Biology subjects

Somlo, S.

Publications and source records attributed to Somlo, S..

6 recordsLinked to original sources

bioRxiv2025

A T-cell Intrinsic Role for APOL1 Risk Alleles in Allograft Rejection

African Americans have an increased risk of kidney disease due to exonic variants in Apolipoprotein-L1 (G1 and G2). These prevalent variants have also been linked with kidney rejection, but outside of association with African ancestry, underpinning causal mechanisms are unknown. We investigated T-cell function using transgenic mice with physiologic expression of wild type (G0-), G1-, or G2-APOL1. Mice with variant APOL1 showed greater CD8+T-cell activation with expansion of a central memory (TCM) subset. Stimulated G1-CD8+T-cells showed enhanced proliferation and cytokine production, which reversed with APOL1 inhibition. In MHC-mismatched cardiac transplants, G1-mice demonstrated greater CD8+T-cell infiltration and reduced survival. Bulk transcriptome of G1-CD8+T-cells, and single-cell transcriptome of graft infiltrating TCMs, showed enrichment of canonical T-cell receptor (TCR) pathways including Ca2+-signaling. G1-CD8+T-cells demonstrated baseline ER-Ca2+ depletion followed by sustained increases in cytosolic-Ca2+ upon TCR stimulation. G1-CD8+T-cells were more sensitive to Ca2+ chelation, or store-operated Ca2+ entry inhibition, and relatively resistant to calcineurin antagonism vs. G0-CD8+T-cells. Analogously, in a kidney transplant cohort, APOL1-variant recipients developed rejection when they had elevated peripheral TCMs before transplantation and despite significantly higher tacrolimus levels vs G0/G0-AAs with rejection. In summary, we unravel an excitatory T-cell intrinsic mechanism for APOL1 exonic variants, causally linking them with kidney rejection.

immunology↗

bioRxiv2025

Glis3 is a modifier of cyst progression in autosomal dominant polycystic kidney disease

BackgroundAutosomal dominant polycystic kidney disease (ADPKD) is caused by mutations affecting polycystin-1 (PC1) or -2 (PC2). The existence of a cilia-dependent cyst activation (CDCA) pathway has been identified by demonstrating that structurally intact primary cilia are crucial for cyst growth following loss of polycystins. We previously used translating ribosome affinity purification (TRAP) RNA-Seq on pre- cystic mouse kidneys to determine the translatome that meet the criteria for CDCA and identified Glis2 as an early effector of polycystin signaling. Here, we investigate the potential role of Glis3 in ADPKD, which, while not transcriptionally altered, encodes a cilia-localized transcription factor belonging to the same family of genes as Glis2. MethodsWe used live cell confocal imaging to study the subcellular localization of Glis3 in the presence or absence of Pkd1. We used Glis3 conditional knockout mice to investigate the genetic interaction between Glis3 and Pkd1. Changes in gene expression and chromatin accessibility were assessed by RNA-Seq and ATAC-Seq on an allelic series of Glis3 and Pkd1 kidney selective inactivation models at 7-weeks age to evaluate the function of Glis3. ResultsThe ciliary localization of Glis3 is not affected by Pkd1 mutation status. Kidney selective Glis3 by itself does not affect kidney structure or function, but dual inactivation of Glis3 and Pkd1 significantly worsen polycystic kidney disease. Integration of transcriptomic profiling and chromatin accessibility assays suggested that kidney tubule specific Glis3 inactivation results in dysregulated fatty acid metabolism and circadian. ConclusionsGlis3 is a primary cilium localized transcription factor that genetically interacts with Pkd1 and modifies kidney epithelial cell metabolism and circadian function.

genetics↗

bioRxiv2025

Polycystin-1 acts as an atypical adhesion GPCR that responds to novel Wnt signaling and mechanical stimuli

Mutations in the genes encoding Polycystin-1 and 2 cause autosomal dominant polycystic kidney disease (ADPKD). These proteins cellular functions and the mechanisms through which their absence causes disease are unknown. We find that the behavior of the 11 transmembrane domain polycystin-1 protein resembles that of an adhesion G protein-coupled receptor when activated by Wnt ligands. Exposure to Wnt ligands causes shedding of the polycystin-1 N terminal region, exposing a tethered agonist that activates G protein-dependent functions of the membrane-associated C terminal fragment. Activated polycystin-1 communicates through G13 to activate RhoA, leading in turn to the ROCK-dependent phosphorylation and inactivation of GSK3{beta}. Activated polycystin-1 traffics out of the primary cilium through an arrestin-dependent mechanism, and arrestin involvement is required for signaling to occur. These data elaborate a function for polycystin-1 that is structurally non-canonical and that is directly connected to pathways whose perturbation results in cystic disease. SummaryThe polycystin-1 protein can activate a signaling pathway resembling those employed by non-canonical adhesion G protein coupled receptors, which is induced by Wnt9b binding and which leads to leads to inhibition of the GSK3{beta} kinase and removal of polycystin-1 from the primary cilium. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/655326v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@1b32dc1org.highwire.dtl.DTLVardef@80ee43org.highwire.dtl.DTLVardef@9aa441org.highwire.dtl.DTLVardef@95ceb1_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract PC1 resides at baseline in the primary cilium. PC1 behaves as an aGPCR that responds to Wnt9b and to flow-induced ATP release by departing from the cilium and initiating the inhibition of GSK3. The schematic diagram presents a model that integrates the findings presented here. Wnt9b binding to the PC1 NTF leads to shedding of the NTF, exposing the tethered agonist to activate the PC1 receptor-mediated signaling cascade, which involves triggering G13 binding and the subsequent nucleotide exchange and GTP-loading of RhoA. GTP-bound RhoA stimulates the kinase activity of ROCK, which phosphorylates and inhibits GSK3. C_FIG

cell biology↗

bioRxiv2025

Anks3 mediates cilia dependent polycystin signaling and is essential for adult kidney homeostasis

The existence of a cilia-dependent cyst activation (CDCA) pathway underlying autosomal dominant polycystic kidney disease was identified by showing that cyst progression following loss of polycystins is significantly suppressed by removal of structurally intact cilia. We applied translating ribosome affinity purification RNASeq on pre-cystic mouse kidneys to determine a cell-autonomous in vivo translatome associated with CDCA and identified Glis2 as an early effector of polycystin signaling. Here, to discover additional components of CDCA, we used polycystin-dependent Glis2 expression as a functional readout and identified Anks3, from the CDCA pattern translatome, as a candidate cytosolic regulator of polycystin signaling. Anks3 regulates polycystin-dependent Glis2 expression both in vitro and in vivo. Anks3 also undergoes polycystin-dependent changes in phosphorylation state. Inactivation of Anks3 in Pkd1 mouse models suppresses cyst progression, but also results in rapidly progressive kidney injury independent of polycystins. Anks3 inactivation also normalizes a broader spectrum of polycystin-dependent CDCA translatome changes. These findings define Anks3 as a central regulator of cilia dependent polycystin signaling, functioning downstream of cilia and polycystins and upstream of Glis2, and show that Anks3 has broader functions in maintaining renal structural and functional homeostasis.

genetics↗

bioRxiv2025

PERADIGM: Phenotype Embedding Similarity-based Rare Disease Gene Mapping

Identifying genes associated with rare diseases remains challenging due to the scarcity of patients and the limited statistical power of traditional association methods. Here, we introduce PERADIGM (Phenotype Embedding similarity-based RAre DIsease Gene Mapping), a novel framework that leverages natural language processing techniques to integrate comprehensive phenotype information from electronic health records for rare disease gene discovery. PERADIGM employs an embedding model to capture relationships between ICD-10 codes, providing a nuanced representation of individual phenotypes. By utilizing patient similarity scores, it enhances the identification of candidate genes associated with disease-specific phenotypes, surpassing conventional methods that rely on binary disease status. We applied PERADIGM to the UK Biobank dataset for three rare diseases: autosomal dominant polycystic kidney disease (ADPKD), Marfan syndrome, and neurofibromatosis type 1 (NF1). PERADIGM identified additional candidate genes associated with ADPKD-related and Marfan syndrome-related phenotypes, some of which are supported by existing literature, and demonstrated enhanced signal detection for NF1-specific phenotypes beyond traditional methods. Our findings demonstrate the potential of PERADIGM to identify genes associated with rare diseases and related phenotypes by incorporating phenotype embeddings and patient similarity, providing a powerful tool for precision medicine and a deeper understanding of rare disease genetics and clinical manifestations.

genetics↗

bioRxiv2021

The C-terminal tail of polycystin-1 suppresses cystic disease in a mitochondrial enzyme-dependent fashion

Autosomal dominant polycystic kidney disease (ADPKD) is the most prevalent potentially lethal monogenic disorder. Approximately 78% of cases are caused by mutations in the PKD1 gene, which encodes polycystin-1 (PC1). PC1 is a large 462-kDa protein that undergoes cleavage in its N and C-terminal domains. C-terminal cleavage produces fragments that translocate to mitochondria. We show that transgenic expression of a protein corresponding to the final 200 amino acid residues of PC1 in a Pkd1-KO orthologous murine model of ADPKD dramatically suppresses cystic phenotype and preserves renal function. This suppression depends upon an interaction between the C-terminal tail of PC1 and the mitochondrial enzyme Nicotinamide Nucleotide Transhydrogenase. This interaction modulates tubular/cyst cell proliferation, the metabolic profile, mitochondrial function and the redox state. Together, these results suggest that a short fragment of PC1 is sufficient to suppress cystic phenotype and open the door to the exploration of gene therapy strategies for ADPKD.

physiology↗