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JCI Insight

American Society for Clinical Investigation

All preprints, ranked by how well they match JCI Insight's content profile, based on 277 papers previously published here. The average preprint has a 0.28% match score for this journal, so anything above that is already an above-average fit. Older preprints may already have been published elsewhere.

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Integrated transcriptomic and proteomic analyses identify novel biomarkers of bladder outlet obstruction

Bigger-Allen, A. A.; Das, B.; Tang, Y.; Costa, K.; Ocampo, G.-L.; Hashemi Gheinani, A.; DiMartino, S.; Kaull, J.; Froehlich, J.; Lee, R. S.; Adam, R.

2026-05-04 bioinformatics 10.64898/2026.04.29.721732 medRxiv
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Bladder outlet obstruction leads to pathological remodeling and emergence of lower urinary tract symptoms. Although relief of obstruction is associated with symptomatic improvement, it is not universally successful, reflecting persistent alterations in the bladder. Reliable surrogate biomarkers of obstruction are lacking, particularly early in the disease course before irreversible damage to the bladder may have occurred. In this study, re-analysis of publicly available transcriptomic datasets from diverse rodent models of obstruction identified tissue transcripts including Cthrc1, Grem1, Ltbp2 and Msn that were induced in response to injury. Candidate markers were validated experimentally in an independent model of neurogenic obstruction demonstrating time-dependent changes. Candidate markers were also attenuated with either surgical removal of obstruction or treatment with anticholinergic medication or inosine. Integrated analysis of tissue transcriptomics data and tissue and urine proteomics data from a model of neurogenic obstruction revealed significant concordance between markers observed in tissue and urine. Urinary proteomics analysis identified a statistically significant increase in MSN in patients with neurogenic bladder compared to unaffected controls. These findings identify tissue and urine biomarkers of both non-neurogenic and neurogenic obstruction that may reflect early changes in obstructive uropathy that could be monitored in a non-invasive manner.

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Serum proteomic atlas reveals distinct molecular signatures of lupus nephritis activity, chronicity, and treatment response

Lu, R.; Wagner, C. A.; Fava, A.; Jones, B.; Izmirly, P.; Belmont, H. M.; Clancy, R. M.; Anolik, J.; Barnas, J. L.; Putterman, C.; Wofsy, D.; Weisman, M. H.; Davidson, A.; Fine, D. M.; Holers, V. M.; Utz, P. J.; Accelerating Medicines Partnership in RA/SLE Network, ; diamond, b.; Buyon, J.; Petri, M.; Guthridge, J. M.; James, J. A.

2026-05-12 immunology 10.64898/2026.05.08.723858 medRxiv
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Lupus nephritis (LN), a severe manifestation of systemic lupus erythematosus (SLE), features heterogeneous renal pathology and reliance on invasive biopsies for diagnosis, prognosis, and treatment selection. Current peripheral clinical markers inadequately capture disease activity and progression. Here, we performed comprehensive serum proteomic profiling of over 5,000 proteins in the large, longitudinal Accelerating Medicines Partnership Rheumatoid Arthritis/SLE cohort of 270 LN patients and 63 healthy controls. Machine learning identified distinct molecular signatures that classified LN versus controls, differentiated histological classes, and delineated activity- and chronicity-associated pathways, including inflammatory cytokine, PI3K/AKT, TGFb, and complement/coagulation pathways. An increase in VSIG4, CD27, HAVCR1, and LAIR1 consistently emerged as top biomarkers across multiple clinical contexts, and early decreases in these markers at 3 months were associated with complete treatment response at 1 year. By resolving coordinated serum protein modules linked to key inflammatory, PI3K/AKT, TGFb, and complement pathways, these signatures mechanistically connect circulating proteomic perturbations to intrarenal immune activation, tissue injury, and repair in LN. These findings demonstrate that serum proteomics reflect complex intrarenal immunopathology and offer a promising noninvasive "liquid biopsy" approach to refine LN classification and guide personalized management, potentially reducing the need for repeated invasive biopsies and improving therapeutic decision-making.

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The Function of Efhd1+ Telocytes in the Synovial Lymphatic System and Inflammatory-Erosive Arthritis

Peng, Y.; Kenney, H. M.; Lydon, S.; de Mesy Bentley, K. L.; Xing, L.; Korman, B.; Ritchlin, C.; Schwarz, E.

2025-11-05 cell biology 10.1101/2025.11.03.685859 medRxiv
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Resting collecting lymphatic vessels (cLVs) sense edema in distal joints and initiate contractions via unknown mechanisms. Rheumatoid arthritis (RA) patients have lymphatic drainage deficiencies from affected joints, and defects in the synovial lymphatic system exacerbate inflammatory-erosive arthritis in animal models. To understand this, we generated Efhd1-CreERT2 and Myoc-CreERT2 mice for cell-specific genetic gain and loss of function studies. These mice were crossed with tdTomato reporter (Ai9) mice, and studies showed selective tamoxifen-induced transgene expression in CD31-/CD34+ telocyte-like cells in knee and ankle synovium, and in networks physically associated with mast cells proximal to popliteal lymphatic vessels (PLVs). Consistent with the known loss of CD31-/CD34+ telocyte in RA synovium, these cells were also decreased in TNF-tg knees and partially recovered by anti-TNF treatment. Ultrastructural and gene expression studies confirmed a distinct telocyte phenotype versus closely related fibroblasts. In vivo depletion studies in tamoxifen-treated Efhd1-CreERT2 and Myoc-CreERT2 mice crossed to diphtheria toxin alpha-floxed (DTAflox) mice demonstrated telocyte requirements for physiologic lymphatic drainage and resolution of joint inflammation and focal erosions from zymosan-induced arthritis in the knee. In vitro studies demonstrated increased sensitivity to osmotic shock and decreased motility versus fibroblasts, and telocyte potential to differentiate into myofibroblasts on stiff matrix. Collectively, these findings support a model of joint homeostasis in which osmotic pressure-sensing telocyte networks extend from the synovium into mast cells proximal to joint-draining cLVs, and telocyte loss is associated with defects in the synovial lymphatic system and increased susceptibility to joint inflammation and structural damage from arthritis. TeaserThis study discovered a unique cell type (telocytes) responsible for draining inflammation from arthritic joints.

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Multi-omics identification of activated T cells and spatial PD-1/PD-L1 signaling as biomarkers of diabetic foot ulcer healing

Bilik, S. M.; Dodson, C.; Rivas, K.; Balukoff, N.; Burgess, J. L.; Griswold, A. J.; Sawaya, A.; Pastar, I.; Strbo, N.; Morasso, M. I.; Tomic-Canic, M.; Stone, R. C.

2025-11-12 immunology 10.1101/2025.11.10.687697 medRxiv
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Diabetic foot ulcers (DFUs) are a common and debilitating complication of diabetes, and amputations from non-healing ulcers carry high morbidity and mortality. A critical need exists for biomarkers that can identify healing potential early and guide targeted interventions. To address this, we applied an integrated multi-omics approach across four patient cohorts comprising 51 DFUs (29 Healing, 22 Non-healing). Bulk RNA-sequencing revealed marked activation of Th1 and Th2 pathways (activation z-score +4.8, p = 3.8x10-{superscript 1}), and immune cell deconvolution predicted higher proportions of T cell populations in Healers. Spatial proteomics in a second cohort identified elevated CD3 T cell density and selective enrichment of PD-1 and PD-L1 expression in vascular niches of the papillary dermis in Healers (p < 0.001). Flow cytometry in a third cohort further demonstrated higher proportions of CD3PD-1 and CD3PD-L1 T cells in Healers compared with Non-healers. Single-cell RNA-sequencing from a fourth cohort showed upregulation of PD-1 and PD-L1 within CD4 T cells from Healers. Complementary immunofluorescence and serological profiling confirmed that both PD-1 and PD-L1 are elevated in tissue and circulating serum of healing DFUs, supporting their potential use as systemic biomarkers. Taken together, vascular-enriched PD-1/PD-L1 signaling and T cell activation were observed in association with healing DFUs, supporting PD-1/PD-L1 as candidate biomarkers in both tissue and blood with potential translational relevance for predicting DFU outcomes and informing precision therapies.

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Inflammatory proteolysis generates pathogenic APOL1 fragments with distinct intracellular toxicities in podocytes derived from children with HIV associated nephropathy.

Li, J.; Yu, Y.; Das, J. R.; Xu, L.; Kumar, P.; Han, Z.; Ray, P.

2026-08-13 cell biology 10.64898/2026.08.12.744497 medRxiv
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APOL1 risk variants are the strongest genetic determinants of HIV-associated nephropathy (HIVAN), yet the mechanisms linking inflammation to APOL1-mediated podocyte injury remain poorly understood because authentic patient-derived human disease models are lacking. Using urine-derived podocytes established from children with HIVAN and endogenous APOL1 reporter cell lines derived from these cells, we identified a previously unrecognized pathway of inflammatory, cathepsin-dependent APOL1 proteolysis. Endogenous APOL1 cleavage was detected in patient-derived podocytes, whereas reporter cell lines enabled the identification and functional characterization of N-terminal and C-terminal APOL1 fragments with distinct intracellular localization and pathogenic functions. The nuclear N-terminal fragment activated inflammatory transcriptional programs and promoted podocyte injury, whereas the membrane-associated C-terminal fragment mediated membrane toxicity and remained susceptible to pharmacologic inhibition by inaxaplin. Cathepsin S directly cleaved APOL1 in vitro, linking inflammatory signaling to APOL1 fragmentation. These findings identify inflammatory APOL1 proteolysis as a mechanism that partitions APOL1 toxicity into distinct pathogenic programs and nominate APOL1 processing as a therapeutic target for HIV-associated and other APOL1-mediated kidney diseases.

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The Harmine and Exendin-4 Combination Markedly Expands Human Beta Cell Mass In Vivo: Quantification and Visualization By iDISCO+ 3D Imaging

Rosselot, C.; Alvarsson, A.; Wang, P.; Li, Y.; Kumar, K.; DeVita, R. J.; Stewart, A. F.; Stanley, S. A.; Garcia-Ocana, A.

2020-07-25 cell biology 10.1101/2020.07.24.220244 medRxiv
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463 million people globally suffer from diabetes. The majority are deficient in insulin-producing pancreatic beta cells, although beta cells remain in most people with diabetes. Unfortunately, although many diabetes drugs exist, none is able to increase adult human beta cell numbers. Recently, small molecules that inhibit the kinase, DYRK1A, have been suggested to induce human beta cell replication in vitro and in vivo as assessed using proliferation markers, and this is enhanced by drugs that stimulate the GLP1 receptor (GLP1R) on beta cells. DYRK1A inhibitors also enhance human beta cell differentiation and function. However, it is unknown whether any drug can actually increase human beta cell mass in vivo, reflecting: 1) the intrinsic resistance of human beta cells to regeneration; and, 2) the current technical inability to accurately assess human beta cell mass in vivo. Here, we demonstrate for the first time that combining a DYRK1A inhibitor with a GLP1R agonist increases actual human beta cell numbers and overall mass in vivo by 400-700% in diabetic and non-diabetic mice over three months. We further describe a novel application of tissue-clearing and 3D imaging for quantification of human beta cell mass. These findings should be transformative for diabetes treatment.

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A first-in-kind MAPK13 inhibitor that can correct stem cell reprogramming and post-injury disease

Zhang, Y.; Wu, K.; Mao, D.; Iberg, C. A.; Yin-Declue, H.; Sun, K.; Wikfors, H. A.; Keeler, S. P.; Li, M.; Young, D.; Yantis, J.; Crouch, E. C.; Chartock, J. R.; Han, Z.; Byers, D. E.; Brody, S. L.; Romero, A. G.; Holtzman, M. J.

2024-08-22 immunology 10.1101/2024.08.21.608990 medRxiv
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The stress kinase MAPK13 (aka p38delta-MAPK) is an attractive entry point for therapeutic intervention because it regulates the structural remodeling that can develop after epithelial injury in the lung and likely other tissue sites. However, a selective, safe, and effective MAPK13 inhibitor is not yet available for experimental or clinical application. Here we identify a first-in-kind MAPK13 inhibitor using structure-based drug design combined with a screening funnel for cell safety and molecular specificity. This inhibitor (designated NuP-4A for intravenous or Nu4-B for inhaled delivery) down-regulates basal-epithelial stem cell reprogramming, structural remodeling, and pathophysiology equivalently to Mapk13 gene-knockout in mouse and mouse organoid models of muco-obstructive lung disease after viral infection. Treatment prevents and reverses disease biomarkers, and this benefit persists after stopping treatment as a sign of disease modification. Similarly, NuP-4 treatment can directly control stimulated growth, immune activation, and mucinous differentiation in human basal-cell organoids. The results thereby provide a new tool and potential correction for stem cell reprogramming towards muco-obstructive lung diseases like asthma and COPD and related diseases that might depend on overactivation of MAPK13. New and noteworthyThis study identifies a highly selective and potent small-molecule inhibitor for stress kinase MAPK13 in controlling the basal-epithelial stem cell response to viral infection and the consequent development of muco-obstructive lung disease. The present model has direct implications for diseases like asthma and COPD that are triggered by respiratory viruses and other inhaled toxins. Further, the tissue distribution of MAPK13 implies related actions at other epithelial sites. The findings also refine a hypothesis for therapeutic intervention based on proper scaling of MAPK13 function including precise down-regulation with a highly selective MAPK13 inhibitor.

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Aberrant Transitional Alveolar Epithelial Cells Promote Pathogenic Activation of Lung Fibroblasts in Preclinical Fibrosis Modeling

Hoffman, E. T.; Barboza, W. R.; Rodriguez, L. R.; Dherwani, R.; Tomer, Y.; Murthy, A.; Bennett, A.; Nottingham, A.; Babu, A.; Chavez, K.; Cooper, C. H.; Basil, M. C.; Raredon, M. S. B.; Katzen, J. B.

2024-06-18 cell biology 10.1101/2024.06.17.599351 medRxiv
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Pulmonary fibrosis (PF) is a chronic progressive lung disease histopathologically characterized by fibrotic remodeling and the presence of pathological epithelial and mesenchymal cell populations in the distal lung parenchyma. Within the epithelial compartment, a subset of alveolar type 2 cells (AT2s) enter and persist in an aberrant transitional state. Whether and how these aberrant transitional cells participate in lung fibrosis is not known. To address this, we exploited the SftpcC121G mouse model, where we previously demonstrated that chronic expression of a PF-associated point mutation (C121G) in the AT2-specific surfactant protein C (Sftpc) gene results in spontaneous and progressive fibrosis driven by intrinsic AT2 dysfunction. We utilized single cell RNA sequencing to demonstrate the emergence of pathologic epithelial and mesenchymal cells in the SftpcC121G murine lung fibrosis model, including aberrant transitional alveolar epithelial cells as well as transitional and fibrotic fibroblasts. Aberrant transitional alveolar epithelial cells share similar transcriptional profiles to human aberrant basaloid cells, including the upregulation of profibrotic gene markers (Fn1, Ctgf, Tgfb2, Pdgfb, Spp1), and develop a unique interactome with pathogenic lung fibroblasts. We developed a method to reliably flow sort aberrant transitional alveolar epithelial cells, and we highlight their ability to cause fibrotic activation of fibroblasts in ex vivo organoid assays and using conditioned supernatant, suggesting a profibrotic secretome. We conclude that aberrant transitional alveolar epithelial cells actively contribute to fibrotic lung remodeling through pathogenic activation of alveolar fibroblasts.

9
Single cell spatial transcriptomic profiling of childhood-onset lupus nephritis reveals complex interactions between kidney stroma and infiltrating immune cells.

Danaher, P.; Hasle, N.; Nguyen, E.; Hayward, K.; Rosenwasser, N.; Alpers, C. E.; Reed, R. C.; Okamura, D.; Baxter, S. K.; Jackson, S. W.

2023-11-13 immunology 10.1101/2023.11.09.566503 medRxiv
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Children with systemic lupus erythematosus (SLE) are at increased risk of developing kidney disease, termed childhood-onset lupus nephritis (cLN). Single cell transcriptomics of dissociated kidney tissue has advanced our understanding of LN pathogenesis, but loss of spatial resolution prevents interrogation of in situ cellular interactions. Using a technical advance in spatial transcriptomics, we generated a spatially resolved, single cell resolution atlas of kidney tissue (>400,000 cells) from eight cLN patients and two controls. Annotated cells were assigned to 35 reference cell types, including major kidney subsets and infiltrating immune cells. Analysis of spatial distribution demonstrated that individual immune lineages localize to specific regions in cLN kidneys, including myeloid cells trafficking to inflamed glomeruli and B cells clustering within tubulointerstitial immune hotspots. Notably, gene expression varied as a function of tissue location, demonstrating how incorporation of spatial data can provide new insights into the immunopathogenesis of SLE. Alterations in immune phenotypes were accompanied by parallel changes in gene expression by resident kidney stromal cells. However, there was little correlation between histologic scoring of cLN disease activity and glomerular cell transcriptional signatures at the level of individual glomeruli. Finally, we identified modules of spatially-correlated gene expression with predicted roles in induction of inflammation and the development of tubulointerstitial fibrosis. In summary, single cell spatial transcriptomics allows unprecedented insights into the molecular heterogeneity of cLN, paving the way towards more targeted and personalized treatment approaches.

10
Costimulatory blockade depletes T peripheral helper, late-activated naive, and DN2 B cells in rheumatoid arthritis

Shwetar, J. J.; Amarnani, A.; Rigby, W.; Skopelia-Gardner, S.; Ruggles, K. V.; Silverman, G. J.

2026-03-16 rheumatology 10.64898/2026.03.14.26348386 medRxiv
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Rheumatoid arthritis (RA) is a chronic inflammatory autoimmune disease that causes joint destruction along with extra-articular morbidity and early mortality. Abatacept (CTLA-4 Ig), a blocker of lymphocyte co-stimulation, has become a well-accepted biologic treatment with proven efficacy in established-RA and for preventing disease onset in predisposed individuals. To investigate the immunologic implications of abatacept treatment, we conducted a prospective, open-label trial with multi-omic single-cell analyses of lymphocytes and BCR repertoire profiling at predefined intervals. Treatment-induced low-disease activity correlated with coordinated depletion of circulating peripheral helper cells (Tph), late-activated naive cells (late-aNAV), and of CD27-IgD- (Double negative, DN) Zeb2+CD11c+ T-box transcription factor 21 (Tbet+) DN2 unconventional memory B cells, implicated in the tertiary lymphoid structures responsible for the propagation of pathologic autoimmune responses and joint destruction. Among B-cell subsets, DN2 had the greatest representation of molecular machinery for antigen-uptake, processing, and presentation. Among memory B-cell subsets, DN2 had the lowest representation of somatically generated N-glycosylation sites and somatic hypermutation. Yet abatacept induced DN2 cells to express elevated CXCR4 levels, which normalized upon drug withdrawal, suggesting that abatacept treatment may cause these cells to traffic out of pathologic synovial infiltrates. In conclusion, we have documented that abatacept affects the circulating immune cellular drivers of disease activity, Tph, late-aNAV and DN2. Therapeutic depletion of these pathologic lymphocyte subsets is associated with clinical benefits that can persist after therapy cessation. Hence, levels of these subsets may serve as surrogates for the overall burden of disease and potential response to abatacept therapy. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=62 SRC="FIGDIR/small/26348386v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@b44131org.highwire.dtl.DTLVardef@241f4eorg.highwire.dtl.DTLVardef@18361f6org.highwire.dtl.DTLVardef@9470b7_HPS_FORMAT_FIGEXP M_FIG C_FIG One Sentence SummaryMulti-omics analyses showed costimulatory blockade depletes trafficking DN2 B cells and Tph cells that correlates with rheumatoid disease response.

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Antibody-induced glomerulonephritis pathology is amplified by RTEC-intrinsic IL-17 signaling and restrained by the endoribonuclease Regnase-1

Li, D.-D.; Bechara, R.; Ramani, K.; Jawale, C.; Li, Y.; Kolls, J.; Gaffen, S.; Biswas, P. S.

2021-01-11 immunology 10.1101/2021.01.11.425972 medRxiv
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Antibody-mediated glomerulonephritis (AGN) is a clinical manifestation of many autoimmune kidney diseases for which few effective treatments exist. Chronic inflammatory circuits in renal glomerular and tubular cells lead to tissue damage in AGN. These cells are targeted by the cytokine IL-17, which has recently been shown to be a central driver of the pathogenesis of AGN. However, surprisingly little is known about the regulation of pathogenic IL-17 signaling in the kidney. Here, using a well characterized mouse model of AGN, we show that IL-17 signaling in renal tubular epithelial cells (RTECs) is necessary for AGN development. We also show that Regnase-1, an RNA binding protein with endoribonuclease activity, is a negative regulator of IL-17 signaling in RTECs. Accordingly, mice with a selective Regnase-1 deficiency in RTECs exhibited exacerbated kidney dysfunction in AGN. Mechanistically, Regnase-1 inhibits IL-17-driven expression of the transcription factor I{kappa}B{xi} and consequently its downstream gene targets including Il6 and Lcn2. Moreover, deletion of Regnase-1 in human RTECs reduced inflammatory gene expression in an I{kappa}B{xi}-dependent manner. Overall, these data identify an IL-17-driven inflammatory circuit in RTECs during AGN that is constrained by Regnase-1.

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Anti-mitochondrial antibodies in systemic sclerosis target enteric neurons and are associated with GI dysmotility

McMahan, Z. H.; Casciola-Rosen, L.; Kaniechi, T.; Gutierrez-Alamillo, L.; Seika, P.; Hong, S. M.; Kulkarni, S.

2024-11-30 rheumatology 10.1101/2024.11.26.24317983 medRxiv
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BackgroundMost patients with systemic sclerosis (SSc) experience gastrointestinal (GI) dysmotility. The enteric nervous system (ENS) regulates GI motility, and its dysfunction causes dysmotility. A subset of SSc patients harbor autoantibodies against the M2 mitochondrial antigen (AM2A). Here, we investigate whether M2 is expressed by specific ENS cells, and if AM2A associate with GI dysmotility in SSc patients. MethodsSera from 154 well-characterized patients with SSc were screened for AM2A by ELISA. Clinical features and GI transit data were compared between AM2A-positive and negative patients. HepG2 cells were cultured with these sera and co-stained with AM2A. ResultsNineteen of 147 patients (12.9%) were AM2A positive. AM2A positivity was significantly associated with slower transit in the esophagus ({beta} -14.4, 95%CI -26.2, -2.6) and stomach ({beta} -7.9, 95% CI -14.1, -1.6). Immunostaining demonstrated pan-mitochondrial antigens TOM-20 and M2 enrichment in human ENS neurons, specifically in mesoderm- derived enteric neurons (MENS). HepG2 cells cultured with SSc sera showed that SSc autoantibodies penetrate live cells and that AM2A and other SSc autoantibodies are localized to subcellular compartments containing target antigens. ConclusionAM2A in SSc patients associate with slower GI transit. MENs are enriched in mitochondria, suggesting enhanced susceptibility to mitochondrial dysfunction and associated GI dysmotility in SSc. Our finding that SSc autoantibodies penetrate live cells in vitro suggests that SSc-AM2A may penetrate MENs in vivo, driving ENS and GI dysfunction. Further studies are warranted to understand whether AM2As contribute to mitochondrial dysfunction, and whether mitochondrial dysfunction contributes to GI dysmotility in SSc. Key messagesO_LIWhat is already known on this topic O_LIsubset of SSc patients have autoantibodies against the M2 mitochondrial antigen (AM2A). Whether AM2A antibodies inform the presence or severity of GI dysfunction in SSc is unknown. C_LI C_LI O_LIWhat this study adds: O_LIAM2A antibodies in SSc patients associate with slower upper GI transit. C_LIO_LIMitochondria are enriched in a recently identified mesoderm-derived lineage of enteric neurons (MENs), which play a major role in GI motility. This suggests that MENS may be more mitochondrial-dependent than other cell types, and thus more susceptible to mitochondrial dysfunction. This may contribute to dysmotility in AM2A-positive SSc patients. C_LIO_LISSc autoantibodies penetrate live cells in vitro and bind to their target antigens intracellularly. C_LI C_LI O_LIHow this study might affect research, practice or policy O_LIAM2A antibodies in SSc patients may penetrate MENs in vivo, driving ENS dysfunction and subsequent GI dysmotility C_LIO_LIThis potentially novel mechanism in SSc GI disease could inform our current approach to diagnosing and managing these patients. C_LI C_LI

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Fatty Acid Oxidation Suppression Reprograms Fibroblasts in Fibrostenotic Crohns Disease

Jihad Aljabban, J.; Awad, A.; McMichael, B. D.; Gartner, V.; Thomas, V.; Huan, B.; Weaver, D.; Lian, G.; Beasley, C.; Lau, G. W.-J.; Silverstein, S.; Kapadia, M.; Salvador, A. C.; Rieder, F.; Thaxton, J. E.; Furey, T. S.; Bhatt, A. P.; Sheikh, S. Z.

2026-05-10 genomics 10.64898/2026.05.06.723289 medRxiv
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Fibrostenotic complications represent a major cause of morbidity in Crohns disease (CD), yet the cellular mechanisms that drive intestinal fibrosis independent of active inflammation remain poorly understood. Here, we identify impaired fatty acid oxidation (FAO) as a defining metabolic feature of fibroblasts in fibrostenotic CD. Untargeted lipidomics of non-inflamed colonic tissue from CD patients demonstrated enrichment of triacylglycerols and long-chain acylcarnitines, suggesting altered lipid utilization. Across three independent RNA-sequencing cohorts, including treatment-naive pediatric ileal biopsies, FAO genes (CPT1A, CPT2, SLC25A20) were selectively downregulated in patients with or destined to develop fibrostenotic disease. Single-cell RNA-sequencing localized these transcriptional alterations specifically to fibroblasts within strictured ileum. Primary fibroblasts derived from fibrostenotic CD exhibited increased neutral lipid accumulation, impaired mitochondrial fatty acid trafficking, and diminished responsiveness to PPAR{gamma}-mediated suppression of TGF{beta}-induced myofibroblast activation. Together, these findings demonstrate that FAO impairment is a conserved, fibroblast-specific metabolic program associated with intestinal fibrosis in CD and suggest that metabolic modulation of stromal cells represents a potential therapeutic strategy for fibrostenotic disease.

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Soluble IL-2R impairs muscle cell mitochondrial respiration in fatigued individuals with post-acute sequelae of COVID-19.

Brown, L. P.; Joshi, J.; Kosmac, K.; Long, D. E.; Montgomery-Yates, A. A.; Kalema, A. G.; Sturgill, J.; Vekaria, H.; Sullivan, P.; Wilburn, D.; Koutakis, P.; Latham, C. M.; Fry, C.; Kern, P. A.; Miller, B.; Dupont-Versteegden, E.; Ismaeel, A.; Mayer, K. P.; Wen, Y.

2024-08-19 rehabilitation medicine and physical therapy 10.1101/2024.08.14.24311980 medRxiv
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Post-acute sequelae of COVID (PASC) persist in many patients for weeks and months after recovery from initial SARS-CoV-2 infection. Recent evidence suggests that pathological changes in skeletal muscle may contribute significantly to ongoing pain and fatigue, particularly post-exertional malaise. This study aimed to investigate the underlying mechanisms of PASC-related fatigue by examining skeletal muscle function and circulating factors in affected individuals. We conducted a cross-sectional case-control study of patients with fatigue-associated PASC who had experienced mild to moderate COVID-19 without hospitalization. Skeletal muscle biopsies revealed reduced mitochondrial respiration and content in PASC participants compared to healthy controls. This lower respiratory capacity was accompanied by markedly elevated circulating levels of soluble IL-2 receptor alpha subunit (sIL2R), a T cell-specific receptor. In vitro experiments demonstrated that sIL2R directly impairs mitochondrial oxygen consumption and reduces mitochondrial complex III subunit protein levels in cultured muscle cells. These findings suggest a mechanism linking systemic immune dysregulation to muscle-specific mitochondrial dysfunction in PASC. This work provides new insights into the pathophysiology of PASC identifying sIL2R as a promising therapeutic target for addressing mitochondrial deficits in PASC-related fatigue and opening avenues for developing targeted interventions.

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Multi-omics Characterization of Neutrophil Extracellular Trap Formation in Severe and Mild COVID-19 Infections

Bramer, L.; Hontz, R.; Eisfeld, A.; Sims, A.; Kim, Y.-M.; Stratton, K.; Nicora, C.; Gritsenko, M.; Schepmoes, A.; Akasaka, O.; Koga, M.; Tsutsumi, T.; Nakamura, M.; Nakachi, I.; Baba, R.; Tateno, H.; Suzuki, S.; Nakajima, H.; Kato, H.; Ishida, K.; Ishii, M.; Uwamino, Y.; Mitamura, K.; Paurus, V.; Nakayasu, E.; Attah, I.; Letizia, A. G.; Waters, K.; Metz, T.; Corson, K.; Kawaoka, Y.; Gerbasi, V. R.

2022-04-28 infectious diseases 10.1101/2022.04.26.22274196 medRxiv
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The detailed mechanisms of COVID-19 infection pathology remain poorly understood. To improve our understanding of SARS-CoV-2 pathology, we performed a multi-omics analysis of an immunologically naive SARS-CoV-2 clinical cohort from the plasma of uninfected controls, mild, and severe infections. A comparison of healthy controls and patient samples showed activation of neutrophil degranulation pathways and formation of neutrophil extracellular trap (NET) complexes that were activated in a subset of the mild infections and more prevalent in severe infections (containing multiple NET proteins in individual patient samples). As a potential mechanism to suppress NET formation, multiple redox enzymes were elevated in the mild and severe symptom population. Analysis of metabolites from the same cohort showed a 24- and 60-fold elevation in plasma L-cystine, the oxidized form of cysteine, which is a substrate of the powerful antioxidant glutathione, in mild and severe patients, respectively. Unique to patients with mild infections, the carnosine dipeptidase modifying enzyme (CNDP1) was up-regulated. The strong protein and metabolite oxidation signatures suggest multiple compensatory pathways working to suppress oxidation and NET formation in SARS-CoV-2 infections.

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Functional and Metabolic Adaptations of Blood Flow Restriction Exercise in Rats and Post-surgical Patients

Fosam, A.; Nakandakari, S. C. B. R.; Dworkowitz, M.; Li, Z.; Petrosino, C.; Taber, C.; Allen, C.; Perry, R. J.

2026-06-02 rehabilitation medicine and physical therapy 10.64898/2026.05.26.26353908 medRxiv
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Blood flow restriction exercise (BFR-E) has gained popularity as a therapy used to improve muscle mass and strength in various clinical populations. However, the systemic and intramuscular responses to BFR-E are widely unknown. Here, we describe the functional and metabolic responses to BFR-E in our novel in vivo method of BFR-E in rats. Implementation of the model revealed increase in muscle mass and maximal strength in rats exposed to chronic BFR-E. Systemic metabolites related to glycolysis and redox metabolism were altered following acute BFR-E and metabolites related to amino acids and the TCA cycle were altered following chronic BFR-E. Moreover, transcriptomic analysis revealed a muscle-specific metabolic response to chronic BFR-E that coincided with morphological adaptations. Given the broad application of BFR-E in the rehabilitative setting, we examined the acute, systemic response to BFR-E in post-surgical human subjects. Semi-targeted metabolomic analysis revealed no significant alterations in circulating metabolites following acute BFR-E in humans, mirroring findings in acutely exercised rats. Together, these results suggest that the benefits of BFR-E are not mediated by acute systemic metabolic perturbations but instead arise from tissue-specific adaptations that develop with repeated exposure, establishing a conserved, translational framework for mechanistic investigation.

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Rho-ROCK signaling and α-Catenin mediate β-Catenin-driven hyperplasia in the adrenal via adherens junctions

Berber, M.; Haykir, B.; Guagliardo, N. A.; Chortis, V.; Borges, K. S.; Barrett, P. Q.; Beuschlein, F.; Carlone, D. L.; Breault, D.

2025-10-07 cell biology 10.1101/2025.10.06.680572 medRxiv
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How {beta}-Catenin ({beta}Cat) mediates tissue hyperplasia is poorly understood. To explore this, we employed the adrenal cortex as a model system given its stereotypical spatial organization and the important role {beta}Cat plays in homeostasis and disease. For example, excessive production of aldosterone by the adrenal cortex (primary aldosteronism, PA) constitutes a significant cause of cardiovascular morbidity, which has been associated with {beta}Cat gain-of-function ({beta}Cat-GOF). Adherens junctions (AJs) connect the actin cytoskeletons of adjacent zona Glomerulosa (zG) cells via a cadherin/{beta}Cat/-Catenin (Cat) complex and mediate aldosterone production. Whether {beta}Cat-GOF drives zG hyperplasia, a key feature of PA, via AJs is unknown. Here, we show that aldosterone secretagogues (K+, AngII) and {beta}Cat-GOF mediate AJ enrichment via Rho-ROCK-actomyosin signaling. In addition, Rho-ROCK inhibition leads to altered zG rosette morphology and decreased aldosterone production. Mice with zG-specific {beta}Cat-GOF demonstrate increased AJ formation and zG hyperplasia, which was blunted by Rho-ROCK inhibition and deletion of Cat. Further, analysis of human aldosterone-producing adenomas (APAs) revealed high levels of {beta}Cat expression were associated with increased membranous expression of K-Cadherin. Together, our findings identify Rho-ROCK signaling and Cat as key mediators of AJ enrichment and {beta}-Catenin-driven hyperplasia. One Sentence SummaryThis study demonstrates that {beta}-Catenin-driven hyperplasia in the adrenal cortex, a key feature of primary aldosteronism, is mediated through Rho-ROCK signaling and -Catenin-dependent stabilization of adherens junctions, with significant implications for patients with primary aldosteronism. HighlightsO_LIRho-ROCK signaling drives AJ enrichment in the adrenal C_LIO_LIROCK inhibition via fasudil blunts aldosterone production C_LIO_LI{beta}Cat drives adrenal hyperplasia via enhanced AJ enrichment C_LIO_LIROCK inhibition or [a]Cat deletion block zG hyperplasia C_LI

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Virologic, clinical, and immunological characteristics of a dengue virus 3 human challenge model

Waickman, A. T.; Newell, K.; Lu, J. Q.; Fang, H.; Waldran, M.; Gebo, C.; Currier, J. R.; Friberg, H.; Jarman, R. G.; Klick, M. D.; Ware, L. A.; Endy, T. P.; Thomas, S. J.

2022-10-31 infectious diseases 10.1101/2022.10.24.22281454 medRxiv
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30.9%
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Dengue human infection models present an opportunity to explore a vaccine, antiviral, or immuno-compounds potential for clinical benefit in a controlled setting. Herein, we report the outcome of a phase 1, open-label assessment of a DENV-3 challenge model. In this study, 9 participants received a subcutaneous inoculation with 0.5ml of a 1.4x103 PFU/ml suspension of the DENV-3 strain CH53489. All subjects developed RNAemia within 7 days of inoculation, with peak titers ranging from 3.13x104 to 7.02x108 GE/ml. Symptoms and clinical lab abnormalities consistent with mild dengue infection were observed in all subjects. DENV-3 specific seroconversion was observed by 14 days after inoculation, along with DENV-3 specific memory T cell responses. RNAseq and serum cytokine analysis revealed the presence of an antiviral transcriptional and cytokine response to infection that overlapped with the period of viremia. The magnitude and frequency of clinical and immunologic endpoints correlated with an individuals peak viral titer.

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Hypoxia-inducible factor-2 (HIF2) regulates alveolar regeneration after repetitive injury

McCall, A. S.; Tanjore, H.; Burman, A.; Sherrill, T.; Chapman, M.; Calvi, C. L.; Camarata, J.; Hunt, R. P.; Nichols, D.; Banovich, N.; Lawson, W. E.; Gokey, J. J.; Kropski, J. A.; Blackwell, T. S.

2023-09-17 cell biology 10.1101/2023.09.17.557477 medRxiv
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Idiopathic Pulmonary Fibrosis (IPF) is a progressive and often fatal chronic respiratory disease thought to result from repetitive injury and failed repair of the lung alveoli, and recent studies have identified a number of disease-emergent intermediate/transitional cell states in the IPF lung supporting this concept. In this study, we found that persistent activation of hypoxia-inducible factor (HIF)-signaling in airway-derived, repair-associated cell types/states is a hallmark of dysfunctional epithelial repair in the IPF lung epithelium and experimental models of recurrent lung epithelial injury. Disrupting Hif-signaling attenuated experimental lung fibrosis, reduced mucous-secretory cell polarization, and promoted functional alveolar regeneration following repetitive injury. Mouse and human organoid studies demonstrated that small-molecule-based HIF2 inhibition promoted alveolar epithelial cell proliferation and maturation while preventing the emergence of maladaptive intermediate/transitional states analogous to those in IPF. Together, these studies indicate that targeted HIF2-inhibition represents a novel and effective therapeutic strategy to promote functional lung regeneration, and could be readily translated into human studies of IPF and other chronic interstitial lung diseases with disease modifying effect. One sentence summaryInhibiting hypoxia-inducible-factor 2 (HIF2) promotes functional lung alveolar epithelial repair following recurrent injury.

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Discovery of post-translationally modified self-peptides that promote hypertension

Bloodworth, N.; Chen, W.; Patrick, D.; Palubinsky, A.; Phillips, E.; Roeth, D.; Kalkum, M.; Mallal, S.; Davies, S. S.; Ao, M.; Moretti, R.; Meiler, J.; Harrison, D. G.

2023-07-19 immunology 10.1101/2023.07.18.549523 medRxiv
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Post translational modifications can enhance immunogenicity of self-proteins. In several conditions including hypertension, systemic lupus, and heart failure, isolevuglandins (IsoLGs) are formed by lipid peroxidation and covalently bond with protein lysine residues. Here we show that the murine class-I major histocompatibility complex (MHC-I) variant H-2Db uniquely presents isoLG modified peptides and developed a computational pipeline that identifies structural features for MHC-I accommodation of such peptides. We identified isoLG-adducted peptides from renal proteins including the sodium glucose transporter 2, Cadherin 16, Kelch Domain containing protein 7A and solute carrier family 23, that are recognized by CD8+ T cells in tissues of hypertensive mice, induce T cell proliferation in vitro, and prime hypertension after adoptive transfer. Finally, we find similar patterns of isoLG-adducted antigen restriction in class-I human leukocyte antigens as in murine analogues. Thus, we have used a combined computational and experimental approach to define likely antigenic peptides in hypertension.