bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anti-mitochondrial antibodies in systemic sclerosis target enteric neurons and are associated with GI dysmotility
Authors: McMahan Zsuzsanna H. , Casciola-Rosen Livia , Kaniecki Timothy , Gutierrez-Alamillo Laura , Ming Su Hong , Seika Philippa , Kulkarni Subhash 
Published: November 2024

ABSTRACTBackgroundMost 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 (β -14.4, 95%CI -26.2, -2.6) and stomach (β -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 cellsin vitrosuggests that SSc-AM2A may penetrate MENsin 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 messagesWhat is already known on this topicsubset 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.What this study adds:AM2A antibodies in SSc patients associate with slower upper GI transit.Mitochondria 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.SSc autoantibodies penetrate live cellsin vitroand bind to their target antigens intracellularly.How this study might affect research, practice or policyAM2A antibodies in SSc patients may penetrate MENs in vivo, driving ENS dysfunction and subsequent GI dysmotilityThis potentially novel mechanism in SSc GI disease could inform our current approach to diagnosing and managing these patients.
Detection of Anti-Non-α-Gal Xenoreactive Antibodies in Human Blood Products
Authors: Ladowski Joseph M. , Hu Meghan , Yoon Janghoon , Chen Zheng , Knechtle Stuart , Jackson Annette , Kwun Jean 
Published: November 2024

AbstractBackgroundSurgical bleeding is a risk in any solid organ transplant, and commonly addressed with the transfusion of human blood product to replace or supplement coagulation factors. It is unknown if these blood products would harm xenotransplanted pig organs in human recipients demonstrating coagulopathy. The aim of this study was to investigatein vitroif blood products such as fresh frozen plasma (FFP) or cryoprecipitate (cryo) contain xenoantibodies capable of cytotoxicity to GTKO pig cells.MethodsWe obtained 12 individual single donor (7 FFP and 5 cryo) blood products from our institution’s blood bank for testing. PBMCs were obtained from a GTKO/hCD55 pig for use as target cells. We performed a series of flow cytometry crossmatch and complement-dependent cytotoxicity assays.ResultsWe found that all the tested blood products contained some degree of IgM and IgG xenoantibody. Tests using a 1:50 dilution revealed a significant decrease in IgM xenoantibody binding, but an increase the detection of IgG binding. Multiple preparations were capable of GTKO PBMC cytotoxicity but the level of antibody binding and cell death varied by preparation.ConclusionsBoth FFP and cryo contain IgM and IgG non-αGal xenoantibodies capable of killing GTKO PBMCs, though the level varies by preparation. While some centers utilize a genetic background with mutations in the three enzymes responsible for the known xenoantigens, others are investigating the GTKO pig as a potential option. These results suggest that a center pursuing a human xenotransplantation study with a GTKO genetic background should pre-screen blood products prior to administration.
Hematocrit and Progressive Stroke in Single Small Subcortical Infarction: Insights from the China Stroke Registry III
Authors: Lu Jiancong , Hankey Graeme J. , Zhang Xiaoli , Meng Xia , Zeng Weiqi , Jiang Jun , Wang Anxin , Tan Zefeng 
Published: November 2024

AbstractBackground and PurposeSingle Small Subcortical Infarction (SSSI) is a subtype of ischemic stroke with unique pathophysiology, often leading to poor outcomes. This study investigates the association between admission hematocrit (HCT) levels and the risk of progressive stroke in SSSI patients.MethodsWe conducted a retrospective cohort study using data from the China National Stroke Registry III, including 2,457 SSSI patients. Progressive stroke was defined as an increase in the NIHSS score by ≥2 points during hospitalization. Logistic regression models assessed the association between HCT levels and progressive stroke risk.ResultsAmong 2,457 SSSI patients, 135 (5.50%) experienced progressive stroke. Higher HCT levels were independently associated with a lower risk of progressive stroke (adjusted OR 0.983, 95% CI 0.973-0.994, P = 0.002), with a potential dose-response relationship. The protective effect was more pronounced in patients with severe sensory deficits (P for interaction = 0.013) and younger age (<65 years) (P for interaction = 0.037). Lower HCT levels were also independently associated with increased mortality risk within 3 months after stroke (adjusted OR 0.937, 95% CI 0.892-0.984, P < 0.001).ConclusionsHigher admission HCT levels are associated with a lower risk of progressive stroke in SSSI patients, particularly those with severe sensory deficits and younger age. Lower HCT levels may also increase early mortality risk. These findings highlight the importance of monitoring and optimizing HCT levels in SSSI management. Further research should explore the underlying mechanisms and therapeutic implications.
Affinity maturation of antibody responses is mediated by differential plasma cell proliferation
Authors: MacLean Andrew J. , Deimel Lachlan P. , Zhou Pengcheng , ElTanbouly Mohamed A. , Merkenschlager Julia , Ramos Victor , Santos Gabriela S. , Hägglöf Thomas , Mayer Christian T. , Hernandez Brianna , Gazumyan Anna , Nussenzweig Michel C. 
Published: November 2024

AbstractIncreased antibody affinity over time after vaccination, known as affinity maturation, is a prototypical feature of immune responses. Recent studies have shown that a diverse collection of B cells, producing antibodies with a wide spectrum of different affinities, are selected into the plasma cell (PC) pathway. How affinity-permissive selection enables PC affinity maturation remains unknown. Here we report that PC precursors (prePC) expressing high affinity antibodies receive higher levels of T follicular helper (Tfh)-derived help and divide at higher rates than their lower affinity counterparts once they leave the GC. Thus, differential cell division by selected prePCs accounts for how diverse precursors develop into a PC compartment that mediates serological affinity maturation.
Measuring Microbial Community-Wide Antibiotic Resistance Propagation via Natural Transformation in the Human Gut Microbiome
Authors: Chowdhury Nadratun N. , Forry Samuel P. , Servetas Stephanie L. , Hunter Monique E. , Dootz Jennifer N. , Dunkers Joy P. , Jackson Scott A. 
Published: November 2024

1)AbstractThis work explored the role of natural transformation – a mechanism by which bacteria uptake and express extracellular genes - in driving antibiotic resistance propagation in the human gut microbiome. The model extracellular antibiotic resistance gene (eARG) – a plasmid containing a kanamycin resistance (kanR) gene and a green fluorescence protein (GFP) gene – was dosed into pooled and homogenized human stool and incubated anaerobically. Cellular uptake of the eARG was assessed via droplet digital PCR, the expression of newly acquired genes was assessed by culturing on selective media and fluorescent microscopy, newly resistant isolates were identified by long-read Nanopore sequencing and the impacts on the taxonomy of the gut microbiome was assessed using shotgun Illumina sequencing. Significant gene uptake of bothkanRand GFP was quantified in gut microbes, and extent of gene accumulation correlated with background kanamycin levels. Gut microbes dosed with background kanamycin expressed kanamycin resistance acquired by the eARG (as quantified by CFU on kanamycin-containing media). Newly resistant isolates, identified asEnterococcus faeciumby long-read sequencing, also expressed green fluorescence acquired from the eARG. Though compositional changes of the kanamycin-resistant subpopulation were observed in the gut microbiome in response to eARG and antibiotic exposure, these changes were not reproducible among replicates and trends in taxonomy due to transformation could not be identified. This comprehensive analysis therefore establishes the significant propagation of antibiotic resistance within the human gut microbiome due to eARG exposure, while evaluating the utility of various measurements in characterizing transformation in a complex microbial community.2)ImportanceInfections from antibiotic resistant bacteria in the human gut microbiome are a growing public health concern. Antibiotic resistance may develop in gut microbiota from exposure to environmentally prevalent extracellular antibiotic resistance genes (eARGs). This work explores the impact of eARG exposure on a complex human gut microbial community. It quantifies significant accumulation and expression of eARG-borne genes by endogenous gut microorganisms, thereby demonstrating that natural transformation may play a role in resistance propagation in the human gut. It also demonstrates the highly variable changes in gut taxonomy in response to eARG exposure, implying that eARGs may impact gut composition and therefore downstream human health effects. These data may be useful in characterizing and mitigating resistance propagation in the human gut, and in general, the suite of genotypic and phenotypic measurements used constitute a quantitative framework to characterize the effects of perturbations on complex microbiomes.
Mapping essential somatic hypermutations in a CD4-binding site bNAb informs HIV-1 vaccine design
Authors: Dam Kim-Marie A. , Gristick Harry B. , Li Yancheng E. , Yang Zhi , Gnanapragasam Priyanthi N.P. , West Anthony P. , Seaman Michael S. , Bjorkman Pamela J. 
Published: November 2024

SummaryHIV-1 broadly-neutralizing antibodies (bNAbs) targeting the CD4-binding site (CD4bs) contain rare features that pose challenges to elicit these bNAbs through vaccination. The IOMA-class of CD4bs bNAbs includes fewer rare features and somatic hypermutations (SHMs) to achieve broad neutralization, thus presenting a potentially accessible pathway for vaccine-induced bNAb development. Here, we created a library of IOMA variants in which each SHM was individually reverted to the inferred germline (iGL) counterpart to investigate the roles of SHMs in conferring IOMA’s neutralization potency and breadth. Impacts on neutralization for each variant were evaluated, and this information was used to design minimally-mutated IOMA-class variants (IOMAmin) that incorporated the fewest SHMs required for achieving IOMA’s neutralization breadth. A cryo-EM structure of an IOMAmin variant bound to Env was used to further interpret characteristics of IOMA variants to elucidate how IOMA’s structural features correlate with its neutralization mechanism, informing the design of IOMA-targeting immunogens.HighlightsIOMAmin variants with reduced SHMs retain neutralization potency and breadth.Cryo-EM structure reveals IOMAmin preserves key Env interactions despite fewer SHMs.IOMA variants with mutations in CDRH3 and CDRL1 fail to improve neutralization.
Multiple pathways to red carotenoid coloration: House finches (Haemorhous mexicanus) do not use CYP2J19 to produce red plumage
Authors: Koch Rebecca E. , Truong Christy N. , Reeb Hannah R. , Joski Brooke H. , Hill Geoffrey E. , Zhang Yufeng , Toomey Matthew B. 
Published: November 2024

AbstractThe carotenoid-based colors of birds are a celebrated example of biological diversity and an important system for the study of evolution. Recently, a two-step mechanism, with the enzymes cytochrome P450 2J19 (CYP2J19) and 3-hydroxybutyrate dehydrogenase 1-like (BDH1L), was described for the biosynthesis of red ketocarotenoids from yellow dietary carotenoids in the retina and plumage of birds. A common assumption has been that all birds with ketocarotenoid-based plumage coloration used this CYP2J19/BDH1L mechanism to produce red feathers. We tested this assumption in house finches (Haemorhous mexicanus) by examining the catalytic function of the house finch homologs of these enzymes and tracking their expression in molting birds. We found that CYP2J19 and BDH1L did not catalyze the production of 3-hydroxy-echinenone (3-OH-echinenone), the primary red plumage pigment of house finches, when provided with common dietary carotenoid substrates. Moreover, gene expression analyses revealed little to no expression ofCYP2J19in liver tissue or growing feather follicles, the putative sites of pigment metabolism in molting house finches. Finally, although the hepatic mitochondria of house finches have high concentrations of 3-OH-echinenone, observations using fluorescent markers suggest that both CYP2J19 and BDH1L localize to the endomembrane system rather than the mitochondria. We propose that house finches and other birds that deposit 3-OH-echinenone as their primary red plumage pigment use an alternative enzymatic pathway to produce their characteristic red ketocarotenoid-based coloration.
Divergent reference genomes compromise the reconstruction of demographic histories, selection scans, and population genetic summary statistics
Authors: Akopyan Maria , Genchev Matthew , Armstrong Ellie E. , Mooney Jazlyn A. 
Published: November 2024

AbstractCharacterizing genetic variation in natural populations is central to evolutionary biology. However, most non-model organisms lack integral genomic resources such as reference genomes and recombination maps, limiting accurate evolutionary inference. Here, we explore the consequences of reference genome bias on the inference of genetic diversity, demographic histories, and recombination rates using gray foxes (Urocyon cinereoargenteus), which, like most members ofCanidae,are traditionally mapped to the dog (Canis lupus familiaris) reference genome. Whole genome sequence data from gray foxes were mapped to the gray fox reference genome and two heterospecific canid references (dog and Arctic fox;Vulpes lagopus). Our results reveal that reference bias significantly affects population genomic analyses. Mapping to the conspecific gray fox genome improved read pairing, increased detection of SNPs, especially rare variants, and reduced spurious variants. Estimates of nucleotide diversity (π) and genetic differentiation (FST) were higher using the gray fox genome. We observed that mapping to heterospecific references leads to underestimates of population sizes, distorted demographic trajectories, and more variable recombination rates. These effects are further complicated by population-specific biases, which vary in their magnitude and direction across populations, highlighting the need for tailored approaches to mitigate reference bias. Importantly,FSToutlier detection also differed among references, affecting functional interpretations. Collectively, this work addresses a critical gap in the rapidly expanding field of non-model species genomics by demonstrating the importance of using conspecific genomic resources in evolutionary research and illustrating how reliance on distantly related reference genomes can distort population genetic analyses.
The Potential of CCA-associated Bacteria to Fight Antimicrobial-Resistant Pathogens: a Genomic Survey
Authors: Lera-Lozano Diego , Ruiz-Toquica Jordan S. , Holt Matthew W. , Jones Elizabeth K. , Ritchie Kim B. , Medina Mónica , González-Pech Raúl A. 
Published: November 2024

ABSTRACTThe global rise of antimicrobial resistance has intensified efforts in bioprospecting, with researchers increasingly exploring unique marine environments for novel antimicrobials. In line with this trend, our study focused on bacteria isolated from the unique microbiome of crustose coralline algae (CCA), which has yet to be investigated for antimicrobial discovery. In the present work, bacteria were isolated from the CCAHydrolithon boergesenii. After running antimicrobial assays against antibiotic-resistant human and marine pathogens, three isolates were selected for genome sequencing using the Oxford Nanopore technology. Genome mining of the high-quality assemblies revealed 100 putative Biosynthetic Gene Clusters (BGCs) across the three genomes. Further analysis uncovered BGCs potentially involved in the biosynthesis of novel antimicrobial compounds. Our study provides valuable resources for future research aimed at the discovery of novel antimicrobials, particularly in the face of the antibiotic-resistance global crisis and highlights the potential of specialized marine environments like CCA biofilms.
Patient-Reported Treatment Outcomes in ME/CFS and Long COVID
Authors: Eckey Martha , Li Peng , Morrison Braxton , Davis Ronald W , Xiao Wenzhong 
Published: November 2024

AbstractMyalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) and Long COVID are persistent multi-system illnesses affecting many patients. With no known effective FDA-approved treatments for either condition, patient-reported outcomes of treatments are invaluable for guiding management strategies in patient care and generating new avenues for research. Here, we present the results of an ME/CFS and Long COVID treatment survey with responses from 3,925 patients. We assessed the experiences of these patients with more than 150 treatments, as well as their demographics, symptoms, and comorbidities. Patients with each condition who participated in the study shared similar symptom profiles, including all the core symptoms of ME/CFS, e.g., 89.7% of ME/CFS and 79.4% of Long COVID reported post-exertional malaise (PEM). Treatments with the greatest perceived benefits were identified, which had varied effects on different core symptoms. In addition, treatment responses were significantly correlated (R² = 0.68) between the two patient groups. Patient subgroups with distinct profiles of symptoms and comorbidities showed varied responses to treatments, e.g., a POTS-dominant cluster benefiting from autonomic modulators and a cognitive-dysfunction cluster from CNS stimulants. This study underscores the symptomatic and therapeutic similarities between ME/CFS and Long COVID and highlights the commonalities and nuanced complexities of infection-associated chronic diseases and related conditions. Insights from patient-reported experiences, in the absence of approved treatments, provide urgently needed real-world evidence for targeted therapies in patient care and for developing future clinical trials.(Disclaimer: The findings presented in this paper are based on patient-reported information and are intended for research purposes only. They should not be interpreted as medical advice. Patients are advised to consult their healthcare provider before initiating or altering any treatment.)
Incident benzodiazepine and Z-drug use and subsequent risk of alcohol- and drug-related problems: a nationwide matched cohort study with co-twin comparison
Authors: Wang Xinchen , Chang Zheng , Molero Yasmina , Isomura Kayoko , de la Cruz Lorena Fernández , Lichtenstein Paul , Kuja-Halkola Ralf , D’Onofrio Brian M , Quinn Patrick D , Larsson Henrik , Brikell Isabell , Hellner Clara , Hasselström Jan , Jayaram-Lindström Nitya , Mataix-Cols David , Sidorchuk Anna 
Published: November 2024

AbstractBackgroundDespite considerable interest in the consequences of benzodiazepine and benzodiazepine-related Z-drug (BZDR) use, little is known about whether and how initiation of BZDR treatment contributes to the development of alcohol- and drug-related problems.AimTo examine the association of incident BZDR dispensing with subsequent development of broadly defined alcohol- and drug-related problems.MethodsThis nationwide register-based study included demographically matched and co-twin control cohorts. Among all Swedish residents aged ≥10 years and BZDR-naïve by 2007, 960,430 BZDR-recipients with incident dispensation in 2007-2019 and without any recorded pre-existing substance-related conditions were identified and matched (1:1) to nonrecipients from the general population. Twin BZDR-recipients (n=12,048) were linked to 12,579 unexposed co-twins. Outcomes included alcohol and drug use disorders, poisoning, deaths, and related suspected criminal offences. Flexible parametric survival models estimated outcome risks across up to 14 years of follow-up.ResultsIn the demographically matched cohort (60% women, median age at BZDR initiation 51 years), incidence rates in BZDR-recipients and nonrecipients (per 1000 person-years) were 5.60 vs 2.79 for alcohol-related and 4.15 vs 1.23 for drug-related problems, respectively. In fully-adjusted models, relative risks were increased for alcohol- and drug-related problems (adjusted hazard ratio [95% confidence interval]: 1.56 [1.53-1.59] and 2.11 [2.05-2.17], respectively). The risks persisted within the co-twin comparison, different follow-ups, and all additional and sensitivity analyses.ConclusionsBZDR initiation was associated with a small but robust increase in absolute and relative risks of developing alcohol- and drug-related problems. The findings contribute to evidence base for making decisions on BZDR treatment initiation.
De novo functional discovery of peptide-MHC restricted CARs from recombinase-constructed large-diversity monoclonal T cell libraries
Authors: Wang Zening , Sarkar Abhijit , Ge Xin 
Published: November 2024

ABSTRACTChimeric antigen receptors (CAR) that mimic T cell receptors (TCR) on eliciting peptide-major histocompatibility complex (pMHC) specific T cell responses hold great promise in the development of immunotherapies against solid tumors, infections, and autoimmune diseases. However, broad applications of TCR-mimic (TCRm) CARs are hindered to date largely due to lack of a facile approach for the effective isolation of TCRm CARs. Here, we establish a highly efficient process forde novodiscovery of TCRm CARs from human naïve antibody repertories by combining recombinase-mediated large-diversity monoclonal library construction with T cell activation-based positive and negative screenings. Panels of highly functional TCRm CARs with peptide-specific recognition, minimal cross-reactivity, and low tonic signaling were rapidly identified towards MHC-restricted intracellular tumor-associated antigens MAGE-A3, NY-ESO-1, and MART-1. Transduced TCRm CAR-T cells exhibited pMHC-specific functional avidity, potent cytokine release, and efficacious and persistent cytotoxicity. The developed approach could be used to generate safe and potent immunotherapies targeting MHC-restricted antigens.