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Science Translational Medicine

American Association for the Advancement of Science (AAAS)

All preprints, ranked by how well they match Science Translational Medicine's content profile, based on 127 papers previously published here. The average preprint has a 0.12% match score for this journal, so anything above that is already an above-average fit. Older preprints may already have been published elsewhere.

1
Pathology-Targeted EP4 Agonism Reverses Fibrosis in a Rat Model of DMD

Kajabadi, N.; Narasimhan, A.; Chen, G.; Yi, L.; Rodriguez-Rodriguez, C.; Coccimiglio, I. F.; Huang, T.; Rendeiro, M.; Yamanouchi, K.; Häfeli, U. O.; Kostenuik, P.; Young, R. N.; Rossi, F.

2026-06-02 pharmacology and toxicology 10.64898/2026.05.29.728674 medRxiv
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Duchenne muscular dystrophy (DMD) presents a critical therapeutic gap in adolescent patients, where extensive fibro-fatty muscle replacement and depletion of the regenerative niche render existing interventions insufficient. Prostaglandin E2 signaling through the EP4 receptor stimulates bone and muscle regeneration and repair, but systemic off-target effects have limited the clinical translation of EP4 agonism in diseases such as DMD. We therefore evaluated irodanoprost (IROD), a bone-targeted prodrug of an EP4-selective agonist, in a DMD rat model, comparing early- and late-intervention cohorts. In adolescent rats, 8 weeks of treatment reduced body weight deficit by 41.4% and restored hindlimb muscle mass and maximum tetanic force to wild-type levels. IROD dose-dependently inhibited fibro-adipogenic progenitor differentiation into -SMA myofibroblasts, facilitating active resolution of established fibrosis below pre-treatment baseline. This was accompanied by re-activation of a synchronized regenerative program marked by clustered eMHC fibers, restoring the total myofiber pool to wild-type levels. A strong linear correlation between intramuscular fat reduction and fibrosis resolution suggests that MRI-based fat imaging may serve as a non-invasive surrogate for monitoring anti-fibrotic efficacy. The efficacy of IROD is likely aided by the fact that while it selectively distributes to bone in healthy animals, we observed markedly enhanced accumulation of the drug in dystrophic muscle. These findings establish IROD as a pathology-targeted approach capable of resolving the fibro-fatty niche and restoring regenerative capacity in advanced DMD. SummaryPathology-targeted EP4 agonism resolves established fibrosis and restores myofiber regeneration in a rat model of adolescent Duchenne dystrophy. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/728674v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@141d591org.highwire.dtl.DTLVardef@12c4723org.highwire.dtl.DTLVardef@1f26514org.highwire.dtl.DTLVardef@ca146e_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Allometric tissue-scale forces activate mechanoresponsive immune cells to drive pathological foreign body response to biomedical implants

Padmanabhan, J.; Chen, K.; Sivaraj, D.; Kuehlmann, B. A.; Bonham, C. A.; Dohi, T.; Henn, D.; Stern-Buchbinder, Z. A.; Than, P. A.; Hosseini, H. S.; Barrera, J. A.; Kussie, H. C.; Magbual, N. J.; Borrelli, M. R.; Trotsyuk, A. A.; Kwon, S. H.; Dunn, J. C. Y.; Maan, Z. N.; Januszyk, M.; Prantl, L.; Gurtner, G. C.

2022-01-15 bioengineering 10.1101/2022.01.14.476395 medRxiv
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For decades, it has been assumed that the foreign body response (FBR) to biomedical implants is primarily a reaction to the chemical and mechanical properties of the implant. Here, we show for the first time that a third independent variable, allometric tissue-scale forces (which increase exponentially with body size), can drive the biology of FBR in humans. We first demonstrate that pathological FBR in humans is mediated by immune cell-specific Rac2 mechanotransduction signaling, independent of implant chemistry or mechanical properties. We then show that mice, which are typically poor models of human FBR, can be made to induce a strikingly human-like pathological FBR by altering these extrinsic tissue forces. Altering these extrinsic tissue forces alone activates Rac2 signaling in a unique subpopulation of immune cells and results in a human-like pathological FBR at the molecular, cellular, and local tissue levels. Finally, we demonstrate that blocking Rac2 signaling negates the effect of increased tissue forces, dramatically reducing FBR. These findings highlight a previously unsuspected mechanism for pathological FBR and may have profound implications for the design and safety of all implantable devices in humans. One-Sentence SummaryAllometric tissue-scale forces at the implant-tissue interface drive pathological foreign body response.

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A Single Multipurpose FSH-Blocking Therapeutic for Osteoporosis and Obesity

Gera, S.; Kuo, T.-C.; Korkmaz, F.; Sant, D.; DeMambro, V.; Gumerova, A. A.; Sudha, K.; Padilla, A.; Prevot, G.; Munitz, J.; Teunissen, A.; van Leent, M. M. T.; Post, T. G. J. M.; Fernandes, J. C.; Netto, J.; Sultana, F.; Shelly, E.; Kumar, P.; Cullen, L.; Chatterjee, J.; Miyashita, S.; Kannangara, H.; Bhongade, M.; Ievleva, K.; Muradova, V.; Batista, R.; Robinson, C.; Macdonald, A.; Babunovic, S.; Saxena, M.; Meseck, M.; Caminis, J.; Iqbal, J.; New, M. I.; Ryu, V.; Kim, S.-M.; Cao, J.; Zaidi, N.; Fayad, Z. A.; Lizneva, D.; J. Rosen, C.; Yuen, T.; Zaidi, M.

2022-03-02 pharmacology and toxicology 10.1101/2022.02.28.482279 medRxiv
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Pharmacological and genetic studies over the past decade have established FSH as an actionable target for diseases affecting millions, notably osteoporosis, obesity and Alzheimers disease (AD). Blocking FSH action prevents bone loss, fat gain and AD-like features in mice. We recently developed a first-in-class, humanized, epitope-specific FSH blocking antibody, MS-Hu6, with a KD of 7.52 nM. Using a GLP-compliant platform, we now report the efficacy of MS-Hu6 in preventing obesity and osteoporosis in mice, and parameters of acute safety in monkeys. Biodistribution studies using 89Zr-labelled, biotinylated or unconjugated MS-Hu6 in mice and monkeys showed localization to bone, bone marrow and fat depots. MS-Hu6 displayed a {beta} phase t[1/2] of 13 days (316 hours) in humanized Tg32 mice, and bound endogenous FSH. We tested 215 variations of excipients using the protein thermal shift assay to generate a final formulation that rendered MS-Hu6 stable in solution upon freeze-thaw and at different temperatures, with minimal aggregation, and without self-, cross-, or hydrophobic interactions or appreciable binding to relevant human antigens. MS-Hu6 showed the same level of "humanness" as human IgG1 in silico, and was non-immunogenic in ELISPOT assays for IL-2 and IFN{gamma} in human peripheral blood mononuclear cell cultures. We conclude that MS-Hu6 is efficacious, durable and manufacturable, and is therefore poised for future human testing as a multipurpose therapeutic.

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Patient-Derived Inner Ear Organoids as a Disease Modeling and Therapy Validation Platform For Hereditary Inner Ear Disorders

Fousert, E.; van den Boogaard, W. M. C.; Lucassen, A. W. A.; Udayappan, S. D.; Oostrik, J.; van Benthem, P. P. G.; Kremer, H.; van Wijk, E.; van der Valk, W. H.; de Vrieze, E.; Locher, H.

2026-07-20 neuroscience 10.64898/2026.07.14.738390 medRxiv
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BackgroundHereditary inner ear disorders comprise a highly heterogenous group of disorders and are a major cause of hearing and vestibular dysfunction. Despite advances in genetic diagnosis, the development of precision therapies has been limited by the lack of relevant and scalable human model systems that can accommodate the wide spectrum of disease-causing variants and support the evaluation of therapeutic interventions. We established patient-derived inner ear organoids (IEOs) as a platform to assess antisense oligonucleotide (ASO)-based therapeutic strategies for hereditary hearing loss. MethodsTwo representative genetic models were selected: recessive syndromic Usher syndrome type IIa (USH2A) and dominant non-syndromic DFNA9 (COCH). Human induced pluripotent stem cells (iPSCs) were generated from a patient carrying a homozygous pathogenic USH2A variant and a patient carrying a frequently occurring pathogenic COCH variant. In parallel, isogenic iPSC lines were created by introducing the same disease-causing variants into a healthy donor background. Following differentiation into IEOs, disease-associated transcript expression was evaluated. Splice-switching and RNase H1-mediated gapmer ASOs were assessed for target engagement. ASO biodistribution and cellular uptake was also examined in both IEOs and adult human vestibular tissue. ResultsPatient-derived and isogenic iPSCs were successfully differentiated into IEOs that recapitulated disease-associated transcript expression. ASOs showed efficient uptake into disease-relevant cell populations in both IEOs and adult human vestibular tissue. In USH2A-variant IEOs, splice-switching ASO treatment corrected aberrant splicing. In COCH-variant IEOs, gapmer ASO treatment reduced total COCH transcript levels, achieving up to 75% knockdown in patient-derived IEOs. ConclusionsPatient-derived and isogenic variant IEOs provide a versatile and scalable human platform for evaluating ASO therapies for hereditary hearing loss. Their adaptability to diverse genetic variants, inheritance patterns, and ASO modalities makes them well suited to address the genetic heterogeneity of hereditary inner ear diseases and establishes IEOs as a broadly applicable preclinical model for rare hereditary inner ear diseases.

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SARS-CoV-2 serology across scales: a framework for unbiased seroprevalence estimation incorporating antibody kinetics and epidemic recency

Takahashi, S.; Peluso, M. J.; Hakim, J.; Turcios, K.; Janson, O.; Routledge, I.; Busch, M. P.; Hoh, R.; Tai, V.; Kelly, J. D.; Martin, J. N.; Deeks, S. G.; Henrich, T. J.; Greenhouse, B.; Rodriguez-Barraquer, I.

2021-09-14 epidemiology 10.1101/2021.09.09.21263139 medRxiv
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Serosurveys are a key resource for measuring SARS-CoV-2 cumulative incidence. A growing body of evidence suggests that asymptomatic and mild infections (together making up over 95% of all infections) are associated with lower antibody titers than severe infections. Antibody levels also peak a few weeks after infection and decay gradually. We developed a statistical approach to produce adjusted estimates of seroprevalence from raw serosurvey results that account for these sources of spectrum bias. We incorporate data on antibody responses on multiple assays from a post-infection longitudinal cohort, along with epidemic time series to account for the timing of a serosurvey relative to how recently individuals may have been infected. We applied this method to produce adjusted seroprevalence estimates from five large-scale SARS-CoV-2 serosurveys across different settings and study designs. We identify substantial differences between reported and adjusted estimates of over two-fold in the results of some surveys, and provide a tool for practitioners to generate adjusted estimates with pre-set or custom parameter values. While unprecedented efforts have been launched to generate SARS-CoV-2 seroprevalence estimates over this past year, interpretation of results from these studies requires properly accounting for both population-level epidemiologic context and individual-level immune dynamics.

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Autoantibodies neutralizing type I IFNs in 40% of patients with WNV encephalitis in seven new cohorts

Gervais, A.; Trespidi, F.; Ferrari, A.; Rovida, F.; Marchal, A.; Croce, S.; Cassaniti, I.; Moratti, M.; Uhrlaub, J. L.; Florian, D. M.; Stiasny, K.; Burdino, E.; Angelini, M.; Bizien, L.; Lilleri, D.; Codullo, V.; Freund, T.; Paran, Y.; Gadoth, A.; Biran, R.; Mancon, A.; Lucca, C.; Vogiatzis, S.; Pacenti, M.; Aubart, M.; Zecca, M.; Comoli, P. A.; Avanzini, M.; Fellay, J.; Piralla, A.; Conti, F.; Dolci, A.; Barzon, L.; Ghisetti, V.; Lazzarotto, T.; Cereda, D.; Aiuti, A.; Jouanguy, E.; Bastard, P. R.; MacDonald, M. M.; Rice, C.; Puel, A.; Abel, L.; Rossini, G.; Mileto, D.; Simonin, Y.; Nagy, A.;

2025-09-04 infectious diseases Community evaluation 10.1101/2025.08.31.25334556 medRxiv
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Mosquito-borne West Nile virus (WNV) infection is a growing global health problem. About 0.5% of infected individuals develop encephalitis. We previously showed that 40% of patients in six cohorts had WNV encephalitis because of circulating auto-antibodies (auto-Abs) neutralizing type I IFNs. In seven new cohorts, we found that the prevalence of auto-Abs was highest (40% [17-44%]) in patients with encephalitis, and very low in a small sample of individuals with asymptomatic or mild infection. In the 13 European, Middle-Eastern and American cohorts available, odds ratios for WNV encephalitis in individuals with these auto-Abs relative to those without them in a large sample of the general population untested for WNV infection range from [~]20 (OR=17.7; 95% CI: 13.8-22.8, p<10-16) for auto-Abs neutralizing only 100 pg/mL IFN-2 and/or IFN-{omega} to >2000 (OR=2218.4; 95% CI: 125.1-39337.7, p<10-16) for auto-Abs neutralizing high concentrations of IFN-2 and high or low concentrations of IFN-{omega}. Pre-existing autoantibodies neutralizing type I IFNs are therefore causal for WNV encephalitis in about 40% of patients. SummaryIn 13 cohorts of individuals with WNV infection, the risk of WNV encephalitis is increased 20 to >2,000 times by circulating auto-Abs neutralizing type I IFNs, depending on the concentration and combination of type I IFNs neutralized and patient age.

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Random survival forests identify myocardial gene signatures associated with survival in heart failure with preserved ejection fraction

Kannan, S.; Knutsdottir, H.; Vaishnav, J.; Bader, J. S.; Kass, D. A.; Sharma, K.; Hahn, V. S.

2025-06-11 genomics 10.1101/2025.06.08.658488 medRxiv
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Heart failure with preserved ejection fraction (HFpEF) continues to be poorly understood at the molecular level. While previous studies have identified gene expression signatures unique to HFpEF, genes associated with clinical decompensation have not been determined. Here, we performed exploratory analysis of myocardial RNA-seq data to identify genes associated with event-free survival in HFpEF. We analyzed previously published RNA sequencing data of right ventricular septal endomyocardial biopsies from HFpEF patients (n=41) with paired clinical, echocardiographic, and outcome data (including mortality and heart failure hospitalizations). We constructed random survival forests with forward stepwise regularization (the "variable hunting" method) to determine genes associated with time to first event using a combined end-point of heart failure hospitalization or all-cause death. Selection of candidate forest variables was tested with both random and weighted sampling methods. We identified 33 genes that are predictive of survival in HFpEF. This set includes genes previously implicated in heart failure, including ADAMTSL2, ADRB1, BMP6, and METRNL. Survival forests constructed using these genes outperform those constructed from clinical and hemodynamic parameters alone (out-of-bag C-index 0.894 vs 0.545). Moreover, in survival forests constructed from both gene data and hemodynamic measurements, individual survival genes consistently showed higher variable importance than clinical/hemodynamic parameters. Our study shows that random survival forests identify myocardial gene signatures that may better model HFpEF prognosis than clinical measurements. Further studies are warranted to validate findings in independent cohorts.

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Galectin-anchored indoleamine 2,3-dioxygenase suppresses local inflammation

Bracho-Sanchez, E.; Rocha, F.; Bedingfield, S. K.; Partain, B. D.; Brusko, M. A.; Colazo, J. M.; Fettis, M. M.; Farhadi, S. A.; Helm, E. Y.; Koenders, K.; Kwiatkowski, A. J.; Macias, S. L.; Restuccia, A.; Wanchoo, A.; Avram, D.; Allen, K. D.; Duvall, C. L.; Wallet, S. M.; Hudalla, G. A.; Keselowsky, B. G.

2021-05-09 bioengineering 10.1101/2021.05.07.443161 medRxiv
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Summary paragraphChronic inflammation underlies the onset, progression and associated pain of numerous diseases.(1) Current anti-inflammatory treatments administered systemically are associated with moderate-to-severe side effects, while locally administered drugs have short-lived efficacy, and neither approach successfully modifies the underlying causality of disease.(2) We report a new way to locally modulate inflammation by fusing the enzyme indoleamine 2,3-dioxygenase 1 (IDO) to galectin-3 (Gal3). A general regulator of inflammation(3), IDO is immunosuppressive(4), catabolizing the essential amino acid tryptophan into kynurenine.(5) Recently we demonstrated that extracellular exogenous IDO regulates innate immune cell function(6), and envisioned delivering IDO into specific tissues would provide control of inflammation. However, proteins problematically diffuse away from local injection sites. Addressing this, we recently established that fusion to Gal3 anchors enzymes to tissues(7) via binding to extracellular glycans. Fusion protein IDO-Gal3 was retained in injected tissues and joints for up to a week or more, where it suppressed local inflammation in rodent models of endotoxin-induced inflammation, psoriasis, periodontal disease and osteoarthritis. Amelioration of local inflammation, disease progression and inflammatory pain were concomitant with homeostatic preservation of tissues without global immune suppression. Thus, IDO-Gal3 presents a new concept of anchoring immunomodulatory enzymes for robust control of focal inflammation in multiple disease settings.

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T cell-derived IFNγ instructs ECM crosslinking by cardiac fibroblasts through LOXL3 in experimental cardiometabolic HFpEF

Emig, R.; Robbe, Z. L.; Kley, C.; Smolgovsky, S.; Travers, J. G.; Blanton, R. M.; McKinsey, T. A.; Black, L. D.; Alcaide, P.

2026-03-18 pathology 10.64898/2026.03.16.712110 medRxiv
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BackgroundHeart failure with preserved ejection fraction (HFpEF) is a major clinical challenge characterized by diastolic dysfunction. Left ventricular stiffening and inflammation are hallmarks of HFpEF, yet the contribution of extracellular matrix (ECM) stiffness and the immune-stromal mechanisms driving ECM stiffening in cardiometabolic HFpEF remain poorly understood. MethodsWe used the murine "2-hit model" of cardiometabolic HFpEF, in which the combination of high fat diet and hypertension induced by L-NAME causes diastolic dysfunction. We evaluated diastolic function by echocardiography and ECM mechanics by uniaxial tensile testing of decellularized cardiac tissue. Functional in vivo studies included genetic depletion of T cells, interferon-{gamma} (IFN{gamma}) knockout mice, and pharmacological lysyl oxidase inhibition. We combined co-cultures of CD4+ T cells and cardiac fibroblasts (CFB) with mechanical testing of cardiac ECM and molecular biology to elucidate cellular and molecular mechanisms. ResultsLeft ventricular ECM stiffness strongly correlated with impaired diastolic function in experimental cardiometabolic HFpEF. Cardiac CD4 T cell infiltration was required for ECM stiffening and upregulation of lysyl oxidase enzymes in CFB. CD4+ T cell-derived IFN{gamma} was both necessary and sufficient to induce LOXL3 in CFB, which increased ECM stiffness in vitro. Mechanistically, IFN{gamma} signaling activated hypoxia-inducible factor-1 (HIF1) in CFB, driving LOXL3 expression and subsequent collagen crosslinking. Genetic or pharmacologic disruption of this IFN{gamma}-HIF1-LOXL3 axis in vivo attenuated adverse ECM remodeling and improved diastolic function. ConclusionsCD4 T cells promote pathological ECM stiffening in cardiometabolic HFpEF through IFN{gamma}-mediated, LOXL3-dependent ECM crosslinking by CFB. Targeting this immune-stromal pathway may offer a novel therapeutic strategy for HFpEF.

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Divergence of variant binding/neutralizing antibodies following SARS-CoV-2 booster vaccines in myeloma: Impact of hybrid immunity

Moreno, A.; Manning, K.; Azeem, M. I.; Nooka, A. K.; Ellis, M.; Manalo, R. J.; Switchenko, J. M.; Wali, B.; Kaufman, J. L.; Hofmeister, C. C.; Joseph, N. S.; Lonial, S.; Dhodapkar, K. M.; Dhodapkar, M. V.; Suthar, M. S.

2023-08-25 immunology 10.1101/2023.08.17.553767 medRxiv
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We characterized virus-neutralization and spike-binding antibody profiles in myeloma patients following monovalent or bivalent-SARS-CoV-2 booster vaccination. Vaccination improves the breadth of binding antibodies but not neutralization activity against current variants. Hybrid immunity and immune imprinting impact vaccine-elicited immunity.

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WBC population dynamics differ in response to acute ischemic and infectious insults and can discriminate clinically maladaptive responses to myocardial infarction.

Ranjeva, S.; Foy, B.; Mow, C.; Carlson, J.; Aguirre, A.; Nahrendorf, M.; Higgins, J.

2026-05-05 intensive care and critical care medicine 10.64898/2026.05.03.26352288 medRxiv
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Leukocytosis, or elevated white blood cell count (WBC), is a clinical hallmark of the systemic inflammatory response following acute ischemia or infection. However, WBC population dynamics during the initial inflammatory response are poorly understood. It is unknown whether early WBC dynamics differ by etiology or impact clinical risk. We fit mathematical models to WBC trajectories for patients hospitalized following acute ischemia or infection. We found differences between responses to strong ischemic insult (acute myocardial infarction, AMI) and strong infectious insult (sepsis). Among patients who recovered and survived hospitalization, net WBC growth following ischemia was [~]1.8x faster than following infection. Response kinetics and dynamics were correlated with short-term mortality in AMI. Increased immature neutrophil production over 24h preceding WBC peak was associated with [~]2x increased odds of short-term AMI mortality, suggesting that dysregulated responses to ischemia may involve bone marrow overactivation towards increased proliferation. Our work provides novel insight into fundamental etiology-specific differences in acute inflammatory responses from routine clinical data and is consistent with recent evidence of a maladaptive role for emergency granulopoiesis in AMI. One Sentence SummaryWBC dynamics differ between ischemia and infection in the early response to acute inflammatory insult, and can discriminate clinically maladaptive responses to myocardial infarction.

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Dysregulated STAT3 signaling and T cell immunometabolic dysfunction define a targetable, high mortality subphenotype of critically ill children

Lindell, R. B.; Sayed, S.; Campos, J. S.; Knight, M.; Mauracher, A. A.; Hay, C. A.; Conrey, P. E.; Fitzgerald, J. C.; Yehya, N.; Famularo, S. T.; Arroyo, T.; Tustin, R.; Fazelinia, H.; Behrens, E. M.; Teachey, D. T.; Freeman, A. F.; Bergerson, J. R. E.; Holland, S. M.; Leiding, J. W.; Weiss, S. L.; Hall, M. W.; Zuppa, A. F.; Taylor, D. M.; Feng, R.; Wherry, E. J.; Meyer, N. J.; Henrickson, S. E.

2024-06-11 intensive care and critical care medicine 10.1101/2024.06.11.24308709 medRxiv
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Sepsis is a leading cause of morbidity and mortality in critically ill children, yet heterogeneity in immune responses complicates the development of targeted therapies. Although immune dysregulation is associated with poor outcomes in sepsis, it remains unclear which host immune factors contribute causally to sepsis morbidity and mortality. To address this gap, we integrated deep immune phenotyping, plasma proteomics, single-cell transcriptomics, and phosphoflow cytometry in a prospective cohort of 88 critically ill children to elucidate the immunologic mechanisms which underly disease heterogeneity. Unsupervised clustering of plasma cytokines identified three immunologic subgroups, including a high-severity group ("Group C") characterized by marked hypercytokinemia, driven primarily by IL-6 and IFN-{gamma}. Group C exhibited distinct alterations in immune cell frequency and activation status, along with a strong association between hyperinflammatory signaling and lymphocyte dysfunction. Single-cell RNA sequencing revealed transcriptional signatures of T cell activation and metabolic stress, and identified widespread suppression of a lymphoid protective gene program across CD8 T cell subsets. In the setting of increased expression of activation markers, T cell receptor repertoire analysis revealed no dominant clonotypes, consistent with a bystander mechanism of T cell activation. Using phosphoflow cytometry, we demonstrated baseline hyperactivation of STAT1 and STAT3 in CD8 T cells from patients in Group C, and these cells failed to respond to aCD3/aCD28 stimulation. Together, these findings define IL-6/IFN-{gamma}-driven T-cell dysfunction as a distinct endotype of immune dysregulation in pediatric sepsis, highlighting the JAK/STAT axis as a potential future target for immunomodulatory therapy.

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Autoantibodies neutralizing type I interferons underlie a third of cases of Chikungunya virus encephalitis or myelitis

Tran, V. L.; Gervais, A.; Champeaux, M.-M.; de Souza Sampaio, M. P.; Abel, S. L.; Calmont, I.; do Rosario, M. S.; Schidlowski, L.; Simione, J. D.; Alves, P. A.; Puel, A.; Bastard, P.; Abel, L.; Prando, C.; Franca, R. F. d. O.; de Siqueira, I. C.; Cabie, A.; Cobat, A.; Zhang, S.-Y.; Casanova, J.-L.

2026-07-27 infectious diseases 10.64898/2026.07.23.26358609 medRxiv
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Chikungunya virus (CHIKV) infection is typically not life-threatening but may, in rare cases, affect the central nervous system (CNS). In three cohorts of confirmed CHIKV cases from Martinique (French overseas territory) and Brazil (patients aged 0--89 years, n = 245), 20 patients had CNS infection (aged 17--87 years). Autoantibodies neutralizing type I interferons (AAN-I-IFN) were found in 35% of patients (4 male and 3 female, aged 17--87 years) with encephalitis (4/15), encephalomyelitis (1/2), or myelitis (2/3), but were absent in 225 patients without CNS infection. They neutralized high concentrations (10--1,000 ng/mL) of IFN-2, IFN-8, and IFN-{omega}, and the antibodies of one patient also neutralized IFN-{beta}. All samples also neutralized the other 10 IFN- subtypes (at least 100 pg/mL). This combination of blood autoantibodies occurs in ~0.02% and 0.6% of healthy individuals under and over 70 years of age, respectively. The presence of AAN-I-IFN before CHIKV infection therefore increased the risk of CNS disease ~850-fold relative to the general population.

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Pix2Path: Integrating Spatial Transcriptomics and Digital Pathology with Deep Learning to Score Pathological Risk and Link Gene Expression to Disease Mechanisms

Fu, X.; Chen, Y.

2024-08-19 pathology 10.1101/2024.08.18.608468 medRxiv
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Spatial transcriptomics (ST) provides high-resolution mapping of gene expression within tissues, and integrating ST with digital pathology can offer unprecedented insights into the molecular mechanisms underlying various diseases. However, existing methods primarily focus on aligning these two distinct datasets, often neglecting the causal connections between spatial gene activity and pathological phenotype. We introduce Pix2Path, a deep learning-based approach utilizing conditional generative adversarial networks (cGANs), to bridge the gap between spatial transcriptomics and digital pathology. Pix2Path can process data from various spatial transcriptomics (ST) technologies, assess pathological risk scores across different conditions, and supports a leave-one-out spatial in silico gene perturbation strategy. As demonstrated in AD A{beta} plaques pathology, this approach allows to link gene expression changes to tissue morphology and pathology without relying on predefined conditions, providing a new perspective on understanding disease mechanisms.

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SARS-CoV-2 spike conformation determines plasma neutralizing activity

Bowen, J. E.; Walls, A. C.; Joshi, A.; Sprouse, K. R.; Stewart, C.; Tortorici, M. A.; Franko, N. M.; Logue, J. K.; Mazzitelli, I. G.; Tiles, S. W.; Ahmed, K.; Shariq, A.; Snell, G.; Iqbal, N. T.; Geffner, J.; Bandera, A.; Gori, A.; Grifantini, R.; Chu, H. Y.; Van Voorhis, W. C.; Corti, D.; Veesler, D.

2021-12-21 immunology 10.1101/2021.12.19.473391 medRxiv
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Numerous safe and effective COVID-19 vaccines have been developed that utilize various delivery technologies and engineering strategies. The influence of the SARS-CoV-2 spike (S) glycoprotein conformation on antibody responses induced by vaccination or infection in humans remains unknown. To address this question, we compared plasma antibodies elicited by six globally-distributed vaccines or infection and observed markedly higher binding titers for vaccines encoding a prefusion-stabilized S relative to other groups. Prefusion S binding titers positively correlated with plasma neutralizing activity, indicating that physical stabilization of the prefusion conformation enhances protection against SARS-CoV-2. We show that almost all plasma neutralizing activity is directed to prefusion S, in particular the S1 subunit, and that variant cross-neutralization is mediated solely by RBD-specific antibodies. Our data provide a quantitative framework for guiding future S engineering efforts to develop vaccines with higher resilience to the emergence of variants and longer durability than current technologies.

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Vaccination boosts protective responses and counters SARS-CoV-2-induced pathogenic memory B cells

Mishra, P. K.; Bruiners, N.; Ukey, R.; Datta, P.; Onyuka, A.; Handler, D.; Hussain, S.; Honnen, W.; Singh, S.; Guerrini, V.; Yin, Y.; Dewald, H.; Choudhary, A.; Horton, D. B.; Barret, E. S.; Roy, J.; Weiss, S. H.; Fitzgerald-Bocarsly, P.; Blaser, M. J.; Carson, J. L.; Panettieri, R. A.; Lardizabal, A.; Chang, T. L.; Pinter, A.; Gennaro, M. L.

2021-05-12 infectious diseases 10.1101/2021.04.11.21255153 medRxiv
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Given the rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the recent implementation of SARS-CoV-2 vaccination, we have much to learn about the duration of immune protection and the interface between the immune responses to infection and to vaccination. To address these questions, we monitored immune responses to SARS-CoV-2 infection in convalescent individuals over seven months and following mRNA vaccination. Spike Receptor-Binding-Domain (RBD)-specific circulating antibodies and plasma neutralizing activity generally decreased over time, whereas RBD-specific memory B cells persisted. Additionally, using antibody depletion techniques, we showed that the neutralizing activity of plasma specifically resides in the anti-RBD antibodies. More vigorous antibody and B cell responses to vaccination were observed in previously infected subjects relative to uninfected comparators, presumably due to immune priming by infection. SARS-CoV-2 infection also led to increased numbers of double negative B memory cells, which are described as a dysfunctional B cell subset. This effect was reversed by SARS-CoV-2 vaccination, providing a potential mechanistic explanation for the vaccination-induced reduction in symptoms in patients with "Long-COVID".

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High-level clarithromycin resistance: a metabolic vulnerability exploited by bismuth in Helicobacter pylori

He, C.; Huang, Y.

2026-05-01 gastroenterology 10.64898/2026.04.29.26351907 medRxiv
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Background & AimsClarithromycin (CLA) resistance severely compromises the efficacy of triple therapy (TT) against Helicobacter pylori (H. pylori). Bismuth-based regimens exhibit greater efficacy against CLA-resistant H. pylori than against strains resistant to other antibiotics, suggesting a resistance-specific vulnerability rather than broad antimicrobial activity. The mechanistic basis for this selectivity, however, remains unknown. We hypothesized that high-level CLA resistance confers a metabolically targetable vulnerability that can be exploited by bismuth, and that a quantitative MIC of CLA threshold could identify this responsive subset. MethodsWe conducted a real-world retrospective analysis of 4,610 pediatric patients with H. pylori infection treated between 2019 and 2024, among whom 1,844 (40%) had complete follow-up data for eradication assessment. In parallel, we prospectively enrolled 51 patients with culture-positive isolates--the largest liquid checkerboard panel reported to date--to evaluate bismuth-CLA interactions and track treatment outcomes. Mechanistic validation included transcriptomic profiling and functional assays of iron and ATP metabolism, with iron chelation and supplementation experiments. ResultsIn the retrospective real-world cohort (n = 4,610; 1,844 with follow-up), bismuth quadruple therapy (BQT) achieved superior eradication specifically in CLA-resistant infections (93.1% vs 68.8% with TT; p = 0.017). In vitro, bismuth-CLA synergy was exclusive to resistant strains and intensified with increasing MIC of CLA. Mechanistically, bismuth triggered coordinated depletion of intracellular iron and ATP--a phenotype mimicked by iron chelation and reversed by iron supplementation. A baseline MIC of CLA [&ge;]16 g/mL robustly predicted this synergy (AUC = 0.991) and was prospectively validated in an independent patient subset: bismuth cured 96% of high-level resistant patients (MIC [&ge;] 16 g/mL) versus 0% with triple therapy (p < 0.001). ConclusionHigh-level CLA resistance defines an iron-dependent metabolic vulnerability in H. pylori that is selectively targeted by bismuth. The MIC threshold of [&ge;] 16 g/mL provides the first clinically actionable biomarker for resistance-guided therapy, transforming a marker of treatment failure into a positive predictor of bismuth response. These findings establish the mechanistic and clinical foundation for MIC-stratified eradication strategies and inform future randomized trials aimed at precision management of antibiotic-resistant H. pylori infection. Graphical abstractO_ST_ABSLeftC_ST_ABSHigh-level clarithromycin (CLA) resistance defines a distinct physiological phenotype in Helicobacter pylori, in which an elevated MIC of CLA ([&ge;] 16 {micro}g/mL) predicts poor eradication with triple therapy (TT) but favorable response to bismuth-containing quadruple therapy (BQT). MiddleMechanistically, CLA resistance is associated with upregulation of the ferric uptake regulator Fur, leading to reprogrammed iron homeostasis and an increased metabolic burden. Colloidal bismuth subcitrate (CBS) disrupts Fur-dependent iron regulation, exacerbates iron-restricted metabolic stress, and compromises cellular integrity, thereby selectively sensitizing CLA-resistant bacteria to antibiotic killing. RightTranslational implication of reframing antibiotic resistance as a therapeutic vulnerability--bismuth-based regimens function as a "key" that unlocks resistance-associated metabolic liabilities, delays resistance evolution, and improves treatment outcomes. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/26351907v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@28fb58org.highwire.dtl.DTLVardef@8d5190org.highwire.dtl.DTLVardef@1e5fc9dorg.highwire.dtl.DTLVardef@2bc102_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Garetosmab, an inhibitor of activin A, reduces heterotopic ossification and flare-ups in adults with fibrodysplasia ossificans progressiva: a randomized, double-blind, placebo-controlled phase 2 trial

Di Rocco, M.; Forleo-Neto, E.; Pignolo, R.; Keen, R.; Orcel, P.; Funck-Brentano, T.; Roux, C.; Kolta, S.; Madeo, A.; Bubbear, J. S.; Tabarkiewicz, J.; Szczepanek, M.; Bachiller-Corral, J.; Cheung, A. M.; Dahir, K. M.; Botman, E.; Raijmakers, P. G.; Al Mukaddam, M.; Tile, L.; Portal-Celhay, C.; Sarkar, N.; Hou, P.; Musser, B.; Boyapati, A.; Mohammadi, K.; Mellis, S.; Economides, A. N.; Gonzalez Trotter, D.; Herman, G.; O'Meara, S. J.; DelGizzi, R.; Weinreich, D. M.; Yancopolous, G. D.; Eekhoff, E. M. W.; Kaplan, F. S.

2023-01-12 infectious diseases 10.1101/2023.01.11.23284254 medRxiv
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BackgroundFibrodysplasia ossificans progressiva (FOP), an ultra-rare disorder caused by mutations in the gene encoding activin A receptor type 1 (ACVR1), is characterized by painful flare-ups and cumulative heterotopic ossification (HO). Garetosmab, a fully-human monoclonal antibody blocking activin A, prevents HO in FOP mice. MethodsLUMINA-1 (NCT03188666) was a phase 2, multi-center, randomized, double-blind, placebo-controlled study evaluating the safety, tolerability, and effects on HO of intravenous (IV) garetosmab 10 mg/kg every 4 weeks (Q4W). Adult patients with FOP were randomized to garetosmab or placebo for 28 weeks (Period_1), followed by an open-label period (Period_2). After Period_2, patients were allowed to stay on garetosmab in an open-label extension. For Period_1, primary endpoints were HO total lesion activity (HO-TLA) by 18F-sodium fluoride positron emission tomography (18F-NaF PET) and HO total lesion volume by computed tomography (CT). The Period_2 primary endpoint compared the number of new lesions in Period_2 versus Period_1. The safety primary endpoint was incidence and severity of TEAEs through the end of the Period 1 at week 28. FindingsPatients (n=44) were randomized to garetosmab (n=20) or placebo (n=24). In Period_1, there was a trend for garetosmab to decrease HO-TLA versus placebo (24.6%; P=0.07), primarily driven by near complete prevention of new lesions (97% decrease by 18F-NaF PET, post-hoc P=0.009; 90% relative reduction by CT, post-hoc P=0.017); flare-ups were significantly reduced (P=0.0005). For placebo patients transitioning to garetosmab in Period_2, no patients developed new HO lesions (0% in Period_2 versus 40.9% in Period_1; P=0.0027) by CT. All 44 patients met primary safety endpoint of at least one TEAE during Period 1. Garetosmab was associated with more adverse events than placebo: mild recurrent epistaxis, madarosis, and skin/soft tissue infections. Overall, the AEs were predominantly mild in severity, with no effect on patients ability to receive garetosmab. Five deaths (5/44; 11.4%) occurred either in Period_2 or the open-label extension. The deaths were associated with baseline disease severity in some, preexisting comorbidities in others and occurred following 8-16 doses (median: 15) of garetosmab in the open label/follow-up periods. InterpretationGaretosmab reduced flare-ups and prevented new HO lesions in FOP patients. Although side effects were mild to moderate, there were a relatively high number of deaths for a small study; the deaths were not related to epistaxis and considered unlikely to be related to garetosmab. FundingRegeneron Pharmaceuticals, Inc.

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Germline NF2 variant position constrains somatic second hits and determines clinical severity in Neurofibromatosis Type 2-related schwannomatosis

Ravindra, N.; Asuzu, D. T.; Celano, E.; Kumar, S.; Chopra, A.; Mandal, D.; Mullaney, D.; Bhatt, D.; Laws, M. T.; Hayes, C.; Kunnath, I.; Sisay, B.; Elkahloun, A.; Asthagiri, A. R.; Lehky, T.; Zalewski, C.; Heiss, J. D.; Kim, H. N.; Chittiboina, P.

2026-07-28 oncology 10.64898/2026.07.27.26359036 medRxiv
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Purpose: Neurofibromatosis type 2-related schwannomatosis (NF2-SWN) is an autosomal dominant tumor syndrome with complete penetrance and variable expressivity. Underlying patterns of disease burden and severity are largely unexplained. Methods: We comprehensively phenotyped 168 NF2-SWN patients over a mean duration of 4.5 years. We used a custom sequencing panel of NF2 and schwannomatosis genes to identify germline (n=166) and somatic variants in tumors (n=37). An optimized composite severity (CSS) score based on clinical and radiological data was created to analyze the effect of genetic variants on phenotype. Results: We found significant variable expressivity not explainable by demographic variables. Germline variants included premature termination (42%), splice-site (18%), and large deletions (16%). The CSS successfully predicted worsening clinical function in patients. Unsupervised clustering of clinical data revealed distinct phenotypic clusters that corresponded to CSS. Mosaicism, however, was not associated with CSS or any other disease severity marker. CSS was significantly associated with germline variant location along the NF2 locus. Specifically, FERM-F1 and the -helical variants were associated with increased disease severity. Within tumors, germline variants with severe effects on merlin acquired milder somatic second-hits at the NF2 locus. Conclusion: We identified a second-hit modifier to the Mendelian first-hit: severe germline variants were associated with milder somatic variants, and vice versa. This phenomenon partly explains the variable expressivity in NF2-SWN.

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The hyperacute plasma proteome reports injury severity and defines distinct trauma endotypes

Masarone, S.; Hernandez Mir, G.; Ross, J.; Pott, J.; Brohi, K.; Barnes, M. R.; Pennington, D. J.

2026-02-03 intensive care and critical care medicine 10.64898/2026.01.31.26345281 medRxiv
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The host response to traumatic injury is varied and unpredictable. Patients with subjectively similar injuries progress along divergent clinical paths, from uncomplicated recovery to extended hospitalisation, multiple organ dysfunction, and life-long ill health. The temporal certainty of trauma nonetheless provides immediate opportunity to predict clinical trajectory and intervene therapeutically. We demonstrate using machine-learning that the hyperacute plasma proteome can function as a physiology-driven indicator of injury severity. Moreover, it identifies two serious-injury endotypes that differentially predict unfavourable clinical trajectories. Notably, a prominent neuronal guidance protein signature, that reports vascular dysfunction and immune activation, together with an anti-coagulation/pro-fibrinolytic state, identify those patients who progress to adverse clinical outcomes. Together, these mechanistic insights into immediate host responses to serious trauma reveal tractable targets for future therapeutic interventions.