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Abstract
Sustained injury to renal tubular epithelial cells (TECs), driven by excessive autophagy, is a critical mechanism underlying kidney fibrosis. Our previous work identified JLP—a TEC-expressed scaffolding protein—as an endogenous anti-fibrotic factor that counteracts TGF-β1–induced autophagy and fibrogenesis. However, the mechanism underlying JLP downregulation in renal fibrosis remains unclear. Here, we delineated a TGF-β1/LEF1/β-catenin/JLP axis that governed TEC autophagy through a dichotomous regulatory circuit. Under physiological conditions, low levels of β-catenin and LEF1 with minimal nuclear localization permit normal JLP expression, which in turn maintains autophagy in check. In contrast, during renal injury, TGF-β1 promoted the expression and nuclear translocation of β-catenin and LEF1, which together suppressed JLP transcription. This loss of JLP-mediated inhibition led to unchecked autophagy and exacerbated fibrotic damage. Analyses of kidney tissues from patients with CKD, murine fibrotic kidneys, and cultured HK-2 cells confirmed consistent JLP downregulation accompanied by upregulation and nuclear accumulation of LEF1 and β-catenin. Therapeutic intervention using the β-catenin/LEF1 inhibitor iCRT3 or LEF1-targeted silencing in murine fibrosis models restored JLP expression, attenuated TEC autophagy, and ameliorated renal fibrosis. These findings revealed an autoregulatory circuit controlling TEC autophagy and fibrogenesis, and supported LEF1 and β-catenin as potential therapeutic targets in CKD.
Authors
Chen Li, Meng Zhang, Maoqing Tian, Zeyu Tang, Yuying Hu, Yuyu Long, Xiaofei Wang, Liwen Qiao, Jiefei Zeng, Yujuan Wang, Xinghua Chen, Cheng Chen, Xiaoyan Li, Lu Zhang, Huiming Wang
Abstract
Next generation sequencing can identify previously uncharacterized gene expression patterns in disease. Beyond differentially expressed genes analysis, we investigated the ability of within-population diversity (α-diversity) of the transcriptome to reveal additional biological information in alcohol-associated liver disease (ALD), comparing Differential Shannon diversity (DSD) to transcriptome heterogeneity changes. RNA sequencing data from normal livers and patients with early ALD and severe AH were analyzed. α-diversity indices and Percent Shannon Diversity of a gene, which refers to this gene's contribution to total Shannon entropy, were calculated. Ingenuity pathway analysis identified canonical pathways determined by differentially expressed genes (DEG) and DSD approaches. ALD significantly decreased hepatic transcriptome α-diversity correlating with increased relative contribution of select genes. These changes were driven by lower abundance gene expression loss. DEG and DSD analyses showed overlapping genes and canonical pathways, but DSD also identified additional genes and pathways not highlighted by DEG, including fatty acid oxidation, extracellular matrix degradation, and cholesterol metabolism pathways that may represent additional therapeutic targets. Importantly, DSD more effectively identified differences between ASH and AH. Overall, α-diversity analysis revealed that ALD progressively reduces transcriptome heterogeneity, and that DSD provides complementary insights into disease mechanisms missed by standard approaches.
Authors
Sudrishti Chaudhary, Jia-Jun Liu, Silvia Liu, Marissa Di, Juliane I. Beier, Ramon Bataller, Josepmaria Argemi, Panayiotis V. Benos, Gavin E. Arteel
Abstract
Activation of lung fibroblasts in response to epithelial injury and inflammation provokes pulmonary fibrosis (PF). Endogenous molecular brakes counteracting fibroblast activity can be targets for therapies. Preclinical studies of synthetic C-type natriuretic peptide (CNP) indicated that this hormone might provide such a brake. As shown here, CNP exerts antifibrotic effects in cultured lung fibroblasts as well as precision cut lung slices from patients with PF, supporting clinical relevance. Therefore, augmenting or supplementing endogenous CNP could improve the treatment of such patients. To unravel whether paracrine CNP counteracts inflammation-driven PF, we studied mice with fibroblast-restricted knock-out of guanylyl-cyclase-B (GC-B), its cGMP-synthesizing receptor. Fibroblast GC-B-KO mice had enhanced bleomycin-induced lung inflammation, with increased expression of proinflammatory, profibrotic cytokines. Nevertheless, subsequent PF was not exacerbated. Molecular studies revealed that inflammation led to inhibition of CNP signaling in resident myofibroblasts, namely GC-B downregulation and induction of CNP/cGMP-degrading pathways. Despite this, a single subcutaneous injection of the recently developed long-acting CNP analog, MS~[Gln6,14]CNP-38, abrogated experimental lung inflammation and fibrosis. We conclude that CNP signaling in lung fibroblasts has anti-inflammatory and antifibrotic effects. Attenuation of this endogenous brake participates in the pathogenesis of PF and rescuing this pathway with long-acting CNP-analogs may have therapeutic potential.
Authors
Rene Weyer, Katharina Völker, Tamara Potapenko, Lisa Krebes, Marco Abesser, Anna-Lena Friedrich, Eva Lessmann, Ali Khadim, Clemens Ruppert, Elie El Agha, Dalia Sheta, Andreas Beilhack, Daniel V. Santi, Eric L. Schneider, Michaela Kuhn, Swati Dabral
Abstract
Iron regulatory protein 1 (IRP1) is a post-transcriptional regulator of cellular iron metabolism. In mice, loss of IRP1 causes polycythemia through translational de-repression of hypoxia-inducible factor 2α (HIF2α) mRNA, which increases renal erythropoietin production. Here we show that Irp1-/- mice develop fasting hypoglycemia and are protected against high-fat diet–induced hyperglycemia and hepatic steatosis. Discovery-based proteomics of Irp1-/- livers revealed a mitochondrial dysfunction signature. Seahorse flux analysis in primary hepatocytes and differentiated skeletal muscle myotubes confirmed impaired respiratory capacity, with a shift from oxidative phosphorylation to glycolytic ATP production. This metabolic rewiring was associated with enhanced insulin sensitivity and increased glucose uptake in skeletal muscle. Under metabolic stress, IRP1 deficiency altered the redox balance of mitochondrial iron, resulting in inefficient energy production and accumulation of amino acids and metabolites in skeletal muscle, rendering them unavailable for hepatic gluconeogenesis. These findings identify IRP1 as a critical regulator of systemic energy homeostasis.
Authors
Wen Gu, Nicole Wilkinson, Carine Fillebeen, Darren Blackburn, Korin Sahinyan, Eric Bonneil, Tao Zhao, Zhi Luo, Vahab Soleimani, Vincent Richard, Christoph H. Borchers, Albert Koulman, Benjamin Jenkins, Bernhard Michalke, Hans Zischka, Judith Sailer, Vivek Venkataramani, Othon Iliopoulos, Gary Sweeney, Kostas Pantopoulos
Abstract
Multisystemic Smooth Muscle Dysfunction Syndrome (MSMDS) is a rare disorder caused by ACTA2 mutations, including the R179H variant, which alters actin filament stability and dynamics and smooth muscle contractility. While cardiovascular complications dominate its clinical presentation, gastrointestinal (GI) dysfunction significantly impacts quality of life. To investigate the structural, functional, and cellular basis of gut dysmotility in MSMDS, we reviewed clinical data from 24 MSMDS patients and studied the ACTA2 R179H mouse model Patients exhibited severe gut dysmotility, with 75% requiring medication for chronic constipation. ACTA2 mutant mice displayed cecal and colonic dilatation, reduced intestinal length, and disrupted colonic migrating motor complexes (CMMCs). Delayed whole-gut transit and impaired contractile responses to electrical and pharmacological stimulation were observed. Transcriptomic analysis revealed significant actin cytoskeleton-related gene changes in smooth muscle cells, and immune profiling identified increased lymphocytic infiltration. Despite functional abnormalities, there were no obvious changes in the enteric nervous system. These findings establish ACTA2 mice as a robust model for studying GI pathology in MSMDS, elucidating the role of smooth muscle dysfunction in gut dysmotility. This model provides a foundation for developing targeted therapies aimed at restoring intestinal motility by directly addressing actin cytoskeletal disruptions in smooth muscle cells.
Authors
Ahmed A. Rahman, Rhian Stavely, Leah C. Ott, Christopher Y. Han, Kensuke Ohishi, Ryo Hotta, Alan J. Burns, Sabyasachi Das, Emily Da Cruz, Diana Tambala, Mark E. Lindsay, Patricia L. Musolino, Allan M. Goldstein
Abstract
Functional antibody responses to malaria transmission-blocking vaccines (TBVs) are assessed using the Standard Membrane Feeding Assay (SMFA). This assay quantifies percentage reduction of oocyst levels in mosquitoes fed gametocytes mixed with antisera/antibodies, referred to as transmission-reducing activity (TRA). As TBVs advance to large clinical trials, new scalable assays are needed to characterize vaccine responses. Here, we developed an epitope-specific competitive ELISA platform (P230Compete) for TBV candidate Pfs230D1, based on single-chain variable fragments (scFv) against epitopes recognized by human monoclonal antibodies with high TRA. We quantified functional epitope-specific antibody responses (F) in Phase 1 Pfs230D1-EPA/AS01 vaccine trial participants, using 171 serum samples collected at two post-vaccination timepoints. Five antibody features were examined by P230Compete including total IgG (reported as ELISA units, EUF), IgG subclasses (IgG1F, IgG3F, IgG4F), and bound complement factor C1q (C1qF). EUF and IgG1F demonstrated strong correlation and excellent prediction of TRA≥80% in logistic regression analysis (AUC of 0.81 for both assays post-dose 3, and 0.80 and 0.76 post-dose 4). Furthermore, combining EUF and IgG1F showed even better predictive performance at each timepoint. P230Compete offers a promising proxy assay to replace SMFA in late-stage Pfs230D1 trials.
Authors
Cristina A. Meehan, Matthew V. Cowles, Robert D. Morrison, Yuyan Yi, Jingwen Gu, Jen C.C. Hume, Mina P. Peyton, Issaka Sagara, Sara A. Healy, Jonathan P. Renn, Patrick E. Duffy
Abstract
This investigation leverages single-cell RNA sequencing (scRNA-Seq) to delineate the contributions of muscle-resident Schwann cells to neuromuscular junction (NMJ) remodeling by comparing a model of stable innervation with models of reinnervation following partial or complete denervation. The study discovered multiple distinct Schwann cell subtypes, including a novel terminal Schwann cell (tSC) subtype integral to the denervation-reinnervation cycle, identified by a transcriptomic signature indicative of cell migration and polarization. The data also characterizes three myelin Schwann cell subtypes, which are distinguished based on enrichment of genes associated with myelin production, mesenchymal differentiation or collagen synthesis. Importantly, SPP1 signaling emerges as a pivotal regulator of NMJ dynamics, promoting Schwann cell proliferation and muscle reinnervation across nerve injury models. These findings advance our understanding of NMJ maintenance and regeneration and underscore the therapeutic potential of targeting specific molecular pathways to treat neuromuscular and neurodegenerative disorders.
Authors
Steve D. Guzman, Ahmad Abu-Mahfouz, Carol S. Davis, Lloyd P. Ruiz, Peter C.D. Macpherson, Susan V. Brooks
Abstract
C-type natriuretic peptide (CNP) is known to promote chondrocyte proliferation and bone formation; however, CNP’s extremely short half-life necessitates continuous intravascular administration to achieve bone-lengthening effects. Vosoritide, a CNP analog designed for resistance to neutral endopeptidase, allows for once daily administration. Nonetheless, it distributes systemically rather than localizing to target tissues, which may result in adverse effects such as hypotension. To enhance local drug delivery and therapeutic efficacy, we developed a novel synthetic protein by fusing a collagen-binding domain (CBD) to CNP, termed CBD-CNP. This fusion protein exhibited stability under heat conditions and retained the collagen-binding ability and bioactivity as CNP. CBD-CNP localized to articular cartilage in fetal murine tibiae and promoted bone elongation. Spatial transcriptomic analysis revealed that the upregulation of chondromodulin expression may contribute to its therapeutic effects. Treatment of CBD-CNP mixed with collagen powder to a fracture site of a mouse model increased bone mineral content and bone volume rather than CNP-22. Intra-articular injection of CBD-CNP to a mouse model of knee osteoarthritis suppressed subchondral bone thickening. By addressing the limitations of CNP’s rapid degeneration, CBD-CNP leverages its collagen-binding capacity to achieve targeted, sustained delivery in collagen-rich tissues, offering a promising strategy for enhancing chondrogenesis and osteogenesis.
Authors
Kenta Hirai, Kenta Sawamura, Ryusaku Esaki, Ryusuke Sawada, Yuka Okusha, Eriko Aoyama, Hiroki Saito, Kentaro Uchida, Takehiko Mima, Satoshi Kubota, Hirokazu Tsukahara, Shiro Imagama, Masaki Matsushita, Osamu Matsushita, Yasuyuki Hosono
Abstract
Clonal haematopoiesis of indeterminate potential (CHIP) is the expansion of blood stem cells and progeny after somatic mutation. CHIP associates with increased cardiovascular disease (CVD) with inflammation from macrophages a proposed common effector. However, mouse CHIP studies are discordant for clonal expansion and inflammation. Similarly, directionality of association between CHIP and CVD remains debated. We investigated effects of three CHIP mutations on macrophage cytokines, clonal expansion and atherosclerosis in parallel. We find that Tet2 and Dnmt3a mutations increase cytokines and inflammasome activation in Tet2 but decrease in Dnmt3a. However, Jak2 mutant macrophages produced equivalent cytokine as wild-type. In mice, Tet2 mutants clonally expanded, but Dnmt3a and Jak2 mutants didn’t. Expansion was unaffected by systemic inflammation, while hyperlipidemia expanded Tet2-/- cells, but not mono-allelic mutants. Similarly, human Mendelian randomisation showed no effect of serum cytokines or CVD on CHIP risk. Experimental atherosclerosis was increased in females with Tet2 and males with Jak2, but unchanged with Dnmt3a mutations. Together, common CHIP mutations have disparate effects on macrophage cytokines and clonal expansion, and sex-dependent effects on atherogenesis, suggesting a common mechanism across CHIP is unlikely. Thus, CHIP mutations differ in pathophysiology and clinical sequalae across sexes and should be treated as different entities.
Authors
Paul R. Carter, Lauren Kitt, Amanda Rodgers, Nichola Figg, Ang Zhou, Chengrui Zhu, Ziyang Wang, Peter Libby, Stephen Burgess, George S. Vassiliou, Murray CH. Clarke
Abstract
Background: Sleep is increasingly recognized as essential to human health, yet the adverse health consequences of acute sleep deprivation are unknown. We hypothesized that acute sleep deprivation is associated with health outcomes and modulated by sleep-associated genotypes. Methods: LOESS smoothing was performed on sleep estimates from Fitbit users (N = 14,681) between June 1, 2016 and July 1, 2022. Dates when population minutes slept were less than the 90% confidence interval of the LOESS regression were named acute sleep deprivation events (ASDEs). Phenome-wide disease incidence among the AoU population (N = 287,012) in the 10 days post-ASDE was compared to a preceding reference period by McNemar test. Circadian rhythm and sleep duration-associated SNPs were screened to identify genotypes associated with shorter ASDE sleep duration. Influences of sleep and circadian genotype on post-ASDE influenza risk were modeled using binomial family generalized estimating equations. Results: We identified 32 ASDEs spanning major national events. A phenome-wide screen found increased risk of influenza (OR = 1.54 [1.40, 1.70], P-value = 1.00 x 10-18) following ASDEs. 56 SNPs were associated with decreased sleep duration on ASDEs. Higher quantiles of ASDE-related SNP genotype burden were associated with less ASDE sleep duration and a greater risk of influenza-associated healthcare visits. Conclusion: Major national events are associated with acute sleep deprivation and greater influenza risk which is amplified by sleep genotypes. These findings should inform public health vigilance surrounding major national events.
Authors
Neil J. Kelly, Rahul Chaudhary, Wadih El Khoury, Nishita Kalepalli, Jesse Wang, Priya Patel, Irene Chan, Haris Rahman, Aisha Saiyed, Anisha N. Shah, Colleen A. McClung, Satoshi Okawa, Mehdi Nouraie, Stephen Y. Chan
Abstract
Hofbauer cells (HBC) are fetal-derived macrophages located in the placenta that contribute to antimicrobial defense, angiogenesis, tissue remodeling, and metabolic processes within the chorionic villi. Although their roles in placental biology are increasingly recognized, the mechanisms that regulate HBC identity and function are not yet fully defined. This study aimed to define the core transcriptomic and epigenomic features of HBCs in term placentas and to examine their capacity for transcriptional responsiveness and phenotypic variation. Using chromatin accessibility profiling and bulk RNA sequencing, we found that HBCs exhibit a unique gene expression and chromatin accessibility profile compared to other fetal and adult macrophages. We identified a coordinated transcriptional network involving nuclear receptors NR4A1–3, the glucocorticoid receptor (GR), and RFX family members (RFX1, RFX2, RFX5) that appears to shape HBC identity, particularly through pathways linked to lipid metabolism and angiogenesis. Although exploratory in nature, in vitro stimulation studies showed that HBCs exhibited increased transcriptional activity in response to combined IL-4 and RSG treatment, including induction of the lipid transporter CD36. Mass cytometry analysis revealed surface markers indicative of both immature and mature macrophage states. Together, these results indicated that HBCs represent a distinct and diverse macrophage population with specialized and adaptable regulatory program in the human placenta.
Authors
Benjámin R. Baráth, Dóra Bojcsuk, Krisztian Bene, Noemí Caballero-Sánchez, Tímea Cseh, João CR. de Freitas, Petros Tzerpos, Marta Toth, Zhonghua Tang, Seth Guller, Zoárd Tibor Krasznai, Patrícia Neuperger, Gabor J. Szebeni, Gergely Nagy, Tamás Deli, Laszlo Nagy
Abstract
Mucosal secretory IgA (sIgA) plays a central role in protecting against the invasion of respiratory pathogen via the upper respiratory tract. To understand how intranasal booster induces mucosal sIgA response in humans, we first used liquid chromatography-tandem mass spectrometry for peptide identification of immunoglobulin (MS Ig-Seq) and single-cell B-cell receptor sequencing (scBCR-seq) to identify mucosal spike-specific sIgA monoclonal antibodies (mAbs) after intranasal booster. These mucosal sIgA mAbs exhibited enhanced neutralization up to 100-fold against SARS-CoV-2 variants compared to their monomeric IgG and IgA isotypes. Deep sequencing and longitudinal analysis of B-cell receptor repertoires revealed that nasal booster re-stimulates memory B cells primed by intramuscularly vaccination to undergo IgA class switching, somatic hypermutation, and clonal expansion. Single-cell sequencing revealed that intranasal booster upregulated the expression of mucosal homing receptors in spike-specific IgA-expressing B cells. This increase coincided with a transient increase of cytokines and chemokines that facilitate B cell recruitment in the nasal mucosa. Our findings demonstrate that intranasal booster can be an effective strategy for inducing upper respiratory mucosal sIgA and establishing mucosal immune protection.
Authors
Si Chen, Zhengyuan Zhang, Zihan Lin, Li Yin, Lishan Ning, Wenming Liu, Qian Wang, Chenchen Yang, Bo Feng, Ying Feng, Yongping Wang, Hengchun Li, Ping He, Huan Liang, Yichu Liu, Zhixia Li, Bo Liu, Yang Li, Diana Boraschi, Linbing Qu, Xuefeng Niu, Nanshan Zhong, Pingchao Li, Ling Chen
Abstract
Pathogenic variants in kinesin KIF11 underlie microcephaly-lymphedema-chorioretinopathy (MLC) syndrome. Although well known for regulating spindle dynamics ensuring successful cell division, the association of KIF11 (encoding EG5) with development of the lymphatic system, and how KIF11 pathogenic variants lead to lymphatic dysfunction and lymphedema remain unknown. Using patient-derived lymphoblastoid cells, we demonstrated that MLC patients carrying pathogenic stop-gain variants in KIF11 have reduced mRNA and protein levels. Lymphoscintigraphy showed reduced tracer absorption, and intestinal lymphangiectasia was detected in one patient, pointing to impairment of lymphatic function caused by KIF11 haploinsufficiency. We revealed that KIF11 is expressed in early human and mouse development with the lymphatic markers VEGFR3, Podoplanin and PROX1. In zebrafish, scRNA-seq identified kif11 specifically expressed in endothelial precursors. In human lymphatic endothelial cells (LECs), EG5 inhibition with Ispinesib, reduced VEGFC-driven AKT phosphorylation, migration and spheroid sprouting. KIF11 knockdown reduced PROX1 and VEGFR3 expression, providing for the first time a link between KIF11 and drivers of lymphangiogenesis and lymphatic identity.
Authors
Kazim Ogmen, Sara E. Dobbins, Rose Yinghan Behncke, Ines Martinez-Corral, Ryan C.S. Brown, Michelle Meier, Sascha Ulferts, Nils Rouven Hansmeier, Ege Sackey, Ahlam Alqahtani, Christina Karapouliou, Dionysios Grigoriadis, Juan C. Del Rey Jimenez, Michael Oberlin, Denise Williams, Arzu Ekici, Kadri Karaer, Steve Jeffery, Peter Mortimer, Kristiana Gordon, Kazuhide S. Okuda, Benjamin M. Hogan, Taija Mäkinen, René Hägerling, Sahar Mansour, Silvia Martin-Almedina, Pia Ostergaard
Abstract
Developing biomarkers to quantitatively monitor disease-specific T cell activity is crucial for assessing type 1 diabetes (T1D) progression and evaluating immunotherapies. This study presents an approach using V-gene targeted sequencing to quantify T cell receptor (TCR) clonotypes as biomarkers for pathogenic T cells in T1D. We identified "public" TCR clonotypes shared among multiple non-obese diabetic (NOD) mice and human organ donors, with a subset expressed exclusively by islet antigen-reactive T cells in those with T1D. Employing V-gene targeted sequencing of only TCRs containing TRAV16/16D allowed quantitative detection of the public islet antigen-reactive TCR clonotypes in peripheral blood of NOD mice. Frequencies of these public TCR clonotypes distinguished prediabetic NOD mice from those protected from diabetes. In human islets, public TCR clonotypes identical to preproinsulin-specific clones were exclusively found in T1D donors. This quantifiable TCR sequencing approach uncovered public, disease-specific clonotypes in T1D, providing biomarker candidates to monitor pathogenic T cell frequencies in blood for assessing disease activity and therapeutic response.
Authors
Laurie G. Landry, Kristen L. Wells, Amanda M. Anderson, Kristen R. Miller, Kenneth L. Jones, Aaron W. Michels, Maki Nakayama
Abstract
BACKGROUND. Chimeric antigen receptor (CAR) T-cells are a leading immunotherapy for refractory B-cell malignancies; however, their impact is limited by toxicity and incomplete efficacy. Daily (circadian) rhythms in immune function may offer a lever to boost therapeutic success; however, their clinical relevance to CAR T-cell therapy remains unknown. METHODS. We retrospectively analyzed CAR T-cell survival and complications based on infusion time at two geographically distinct hospitals in St. Louis, Missouri (n=384), and Portland, Oregon (n=331) between 1/2018 and 3/2025. The primary outcome was 90-day overall survival (OS). Secondary outcomes included event-free survival (EFS), cytokine release syndrome (CRS), immune cell-associated neurotoxicity syndrome (ICANS), ICU admission, shock, respiratory failure, and infection. We quantified the independent relationship between infusion time and outcomes using multivariable mixed-effects logistic regression and time-to-event models, adjusting for patient, oncologic, and treatment characteristics. RESULTS. The therapeutic index of CAR-T cells inversely correlated with administration time, with later infusions associated with lower effectiveness and more adverse outcomes. For each hour that CAR T-cell treatment was delayed, the adjusted odds of 90-day mortality increased by 24% (aOR 0.64-0.88, p=<0.001), severe neurotoxicity by 17% (p=0.023), and mechanical ventilation by 27% (p=0.026). These temporal patterns were most pronounced in patients receiving CD19-targeting CAR T-cell products. In contrast, we did not find an association between infusion time and severe CRS (aOR 0.99, 95% CI 0.75–1.27, p=0.92). CONCLUSION. Time of day is a potent and easily modifiable factor that could optimize CAR T-cell clinical performance. FUNDING. National Institutes of Health.
Authors
Patrick G. Lyons, Emily Gill, Prisha Kumar, Melissa Beasley, Brenna Park-Egan, Zulfiqar A. Lokhandwala, Katie M. Lebold, Brandon Hayes-Lattin, Catherine L. Hough, Nathan Singh, Guy Hazan, Huram Mok, Janice M. Huss, Colleen A. McEvoy, Jeffrey A. Haspel
Abstract
Few HIV-specific epitopes restricted by non-classical HLA-E have been described, and even less is known about the functional profile of responding CD8 T cells (CD8s). This study evaluates the functional characteristics of CD8s targeting the Gag epitope KF11 (KAFSPEVIPMF) restricted by either HLA-E (E-CD8s) or HLA-B57 (B57-CD8s). CD8s from eight people with HIV (PWH) were cocultured with KF11 peptide presented by cell lines expressing HLA-B*57:01, HLA-E*01:01 or E*01:03. CD8 responses were analyzed using scRNA-seq and scTCR-seq. Supernatants were also assessed for soluble protein profiling. HLA-I multimers were developed to identify CD8s restricted by HLA-B57 and/or HLA-E ex vivo. B57-CD8s secreted higher levels of cytotoxic cytokines such as IFNγ, whereas E-CD8s produced more chemotactic cytokines, including RANTES, CXCL10 (IP-10), and IL27, findings which were corroborated through scRNA sequencing. TCR clonotypes stimulated by KF11 were cross-restricted by HLA-B*57 and HLA-E*01/03 as demonstrated by in vitro T cell reporter assays and ex vivo multimer screening. Ex vivo CD8s were singly restricted by HLA-B57 and HLA-E, with dual restriction only observed in PWH with lower viral load. These findings demonstrate that certain HIV-specific CD8s in PWH exhibit dual restriction by HLA-B*57 and HLA-E*01/03, leading to functionally distinct immune responses depending upon the restricting allele(s).
Authors
Kevin J. Maroney, Michael A. Rose, Allisa K. Oman, Abha Chopra, Hua-Shiuan Hsieh, Zerufael Derza, Rachel Waterworth, Mark A. Brockman, Spyros A. Kalams, Anju Bansal, Paul A. Goepfert
Abstract
Kidney organoids are an emerging tool for disease modeling, especially genetic diseases. Among these diseases, X-linked Alport syndrome (XLAS) is a hematuric nephropathy affecting the glomerular basement membrane (GBM) secondary to pathogenic variations in the COL4A5 gene encoding the α5 subunit of type IV collagen [α5(IV)]. In patients carrying pathogenic variations affecting splicing, the use of antisense oligonucleotides (ASOs) offers immense therapeutic hope. In this study, we develop a framework combining the use of patient-derived cells and kidney organoids to provide evidence of the therapeutic efficacy of ASOs in XLAS patients. Using multiomics analysis, we describe the development of GBM in wild-type and mutated human kidney organoids. We show that GBM maturation is a dynamic process, which requires long organoid culture. Then, using semi-automated quantification of α5(IV) at basement membranes in organoids carrying the splicing variants identified in patients, we demonstrate the efficacy of ASO treatment for α5(IV) restoration. These data contribute to our understanding of the development of GBM in kidney organoids and pave the way for a therapeutic screening platform for patients.
Authors
Hassan Saei, Bruno Estebe, Nicolas Goudin, Mahsa Esmailpour, Julie Haure, Olivier Gribouval, Christelle Arrondel, Vincent Moriniere, Pinyuan Tian, Rachel Lennon, Corinne Antignac, Geraldine Mollet, Guillaume Dorval
Abstract
Uncovering the early interactions and spatial distribution of dermal fibroblasts and immune cells in treatment-naïve diffuse cutaneous systemic sclerosis (dcSSc) patients is critical to understanding the earliest events of skin fibrosis. We generated an integrated multiomic dataset of early, treatment-naïve dcSSc skin. Skin biopsies were analyzed by single-nuclei multiome sequencing (snRNA-seq and snATAC-seq) and two different spatial transcriptomic methods to comprehensively determine the molecular changes in these individuals. We identified an immunomodulatory niche within the papillary, hypodermis, and vascular regions that are enriched for activated myeloid cells and fibroblasts characterized by expression of genes such as CXCL12, APOE, and C7. Pathway analyses showed significant enrichment of PI3K-AKT-mTOR signaling pathway expression in these cellular niches, driven by profibrotic growth factor signaling networks. Macrophage subclustering showed SSc-specific macrophage activation of the IL6-JAK-STAT signaling and the enrichment of oxidative phosphorylation pathways. Ligand-receptor analysis revealed that SSc macrophages secrete PDGF and TGF-β to activate the SSc-dominant fibroblast subclusters. Spatial transcriptomic analyses showed monocyte-derived MRC1+ macrophages express PDGF near PDGFRhighTHY1high fibroblasts. Multi-omic data integration and spatial transcriptomic neighborhood analysis revealed the co-localization of fibroblasts, macrophages, and T cells around the vasculature. These data suggest that interactions between activated immune cells and immunomodulatory fibroblasts around vascular niches are an early event in scleroderma pathogenesis.
Authors
Helen C. Jarnagin, Rezvan Parvizi, Zhiyun Gong, Rosemary Gedert, Xianying Xing, Lam (Alex) C. Tsoi, Rachael Bogle, Madeline J. Morrisson, Laurent Perreard, Patricia A. Pioli, Fred Kolling IV, Johann E. Gudjonsson, Dinesh Khanna, Michael L. Whitfield
Abstract
Induction of heme oxygenase-1 (HO-1/Hmox1) is broadly considered cytoprotective, but the role of colonic epithelial HO-1 in colitis-associated tumorigenesis is poorly defined. HO-1 catabolizes heme, releasing ferrous iron, a key driver of oxidative stress and lipid peroxidation. We observed that colonic epithelial HO-1 is induced during colitis and tumorigenesis. We also found that HO-1 is upregulated in ferroptosis-inducing conditions in murine and human colonic epithelial organoids, and correlated with lipid peroxidation and ferroptosis markers in colonic tumors. In colonic epithelial organoids exposed to heme, deletion of Hmox1 amplified a compensatory oxidative stress and detoxification transcriptional program, likely reflecting unresolved oxidative and non-oxidative toxicity from heme. In vivo, epithelial HO-1 deficient mice developed significantly fewer and smaller tumors compared to littermate controls in a colitis-associated tumorigenesis model, despite similar inflammatory injury. Tumors from knockout mice exhibited reduced iron levels, decreased lipid peroxidation, lower oxidative DNA damage, and decreased proliferation. Single-cell RNA sequencing of tumor epithelial cells revealed a shift from a proliferative to a stress-adaptive program with loss of HO-1. These findings identify epithelial HO-1 as a context-dependent regulator of tumorigenesis: protective against acute heme toxicity, but promoting iron-dependent oxidative damage and proliferation in the setting of chronic inflammation.
Authors
Rosemary C. Callahan, Jillian C. Curry, Geetha Bhagavatula, Alyse W. Staley, Rachel E.M. Schaefer, Faiz Minhajuddin, Liheng Zhou, Rane M. Neuhart, Shaikh M. Atif, David J. Orlicky, Ian M. Cartwright, Mark E. Gerich, Calen A. Steiner, Arianne L. Theiss, Caroline H.T. Hall, Sean P. Colgan, Joseph C. Onyiah
Abstract
Fusion-positive rhabdomyosarcoma (FP-RMS), driven by PAX-FOXO1, represents the subtype of RMS with the poorest prognosis. However, the oncogenic mechanisms and therapeutic strategies of PAX-FOXO1 remain incompletely understood. Here, we discovered that N-Myc, in addition to being a classic downstream target of PAX-FOXO1, can also activate its expression and form a transcriptional complex with PAX-FOXO1, thereby markedly amplifying oncogenic signaling. The reciprocal transcriptional activation of PAX3-FOXO1 and N-Myc is critical for FP-RMS malignancy. We further identified YOD1 as a deubiquitinating enzyme (DUB) that stabilizes both PAX-FOXO1 and N-Myc. Knocking down YOD1 or inhibiting it by G5 could suppress FP-RMS growth both in vitro and in vivo, through promoting the degradation of both PAX-FOXO1 and N-Myc. Collectively, our results identify that YOD1 promotes RMS progression by regulating the PAX3-FOXO1-N-Myc positive feedback loop, and highlight YOD1 inhibition as a promising therapeutic strategy that concurrently reduces the levels of both oncogenic proteins.
Authors
Wenwen Ying, Jiayi Yu, Xiaomin Wang, Jiayi Liu, Boyu Deng, Xuejing Shao, Jinhu Wang, Ting Tao, Ji Cao, Qiaojun He, Bo Yang, Yifan Chen, Meidan Ying
