👤 Michael Lindsey

Type 2 diabetes (T2D) is a complex metabolic disorder driven by genetic and environmental factors. While genome-wide association studies (GWAS) have identified numerous T2D-associated variants, many remain functionally uncharacterized. Integration of GWAS with molecular phenotyping offers a path to revealing biological relevance. We investigated the influence of GWAS-variants, including sub-threshold T2D-associated variants (GWAS p-value ≤ 0.0001), on gene and protein expression to assign functional relevance. Genetic variants associated with T2D in the GWAS Catalog and present in our whole-genome sequencing (WGS) data were used to perform expression quantitative trait loci (eQTL) analysis in 242 whole-blood mRNA-sequenced samples. The same variants were used to perform protein quantitative trait loci (pQTL) analysis in a set of 362 plasma samples profiled on the Olink platform. For each analysis, the datasets were randomly split into discovery and validation subsets. Associations between variants and mRNA or protein levels were tested by multiple linear regression, and only QTLs that reached a false discovery rate adjusted p-value ≤ 0.05 in the discovery dataset and replicated in the validation dataset (p ≤ 0.05) with same direction of effect were carried forward. QTL-linked mRNAs and proteins were subsequently evaluated for their relationship with T2D status to connect them with T2D pathophysiology. We identified 1,291 eQTLs linked to 97 mRNAs and 1,273 pQTLs linked to 22 proteins. Among these, 10 mRNAs and 5 proteins were differentially expressed between non-diabetic and diabetic individuals. Notably, LPL, APOBR, APOM (lipid metabolism), NOTCH2, TREH (β-cell/endocrine regulation), and HLA-A, OAS3 (immune response) converged on three biological axes central to T2D pathophysiology. The directionality of molecular effects was consistent with known disease mechanisms, including insulin resistance (LPL, APOBR), β-cell stress (TREH, NOTCH2), and chronic inflammation (OAS3). Our findings indicate that variants falling below conventional GWAS significance thresholds can have demonstrable effects on gene expression and protein levels. This underscores the importance of prioritizing biological relevance alongside statistical significance, rather than relying solely on rigid p-value cutoffs. Show less

The claudin (Cldn) family comprises 27 members of 20 to 34 kDa transmembrane tight junction proteins. In addition to Cldns' established canonical role as barriers controlling paracellular flow of molecules, a distinct noncanonical role for them as mediators of cell signaling is now emerging. In our studies evaluating Cldn family expression levels during osteoblast differentiation, Cldn-11 showed the largest increase (60-fold). Immunohistochemistry studies revealed high Cldn-11 expression in trabecular (Tb) bone lining cells. Micro-CT analysis of femurs and vertebrae of Cldn-11 knock-out (KO) mice at 12 weeks of age exhibited a 40% (p < 0.01) reduction in Tb bone volume adjusted for tissue volume compared with control mice, a change caused by significant reductions in Tb number and thickness and increase in Tb separation. Histomorphometry and serum biomarker studies revealed that reduced bone formation, not increased resorption, is the cause for reduced Tb bone volume in the Cldn-11 KO mice. Cldn-11 KO osteoblasts expressed reduced ALP and BSP, whereas Cldn-11 overexpression in MC3T3-E1 cells increased expression of ALP and BSP. Mechanistically, Cldn-11 interacted with tetraspanin (Tspan)3 in osteoblasts, and Tspan3 knockdown reduced osteoblast differentiation. Because members of the Tspan family regulate cell functions via Notch signaling, we evaluated whether Cldn-11/Tspan3 regulates Notch signaling in osteoblasts. Accordingly, Notch targets Hey1 and Hey2 were significantly upregulated in Cldn-11 overexpressing cultures but downregulated in both Cldn-11 KO and Tspan3 knockdown osteoblasts. Because ADAM10 has been shown to interact with Tspan family members to regulate Notch signaling, we evaluated whether Cldn-11 regulates ADAM10 expression. Cldn-11 overexpressing cells express more mature ADAM10, and an ADAM10 inhibitor blocked the Cldn-11 effect on osteoblast differentiation. Based on these data, we propose Cldn-11 as a novel component of an osteoblast cell surface protein complex, comprising Tspan3 and ADAM10, which regulates Notch signaling and cell differentiation. © 2019 American Society for Bone and Mineral Research. Show less

PURPOSE. Jeune's asphyxiating thoracic dystrophy (JATD) is an autosomal recessive disorder with symptoms of retinal degeneration, kidney cysts, and chondrodysplasia and results from mutations in the ift80 gene. This study was conducted to characterize zebrafish lacking ift80 function for photoreceptor degeneration and defects in ciliogenesis to establish zebrafish as a vertebrate model for visual dysfunction in JATD and to determine whether ift80 interacts genetically with Bardet-Biedl syndrome (BBS) genes. METHODS. Zebrafish were injected with morpholinos (MOs) targeted to the ift80 gene. Retinas were analyzed by histology, transmission electron microscopy, and immunohistochemistry. Ear and kidney cilia were analyzed by whole-mount immunostaining. Intraflagellar transport (IFT) particle composition was subjected to Western blot analysis. Genetic interactions were tested by coinjection of MOs against ift80 and bbs4 or bbs8 followed by in situ hybridization. RESULTS. Zebrafish lacking ift80 function exhibited defects in photoreceptor outer segment formation and photoreceptor death. Staining with opsin antibodies revealed opsin mislocalization in both rods and cones. Ultrastructural analysis showed abnormal disc stacking and shortened photoreceptor outer segments. The kinocilia of the ear and motile cilia in the kidney were shorter and reduced in number. Western blot analysis revealed a slight increase in the stability of other IFT proteins. Coinjection of MOs against ift80 and BBS genes led to convergent-extension defects. CONCLUSIONS. Zebrafish lacking ift80 exhibited defects characteristic of JATD. Because the developing outer segments degenerated, Ift80 could possibly act as a maintenance factor for the IFT particle. Show less