Biology subjects

Mehta, B.

Publications and source records attributed to Mehta, B..

5 recordsLinked to original sources

bioRxiv2026

Integrated transcriptomic and epigenomic profiling of human cartilage reveals coordinated changes in fibronectin expression, splicing, and receptor signaling during osteoarthritis progression

Osteoarthritis (OA) is defined by progressive loss of articular cartilage, but how chondrocytes change as the disease advances is unclear because most studies have focused on end-stage tissue. We profiled human knee articular cartilage across the full range of macroscopic OA grade, from young healthy to aged severe OA donors, by bulk RNA sequencing of 92 knees, single-nucleus RNA sequencing of 108,600 chondrocyte nuclei from 30 donors and single-nucleus multiome sequencing of 24 of these donors, treating grade as a continuous variable. With increasing grade, cartilage increased extracellular matrix (ECM) synthesis and remodeling genes, lost glucocorticoid-responsive, lipid-metabolic and antioxidant programs, and changed the splicing of a small set of ECM transcripts, led by the extra domain B (EDB) exon of fibronectin (FN1). Nine chondrocyte clusters were present in every disease stage and formed a continuum ordered by cartilage zone and hypertrophic differentiation, with PRG4+ superficial and COL10A1+ hypertrophic chondrocytes as the only distinct cell types at its ends and a pre-hypertrophic state between them. With grade, all clusters shared a response in which ECM production rose and homeostatic programs fell, and they differed in which of its components was strongest: ECM production in the superficial cells, the secretory pathway in the hypertrophic and CYTL1+ cells, and inflammatory signaling in the ANXA1+ and CRISPLD2+ cells. Inferred communication between chondrocytes was remodeled with stage. FN1 was induced in every cluster in excess of its fibril-assembly machinery, together with the fibronectin-cleaving protease HTRA1, and FN1 signaling shifted in receptor use from integrin 5{beta}1 toward CD44 and, less robustly, v{beta}8, accompanied by a rise in TGF-{beta}/SMAD response genes. In four early-OA donors, tenascin-C was already largely induced and the FN1 receptor shift from 5{beta}1 toward CD44 was partly present, whereas the rise of FN1 outside superficial chondrocytes, of FGF1 and of developmental and ossification programs came with progression. Chromatin accessibility changed in the same direction across clusters, with regions linked to FN1 opening and regions linked to ITGA5 closing. OA progression in human cartilage therefore appears to be a change of chondrocyte state that differs in emphasis along a zonal and hypertrophic continuum and includes changes in fibronectin regulation, production, processing, and receptor engagement.

bioinformatics↗

bioRxiv2026

Single-nucleus multiome profiling reveals osteocyte-centered remodeling of human subchondral bone across osteoarthritis severity

Objective: Subchondral bone remodeling is a hallmark of osteoarthritis (OA), but osteocytes, the principal regulators of bone homeostasis, have been inaccessible to single-cell studies because they are embedded in mineralized matrix. We aimed to define the cellular, transcriptional and chromatin changes of human subchondral bone across OA severity, osteocytes included, and to identify candidate signals between cartilage and bone. Design: Subchondral bone from the medial femoral condyle of human knees graded by the Outerbridge system was analyzed by bulk RNA sequencing (89 knees) and by single-nucleus multiome sequencing of gene expression and chromatin accessibility after mechanical nuclear isolation (16 donors). Three hypotheses were prespecified: with increasing OA severity, (1) the osteoprogenitor fraction increases, (2) the osteocyte fraction increases, and (3) osteocyte SMAD2/3 motif activity increases. Results: With OA severity, bulk expression shifted toward extracellular matrix and ossification programs. The atlas resolved 26 cell states among 61,570 nuclei, including 906 osteocytes. Osteoprogenitors (p = 0.003) and osteocytes (p = 0.036) increased in share along an osteogenic continuum that starts from CXCL12-abundant reticular cells. Chondrocytes at the osteochondral junction upregulated FN1, FGF1, FGF2 and TNFSF11 without increased hypertrophic gene expression, and their share of the inferred FN1 signal received by osteocytes rose from 4% in normal knees to 33% in severe OA. Osteocyte SMAD2/3 motif activity increased with severity (rho = 0.70, p = 0.003), and all three hypotheses remained significant after Holm correction. Across the osteogenic lineage, SMAD2/3 activity correlated with junction chondrocyte FN1 (rho = 0.63, p = 0.017), and in osteocytes it was accompanied by TGF-{beta}-responsive matrix genes and perilacunar-remodeling genes. Conclusions: This osteocyte-inclusive atlas of human OA subchondral bone shows expansion of the osteogenic compartment and a rise of osteocyte SMAD2/3-linked matrix remodeling with disease, and identifies chondrocyte-derived FN1 as a candidate contributor to cartilage-bone communication associated with osteocyte TGF-{beta}/SMAD2/3 signaling.

molecular biology↗

bioRxiv2026

Synovial transcriptional clusters link cartilage degeneration to cell-type-specific gene expression in knee osteoarthritis

ObjectivesTo identify synovial transcriptional clusters in human knee osteoarthritis (OA) and determine how these relate to synovial histologic features, cell-type-associated gene expression, and cartilage degeneration severity. MethodsBulk RNA sequencing (RNA-seq) of synovial tissue from n = 135 patients with knee OA was analyzed using consensus clustering. Clusters were compared by clinical and histologic features, including cartilage degeneration severity (OARSI score). Single-cell RNA-seq (n = 18) and spatial transcriptomics were used to relate cartilage degeneration-associated gene expression patterns to synovial cell populations. ResultsFour synovial transcriptional clusters that differed in synovial histologic features and cartilage degeneration severity were identified. Greater cartilage degeneration was associated with enrichment of lining fibroblast- and inflammatory myeloid-associated gene expression, whereas lesser cartilage degeneration was associated with enrichment of sublining fibroblast, endothelial, mural cell, and adipocyte-associated gene expression. ConclusionsHuman knee OA synovium segregates into transcriptional clusters associated with cartilage degeneration severity. Synovial transcriptional heterogeneity corresponds to cell-type-associated gene expression. Key messagesO_ST_ABSWhat is already known on this topicC_ST_ABSO_LIOsteoarthritis synovium exhibits marked histologic and molecular heterogeneity. C_LIO_LISynovial inflammation detected by MRI correlates with cartilage degeneration and predicts progressive cartilage loss in knee OA. C_LIO_LIPrior transcriptomic studies have identified molecular subsets of OA synovium, but their relationship to cartilage degeneration severity remains unclear. C_LI What this study addsO_LIOA synovium segregates into four transcriptional clusters: Sublining (C1), Lymphomyeloid (C2), Myeloid (C3), and Major trauma (C4). C_LIO_LIGreater cartilage degeneration is associated with enrichment of inflammatory myeloid and lining fibroblast gene expression, whereas lesser degeneration is associated with enrichment of adipocyte, sublining fibroblast, endothelial, and mural cell-associated gene expression. C_LI How this study might affect research, practice or policyO_LIProvides a framework for a clinically relevant biological stratification of OA patients based on synovial molecular features. C_LIO_LIInforms future efforts to link synovial biology with OA prognosis, cartilage degeneration, treatment allocation, and development of targeted therapeutic strategies. C_LI

genomics↗

bioRxiv2023

Aging-related changes in expression and function of glutamate transporters in rat spinal cord astrocytes

Astrocytes are abundant and heterogeneous cell types in the CNS [1]. They promote neuronal health and survival and protect neurons from glutamate-induced excitotoxicity. In the spinal cord, astrocytes are present in both the dorsal horn (DH) and ventral horns (VH). However, only motor neurons in the VH are highly vulnerable to glutamate excitotoxicity. We hypothesize that the preferential vulnerability of motor neurons may underlie their spatial confinement to the VH, where astrocytes are differentially equipped with glutamate-handling machinery. With aging, glutamate excitotoxicity increases, suggesting compromised astrocytic glutamate handling. We tested our hypotheses by comparing astrocytic morphology, expression of glutamate transporters, and glutamate uptake function in the DH and VH using immunohistochemical staining, western blotting, and whole-cell patch-clamp electrophysiology. We found a global reduction in the numerical density and astroglial coverage in the spinal cord, with a prominent decline in the VH with aging. Astrocytic glutamate transporters, Excitatory amino acid transporter 1 (EAAT1) and Excitatory amino acid transporter 2 (EAAT2), show an overall reduction in expression with aging, with a more progressive decrease in the VH than DH. We performed whole-cell patch-clamp studies on DH and VH astrocytes to assess the functional outcome of the altered expression of EAATs with aging. Both VH and DH astrocytes showed a dramatic decline in glutamate uptake currents with aging, suggesting compromised glutamate handling in aging astrocytes. Our study suggests that astrocytes in the DH and VH undergo differential changes with aging, exhibiting compromised glutamate handling properties, which may be one of the key contributors to the late onset of neurodegenerative disorders.

neuroscience↗

bioRxiv2018

Novel KCNJ10 mutation identified in a SeSAME family compromise channel function and impairs Drosophila locomotor behavior

Dysfunction in inwardly-rectifying potassium channel Kir4.1 has been implicated in SeSAME syndrome, an autosomal-recessive (AR), rare, multi-systemic disorder. However, not all neurological, intellectual disability and comorbid phenotypes in SeSAME syndrome can be mechanistically linked solely to Kir4.1 dysfunction. We therefore performed whole exome sequencing and identified additional genetic risk-elements that might exert causative effects either alone or in concert with Kir4.1 in a family diagnosed with SeSAME syndrome. Two variant prioritization pipelines based on AR inheritance and runs of homozygosity (ROH), identified two novel homozygous variants in KCNJ10 and PI4KB and five rare homozygous variants in PVRL4, RORC, FLG2, FCRL1, NIT1 and one common homozygous variant in HSPA6 segregating in all four patients. The novel mutation in KCNJ10 resides in the cytoplasmic domain of Kir4.1, a seat of phosphatidyl inositol bisphosphate (PIP2) binding. The mutation altered the subcellular localization and stability of Kir4.1 in patient-specific lymphoblastoid cells (LCLs) compared to parental controls. Barium-sensitive endogenous K+ currents in patient-specific LCLs using whole-cell patch clamp electrophysiology revealed membrane depolarization and defects in inward K+ ion conductance across the membrane, thereby suggesting a loss-of-function effect of KCNJ10 variant. Altogether our findings implicate the role of new genes in SeSAME syndrome without electrolyte imbalance and thereby speculate the regulation of Kir4.1 channel activity by PIP2 and integrin-mediated adhesion signaling mechanisms.

neuroscience↗