Biology subjects

Lang, S.

Publications and source records attributed to Lang, S..

At least 19 recordsLinked to original sources

bioRxiv2026

The early-life determinant LIN28B constrains immunoglobulin light chain secondary rearrangements independent of BCR specificity

The early-life B cell repertoire is disproportionately enriched for self-reactive specificities in mice and humans, raising the question of how this ontogenic permissiveness is achieved. The predominant B cell central tolerance mechanism edits away self-reactivity by secondary rearrangements of the immunoglobulin light chain (IgL) following strong B cell receptor (BCR) engagement during the immature B cell stage. Here, we demonstrate a layer of developmental regulation, imposed by the early-life restricted RNA-binding protein LIN28B, that suppresses the incidence and capacity for IgL secondary rearrangements during ontogeny. Genetic dissection demonstrated that the underlying mechanisms operate independent of BCR specificity or pre-BCR requirement, dissociating the receptor editing fate from strict BCR instruction. We identified an adult-specific receptor editing-biased pre-B cell state marked by CD25 expression and metabolic quiescence. LIN28B subverted this state, shifting the balance from secondary rearrangements to positive selection and bone marrow egress. Together, our results demonstrate that the central tolerance threshold is an ontogenically tuned parameter, providing insights into the self-reactivity bias that characterizes the early-life B cell repertoire.

immunology↗

bioRxiv2026

Development of a Fully Non-Viral 1XX-enhanced BCMA CAR-T Cell Therapy for Multiple Myeloma

Multiple myeloma (MM) is a clonal plasma cell malignancy characterized by bone marrow infiltration, monoclonal immunoglobulin production, and microenvironmental dysregulation that leads to systemic organ damage. The advent of B-cell maturation antigen (BCMA)-directed chimeric antigen receptor (CAR) T-cell therapy has induced unprecedented responses and durability for patients with relapsed/refractory MM. These outcomes are rarely observed with prior salvage strategies, although relapse remains the predominant long-term challenge for most patients. The two currently approved BCMA CAR-T cell products use viral vectors to semi-randomly insert the CAR gene, which results in heterogeneous genomic composition and variability in efficacy, safety, and product consistency. To address these challenges, we integrated targeted CRISPR genome engineering with precise CAR transgene insertion at the T-cell receptor alpha constant (TRAC) locus, 1XX CAR signaling architecture to enhance potency and durability, and non-viral manufacturing with a single-stranded DNA repair template to improve efficiency and yield. This approach confers physiological CAR expression, reduces insertional mutagenesis, and improves persistence by mitigating tonic signaling and exhaustion. Our GMP manufacturing process consistently achieved high CAR integration (37.7-72.7%) and yields across all full-scale runs and met predefined release criteria for identity, purity, safety, and quality. In NSG mouse models of MM, the UCCT-BCMA-1 product exhibited exceptionally potent tumor control, CAR-T cell expansion 100-1000-fold greater than that of lentiviral constructs, and durable clearance of myeloma cells after multiple rechallenges. These findings establish a CRISPR-edited, fully non-viral manufacturing platform for next-generation 1XX-BCMA CAR-T therapies with enhanced persistence, safety, and efficacy. One Sentence SummaryCRISPR-engineered, TRAC-targeted 1XX-BCMA CAR-T therapy with improved safety, potency, and persistence in relapsed and refractory multiple myeloma.

cancer biology↗

bioRxiv2026

Identification of disease-specific alleles and gene duplications from 1,600 Haemophilus influenzae genomes using predicted protein analyses from an unsupervised language model and clinical metadata

Haemophilus influenzae, a Gram-negative bacterium that is an obligate commensal of the human nasopharynx, is associated with both acute and chronic infections of the ears, adenoids, sinuses, and lungs, as well as pelvic inflammatory disease, sepsis, and meningitis. This diverse array of clinical disease phenotypes is due to H. influenzaes natural competence providing for frequent distributed gene exchange among strains during polyclonal colonizations. We performed whole genome sequencing (WGS) on [~]1000 H. influenzae strains and combined these data with [~]600 publicly available genomes. Clinical metadata including isolation site and disease were available for all strains. Our goal was to identify variations in protein sequences inferred from the WGS that correlate with the clinical metadata. We employed the alpha-fold unsupervised machine-learning model to all protein sequences. For each unique AA sequence, a numerical vector was generated reflecting the proteins biochemical properties. Multidimensional clustering was used to group variants into clusters by distance. For gene groups with two or more clusters, clinical metadata from the strain of origin was overlayed and subsequently tested for correlation with the clustering. This allowed identification of multiple gene groups with clusters of variants that correlated significantly with the patients disease. COG category analysis showed that many of the significant gene groups were associated with antibiotic targets. The TbpA gene group type was found to be significantly correlated with disease type with three of five variant clusters having a 95% prevalence among strains that were isolated from the lungs of COPD patients or other lower pulmonary tract infections.

genomics↗

bioRxiv2026

Maximum Unified Fatty Acid Signature Analysis: a new approach to QFASA

Accurately estimating predator diets is crucial for understanding and predicting ecosystem changes. The desire for non-lethal but accurate diet estimation techniques has led to new approaches such as quantitative fatty acid signature analysis (QFASA), a now widely accepted method for estimating the diets of marine predators. We propose a novel alternative to QFASA, namely maximum unified fatty acid signature analysis (MUFASA), to estimate dietary proportions using fatty acid signatures. MUFASA is based on maximum likelihood estimation principles and consequently offers several theoretical advantages over QFASA, including estimates that possess desirable properties when model assumptions hold. In addition, the availability of a likelihood function enables the use of a broad range of existing methodologies that may have the capacity to address current well-known challenges associated with diet estimation via fatty acids. MUFASA and QFASA are compared using simulations based on wide-ranging diets, as well as real-life data from a captive study of harbour seals, for which diets are known. Estimates derived from QFASA and MUFASA are similar, suggesting that diet estimation in this context can potentially be viewed through an MLE framework. While not the primary focus of this work, bootstrap confidence intervals are also developed and preliminary results yield high coverage probabilities when the diet proportions are not near 0 or 1.

ecology↗

bioRxiv2026

IL-1α drives a tumor-stroma-neutrophil axis through inflammatory fibroblast activation in head and neck cancer

In head and neck squamous cell carcinoma (HNSCC), high tumor-associated neutrophil (TAN) density is a robust biomarker of poor prognosis. TANs predominantly localize to the stroma and their intratumoral density strongly correlates with adverse outcome. Here, we investigated how tumor-stroma communication regulates TAN recruitment, activation, and spatial organization. We identified interleukin-1 (IL-1), released by viable or necrotic tumor cells, as an upstream signal that induces an inflammatory cancer associated fibroblast (iCAF)-like transcriptional program in patient-derived mesenchymal stromal cells (MSCs) of the oral cavity. IL-1-stimulated MSCs secrete factors associated with neutrophil recruitment, survival, and function, together with mediators of extracellular matrix remodeling and angiogenesis. Notably, the IL-1-induced iCAF-like transcriptional program closely resembles CAF subsets in HNSCC that are associated with poor clinical outcome. Functionally, conditioned media from IL-1-stimulated MSCs promoted tumor growth and enhanced polymorphonuclear neutrophil survival, activation, trans-well migration and infiltration into spheroids, in vitro. In zebrafish xenografts, co-injection of IL-1-overexpressing tumor cells and MSCs markedly amplified neutrophil infiltration. TCGA analysis demonstrated robust correlations between the IL-1-induced MSC gene signature and neutrophil signatures across multiple TAN subsets in human HNSCC. Spatial analysis of HNSCC tissues showed that stromal regions adjacent to IL1A-positive tumor islets were enriched for CXCL8/CSF3 double-positive cells and exhibited increased TAN density, including higher frequencies of NE- and MPO-positive neutrophils. Collectively, these findings define an IL-1-dependent tumor-stroma signaling circuit that links tumor inflammation to stromal remodeling and neutrophil infiltration in HNSCC. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=180 SRC="FIGDIR/small/700440v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@f8d282org.highwire.dtl.DTLVardef@1c4575aorg.highwire.dtl.DTLVardef@1430cfcorg.highwire.dtl.DTLVardef@1098887_HPS_FORMAT_FIGEXP M_FIG Graphical abstract: IL-1 drives tumor-stroma communication and neutrophil recruitment in HNSCC. Here, we describe a mechanism in HNSCC that promotes high tumor-associated neutrophil (TAN) density, a biomarker associated with poor prognosis. Tumor-derived IL-1 activates stromal cells to adopt an inflammatory phenotype, resulting in the release of CXCL8, GM-CSF, and G-CSF to enhance neutrophil recruitment, activation, and survival. IL1A-positive tumor islets are surrounded by CXCL8/CSF3-rich stroma with elevated TAN densities in both tumor and stromal compartments. These TANs exhibit increased frequencies of MPO- and NE-positive cells, revealing a spatially organized inflammatory tumor microenvironment. Figure was created using BioRender. C_FIG

cancer biology↗

bioRxiv2026

Deletion of Dock7 Exons 3 and 4 Results in Reduced Trabecular Microarchitecture and a Decrease in Mineralization

Dedicator of Cytokinesis 7 (DOCK7) has recently emerged as a regulator of skeletal homeostasis, but existing Dock7 mutant models harbor only global mutations and are incompatible with tissue-specific deletion studies. We previously generated a Dock7-floxed allele in which exons 3-4 are flanked by LoxP sites. To validate the utility of this allele for future conditional strategies, we globally deleted exons 3-4 to generate Dock7em2/em2 mice and characterized their skeletal phenotype. Homozygous Dock7em2/em2 mice exhibited a diluted coat color and white belly spot, consistent with spontaneous Dock7 mutations, whereas heterozygotes exhibited no spotting or coat changes. Bone microarchitecture was assessed in 21-week-old males and females. Global deletion of Dock7 exons 3-4 resulted in a 30-37% reduction in trabecular bone volume in the distal femur and L5 vertebrae. Cortical bone thickness was unchanged, though sex-specific alterations in femoral area suggested altered appositional bone growth. Mass spectrometry (SWATH) analysis of Dock7em2/em2 bone marrow stromal cells (BMSCs) identified DOCK7 protein levels similar to control mice, likely resulting from an alternative translational start site. Despite stable protein abundance prior to differentiation, BMSCs from Dock7em2/em2 mice exhibited reduced mineralization and decreased Bglap expression, indicating attenuated osteoblast differentiation. These findings demonstrate that Dock7 exons 3-4 are required for normal trabecular bone acquisition and osteoblast function. While the Dock7-em2 allele likely encodes a truncated protein product, its recapitulation of the Misty skeletal phenotype confirms that exons 3-4 are essential for DOCK7 activity. These studies in the Dock7em2/em2 mouse provide a foundation for future tissue-specific deletion studies utilizing the Dock7 exon 3-4 deletion model to define the cellular roles of DOCK7 in regulating bone formation and trabecular architecture. Lay SummaryIdentifying genes that regulate bone mass is essential for understanding osteoporosis. Mutation of the Dock7 gene in mice results in low bone mass, similar to human osteoporosis. Previous models could not isolate its role in specific tissues, limiting our ability to understand how DOCK7 controls bone mass. We developed a new mouse model where Dock7 can be mutated in specific tissues. In this study, we bred mice to carry this mutation across all tissues, causing significant bone loss. This validates a flexible tool for future research to mutate DOCK7 in specific cell types and map its role in skeletal health.

cell biology↗

bioRxiv2025

A non-canonical AKT1-TERT pathway coordinates autophagy and ERphagy

The retinal pigment epithelium (RPE) sustains lifelong proteostasis under chronic stress, yet how post-mitotic cells activate autophagy when canonical kinase pathways suppress it remains unresolved. Here we demonstrate that AKT1, conventionally regarded as an autophagy suppressor, drives autophagy through a non-canonical transcriptional mechanism triggered by isoform imbalance. In RPE and age-related macular degeneration (AMD) models, AKT2 hyperactivation destabilizes mTORC2 and engages S6K-mediated IRS-1 inhibition, creating a feedforward autophagic arrest. Compensatory AKT1 activation via mTORC2 phosphorylates telomerase reverse transcriptase (TERT) at Serine 824, driving nuclear translocation that is independent of telomere maintenance. In the nucleus, TERT assembles with FOXO3 and MYC into a tripartite transcriptional complex that occupies the EIF2AK3 promoter, enabling PERK transcriptional activation. This activity converts the unfolded protein response from pro-apoptotic to cytoprotective: PERK-ATF4 signaling drives biogenesis of core autophagy machinery while simultaneously inducing selective ERphagy through the receptors TEX264 and CCPG1, which prevents pathological PERK clustering and preserves tubular ER architecture in diseased RPE. Using C. elegans phosphorylation-deficient mutants, mouse models and AMD patient induced pluripotent stem cell-derived retinal pigment epithelium (iPSC-RPE), we establish that AKT1-mediated TERT phosphorylation is an evolutionarily conserved prerequisite for FOXO/DAF-16 nuclear function and lysosomal homeostasis in post-mitotic cells. Pharmacologic targeting of AKT2 with a first-in-class dual-pocket allosteric inhibitor selectively enhances AKT1 compensation, restoring macroautophagic and ERphagy flux across disease models. These findings reveal a kinase-to-transcription axis that reprograms organelle quality control and identify the AKT1-TERT-PERK-ATF4 pathway as a therapeutic target in proteostasis-driven disease.

cell biology↗

bioRxiv2025

Salivary Extracellular Vesicle RNA Profiling Reveals Biomarkers for Sjogrens

Sjogrens is a chronic autoimmune disease affecting exocrine glands and is subclassified into SSA-positive (SSA+) and SSA-negative (SSA-) subtypes, with a complex diagnostic journey and an average diagnostic delay of almost 4 years. While SSA+ cases can be detected via serological testing, current assays lack specificity. For SSA-patients, no non-invasive diagnostic tools exist, and diagnosis often requires invasive lip biopsy. A saliva-based liquid biopsy capable of diagnosing both subtypes is therefore of high clinical interest. However, saliva poses challenges due to its abundant oral microbiome, which complicates unbiased biomarker discovery. In this study, we present a novel RNA sequencing workflow that efficiently depletes microbial content, enabling deep profiling of long RNAs within salivary extracellular vesicles (EVs). This approach identified both known and novel RNA biomarkers capable of diagnosing SSA+ and SSA-subtypes with high sensitivity and specificity. Moreover, we uncovered distinct RNA signatures that allow molecular stratification of Sjogrens subtypes. Pathway analysis in SSA+ cases revealed enrichment of immune and glandular pathways consistent with prior tissue-based studies, supporting the utility of salivary EVs as a non-invasive surrogate for tissue biopsy. Importantly, our data provides new molecular insights into the under-characterized SSA-subtype, laying the foundation for future mechanistic studies and facilitating their broader inclusion in clinical trials.

genomics↗

bioRxiv2025

Ultra-wide-field, deep, adaptive two-photon microscopy

Observing the activity patterns of large neural populations throughout the brain is essential for understanding brain function. However, capturing neural interactions across widely distributed brain regions from both superficial and deep cortical layers remains challenging with existing microscopy technologies. Here, we introduce a state-of-the-art two-photon microscopy system, ULTRA, capable of single-cell resolution imaging across an ultra-large field of view (FOV) exceeding 50 mm{superscript 2}, enabling deep and very wide field in vivo imaging. To demonstrate its capabilities, we conducted a series of experiments under multiple imaging conditions, successfully visualizing brain structures and neuronal activities spanning a spatial range of over 7 mm from superficial layers to depths of up to 900 m, while covering a volume of 45.24 mm3 in the mouse brain. This versatile imaging platform overcomes traditional spatial constraints, providing a powerful tool for comprehensive exploration of neuronal circuitry over extensive spatial scales with cellular resolution.

neuroscience↗

bioRxiv2025

Whole-brain chemosensory responses of both C. elegans sexes

Sexually-dimorphic neural circuits play a critical role in shaping sex-specific animal behaviors. Maps of the structural dimorphisms in these circuits have been explored by analyzing "synaptic connectomes", electron micrograph reconstructions of synaptic connectivity. Nevertheless, recent studies in the model organism C. elegans have shown little to no correlation between the synaptic connectome and dynamic neural activity. Therefore, the extent of sexual dimorphism in functional neural activity remains unknown. To determine the extent of functional sexual-dimorphisms in C. elegans we compared activity, neuron-by-neuron, across all neurons in the heads of both sexes. To sample a broad view of responses to different sensory modalities, we tested a diverse panel of ethologically-relevant olfactory, gustatory, and chemical stimuli, representing both attractive and aversive cues. We found that nearly every sensory neuron responded dimorphically to at least one cue and monomorphically to other cues, indicating that sexually-dimorphic circuits are pervasive and stimulus dependent. This dimorphic and monomorphic activity was present to a lesser extent in downstream interneurons and even less so in motoneurons, implicating sensory neurons as the primary source and location of sexually-dimorphic activity. Comparing the functional activity we measured to the published synaptic connectomes of both sexes revealed that sexual dimorphism in functional connectivity was distinct from and complementary to sexual dimorphism in synaptic connectivity. Our results provide a first-of-its-kind comparison of whole-brain dynamics between sexes at the level of single neurons, serving as an extensive resource for further investigations of functional sex differences.

neuroscience↗

bioRxiv2025

Transcriptional Roadmap of the Human Airway Epithelium Identifying HLF as a Novel Regulator of Basal Stem Cell Function

RationaleThe human airway epithelium depends on a coordinated hierarchy of stem-and differentiated cells to maintain tissue integrity and respond to injury. Defining the transcriptional and translational programs that govern these processes is critical for understanding airway disease and advancing regenerative therapies. ObjectivesTo map the transcriptional landscape of the human airway epithelium and identify regulatory factors controlling basal stem cell function and epithelial differentiation. MethodsWe performed single-cell RNA sequencing on bronchial biopsies from nine healthy never-smokers, categorized into young (<40 years) and aged (>60 years) cohorts. Unbiased cell type annotation and pseudotime trajectory analysis were used to define cell states and transcription factor dynamics. Measurements and Main ResultsAll major airway epithelial cell types were identified, with conserved composition and transcriptional programs across age groups. Basal stem cells (BSCs) exhibited elevated ribosomal gene expression, indicating increased translational readiness. Pseudotime analysis revealed transitions from basal to differentiated states, with MYC, JUN, and FOS upregulated in proliferative suprabasal cells. HLF emerged as a BSC-enriched transcription factor downregulated upon differentiation. Functional assays showed that HLF overexpression suppresses proliferation in airway BSC and in lung squamous carcinoma cells, while Hlf-deficient mice display basal cell hyperplasia and deficient differentiation. In lung cancer datasets, low HLF expression correlated with worse patient survival. ConclusionsThis study defines conserved gene programs in the human airway epithelium and identifies HLF as a novel regulator of BSC proliferation and potential tumor suppressor. These findings may inform the development of regenerative therapies and contribute to improved understanding and treatment of lung disease.

molecular biology↗

bioRxiv2025

Serpins A1/A3 within tumor-derived extracellular vesicles support pro-tumoral bias of neutrophils in cancer

Neutrophils are known to play an important regulatory role during tumor progression in several types of cancer. However, the mechanisms responsible for their tumorigenic bias and extended lifespan in cancer are not clear to date. This study uncovers a previously unknown mechanism by which tumor-derived small extracellular vesicles (sEVs), via their serpin cargo, reprogram neutrophils to adopt a tumor-supporting phenotype. We demonstrated here an elevated content of plasma sEVs during head and neck cancer progression, and their significant cargo enrichment with inhibitors of neutrophil serine proteases: serpins A1 and A3. Mechanistically, neutrophils educated with serpin-rich tumor-derived sEVs displayed typical pro-tumoral characteristics, including prolonged lifespan and activated CD62Llow CD11bhigh PDL1high phenotype. Functionally, such neutrophils demonstrated a strong ability to promote the epithelial-to-mesenchymal transition of tumor cells. Moreover, such neutrophils induced remarkable suppression of cytotoxic CD8 T cells, significantly reducing their tumor cell-killing capacity. Importantly, serpin cargo was essential for this activity, as serpin-depleted sEVs failed to reprogram neutrophils. These findings again highlight the clinical significance of sEVs and suggest their serpin content as important mediators of pro-tumoral functionality. Targeting the biogenesis or uptake of such immunosuppressive sEVs, or modifying their cargo, could potentially serve as a potent adjuvant anti-cancer therapy.

cancer biology↗

bioRxiv2025

Chronic Antigen Stimulation in Solid Tumors Induces T Cell Exhaustion and Limits Efficacy of T Cell Bispecific Therapies

T cell bispecific antibodies (TCBs) have demonstrated promising results in patients with solid tumors. However, the underlying immunological and molecular mechanisms influencing these clinical outcomes require in depth evaluation. T cell exhaustion, a state induced by prolonged antigen exposure, is known to undermine T cell-based immunotherapies, though its specific impact on TCB efficacy remains unclear. In this study, we assessed the effectiveness of TCBs on tumor-specific T cells, focusing on their functional status. Utilizing a fully immunocompetent mouse model with a solid tumor expressing an immunogenic antigen, we showed that tumor-specific T cells acquire an exhausted phenotype and fail to expand under TCB treatment. By employing both mouse and human tumor-specific T cells in vitro, our study established that chronically stimulated tumor-specific T cells show impaired response to TCB treatment. The comparison of TCB efficacy in T cell-inflamed tumors with immunogenic antigens versus non-inflamed tumors with low antigen presence in mice revealed TCB success in solid tumors is more reliant on T cell functional fitness than on their abundance before treatment. The data also indicate that solid tumors with elevated levels of both, intratumoral regulatory T cells, and T cells expressing co-inhibitory receptors, show diminished responses to TCB therapy, aligning with similar observations described in hematological cancers. These findings highlight the critical role of T cell exhaustion due to chronic antigen exposure and illustrate that exhausted tumor-specific T cells are likely not the driver population redirected by TCBs for tumor elimination. Our research highlights the importance of maintaining T cell fitness and preventing T cell exhaustion to improve TCB therapy outcomes. This may help better identify patient populations with solid tumors that could benefit from TCB treatments most in clinical settings.

cancer biology↗

bioRxiv2024

Blood-borne immune cells carry low biomass DNA remnants of microbes in patients with colorectal cancer or inflammatory bowel disease

The involvement of the human intestinal microbiome in the regulation of immune cell homeostasis, as well as in the pathogenesis of inflammatory bowel disease (IBD) and colorectal cancer (CRC), are well-established1-4. Bacteria interact with immune cells at the sites of intestinal inflammation, but also in the CRC tumor microenvironment1-6. Indeed, bacterial remnants have recently been detected in human intestinal tissue in patients with IBD, at primary tumor sites and in the metastases of patients with CRC, and in whole blood3,7,8. A defective intestinal epithelial barrier is thought to promote bacterial remnant translocation and disease progression6. However, it is unknown, how bacterial remnants translocate from the intestine to sites of metastasis or into the circulation. We hypothesized that bacterial remnants translocate within peripheral blood immune cells into the circulation. Here, we thus explored the composition of the detectable microbiome in peripheral blood mononuclear cells (PBMCs) of patients with CRC or IBD compared to healthy controls. The PBMC microbiome profiles partially align with the tumor- and metastasis-derived or intestinal tissue-derived microbiome signatures obtained from the same patients with CRC or IBD, respectively. Our metagenomics data, supported by 16S-rRNA-FISH-Flow, imaging flow cytometry and species-specific qPCR, reveal the presence of translocated bacterial genetic sequences in the patients with CRC and IBD, likely due to an intestinal barrier defect. Pathway and serum metabolomics analysis connected to the metabolic potential of the PBMC-derived microbiome sequences support the onset of microbial translocation in such patients. Thus, our data suggest that in patients with intestinal barrier leakage, such as those with CRC or IBD, there is the potential for the translocation of bacterial remnants into the circulation via peripheral immune cells.

cancer biology↗

bioRxiv2024

Anatomical and functional analysis of the corticospinal tract in an FRDA mouse model

Friedreichs ataxia (FRDA) is one of the most common hereditary ataxias. It is caused by a GAA repeat in the first intron of the FXN gene, which encodes an essential mitochondrial protein. Patients suffer from progressive motor dysfunction due to the degeneration of mechanoreceptive and proprioceptive neurons in dorsal root ganglia (DRG) and cerebellar dentate nucleus neurons, especially at early disease stages. Postmortem analyses of FRDA patients also indicate pathological changes in motor cortex including in the projection neurons that give rise to the cortical spinal tract (CST). Yet, it remains poorly understood how early in the disease cortical spinal neurons (CSNs) show these alterations, or whether CSN/CST pathology resembles the abnormalities observed in other tissues affected by FXN loss. To address these questions, we examined CSN driven motor behaviors and pathology in the YG8JR FRDA mouse model. We find that FRDA mice show impaired motor skills, exhibit significant reductions in CSN functional output, and, among other pathological changes, show abnormal mitochondrial distributions in CSN neurons and CST axonal tracts. Moreover, some of these alterations were observed as early as two months of age, suggesting that CSN/CST pathology may be an earlier event in FRDA disease than previously appreciated. These studies warrant a detailed mechanistic understanding of how FXN loss impacts CSN health and functionality.

neuroscience↗

bioRxiv2024

Spatial Coherence of DNA Barcode Networks

Sequencing-based microscopy is a novel, optics-free method for imaging molecules in biological samples using molecular DNA barcodes, spatial networks, and sequencing technologies. Despite its promise, the principles determining how these networks preserve spatial information are not fully understood. Current validation methods, which rely on comparing reconstructed positions to expected results, would benefit from a deeper understanding of these principles. Here, we introduce the concept of spatial coherence-- a set of fundamental properties of spatial networks that quantifies the alignment between topological relationships and Euclidean geometry. Our findings show that spatial coherence is an effective method for evaluating a networks capacity to maintain spatial fidelity and identify distortions, independent of prior information. This framework provides a cost-effective validation tool for sequencing-based microscopy by taking advantage of the fundamental properties of spatial networks in nanoscale systems.

bioinformatics↗

bioRxiv2024

Shift in cellular crosstalk reveals the immunosuppressive environment in cholangiocarcinoma patients.

Background and aimsCholangiocarcinoma (CCA) is a deadly disease, and this cancer entity is characterized by an abundant stroma. The tumor microenvironment (TME) plays an important role in aggressive behavior and poor response to therapeutics; however, underlying pathways are unknown. MethodsTo fill this gap, we used multiplexed immunohistochemistry, high-dimensional phenotyping, and transcriptomics to analyze human CCA samples and identify cell cluster crosstalk in patients with a poor prognosis. ResultsOur findings confirmed the presence of Tregs and the lack of effector memory cells in the tumor. New findings are the spatiality of the effector memory cells being more present in the peripheral tissue, for some reason these immune cells fail to reach the tumor niche. We revealed cancer crosstalk with macrophages and stromal cells and identified responsible genes in the poor prognosis group. Amongst the responsible ligand pairs are GAS6-AXL belonging to the TAM family. We then identified VCAN-TLR2 to be present and influencing the ECM in a way to supports immune exhaustion. Last, EGFR-TGF-{beta} is expressed in macrophages and this finding is important in Tregs induction and blocking cytotoxic T cell function. ConclusionsThe multiple mechanisms leading to the exclusion of relevant immune cells needed for an anti-cancer response and mechanisms leading to active immune suppression are part of complex cell-cell crosstalk. This study provides a deeper insight into the immune exhausted phenotype in CCA.

cancer biology↗

bioRxiv2023

Application of an NMR/crystallography fragment screening platform for the assessment and rapid discovery of new HIV-CA binding fragments

Identification and assessment of novel targets is essential to combat drug resistance in the treatment of HIV/AIDS. HIV Capsid (HIV-CA), the protein playing a major role in both the early and late stages of the viral life cycle, has emerged as an important target. We have applied an NMR fragment screening platform and identified molecules that bind to the N-terminal domain (NTD) of HIV-CA at a site close to the interface with the C-terminal domain (CTD). Using X-ray crystallography, we have been able to obtain crystal structures to identify the binding mode of these compounds. This allowed for rapid progression of the initial, weak binding, fragment starting points to compounds 37 and 38, which have 19F-pK values of 5.3 and 5.4 respectively. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=56 SRC="FIGDIR/small/569544v2_ufig1.gif" ALT="Figure 1"> View larger version (6K): org.highwire.dtl.DTLVardef@1c7043corg.highwire.dtl.DTLVardef@e73044org.highwire.dtl.DTLVardef@11c1d9org.highwire.dtl.DTLVardef@1cd99e7_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗