsWe present the successful rejuvenation of a human SIX2-positive renal progenitor cell line derived from the urine of a 30-year-old West African male (UM30-OSN). To achieve partial reprogramming, plasmids expressing the Yamanaka factors OCT4, SOX2, NANOG, c-Myc, and KLF4 were employed. ResultsUM30-OSN expresses the pluripotency-associated marker SSEA4, renal stem cell markers such as SIX2, CD133 and CD24, determined by immunofluorescence, FACS and qPCR. Expression analysis revealed downregulation of senescence markers p21and p53 and upregulation of proliferation-associated genes PCNA, KI67 and TERT, confirming rejuvenation. Upon podocyte differentiation, UM30-OSN cells expressed podocyte-specific markers NPHS1, NPHS2, SYNPO and CD2AP. Comparative transcriptome analyses revealed a correlation co-efficiency (R2 = 0.88) with the immortal podocyte line AB 8/13. To demonstrate the usefulness of UM30-OSN to model APOL1-mediated kidney disease, we investigated the effects of Interferon-{gamma} (IFN-{gamma}) on UM30-OSN derived podocytes and evaluated the potential of the JAK1/JAK2 inhibitor Baricitinib to mitigate IFN-{gamma}-induced cellular responses. IFN-{gamma} stimulation resulting in increased phosphorylation of STAT1, activation of APOL1, upregulation of pro-inflammatory and fibrotic markers such as, IL-6, TGF-{beta}, Vimentin, Fibronectin, and morphological changes indicative of cell stress. Pre-treatment with Baricitinib effectively inhibited STAT1 phosphorylation, reduced expression of pro-inflammatory and fibrosis-associated genes, and preserved podocyte morphology. ConclusionGiven their robust proliferation capacity, UM30-OSN cells represent a valuable additional model for investigating kidney-associated diseases such the contribution of APOL1 high-risk variants to kidney injury and fibrosis.

molecular biology↗

bioRxiv2025

Human Urine-derived SIX2-positive renal progenitor cells improve kidney injury in an IRI mouse model

Cells with the characteristics of renal progenitor cells are shed in urine. The aim of this study was to investigate whether these SIX2-positive urine-derived renal progenitor cells (UdRPC) have therapeutic potential in treating or managing acute to chronic kidney injuries. Human UdRPC were obtained from a woman aged 35 years, expanded, and characterized in vitro and finally transplanted unilaterally under the renal capsule of mouse kidneys that had undergone ischemia reperfusion injury (IRI). Analyses of blood serum from the mice revealed that the transplanted human UdRPC transiently influenced the secretome of the animals by triggering the release of inflammatory and angiogenic factors. Of obvious therapeutic relevance, however, was the finding that the transplanted cells suppressed renal fibrosis resulting from IRI. The expression of genes linked to inflammation and chronic kidney disease was also reduced in mouse kidneys in the presence of UdRPC. Ultimately, the human UdRPC were able to alleviate the severity of the injury through the amelioration of fibrosis but were unable to restore complete kidney function within 21 days. Nevertheless, the findings of this study demonstrate a significant influence of transplanted UdRPC on kidney fibrosis after acute to chronic injury presumably via an altered secretome.

cell biology↗

bioRxiv2025

Evidence for conserved gene expression and biological processes operative in human podocytes and adult brain

BackgroundPodocytes are essential for the proper functioning of the glomerular filtration barrier and are characterized by their intricate structure which includes well-organized primary and secondary foot processes. The brain expresses podocyte-associated proteins such as Nephrin, and Synaptopodin which are well documented. Processing of information and inter-cellular communication between podocytes and neurons employ similar molecular mechanisms which include actin-based projections, adhesion molecules, and signaling pathways. MethodsIn this study, we analysed brain-associated biological processes, transcription factors and pathways significantly regulated in UdPodocytes, i.e. podocytes differentiated from SIX2-positive UdRPCs (urine-derived renal progenitor cells). We compared gene expression in iPSC-derived brain and kidney organoids with UdPodocytes and mapped the overlapping 344 genes to brain regions via the GTEX (Genotype-Tissue Expression) database and investigated their regulation induced by the mediator of the renin-angiotensin system-angiotensin II (ANG II) ResultsThe protein interaction network of UdPodocytes genes associated with brain in GTEX contains modules for pre-synapse, post-synapse, endocrine processes and neural crest differentiation. We also found that the genes overlapping between brain and podocytes are also expressed in iPSC-derived kidney and brain organoids and could map the involved genes to all regions of the brain with the frontal cortex as the most enriched. The genes SUZ12, NFKB1 and PAX2 were the most significantly over-represented transcription factors. We independently confirmed the conserved expression of PAX6, KCNQ3, TUJ1,MAP2, TAU and ACTN4 in Udpodocytes as shown by Western blotting, Immunofluorescence and RT-PCR. We further investigated if the conserved genes are also regulated by ANGII. This unveiled genes down-regulated upon ANGII-stimulation of Udpodocytes to be associated with axon guidance, Calcium, Hippo and cGMP-PKG signaling as over-represented pathways. ConclusionIn conclusion, we have identified 344 genes with overlapping expression in brain and podocytes. These are mainly associated with synaptic signaling and cell projections. This implies that human urine-derived SIX2-renal progenitor cells differentiated into podocytes can serve as a platform for dissecting and understanding the relevance of conserved biological processes in podocytes which are currently annotated as neuron projection, axons, neurogenesis and synaptic signaling.

molecular biology↗

bioRxiv2023

Cytokines in the Urine of AKI patients regulate TP53 and SIRT1 and can be used as biomarkers for the early detection of AKI

Acute kidney injury (AKI) is a major kidney disease with a poor clinical outcome. It is a common complication with an incidence of 10-15% of patients admitted to hospital. This rate even increases for patients who are admitted to the intensive care unit with an incidence of >50%. AKI is characterized by a rapid increase in serum creatinine, decrease in urine output, or both. Associated Symptoms include feeling sick or being sick, diarrhoea, dehydration, decreased urine output-although occasionally urine output remains normal, fluid retention-causing swelling in the legs or ankles, shortness of breath, fatigue and nausea. However, sometimes acute kidney injury causes no signs or symptoms and is detected by lab tests. Therefore, an urgent demand for non-invasive biomarkers for early detection of AKI are highly desirable. This might enable the prevention of the progression from AKI to CKD. In this study, we analysed the secretome of urine of an AKI patient cohort employing a kidney-biomarker cytokine assay. Based on these results we suggest, ADIPOQ, EGF and SERPIN3A as potential biomarkers, which might be able to detect AKI as soon as 24 h post-surgery. For the later stages, common biomarkers for the detection of AKI in both male and female patients we suggest, VEGF, SERPIN3A, TNFSF12, ANPEP, CXCL1, REN, CLU and PLAU. These markers in combination might present a robust strategy to identify the development of AKI as early as 24h or 72h post-surgery. Furthermore, we evaluated the effect of patient and healthy urine on human podocyte cells. We conclude that cytokines in the urine of AKI patients trigger processes which are needed to repair the damaged nephron and activate TP53 and SIRT1 to maintain the balance between proliferation, angiogenesis, and cell cycle arrest. In conclusion, the Renin-Angiotensin pathway seems to have major implications.

molecular biology↗

bioRxiv2022

Urine-based detection of biomarkers indicative of chronic kidney disease in a patient cohort from Ghana

Chronic kidney disease (CKD) is a global health burden with a continuously increasing prevalence associated with an increasing incidence of diabetes and hypertension in aging populations. The CKD definition of a more than three months lasting low glomerular filtration rate (GFR) or other renal impairments including proteinuria implies that multiple factors may contribute to the disease. While there are indications of ethnic differences it is hard to disentangle these from confounding social factors. Usually, CKD is detected in later stages of the disease when irreversible renal damage has already occurred, thus suggesting a need for early non-invasive diagnostic markers. In this study, we explored the urine secretome of a CKD patient cohort from Ghana employing a kidney-injury and a more general cytokine assay. We identified panels of kidney-specific cytokine markers which were also gender-specific and a panel of gender-independent cytokine markers. The gender-specific markers are IL10 and MME for male and CLU, RETN, AGER, EGFR and VEGFA for female. The gender-independent cytokine markers were APOA1, ANGPT2, C5, CFD, GH1, ICAM1, IGFBP2, IL8, KLK4, MMP9 and SPP1 (up-regulated) and FLT3LG, CSF1, PDGFA, RETN and VEGFA (down-regulated). APOA1 - the major component of HDL particles - was up-regulated in Ghanaian CKD patients and its co-occurrence with APOL1 in a subpopulation of HDL particles may point to specific CKD-predisposing APOL1 haplotypes in patients of African descent - this however needs further investigation. The identified panels may lay down the foundation for CKD-biomarker assays to be confirmed in further studies with a larger cohort of patients.

molecular biology↗

bioRxiv2022

Derivation of the immortalized cell line-UM51-PrePodo-hTERT and its responsiveness to Angiotensin II and activation of RAAS

Recent demographic studies predict there will be a considerable increase of elderly people within the next decades. Aging has been recognized as one of the main risk factors of the worlds most prevalent diseases, including neurodegenerative disorders, cancer, cardiovascular disease, and metabolic disease. During the process of aging a gradual loss of tissue volume and organ function is observed, which is partially caused by replicative senescence. The capacity of cellular proliferation and replicative senescence is tightly regulated by their telomere length. When the telomere length with progressive cell division is critically shortened, the cell becomes proliferative arrested and DNA damage response and cellular senescence are triggered. At this time point the so called "Hayflick limit" is attained. Podocytes are a cell type that is found in the kidney glomerulus where they have major implications in blood filtration. Mature podocytes are terminal differentiated cells that are unable to undergo cell division in vivo. For this reason, the establishment of podocyte cell cultures has been very challenging. In our present study, we present the successful immortalization of a human podocyte progenitor cell line, of which the primary cell cells were isolated directly from the urine of a 51-year-old male. The immortalized cell line has been cultured over the course of one year ([~]100 passages) with high proliferation capacity, while still endowed with contact inhibition and P53 expression and activation. Furthermore, by immunofluorescent-based expression and quantitative Real-Time PCR for the podocyte markers NPHS1, SYNPO and WT1 we confirmed the differentiation capacity of the immortalized cells. Finally, we evaluated and confirmed the responsiveness of the immortalized cells on the main mediator Angiotensin II (ANGII) of the renin-angiotensin-system (RAS). Elevated levels of ANGII have been identified as a main risk factor for the initiation and progression of chronic kidney disease (CKD). CKD is characterized by an impairment of podocyte function and subsequently podocyte apoptosis. As a major risk factor for patients to develop CKD, diabetes, hypertension, heart disease and stroke have been recognized - all of which show increased incidence in elderly people. In conclusion, we have shown that it is possible to by-pass cellular replicative senescence (Hayflicks limit) by TERT-driven immortalization of human urine-derived pre-podocyte cells from a 51-year-old African male.

cell biology↗