Biology subjects

King, J.

Publications and source records attributed to King, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Development of immunological reagents for the identification of biomarkers of inflammation in the common marmoset

Marmosets (MAR, Callithrix jacchus) are nonhuman primates extensively studied in a broad array of preclinical biomedical research areas. However, the limited number of available immunological reagents remains a critical shortcoming of these models. We successfully developed monoclonal antibodies (mAbs) pairs that can be used in immunoassays for the identification and quantification of the biomarkers of inflammation C-reactive protein (CRP), CXCL-10 (IP-10), interleukin (IL)-4, IL-6, and IL-10. Recombinant MAR protein variants were produced in mammalian cells, purified and used for mice immunization. Hybridoma clones were selected first for their capacity to bind the recombinant proteins. All possible pair combinations of these mAbs were then tested for their capacity to identify their targets in MAR-derived samples. These MAR samples consisted of supernatant of PBMCs exposed ex vivo to different stimulants, and plasma samples from animals stimulated in vivo with a low-dose intravenous LPS inoculation. The majority of the mAbs that recognized the recombinant proteins failed to bind to the MAR-derived homologs. However, we found MAR-derived reactive mAbs and selected pairs with optimal sensitivity and signal-to-noise ratio for immunoassays that included Luminex multiplexing assays, ELISA, and ELISpot assays. These immunoreagents and assays will improve the translational value of different MAR biomedical models.

immunology↗

bioRxiv2026

Defining biologically directed therapy target signatures in urothelial carcinoma: A transcriptomic framework for precision therapy

IntroductionNectin-4 targeting antibody-drug conjugate (ADC) enfortumab vedotin (EV), in combination with pembrolizumab, is the first-line treatment for patients with locally advanced or metastatic urothelial carcinoma (UC). Optimal treatment strategies for patients who are non-responders or progress on EV with pembrolizumab remain an unmet clinical need. We sought to characterize ADC and immunotherapy (IO)-associated target expression profiles to identify candidate therapeutic vulnerabilities beyond EV. MethodsWe conducted a literature review to identify ADC and IO targets with approved or investigational relevance in UC. Unsupervised hierarchical clustering was used to identify clusters of target gene expression in RNA-seq data. Transcriptomic clustering analyses were performed in 434 patients from The Cancer Genome Atlas Bladder Urothelial Carcinoma cohort (TCGA-BLCA) and validated in an independent cohort of 478 patients from the Oncology Research Information Exchange Network (ORIEN) consortium. Proteomic interrogation of these targets was performed using mass spectrometry data from additional cohort of 116 patients. Differential gene expression analyses evaluated associations between target expression patterns, histologic variants, and consensus molecular subtypes of muscle-invasive bladder cancer (CMIBC). ResultsWe identified 13 ADC and 10 IO-associated targets with translational relevance in UC. Transcriptomic analyses revealed three reproducible clusters of overexpressed target genes across independent cohorts: 1) a luminal/epithelial-associated cluster enriched for VTCN1, SLITRK6, FGFR3, NECTIN4, TACSTD2, ERBB2, and ERBB3; 2) an immune target predominant cluster enriched for BTLA, LAG3, PDCD1, TIGIT, CTLA4, TNFRSF9, TNFRSF18, TNFRSF4; and 3) a basal/neuroendocrine-associated cluster characterized by CD274, F3, NT5E, EGFR, MET and DLL3. Similar clusters were largely conserved at the proteomic level. Adenocarcinomas overexpressed ERBB3 compared to neuroendocrine and squamous cell carcinomas. Pure squamous cell carcinomas overexpressed TACSTD2 compared to adenocarcinomas. In CMIBC subtypes, basal/squamous tumors expressed higher levels of CD274, EGFR, F3, LAG3, NT5E, and TNFRSF18, whereas luminal tumors demonstrated higher ERBB2 and ERBB3 expression. Neuroendocrine-like tumors showed higher DLL3 expression compared to all other subtypes. Tumors with low expression of NECTIN4, TACSTD2, and FGFR3 were enriched for alternative targets including DLL3, CD274, and CD276. Our findings provide a framework for hypothesis-driven therapeutic prioritization in advanced UC. Conclusions: UC is characterized by reproducible, biologically distinct patterns of ADC and IO target expressions. The degree of expression of NECTIN4 was positively associated with TACSTD2, FGFR3 and inversely associated with DLL3, CD276, and CD274, supporting alternative biologically informed treatment strategies besides EV . Histologic variants and molecular subtypes of UC also display distinct patterns of target expression. This study provides the first integrated transcriptomic framework linking ADC and IO target co-expression patterns for hypothesis-driven therapeutic prioritization. These findings provide a basis for rational ADC and immunotherapy development in advanced UC and support prospective proteomic validation in treatment stratified cohorts. Statement of Translational RelevanceEnfortumab vedotin plus pembrolizumab has redefined first-line therapy for advanced urothelial carcinoma, yet treatment selection following resistance or progression remains undefined. In this study, we integrate transcriptomic and proteomic analyses across independent cohorts to define reproducible patterns of antibody-drug conjugate (ADC) and immunotherapy target co-expression in urothelial carcinoma. We identify biologically distinct target-expression patterns that are associated with histologic and molecular subtypes and demonstrate coordinated and, in some cases, mutually exclusive relationships among therapeutically actionable targets. These findings have direct translational implications. First, they provide biologic rationale for rational sequencing and combination strategies based on co-expressed targets in NECTIN4-enriched tumors. Second, they identify alternative therapeutic vulnerabilities, including DLL3- and CD274-associated pathways, in tumors with low NECTIN4 expression, a population potentially enriched for resistance to EV-based therapy. Finally, this framework establishes a foundation for biomarker-driven clinical trials in urothelial carcinoma and supports the development of precision therapeutic approaches beyond current standards.

cancer biology↗

bioRxiv2026

Chromosome-scale genome assembly of diploid halophyte Thinopyrum bessarabicum excludes J genome from polyploid Thinopyrum ancestry

Wild relatives of wheat harbour genetic diversity essential for improving resilience to climate-driven stresses, yet their deployment is hampered by unresolved evolutionary relationships and the absence of reference genomes. Here we present a chromosome-scale reference genome for Thinopyrum bessarabicum, a diploid halophyte and high-priority donor for wheat salt tolerance breeding. A key unresolved question is whether the diploid J genome contributed directly to the subgenome composition of extant polyploid Thinopyrum species, and which genomic features underpin its exceptional salt tolerance. Using this resource, we show that the diploid J genome of Th. bessarabicum is not represented among the subgenomes of polyploid Thinopyrum species, resolving a long-standing ambiguity in Triticeae genomics. Gene-level resolution of the reciprocal 4/5 chromosomal translocation across six related Triticeae species identifies conserved breakpoint gene pairs, supporting a single ancestral rearrangement. Genome-wide gene content analysis shows that halophytic capacity is underpinned by quantitative expansion of conserved stress-response gene families. Salt tolerance phenotyping validates chromosome 5J as a tolerance locus in both Th. bessarabicum and wheat introgression lines. A physically anchored marker framework and dual-reference skim-sequencing pipeline enable precise megabase-resolution characterisation of Th. bessarabicum introgressions in wheat, providing a genomic foundation for deploying J-genome diversity in crop improvement.

plant biology↗

bioRxiv2026

Target RNA abundance controls the collateral activity of RfxCas13d in human cells and zebrafish embryos

Collateral RNA cleavage by CRISPR-Cas13 effectors presents a critical obstacle to their application in biological research and therapeutics, yet the molecular determinants of this activity remain poorly understood. Here, we systematically investigate the collateral activity of various Cas13 variants in human cells in vitro and zebrafish embryos in vivo. Among these nucleases, RfxCas13d displays robust collateral activity that is highly dependent on target abundance. Targeting moderately expressed RNAs activates only a limited subset of RfxCas13d molecules, resulting in selective degradation of ectopically expressed transcripts, while endogenous RNAs remain largely protected. This selectivity indicates higher accessibility to exogenous RNAs through spatial proximity and temporal colocalization with activated RfxCas13d nuclease domains. In contrast, the recognition of highly abundant RNA targets drives simultaneous activation of a large fraction of cellular RfxCas13d, leading to widespread collateral cleavage of cellular RNAs, disruption of proteome homeostasis, and consequent cell toxicity and developmental defects in zebrafish embryos. Notably, transgenic zebrafish with target RNA expression restricted to endothelial or neuronal cell lineages exhibit localized collateral activity, leading to tissue-specific developmental abnormalities and motility deficits. These findings reveal that RfxCas13ds collateral activity is threshold-dependent, with abundant target RNA acting as a molecular switch for widespread collateral RNA degradation. This work underscores the need for careful consideration of target abundance when deploying RfxCas13d, and highlights PspCas13b as an alternative for RNA silencing free of collateral activity.

molecular biology↗

bioRxiv2026

Defining the RNA Modification Landscape of Multiple Myeloma Reveals METTL3-Dependent m6A Regulation of NEAT1

RNA modifications play critical roles in gene regulation. N6-methyladenosine (m6A) is the most abundant modification on mRNA and long noncoding RNA (lncRNA) and regulates RNA processing, stability, and translation. RNA modifications are not well characterized in multiple myeloma (MM), a plasma cell malignancy characterized by relapse and disease progression, and the contribution of m6A-modified lncRNAs to the disease remains unclear. Here, we define the RNA modification landscape of MM by combining mass spectrometry, Nanopore Direct RNA sequencing, and methylated RNA immunoprecipitation sequencing. We identify 20 RNA modification types and > 15,000 m6A sites, including sites on 2,398 lncRNAs. Among these, we validate m6A sites on the paraspeckle-associated lncRNA NEAT1. Functional studies reveal that NEAT1 expression is regulated by the methyltransferase METTL3 and site-specific demethylation of a NEAT1 m6A site reduces MM cell viability. Single-cell RNA sequencing shows consistent NEAT1 enrichment in malignant plasma cells but minimal expression in healthy cells. These findings identify m6A-modified lncRNAs as key regulators of MM biology and establish NEAT1 as an epitranscriptomically controlled driver of MM cell survival.

cancer biology↗

bioRxiv2026

Meditope-Enabled Chimeric Antigen Receptors Facilitate Plug-and-Play Control of T Cells

Chimeric antigen receptor (CAR) T cells have transformed cancer treatment, yet challenges for achieving broader clinical success remain, including overcoming tumor antigen heterogeneity and limited T cell fitness. To address these challenges and enhance CAR T cell functionality, we leveraged meditope technology, a lock-and-key platform where Fab regions of antibodies are modified to bind a small cyclic peptide termed meditope (meP). We developed a panel of meditope-enabled Fab-based CARs (meCARs), which show selective binding to the meP and comparable activity to traditional single-chain variable fragment (scFv)-based CARs. Focusing on HER2-targeted meCARs for evaluating platform utility, we exploited the modularity of the meditope platform to detect meCAR T cells using meP-fused fluorescent agents, promote meCAR T cell expansion via meP-fused IL-15 cytokine, and broaden tumor antigen targeting through meP-fused antibodies to address tumor heterogeneity. These findings establish the meditope technology as a versatile strategy to augment CAR T cell functionality and overcome key limitations of current CAR-based therapies.

bioengineering↗

bioRxiv2025

Conditional Gene Expression in Magnaporthe oryzae via Fungal Nitrate Reductase Promoter Replacement

Functional genomic studies rely on controlled gene expression, which is challenging for essential genes or those active only under specific conditions. We provide a detailed protocol for generating Magnaporthe oryzae (synonym of Pyricularia oryzae) with conditional BUF1 gene expression. This method uses targeted promoter replacement to substitute the native BUF1 promoter with the nitrogen-responsive promoter. This approach enables nitrogen source-dependent control of expression in M. oryzae, leading to observable pigmentation changes that facilitate easy phenotypic screening.

genomics↗

bioRxiv2025

A segment of Triticum timopheevii chromosome 3G confers type II Fusarium head blight resistance and reduces DON accumulation in wheat.

Fusarium head blight (FHB) is a major disease of small grain cereals that is particularly damaging on wheat and can result in yield losses of up to 80%. Resistance to FHB in wheat is broadly classified as resistance to initial infection (type I) or resistance to disease spread within the spike (type II). A high level of type I FHB resistance was reported in an accession of wheat wild relative Triticum timopheevii. Hexaploid wheat-T. timopheevii introgression lines carrying a segment of the short arm of chromosome 3G (Chr3G) of this accession expressed high levels of FHB resistance following spray inoculation. Further analyses of these introgression lines showed that the Chr3G segment confers a potent type II resistance, accompanied by improved grain weight retention, and reduced deoxynivalenol (DON) accumulation in grain. These results indicate that the Chr3G resistance has the potential to dramatically reduce FHB susceptibility and DON accumulation in grain in wheat cultivars. An introgression of a segment of Chr7At into the short arm of chromosome Chr7A also enhanced type II FHB resistance.

plant biology↗

bioRxiv2025

Missense variants in human forkhead transcription factors reveal determinants of forkhead DNA bispecificity

Recognition of specific DNA sequences by transcription factors (TFs) is a key step in transcriptional control of gene expression. While most forkhead (FH) TFs bind either an FKH (RYAAAYA) or an FHL (GACGC) recognition motif, some FHs can bind both motifs. Mechanisms that control whether a FH is monospecific versus bispecific have remained unknown. Screening a library of 12 reference FH proteins, 61 naturally occurring missense variants including clinical variants, and 22 designed mutant FHs for DNA binding activity using universal ("all 10-mer") protein binding microarrays (PBMs) revealed non-DNA-contacting residues that control mono- versus bispecificity. Variation in non-DNA-contacting amino acid residues of TFs is associated with human traits and may play a role in the evolution of TF DNA binding activities and gene regulatory networks. HighlightsO_LIMost forkhead (FH) proteins recognize FKH or FHL motifs, while others are bispecific C_LIO_LIDNA binding activities of 12 reference and 83 variant or designed FHs C_LIO_LIClinical or population FH variants with altered DNA binding affinity or specificity C_LIO_LINon-DNA-contacting amino acid residues synergistically control mono- versus bi- specificity C_LI

genomics↗

bioRxiv2025

StrPhaser constructs tandem repeat alleles from VCF data

Variant calling is a ubiquitous genomic technique that underpins many scientific disciplines. From a computational perspective, variant calling is a form of logical compression; neglecting large variation, a persons genome can be losslessly described as a set of differences (SNP and small InDel alleles) relative to the reference sequence. Another common genomic technique is haplotype phasing, wherein alleles are partitioned into their paternal and maternal components (as haplotypes). Some classes of alleles are more difficult to describe than others, e.g., short tandem repeats (STRs). STRs serve as a critical marker for many genetic assays. However, STRs tend not to be explicitly reported in most genomic workflows. Here, we present StrPhaser, a novel algorithm that leverages phased variant calling datasets in the VCF file format to construct STR alleles. We evaluated StrPhaser on [~]10,000 STR alleles from 284 human genomes, achieving an average allele accuracy of 91%. In addition, StrPhaser better recovers longer STR alleles than competing approaches; in principle, STR alleles that are longer than the maximum read length can be characterized. This capability, combined with its user-friendly interface, speed, and generation of both STR genotypes and visualizations, makes StrPhaser a valuable tool for a wide range of genomic studies. AvailabilityThe StrPhaser is publicly available at https://github.com/XuewenWangUGA/StrPhaser.

bioinformatics↗

bioRxiv2024

Real-Time Spatiotemporal Tracking of Infectious Outbreaks in Confined Environments with a Host-Pathogen Agent-Based System

Deadly infection outbreaks in confined spaces, whether it is a COVID-19 outbreak on a cruise ship or at a veteran home, or measles and stomach flu outbreaks in schools, can be characterized by their rapid spread due to the abundance of common spaces, shared airways, and high population density. Preventing future infectious outbreaks and developing efficient mitigation protocols can benefit from advanced computational modeling approaches. Here, we developed an agent-based modeling approach to study the spatiotemporal dynamics of an infection outbreak in a confined environment caused by a specific pathogen and to determine effective infection containment protocols. The approach integrates the 3D geographic information system of a confined environment, the behavior of the hosts, key biological parameters about the pathogen obtained from the experimental data, and the general mechanics of host-pathogen and pathogen-fomite interactions. To assess our approach, we applied it to the historical data of infectious outbreak caused by norovirus, H1N1 influenza A, and SARS-CoV-2 viruses. As a result our model was able to accurately predict the number of infections per day, correctly identify the day when the CDC vessel sanitation protocol would be triggered, single out key biological parameters affecting the infection spread, and propose important changes to existing containment protocols, specific for different pathogens. This research not only contributes to our understanding of infection spread and containment in cruise ships but also offers insights applicable to other similar confined settings, such as nursing homes, schools, and hospitals. By providing a robust framework for real-time outbreak modeling, this study proposes new, more effective containment protocols and enhances our preparedness for managing infectious diseases and emerging pathogens in confined environments.

bioinformatics↗

bioRxiv2024

Gene identification for ocular congenital cranial motor neuron disorders using human sequencing, zebrafish screening, and protein binding microarrays

PurposeTo functionally evaluate novel human sequence-derived candidate genes and variants for unsolved ocular congenital cranial dysinnervation disorders (oCCDDs). MethodsThrough exome and genome sequencing of a genetically unsolved human oCCDD cohort, we previously identified variants in 80 strong candidate genes. Here, we further prioritized a subset of these (43 human genes, 57 zebrafish genes) using a G0 CRISPR/Cas9-based knockout assay in zebrafish and generated F2 germline mutants for seventeen. We tested the functionality of variants of uncertain significance in known and novel candidate transcription factor-encoding genes through protein binding microarrays. ResultsWe first demonstrated the feasibility of the G0 screen by targeting known oCCDD genes phox2a and mafba. 70-90% of gene-targeted G0 zebrafish embryos recapitulated germline homozygous null-equivalent phenotypes. Using this approach, we then identified three novel candidate oCCDD genes (SEMA3F, OLIG2, and FRMD4B) with putative contributions to human and zebrafish cranial motor development. In addition, protein binding microarrays demonstrated reduced or abolished DNA binding of human variants of uncertain significance in known and novel sequence-derived transcription factors PHOX2A (p.(Trp137Cys)), MAFB (p.(Glu223Lys)), and OLIG2 (p.(Arg156Leu)). ConclusionsThis study nominates three strong novel candidate oCCDD genes (SEMA3F, OLIG2, and FRMD4B) and supports the functionality and putative pathogenicity of transcription factor candidate variants PHOX2A p.(Trp137Cys), MAFB p.(Glu223Lys), and OLIG2 p.(Arg156Leu). Our findings support that G0 loss-of-function screening in zebrafish can be coupled with human sequence analysis and protein binding microarrays to aid in prioritizing oCCDD candidate genes/variants.

neuroscience↗

bioRxiv2024

Genome-wide analysis of somatic non-coding mutation patterns and mitochondrial heteroplasmy in type B1 and B2 thymomas

IntroductionType B1 and B2 thymomas are lymphocyte-rich malignant tumors with few somatic mutations in protein-coding regions of the nuclear genome; nonetheless, non-coding regions remain uncharacterized. Here, we developed a rigorous tumor isolation method from lymphocyte-rich thymoma tissues and identified somatic mutations in non-coding and mitochondrial DNA. MethodsCD205+CD45- pure tumor cells were isolated from fresh-frozen tissues using DEPArray system. Deep whole-genome sequencing was performed, and recurrent somatic alterations in coding, non-coding, and mitochondria regions were systemically identified by computational framework. The mutations were classified according to gene function, cis-regulatory element, and mutational signature. ResultsThe total number of somatic mutations was approximately 80 times higher in non-coding regions than in coding regions in type B1-2 thymomas (1,671.3 vs. 21.1 per case). Coding mutations were identified in epigenetic regulators, DNA repair genes, and some other genes. Nevertheless, 40% of cases exhibited fewer than four mutations in coding regions. A systematic non-coding analysis identified a total of 405.0 mutations per case on cis-regulatory elements, and detected six recurrent mutations: one interferon regulatory factor (IRF8), two E3 ubiquitin ligases (UBR2 and RNF213), and three intergenic regions. Mitochondrial heteroplasmy was observed in 90% of cases, with a significant proportion of mutations located in D-loop region. The single-base substitution pattern was signature 12. ConclusionsNumerous non-coding mutations and mitochondrial heteroplasmy were detected in type B1 and B2 thymomas. Given the paucity of coding mutations observed in this disease entity, disruption of the non-coding landscape and mitochondrial heteroplasmic shift may be the primary cause of thymoma.

genomics↗

bioRxiv2024

Somatic mutation phasing and haplotype extension using linked-reads in multiple myeloma

Somatic mutation phasing informs our understanding of cancer-related events, like driver mutations. We generated linked-read whole genome sequencing data for 23 samples across disease stages from 14 multiple myeloma (MM) patients and systematically assigned somatic mutations to haplotypes using linked-reads. Here, we report the reconstructed cancer haplotypes and phase blocks from several MM samples and show how phase block length can be extended by integrating samples from the same individual. We also uncover phasing information in genes frequently mutated in MM, including DIS3, HIST1H1E, KRAS, NRAS, and TP53, phasing 79.4% of 20,705 high-confidence somatic mutations. In some cases, this enabled us to interpret clonal evolution models at higher resolution using pairs of phased somatic mutations. For example, our analysis of one patient suggested that two NRAS hotspot mutations occurred on the same haplotype but were independent events in different subclones. Given sufficient tumor purity and data quality, our framework illustrates how haplotype-aware analysis of somatic mutations in cancer can be beneficial for some cancer cases.

bioinformatics↗

bioRxiv2024

Limitations in mitochondrial programming restrain the differentiation and maturation of human stem cell-derived β cells

Pluripotent stem cell (SC)-derived islets offer hope as a renewable source for {beta} cell replacement for type 1 diabetes (T1D), yet functional and metabolic immaturity may limit their long-term therapeutic potential. Here, we show that limitations in mitochondrial transcriptional programming impede the formation of SC-derived {beta} (SC-{beta}) cells. Utilizing transcriptomic profiling, assessments of chromatin accessibility, mitochondrial phenotyping, and lipidomics analyses, we observed that SC-{beta} cells exhibit reduced oxidative and mitochondrial fatty acid metabolism compared to primary human islets that are related to limitations in key mitochondrial transcriptional networks. Surprisingly, we found that reductions in glucose-stimulated mitochondrial respiration in SC-islets were not associated with alterations in mitochondrial mass, structure, or genome integrity. In contrast, SC-islets show limited expression of targets of PPAR, which regulate mitochondrial programming, yet whose functions in {beta} cell differentiation are unknown. Importantly, treatment with WY14643, a potent PPAR agonist, induced expression of mitochondrial targets, improved insulin secretion, and increased the formation of SC-{beta} cells both in vitro and following transplantation. Thus, PPAR-dependent mitochondrial programming promotes the differentiation of SC-{beta} cells and may be a promising target to improve {beta} cell replacement efforts for T1D.

developmental biology↗

bioRxiv2024

LINC01432 binds to CELF2 in newly diagnosed multiple myeloma promoting short progression-free survival to standard therapy

Multiple Myeloma (MM) is a highly prevalent and incurable form of cancer that arises from malignant plasma cells, with over 35,000 new cases diagnosed annually in the United States. While there are a growing number of approved therapies, MM remains incurable and nearly all patients will relapse and exhaust all available treatment options. Mechanisms for disease progression are unclear and in particular, little is known regarding the role of long non-coding RNAs (lncRNA) in mediating disease progression and response to treatment. In this study, we used transcriptome sequencing to compare newly diagnosed MM patients who had short progression- free survival (PFS) to standard first-line treatment (PFS < 24 months) to patients who had prolonged PFS (PFS > 24 months). We identified 157 differentially upregulated lncRNAs with short PFS and focused our efforts on characterizing the most upregulated lncRNA, LINC01432. We investigated LINC01432 overexpression and CRISPR/Cas9 knockdown in MM cell lines to show that LINC01432 overexpression significantly increases cell viability and reduces apoptosis, while knockdown significantly reduces viability and increases apoptosis, supporting the clinical relevance of this lncRNA. Next, we used individual-nucleotide resolution cross-linking immunoprecipitation with RT-qPCR to show that LINC01432 directly interacts with the RNA binding protein, CELF2. Lastly, we showed that LINC01432-targeted locked nucleic acid antisense oligonucleotides reduce viability and increases apoptosis. In summary, this fundamental study identified lncRNAs associated with short PFS to standard NDMM treatment and further characterized LINC01432, which inhibits apoptosis. Key points: lncRNA expression was found to be dysregulated in patients with short PFS to standard multiple myeloma therapy. LINC01432-bound CELF2 inhibits apoptosis.

cancer biology↗

bioRxiv2024

Loss of cell junctional components and matrix alterations drive cell desquamation and fibrotic changes in Idiopathic Pulmonary Fibrosis

The distal bronchioles in Idiopathic Pulmonary Fibrosis (IPF) exhibit histopathological abnormalities such as bronchiolization, peribronchiolar fibrosis and honeycomb cysts that contribute to the overall architectural remodeling of lung tissue seen in the disease. Here we describe an additional histopathologic finding of epithelial desquamation in patients with IPF, wherein epithelial cells detach from the basement membrane of the distal bronchioles. To understand the mechanism driving this pathology, we performed spatial transcriptomics of the epithelial cells and spatial proteomics of the basement membrane of the distal bronchioles from IPF patients and patients with no prior history of lung disease. Our findings reveal a downregulation of cell junctional components, upregulation of epithelial-mesenchymal transition signatures and dysregulated basement membrane matrix in IPF distal bronchioles, facilitating epithelial desquamation. Further, functional assays identified regulation between Collagen IV in the matrix, and the junctional genes JUP and PLEC, that is crucial for maintaining distal bronchiolar homeostasis. In IPF, this balanced regulation between matrix and cell-junctions is disrupted, leading to loss of epithelial adhesion, peribronchiolar fibrosis and epithelial desquamation. Overall, our study suggests that in IPF the interplay between the loss of cell junctions and a dysregulated matrix results in desquamation of distal bronchiolar epithelium and lung remodeling, exacerbating the disease. One Sentence SummaryTwo-way regulation of cell junctional proteins and matrix proteins drives cellular desquamation and fibrosis in the distal bronchioles of patients with Idiopathic Pulmonary Fibrosis.

pathology↗

bioRxiv2024

Red knots in Europe - a dead end host species or a new niche for highly pathogenic avian influenza?

The 2020/2021 epidemic in Europe of highly pathogenic avian influenza virus (HPAIV) of subtype H5 surpassed all previously recorded European outbreaks in size, genotype constellations and reassortment frequency and continued into 2022 and 2023. The causative 2.3.4.4b viral lineage proved to be highly proficient with respect to reassortment with cocirculating low pathogenic AIV and seems to establish an endemic status in northern Europe. A specific HPAIV reassortant of the subtype H5N3 was detected almost exclusively in red knots (Calidris canutus islandica) in December 2020. It caused systemic and rapidly fatal disease leading to a singular and self-limiting mass mortality affecting about 3.500 birds in the German Wadden Sea, roughly 1% of the entire flyway population of islandica red knots. Phylogenetic analyses revealed that the H5N3 reassortant very likely had formed in red knots and remained confined to this species. While mechanisms of virus circulation in potential reservoir species, dynamics of spill-over and reassortment events and the roles of environmental virus sources remain to be identified, the year-round infection pressure poses severe threats to endangered avian species, and prompts adaptation of habitat and species conservation practices. One-Sentence SummaryHigh red knot mortality in Europe (December 2020) was associated with infection of a unique genotype of HPAIV H5N3 clade 2.3.4.4b.

ecology↗