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Journal of Clinical Immunology

Springer Science and Business Media LLC

Preprints posted in the last 7 days, ranked by how well they match Journal of Clinical Immunology's content profile, based on 11 papers previously published here. The average preprint has a 0.00% match score for this journal, so anything above that is already an above-average fit.

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Ancestry-specific rewiring of BCR-MAPK signaling in sarcoidosis B cells

Dunn, C. M.; Watkins, C.; Hallum, G.; Pezant, N.; Rasmussen, A.; Gaffney, P. M.; Bagavant, H.; Deshmukh, U. S.; Montgomery, C.

2026-04-22 immunology 10.64898/2026.04.20.718985 medRxiv
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Sarcoidosis is a heterogenous disease of unknown etiology characterized by non-caseating granulomas. Disease prevalence and presentation vary significantly by ancestry and ranges from acute, self-resolving disease to severe, chronic disease. Following previous reports suggesting B cells in the development and pathogenesis of sarcoidosis, we present here results of single-cell RNA sequencing, supporting B cell involvement in sarcoidosis through altered immediate early response, rewiring of MAPK signaling, and ancestry-specific preferential expansion of B cell receptors. Peripheral blood mononuclear cells were obtained from individuals of African or European Ancestry (AA and EA, respectively) including 48 healthy controls, 59 sarcoidosis patients, and 28 systemic lupus erythematosus (SLE) patients. SLE samples were used as a disease control. Differential expression analysis highlighted many differentially expressed genes (DEGs) with almost 5x more in the AA sarcoidosis versus AA control group compared to the EA sarcoidosis versus EA control group. B cells had the most DEGs of all cell types and expression patterns were similar between ancestries, however, sarcoidosis had an opposite transcription pattern than SLE, demonstrating an alternative immune response to acute activation than that seen in a prototypical autoinflammatory disease. This trend was maintained when examining specialized B cell subsets, with the most pronounced effect in the AA sarcoidosis versus AA control comparison. Our results strongly support further investigation of the role of humoral immune response in sarcoidosis and the potential to highlight patient groups likely to benefit from existing B cell therapies.

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Duplication within 14q32.13 implicates a chimeric CLMN::SYNE3 RNA transcript in cerebellar ataxia

Litster, T. M.; Wilcox, R. A.; Carroll, R.; Gardner, A. E.; Nazri, N. M.; Shoubridge, C. A.; Delatycki, M. B.; Lohmann, K.; Agzarian, M.; Turella Divani, R.; Rafehi, H.; Scott, L.; Monahan, G.; Lamont, P. J.; Ashton, C.; Laing, N. G.; Ravenscroft, G.; Bahlo, M.; Haan, E.; Lockhart, P. J.; Friend, K. L.; Corbett, M. A.; Gecz, J.

2026-04-24 genetic and genomic medicine 10.64898/2026.04.23.26350376 medRxiv
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The spinocerebellar ataxias (SCAs) are a clinically heterogenous group of neurodegenerative disorders that affect movement, vision, speech and balance. Here, we reassign the linkage of SCA30 to 14q32.13 based on a cumulative LOD score >12. Within this interval we identified a 331 kb duplication, absent in population controls and not observed in >800 unrelated individuals with genetically unresolved cerebellar ataxia. RNASeq analysis of patient-derived lymphoblastoid cell lines revealed a splice-mediated chimeric transcript resulting from the duplication event. This transcript joined exon 1 of CLMN to exon 2 of SYNE3. In silico translation predicted that this chimeric transcript would produce a short N-terminal peptide corresponding to exon 1 of CLMN and the usually untranslated region of exon 2 of SYNE3 fused to the complete and in-frame SYNE3 protein. Transient overexpression of SYNE3 or the CLMN::SYNE3 fusion protein, in both HeLa cells and mouse primary cortical neurons, resulted in equivalent cellular outcomes including altered nuclear morphology and chromosomal DNA fragmentation. SYNE3 forms part of the linker of nucleoskeleton and cytoskeleton complex and is not usually expressed in cerebellar Purkyn[e] neurons while, CLMN has a Purkyn[e] specific expression pattern within the brain. Our data suggests that ectopic expression of SYNE3 in cerebellar Purkyn[e] neurons, mediated by the CLMN promoter, leads to cerebellar atrophy and causes spinocerebellar ataxia in the SCA30 family. This is an example of Mendelian disease arising from a novel, chimeric transcript with a likely dominant negative effect. Chimeric transcripts are commonly associated with cancers, but they are not often associated with monogenic disorders. Detection of chimeric transcripts as part of structural variant analysis could increase the genetic diagnostic yield of Mendelian disorders.

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Diminished sex hormone levels influence the risk of skewed X chromosome inactivation

Roberts, A. L.; Osterdahl, M. F.; Sahoo, A.; Pickles, J.; Franklin-Cheung, C.; Wadge, S.; Mohamoud, N. A.; Morea, A.; Amar, A.; Morris, D. L.; Vyse, T. J.; Steves, C. J.; Small, K. S.

2026-04-22 genetic and genomic medicine 10.64898/2026.04.20.26351303 medRxiv
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BackgroundX chromosome inactivation (XCI) is the mechanism which randomly silences one X chromosome to equalise gene expression between 46, XX females and 46, XY males. Though XCI is expected to result in a random pattern of mosaicism across tissues, some females display a significantly unbalanced ratio in immune cells, termed XCI-skew, in which [&ge;]75% of cells have the same X inactivated. XCI-skew is associated with adverse health outcomes and its prevalence increases with age - particularly after midlife - yet the specific risk factors have yet to be identified. The menopausal transition, which is driven by profound shifts in sex hormone levels, has significant impact on chronic disease risk yet the molecular and cellular effects are incompletely understood. We hypothesised that the menopausal transition may impact XCI-skew. MethodsUsing XCI data measured in blood-derived DNA from 1,395 females from the TwinsUK population cohort, along with questionnaires, genetic data, and sex hormone measures, we carried out a cross-sectional study to assess the impact of the menopausal transition and sex hormones on XCI-skew. ResultsWe demonstrate that early menopause (<45yrs) is associated with increased risk of XCI-skew. In subset analyses across those who had a surgically induced or natural menopause, we find the association restricted to those who underwent a surgical menopause. We next identify a low polygenic score (PGS) for testosterone levels is significantly associated with XCI-skew, which we replicate in an independent dataset (n=149), while a PGS for age at natural menopause is not associated. Finally, using longitudinal measures across two time points spanning [~]18 years we show XCI-skew is a stable cellular phenotype that typically increases over time. DiscussionThese data represent the first environmental and genetic risk factors of XCI-skew, both of which implicate endogenous sex hormone levels, particularly testosterone. We propose XCI-skew may have clinical relevance in postmenopausal females.

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Diagnostic Classification for Long Covid Patients identifying Persistent Virus and Hyperimmune Pathophysiologies

James-Pemberton, P.; Harper, D.; Wagerfield, P.; Watson, C.; Hervada, L.; Kohli, S.; Alder, S.; Shaw, A.

2026-04-22 infectious diseases 10.64898/2026.04.21.26351402 medRxiv
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A multiplex diagnostic test is evaluated for self-reported long COVID associated persistent symptoms and a poor recovery from a SARS-CoV-2 infection. A mass-standardised concentration of total antibodies (AC), high-quality (HQ) antibodies and percentage of HQ antibodies (HQ%) is assessed against a spectrum of spike proteins to the SARS-CoV-2 variants: Wuhan, , {delta}, and the Omicron variants BA.1, BA.2, BA.2.12.1, BA.2.75, BA.5, CH.1.1, BQ.1.1 and XBB.1.5 in three cohorts. A cohort of control patients (n = 46) recovered (CC) and a cohort of self-declared long COVID patients (n = 113) (LCC). A nested Receiver Operating Characteristic (ROC) analysis, performed for the variant with lowest HQ concentration in the spectrum, produced an area under the curve and AUC = 0.61 (0.53-0.70) for the CC vs LCC cohorts. For the LCC cohort, the cut-off thresholds for AC = 0.8 mg/L, HQ = 1.5 mg/L and HQ% of 34% were determined, leading to a 71% sensitivity and 66% specificity derived by the Youden metric. The cohorts may be fully classified based on ROC and outlier analysis to give an incidence of persistent virus 62% (95% CI 52% - 71%), hyperimmune 12% (95% CI 7% - 20%) and unclassified, 26% (95% CI 18% - 35%). The overall diagnostic accuracy for both the hyper and hypo immune is 69%. All clinical interventions can now be tailored for the heterogenous long COVID patient cohort.

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Multi-ancestral GWAS with the VA Million Veteran Program enables functional interpretation of rheumatoid arthritis alleles

Sakaue, S.; Yang, D.; Zhang, H.; Posner, D.; Rodriguez, Z.; Love, Z.; Cui, J.; Budu-Aggrey, A.; Ho, Y.-L.; Costa, L.; Monach, P.; Huang, S.; Ishigaki, K.; Melley, C.; Tanukonda, V.; Sangar, R.; Maripuri, M.; Sweet, S. M.; Panickan, V.; McDermott, G.; Hanberg, J. S.; Riley, T.; Laufer, V.; Okada, Y.; Scott, I.; Bridges, S. L.; Baker, J.; VA Million Veteran Program, ; Wilson, P. W.; Gaziano, J. M.; Hong, C.; Verma, A.; Cho, K.; Huffman, J. E.; Cai, T.; Raychaudhuri, S.; Liao, K. P.

2026-04-23 genetic and genomic medicine 10.64898/2026.04.22.26351423 medRxiv
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Rheumatoid arthritis (RA) is a heritable and common autoimmune condition. To date, most genetic associations were derived from individuals with either European or East Asian ancestries. Here, we applied a multimodal automated phenotyping strategy to define RA and performed a genome-wide association study (GWAS) of RA in the Million Veteran Program (MVP), including underrepresented African American (AFR) and Admixed American (AMR) populations. Meta-analyses with previous RA cohorts identified 152 autosomal genome-wide significant loci, of which 31 were novel. Inclusion of multi-ancestry data dramatically improved fine-mapping resolution. Functional characterization of these loci using single-cell transcriptomic and chromatin data suggested new RA genes such as CHD7 and CD247. We identified underappreciated functional roles of fine-grained immune cell states other than T cells, such as B cell and myeloid cell states. We observed that multi-ancestry polygenic risk scores using our data demonstrated better predictive ability, especially for AFR and AMR populations.

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PALM3 and hearing loss: a potential dual diagnosis interfering with novel gene discovery

Najarzadeh Torbati, P.; Hallbrucker, L.; Hofrichter, M. A. H.; Owrang, D.; Setzke, J.; Kilimann, M. W.; Hemmatpour, A.; Rajati, M.; Ghayoor Karimiani, E.; Haaf, T.; Vogl, C.; Vona, B.

2026-04-21 genetic and genomic medicine 10.64898/2026.04.20.26351093 medRxiv
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Hereditary hearing loss is highly genetically heterogeneous, with emerging overlap between genes implicated in early-onset and age-related hearing loss. We report a consanguineous family with autosomal recessive, non-syndromic hearing loss in which the proband harbors a homozygous splice-site variant in PALM3 (NM_001145028.2:c.314+1G>A) and a homozygous missense variant in OTOA. A minigene assay for the PALM3 variant demonstrated aberrant splicing with exon skipping, resulting in a frameshift and a large inframe deletion, both consistent with loss of function and impacting all known transcripts. While the organ of Corti from 12-month-old heterozygous Palm3 mice showed preserved overall architecture, published Palm3 knockout mice exhibit auditory dysfunction, supporting an auditory phenotype with loss of function. Although a dual molecular diagnosis cannot be excluded, the combined genetic, functional, and comparative data support PALM3 as a strong candidate gene for autosomal recessive hearing loss.

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Ensemble Approaches to Screening, Diagnosis, and Subtyping of Multiple Sclerosis

Yang, I. Y.; Patil, A.; Jin, O.; Loud, S.; Buxhoeveden, S.; Zhang, D. Y.

2026-04-21 genetic and genomic medicine 10.64898/2026.04.19.26351230 medRxiv
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Multiple sclerosis (MS) is a debilitating disease affecting more than 1 million Americans, and today is assessed primarily through magnetic resonance imaging (MRI) and observational clinical symptoms. Given the autoimmune nature of MS, we hypothesized that high-dimensional gene expression data from peripheral blood mononuclear cells (PBMCs), when analyzed with the assistance of AI, may collectively serve as valuable biomarkers for the real-time risk and progression of MS. Here, we present PBMC RNA sequencing (RNAseq) results from N=997 samples, including 540 MS, 221 neuromyelitis optica (NMO), and 149 healthy controls. We constructed and optimized ensemble models for three clinical outcomes: (1) discrimination of early MS (EDSS [&le;] 2.0) from healthy individuals with 74% AUC at 100% coverage, (2) differential diagnosis of MS from NMO with 91% AUC at 80% coverage, and (3) subtyping RRMS from progressive MS with 79% AUC at 80% coverage. To our knowledge, no prior molecular test has been reported for any of these three MS clinical tasks, and these results may have immediate impact on clinical management of MS patients. Two innovations that improved the stratification accuracy of our models: selection of gene sets based on expression variance in disease states, and use of non-linear rank sort and conviction weighting in the ensemble score calculation.

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Greater intergroup bias in vaccination attitudes among physicians than the general public

Murakami, M.; Ohtake, F.

2026-04-25 infectious diseases 10.64898/2026.04.23.26351641 medRxiv
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While vaccination conflicts have become apparent, physicians' attitudes toward those with differing views remain unclear. Through an online survey of 492 physicians and 5,252 members of the general public in Japan in February 2026, we investigated attitudes toward four vaccines (influenza, measles, HPV, and COVID-19). Intergroup bias was assessed as ingroup minus outgroup attitudes using a feeling thermometer. Multilevel regression examined associations with agreement group and physician status. Intergroup bias was significantly positive in both agreement and disagreement groups across all vaccine types, and was higher in the agreement group. Physicians exhibited higher intergroup bias than the general public. These findings indicate that vaccination conflict is bidirectional: physicians, often viewed as targets of hostility from vaccine-hesitant individuals, themselves exhibit greater intergroup bias toward those with opposing views. Interventions to raise physicians' awareness of their own bias, alongside communication strategies for vaccine-hesitant individuals, are needed.

9
Transcriptome-Wide Alternative Splicing Analysis Implicates Complex Events in Bipolar Disorder

Martinez-Jimenez, M.; Garcia-Ortiz, I.; Romero-Miguel, D.; Kavanagh, T.; Marshall, L. L.; Bello Sousa, R. A.; Sanchez Alonso, S.; Alvarez Garcia, R.; Benavente Lopez, S.; Di Stasio, E.; Schofield, P. R.; Baca-Garcia, E.; Mitchell, P. B.; Cooper, A. A.; Fullerton, J. M.; Toma, C.

2026-04-21 genetic and genomic medicine 10.64898/2026.04.19.26351209 medRxiv
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Alternative-splicing events (ASE) increase transcriptomic variability and play key roles in biological functions. The contribution of ASE to bipolar disorder (BD) remains largely unexplored. We performed a Transcriptome-Wide Alternative-Splicing Analysis (TWASA) to identify ASEs and genes potentially involved in BD. The study comprised 635 individuals: a discovery sample (DS) of 31 individuals from eight multiplex BD families (16 BD cases; 15 unaffected relatives), and a replication sample (RS) of 604 subjects (372 BD cases; 232 controls). Sequencing was conducted on RNA from lymphoblastoid cell lines (DS) and whole blood (RS). TWASA was performed using VAST-TOOLS (VT), rMATS (RM), and MAJIQ/MOCCASIN (MCC). Gene-set association analyses of genes containing ASEs were performed across six psychiatric disorders. Novel ASE (nASE) were investigated in the DS using FRASER. Limited gene overlap was observed across TWASA tools. MCC identified 2,031 complex ASEs involving 1,508 genes, showing the strongest genetic association with BD across psychiatric phenotypes. Prioritization of MCC-identified ASE genes yielded 441 candidates, including DOCK2 as top candidate from the DS. Replication was obtained for 98 genes, five with an identical ASE, and four (RBM26, QKI, ANKRD36, and TATDN2) showing a concordant percentage-spliced-in direction with the DS. Finally, 578 nASE were identified in the DS, with no evidence of familial segregation or differences in ASE types. This first TWASA in BD reveals tool-specific variability, complex ASE for genes specifically associated with BD, and novel candidate genes for BD. Alternative transcript isoform abundance may represent a mechanism contributing to BD pathophysiology.

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Cross-ancestry evaluation of idiopathic pulmonary fibrosis genetic risk variants

Nabunje, R.; Guillen-Guio, B.; Hernandez-Beeftink, T.; Joof, E.; Leavy, O. C.; International IPF Genetics Consortium, ; Maher, T. M.; Molyneux, P.; Noth, I.; Urrutia, A.; Aburto, M.; Flores, C.; Jenkins, R. G.; Wain, L. V.; Allen, R. J.

2026-04-25 genetic and genomic medicine 10.64898/2026.04.17.26349970 medRxiv
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Genome-wide association studies of idiopathic pulmonary fibrosis (IPF) have identified 35 common genetic risk loci associated with IPF susceptibility. In this study, we evaluated the effects of the reported variants in clinically curated non-European individuals. Despite limited sample sizes, we observed partial replication, limited transferability of some variants and evidence of ancestry-specific effects. The MUC5B promoter variant rs35705950 emerged as the dominant and most consistent signal across ancestries. Our findings highlight the need for larger, well-characterised studies in understudied populations to support robust discovery and translation.

11
Invasive alien predators overturn the spatial-scaling laws of biocomplexity

Lemasle, P.-G.; Paillisson, J.-M.; Roussel, J.-M.; Lacroix, R.; Lacroix, P.; Lacroix, G.; Edeline, E.

2026-04-21 ecology 10.64898/2026.04.16.718936 medRxiv
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The theory of island biogeography and its trophic extensions predict that both species richness and food-web complexity should increase with increasing ecosystem surface area. Accordingly, Species-Area Relationships (SARs) and Network-Area Relationships (NARs) are often observed to be positively-sloped, an observation that came to be considered as a law, and on which rest many area-based conservation plans for biodiversity. However, our mechanistic understanding of the driving mechanisms of SARs and NARs slopes remains limited, undermining our ability to predict how biodiversity will respond to habitat gain or loss. We show in 180 rural ponds sampled across five years that invasive alien predators reversed the SAR and NARs from positive in invader-free ponds, to negative in invaded ponds. Relationship reversal resulted from a higher prevalence of invasive alien predators driving magnified prey extinctions and simplified food webs in larger ponds. The ability of invasive alien predators to reverse SAR and NARs presumably reflected disproportionately high predation rates combined with a low sensitivity to prey extinction conferred by a wide trophic generalism. In a world where virtually all ecosystems face biological invasions, omnipresent invasive alien predators stress the pivotal role played by predation in shaping biocomplexity-area relationships, and highlight a growing need to preserve small ecosystems where invasive alien predators are less prevalent.

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A phylogenetic approach reveals evolutionary aspects and novel genes of bradyzoite conversion in Toxoplasma gondii

C A, A.; Upadhayay, R.; Patankar, S. A.

2026-04-21 bioinformatics 10.64898/2026.04.20.719551 medRxiv
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Toxoplasma gondii is a widespread human pathogen that has multiple, clinically relevant stages in its complex life cycle, including fast-replicating tachyzoites and latent bradyzoites. Bradyzoite differentiation is triggered by stress responses that lead to changes in transcription, translation, and metabolism. Two aspects of this process are addressed in this report: first, whether proteins that play roles in bradyzoite differentiation are specific to T. gondii and other bradyzoite-forming parasites of the Sarcocystidae family, and second, whether new bradyzoite differentiation proteins can be identified in T. gondii. To answer these questions, a phylogenetic approach was used, comparing proteomes of select members of the Sarcocystidae family that form morphologically different bradyzoite cysts and members of the Eimeriidae family that do not form cysts. This approach resulted in 8 distinct clusters of T. gondii proteins that reflected different conservation patterns; for example, one cluster showed conservation among all organisms, while another showed conservation in bradyzoite cyst-forming organisms. Known T. gondii proteins involved in bradyzoite differentiation were found in all clusters, indicating that this process uses both highly conserved pathways as well as bradyzoite-specific pathways. Importantly, the cluster containing proteins that are conserved in bradyzoite-forming organisms contained several known regulators of bradyzoites, and will be a source for identifying novel T. gondii proteins that are involved in bradyzoite differentiation.

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3D Reconstruction of Nanoparticle Distribution in Tumor Spheroids with Volume Electron Microscopy

Bottone, D.; Gerken, L. R.; Habermann, S.; Mateos, J. M.; Lucas, M. S.; Riemann, J.; Fachet, M.; Resch-Genger, U.; Kissling, V. M.; Roesslein, M.; Gogos, A.; Herrmann, I. K.

2026-04-21 bioinformatics 10.64898/2026.04.17.719153 medRxiv
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AO_SCPLOWBSTRACTC_SCPLOWSpatially resolved characterization of nanomaterial (NM) distribution within cellular ultrastructure is essential for understanding NM fate and activity in biological systems. Volume electron microscopy (vEM) is uniquely positioned to address this challenge, yet fully documented quantitative pipelines that simultaneously segment NMs and cellular structures remain scarce. Here, an end-to-end analytical pipeline is presented based on the example of serial block-face scanning electron microscopy (SBF-SEM) data of tumor spheroids containing nanoparticles (NPs). A hybrid segmentation strategy is adopted: a fine-tuned Cellpose-SAM model for cells and nuclei, and an empirical Bayes approach for AuNPs. The fine-tuned model outperforms both the pre-trained baseline and benchmark experiments in Amira, and shows good generalization to 2D EM datasets of varying sample types, suggesting potential as a general-purpose segmentation model for electron microscopy. Full 3D reconstruction of NP distributions reveals preferential clustering in the perinuclear region, with a median nucleus-to-NP distance of 2.57 {micro}m and NM uptake spanning several orders of magnitude across cells. Furthermore, morphological analysis of segmented cells and nuclei using 3D shape descriptors and local curvature metrics provides quantitative access to features inaccessible from single sections. Together, these results establish a reproducible, open framework for the joint quantitative analysis of NM distribution and cellular morphology in vEM data.

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A bidirectional interaction between the SREBP pathway and the LINC complex component nesprin-4 controls lipid metabolism

Al-Sammak, B. F.; Mahmood, H. M.; Bengoechea-Alonso, M. T.; Horn, H. F.; Ericsson, J.

2026-04-21 cell biology 10.64898/2026.04.18.719359 medRxiv
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This report identifies a bidirectional signaling axis connecting lipid metabolism to nuclear mechanotransduction, with the potential to control fatty acid/triglyceride metabolism. The sterol regulatory element-binding (SREBP) family of transcription factors control fatty acid, triglyceride and cholesterol synthesis and metabolism. The family consists of three members: SREBP1a, SREBP1c, and SREBP2, that are regulated by intracellular cholesterol levels and insulin signaling. The SREBP2-dependent control of the LDL receptor gene is a well-established target for cholesterol-lowering therapeutics and the activity of SREBP1c is an attractive target in metabolic disease. In the current report, we identify SYNE4 (nesprin-4), a component of the Linker of Nucleoskeleton and Cytoskeleton (LINC) complex, as a direct target of the SREBP family of transcription factors, and show that nesprin-4 in turn supports SREBP1c function. We identify functional SREBP binding sites in the human SYNE4 promoter and demonstrate that these are required for the sterol- and SREBP-dependent regulation of the promoter. Furthermore, we show that the endogenous SYNE4 gene is also regulated by SREBP1/2 and intracellular sterol levels. Interestingly, SREBP2 is responsible for the sterol regulation of the SYNE4 gene in HepG2 cells, while SREBP1 is the major regulator in MCF7 cells, demonstrating that diberent cell types use diberent SREBP paralogs to regulate the same promoter/gene. Importantly, we find that nesprin-4 is a positive regulator of SREBP1c expression and function in HepG2 cells and during the diberentiation of human adipose-derived stem cells. In summary, the current report identifies a novel regulatory interaction between lipid metabolism and the LINC complex. Importantly, we demonstrate that this signaling axis is bidirectional, forming a closed loop that has the potential to control SREBP1c activity and thereby fatty acid and triglyceride synthesis/metabolism. Based on our data, we propose that the nesprin-4-dependent regulation of SREBP1c could represent a novel therapeutic target in metabolic disease.

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Biological invasion drives ecosystem state and metabolism across tipping points

Gaigne, E.; Dezerald, O.; Gorzerino, C.; Coudreuse, J.; Bennevault, Y.; Pannard, A.; Edeline, E.

2026-04-21 ecology 10.64898/2026.04.16.718977 medRxiv
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Abrupt regime shifts of complex ecosystems between alternative stable states are widespread in nature. Yet, our mechanistic understanding of disturbance-shift-ecosystem functioning relationships remains poor, and it is further unclear whether biotic disturbances can drive such shifts. Using a 5-year pond experiment, we demonstrate that invasion by the red swamp crayfish (Procambarus clarkii) drove a regime shift from a clear-water, macrophyte-dominated, to a turbid, phytoplankton-dominated state. The regime shift was associated with increased water temperature due to increased water turbidity enhanced light absorption, and with a seasonal switch of ecosystem metabolism from hetero-to autotrophy due to decreased respiration in summer, despite constant gross primary production. Reducing crayfish population densities by 44 % failed to move ecosystems back towards their initial state and functioning. Our results stress that biotic disturbances may have hardly-reversible consequences on the biophysical and biogeochemical processes that support ecosystem functioning.

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Comparative analysis of transposable elements in jellyfish and hydroid species (Cnidaria: Medusozoa)

Mays, A.; Cabrera, F.; Macias-Munoz, A.

2026-04-21 evolutionary biology 10.64898/2026.04.17.719288 medRxiv
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BackgroundTransposable elements (TEs) are repetitive genetic elements that can jump to new loci causing genome expansions, structural rearrangements, and can, ultimately, propel the evolution of genomes. Despite their significance, the role of TEs in the evolution of genomes and phylogenetic groups remains largely understudied in early diverging lineages. Further, the extent to which TE content varies across species is still an open question. Medusozoa, a group within Cnidaria encompassing jellyfish and hydroids, exhibits an exceptional diversity of life history strategies, body plans, and physiological capabilities. These characteristics, along with its early-diverging phylogenetic position, establish Medusozoa as an ideal system for investigating the composition and evolutionary history of TEs within the group. ResultsWe generated a custom repeat library built from annotations of 25 Medusozoan genomes and used it to characterize TEs, aiming to identify lineage-specific TE content and activity that may correlate with the diversity observed within the group. We found that repetitive element percentage and genome size varied considerably, with Hydrozoa exhibiting the most variation among classes in both respects. DNA transposons were the most prevalent TE classification in all but two genomes, averaging 28% of all genomes. Intra-genus comparisons revealed a surprising degree of differences in TE content. In the genus Aurelia, the expansion of a single DNA transposon superfamily accounted for much of the difference in repetitive element percentage between two species, whereas in the genus Turritopsis, a similar divergence resulted from the proliferation of multiple superfamilies. Interestingly, most genomes showed evidence of recent TE expansions, suggesting ongoing activity in many medusozoan species. ConclusionWe present the first comparative analysis of TEs across all medusozoan classes. Our results reveal class-specific TE dynamics and highlight cases of TE proliferations as lineages diverge. This research provides data on TE activity and diversity that can be used as a resource for future study and fills important gaps in our understanding of TEs in early diverging animal lineages.

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Statistical Model Comparison Supports a Pitcher Origin of Utricularia Suction Traps

Obara, M.; Matzke, N. J.; Fullmer, M. S.; Wright, S. D.

2026-04-21 evolutionary biology 10.64898/2026.04.19.719479 medRxiv
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Carnivorous plants have been the subject of fascination and research ever since Darwin codified the subject in his 1875 book Insectivorous Plants. The origin of complex trapping mechanisms from structures adapted for photosynthesis is of particular interest. While Darwin proposed a plausible scenario for the origin of the snap traps of the Venus flytrap from simpler adhesive traps, the origin of the tiny and complex bladder traps of the genus Utricularia mystified Darwin and many subsequent workers, despite Utricularia being the most diverse genus of carnivorous plants. In this study, we test the "pitcher hypothesis," which proposes that Utricularia bladder traps evolved gradually from an adhesive trap ancestor, via an extinct pitcher trap intermediate. To overcome the lack of any fossil evidence for this scenario, we constructed a variety of continuous-time Markov chain (CTMC) models, each of which consists of a transition matrix allowing or disallowing certain transitions between 11 types of traps. We assembled available phylogenetic trees for 436 carnivorous plant species and noncarnivorous outgroups, classified each species by trap type, and statistically compared the fit of 18 CTMC models using Maximum Likelihood and statistical model comparison with Akaike Information Criterion. The best-fitting model (PH-7R-AAI), consistent with our pitcher hypothesis, had an AIC weight of 60%, with two similar models accounting for the remaining 40%. These results support a circuitous stepwise evolutionary pathway to the bladder trap, and demonstrate how a detailed stepwise evolutionary scenario may be statistically tested even without direct fossil evidence of key intermediate stages.

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Unlocking a flexible set of phylogenetic models for discrete and continuous trait evolution using discretized stochastic diffusion

Revell, L. J.; Alencar, L. R. V.; Alfaro, M. E.; Dain, J.; Hill, N. J.; Jones, M.; Martinet, K. M.; Romero-Alarcon, V.; Harmon, L. J.

2026-04-21 evolutionary biology 10.64898/2026.04.20.719455 medRxiv
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The practical utility of many modern phylogenetic comparative methods can depend on how accurately mathematical models capture the evolutionary process of traits. Boucher and Demery (2016) described a new quantitative trait model, Brownian motion with reflective limits, that they anticipated might be of use in testing hypotheses about a particular sort of constraint on phenotypic character evolution. Since their analytic solution for the probability function under this bounded evolutionary scenario was not practical to evaluate for reasonably-sized trees, Boucher and Demery (2016) also identified a creative technique for computing the likelihood of their model. The basis of this methodology derives from the convergence of an equal-rates, symmetric, ordered Markov chain and continuous stochastic diffusion in the limit as the number of steps in our chain goes to {infty} (or, alternatively, as their widths decrease towards zero). We refer to this convergence in the limit as the discretized diffusion approximation or (more compactly) the discrete approximation. We realized that this discrete approximation of Boucher and Demery (2016) unlocked a number of additional models for the phylogenetic comparative analysis of discrete and continuous trait data, and we explore several of these in the present article. Specifically, we examine application of this discretized diffusion approximation to the threshold model from evolutionary quantitative genetics, to a new "semi-threshold" trait evolution model, to a joint model of discrete and continuous traits in which the discrete trait influences the rate of evolution of our continuous character, as well as a model where precisely the converse is true, and to a discrete character dependent multi-trend trended continuous trait evolution model. We conclude with some context for the origins of our article and discussion of other possible applications of this powerful approach.

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Organelle partitioning in the multi-budding yeast Aureobasidium pullulans

Wirshing, A. C. E.; Yan, M.; Lew, D. J.

2026-04-21 cell biology 10.64898/2026.04.17.719237 medRxiv
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Cellular organelle content is fairly constant within a given cell type. This is accomplished in part by ensuring equitable organelle partitioning during division. Much of our understanding of organelle inheritance has come from investigating cells that divide in half producing two daughter cells. However, more elaborate division strategies that give rise to multiple daughters are not uncommon in nature. Here, we present the first characterization of organelle inheritance in a fungus that grows by multi-budding, producing several (2-20) daughter cells in a single cell cycle. We find that some organelles (mitochondria and ER) are evenly delivered to all growing buds, while others (vacuole and peroxisomes) are more variably inherited. We discuss the implications of even and uneven inheritance for this polyextremotolerant fungus capable of growing in dynamic, and diverse, environments.

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Pancreatic Gαs ablation disrupts tissue architecture and YAP signaling and unveils a compensatory regenerative response

Rossotti, M.; Burgos, J. I.; Ramms, D. J.; Romero, A.; Burgui, V.; Zelicovich, M.; Traba, S. A.; Heidenreich, A. C.; Gutkind, J. S.; Rodriguez-Segui, S. A.

2026-04-21 cell biology 10.64898/2026.04.20.718494 medRxiv
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Diabetes mellitus is characterized by chronic hyperglycemia and loss of pancreatic {beta}-cell function and mass. Current therapies focus on {beta}-cell protection and regeneration, led by GLP-1 receptor agonists. The G protein -subunit (Gs) acts as a key signaling node downstream of numerous GPCRs, integrating diverse signals that impact {beta}-cell mass and function. Elucidating the integrative role of pancreatic Gs signaling is thus crucial for understanding {beta}-cell biology. Our map of the pancreatic Gs-coupled GPCR landscape reveals sophisticated, cell-type-specific networks, positioning Gs as a central hub for intra-pancreatic communication. Previous studies in mice with {beta}-cell-specific or whole-pancreatic Gs deletion demonstrated reduced {beta}-cell mass, impaired insulin secretion, and glucose intolerance. The stronger phenotype in the whole-pancreas model--marked by -cell expansion and abnormal distribution--points to a crucial role for Gs in differential control of postnatal - and {beta}-cell proliferation. Here, we analyze the organ-wide consequences of Gs deletion using pancreas-specific Gs knockout mice (PGsKO). Consistent with prior findings, PGsKO mice exhibit reduced weight gain from four weeks and severe diabetes due to decreased {beta}-cell mass and concomitant -cell expansion. Furthermore, Gs loss induces profound architectural and functional defects in the exocrine pancreas, linked to YAP reactivation in acinar cells. Importantly, we observed attempted {beta}-cell regeneration in PGsKO mice. Although insufficient to reverse diabetes, our results delineate the full pancreatic phenotype that may facilitate these regenerative efforts and suggest that strategically biasing GPCR signaling network away from Gs could be a viable strategy to promote {beta}-cell regeneration from other pancreatic cell types. ARTICLE HIGHLIGHTSO_LIGs is a central signaling hub that integrates diverse GPCR inputs across pancreatic cell types, yet its organ-wide role remained poorly defined. C_LIO_LIWe addressed how pancreas-wide Gs deletion disrupts both endocrine and exocrine compartments, and whether regenerative programs are engaged. C_LIO_LIGs loss caused severe diabetes through {beta}-cell loss and -cell expansion, induced profound exocrine defects with YAP reactivation, and triggered attempted {beta}-cell regeneration from ducts and potentially other cell types. C_LIO_LIOur findings suggest that strategically biasing GPCR signaling away from Gs could promote regeneration from non-{beta}-cell sources, offering new therapeutic avenues for diabetes. C_LI