Deep learning on electronic medical records identifies distinct subphenotypes of diabetic kidney disease driven by genetic variations in the Rho pathway.

Kidney disease affects 50% of all diabetic patients; however, prediction of disease progression has been challenging due to inherent disease heterogeneity. We use deep learning to identify novel genetic signatures prognostically associated with outcomes. Using autoencoders and unsupervised clustering of electronic health record data on 1,372 diabetic kidney disease patients, we establish two clusters with differential prevalence of end-stage kidney disease. Exome-wide associations identify a novel variant in ARHGEF18, a Rho guanine exchange factor specifically expressed in glomeruli. Overexpression of ARHGEF18 in human podocytes leads to impairments in focal adhesion architecture, cytoskeletal dynamics, cellular motility, and RhoA/Rac1 activation. Mutant GEF18 is resistant to ubiquitin mediated degradation leading to pathologically increased protein levels. Our findings uncover the first known disease-causing genetic variant that affects protein stability of a cytoskeletal regulator through impaired degradation, a potentially novel class of expression quantitative trait loci that can be therapeutically targeted.

Electromagnetic Fields Generated by the IteraCoil Device Differentiate Mesenchymal Stem Progenitor Cells Into the Osteogenic Lineage.

Rapid advances in mesenchymal stem progenitor cells (MSPCs) have rendered impetus into the area of cell therapy and regenerative medicine. The main promise of future stem cell therapies is their reliance on autologous stem cells derived from adipose tissue, which also includes treatments of bone fractures and degeneration. The effectiveness of different electric devices utilized to reprogram MSPCs toward osteogenic differentiation has provided varying degrees of effectiveness for clinical use. Adipose tissue-derived MSPCs were flow-cytometrically characterized and further differentiated into osteoblasts by culturing either in growth medium with pro-osteogenic supplements or without supplements with alternating electromagnetic field (EMF) generated by IteraCoil. IteraCoil is a multi-solenoid coil with a specific complex geometry that creates a 3D-EMF with desired parameters without directly applying electrodes to the cells and tissues. The flow-cytometric analysis of highly enriched (≥95%) adipose-derived MSPCs (CD34- , CD73+ , CD90+ , and CD105+ ) was utilized for the study. Osteoblasts and chondrocyte differentiations were then assessed by specific staining and quantified using ImageJ (National Institutes of Health). The osteoblastic differentiation of MSPCs cultured in regular medium and exposed to EMF at 0.05 and 1 kHz frequencies was compared with MSPCs cultured in a pro-osteogenic supplemented medium. In this study, we demonstrated that EMF from IteraCoil might have affected the signaling pathways that induce the osteogenic differentiation of human adipose-derived MSPCs in the absence of exogenous osteogenic factors. Therefore, EMF-generated osteogenic differentiation of reprogrammed adipose-derived autologous MSPCs may treat the loss of osteoblasts and osteoporosis and open new avenues for the development of regenerative cellular therapy. © 2022 Bioelectromagnetics Society.

Prothymosin α variants isolated from CD8+ T cells and cervicovaginal fluid suppress HIV-1 replication through type I interferon induction.

Soluble factors from CD8(+) T cells and cervicovaginal mucosa of women are recognized as important in controlling human immunodeficiency virus type 1 (HIV-1) infection and transmission. Previously, we have shown the strong anti-HIV-1 activity of prothymosin α (ProTα) derived from CD8(+) T cells. ProTα is a small acidic protein with wide cell distribution, to which several functions have been ascribed, depending on its intracellular or extracellular localization. To date, activities of ProTα have been attributed to a single protein known as isoform 2. Here we report the isolation and identification of 2 new ProTα variants from CD8(+) T cells and cervicovaginal lavage with potent anti-HIV-1 activity. The first is a splice variant of the ProTα gene, known as isoform CRA_b, and the second is the product of a ProTα gene, thus far classified as a pseudogene 7. Native or recombinant ProTα variants potently restrict HIV-1 replication in macrophages through the induction of type I interferon. The baseline expression of interferon-responsive genes in primary human cervical tissues positively correlate with high levels of intracellular ProTα, and the knockdown of ProTα variants by small interfering RNA leads to downregulation of interferon target genes. Overall, these findings suggest that ProTα variants are innate immune mediators involved in immune surveillance.

Ha-Ras stabilization mediates pro-fibrotic signals in dermal fibroblasts.

BACKGROUND: Scleroderma (systemic sclerosis; SSc) is a clinically heterogeneous and often lethal acquired disorder of the connective tissue that is characterized by vascular, immune/inflammatory and fibrotic manifestations. Tissue fibrosis is the main cause of morbidity and mortality in SSc and an unmet medical challenge, mostly because of our limited understanding of the molecular factors and signalling events that trigger and sustain disease progression. Recent evidence has correlated skin fibrosis in SSc with stabilization of proto-oncogene Ha-Ras secondary to auto-antibody stimulation of reactive oxygen species production. The goal of the present study was to explore the molecular connection between Ha-Ras stabilization and collagen I production, the main read-out of fibrogenesis, in a primary dermal fibroblast culture system that replicates the early stages of disease progression in SSc. RESULTS: Forced expression of proto-oncogene Ha-Ras in dermal fibroblasts demonstrated the promotion of an immediate collagen I up-regulation, as evidenced by enhanced activity of a collagen I-driven luciferase reporter plasmid and increased accumulation of endogenous collagen I proteins. Moreover, normal levels of Tgfß transcripts and active transforming growth factor-beta (TGFß) implied Ha-Ras stimulation of the canonical Smad2/3 signalling pathway independently of TGFß production or activation. Heightened Smad2/3 signalling was furthermore correlated with greater Smad3 phosphorylation and Smad3 protein accumulation, suggesting that Ha-Ras may target both Smad2/3 activation and turnover. Additional in vitro evidence excluded a contribution of ERK1/2 signalling to improper Smad3 activity and collagen I production in cells that constitutively express Ha-Ras. CONCLUSIONS: Our study shows for the first time that constitutively elevated Ha-Ras protein levels can directly stimulate Smad2/3 signalling and collagen I accumulation independently of TGFß neo-synthesis and activation. This finding therefore implicates the Ha-Ras pathway with the early onset of fibrosis in SSc and implicitly identifies new therapeutic targets in SSc.