Biology subjects

Klein, J.

Publications and source records attributed to Klein, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Systematic comparison of gliflozins identifies a selective anti-calcifying effect of canagliflozin beyond canonical SGLT2 inhibition

Background: Sodium-glucose cotransporter 2 inhibitors (SGLT2i) provide important cardiorenal benefits in chronic kidney disease (CKD), but their effects on vascular calcification remain conflicting. Whether potential anti-calcifying effects are shared across gliflozins or involve mechanisms beyond canonical SGLT2 inhibition is unknown. Methods: We systematically compared canagliflozin, dapagliflozin and empagliflozin in a high-phosphate diet-induced mouse model of vascular calcification and complementary ex vivo and in vitro models, including rodent and human vascular tissues and vascular smooth muscle cells (VSMCs). Aortic transcriptional response was investigated by RNA sequencing. VSMC calcification, proliferation, migration, viability, glucose uptake and bioenergetics were investigated using complementary cellular assays, including OsteoSense staining, Annexin V/propidium iodide staining, radiolabeled 2-deoxyglucose uptake and Seahorse ATP rate analysis. SGLT2/1 expression was examined by RT-qPCR, Western blotting and immunofluorescence. We also evaluated sotagliflozin, a dual SGLT1/2 inhibitor, and mizagliflozin, a selective SGLT1 inhibitor. Results: Among the three gliflozins, only canagliflozin significantly reduced aortic calcification in vivo. Its anti-calcifying effect was also observed in rodent aortic rings, human vascular explants, cultured VSMCs and aortic rings from diabetic db/db mice. Aortic RNA-seq revealed that canagliflozin partially reversed HPD-induced transcriptional alterations, including changes in pro-calcific signaling and cellular metabolism, while some endothelial and inflammatory responses were shared among gliflozins. In mouse VSMCs, canagliflozin reduced calcification across all tested concentrations, dose-dependently decreased osteogenic marker expression, and reduced proliferation and migration. Increased apoptotic and damaged cell fractions were observed at higher concentrations, but not at lower concentrations. Canagliflozin also reduced glucose uptake and mitochondrial ATP production, without significantly affecting glycolytic ATP production. Neither dapagliflozin nor empagliflozin reproduced these cellular and metabolic effects at any of the concentrations tested. SGLT2 and SGLT1 expression was low or undetectable in vascular tissues and cells, and neither sotagliflozin nor mizagliflozin reproduced the anti-calcifying effect of canagliflozin in vivo or in vitro. Conclusions: Canagliflozin exhibits a selective anti-calcifying profile among the gliflozins tested, associated with changes in VSMC responses and cellular metabolism. These findings suggest that its vascular protective effects may involve mechanisms beyond canonical SGLT2 inhibition.

pathology↗

bioRxiv2026

Identification of the Col4a3-/- mouse as a model of chronic kidney disease-associated cachexia

Background: Cachexia is a frequent complication of advanced chronic kidney disease (CKD), i.e. renal cachexia, particularly in patients undergoing hemodialysis in whom it represents one of the strongest predictors of morbidity and mortality. Yet, our understanding of the molecular mechanisms leading to body wasting in CKD and management of cachectic patients are still poorly defined. To date, a preclinical mouse model of robust and reproducible CKD-associated cachexia is missing. Here, we assessed in a systematic manner the cachectic phenotype of the genetic Col4a3-/- mouse model of CKD. Methods: 129/SvJ Col4a3-/- male and female animals were monitored longitudinally until they developed kidney failure. Measured glomerular filtration rate (mGFR), body composition and grip strength were recorded at baseline (6 weeks of age, before onset of kidney dysfunction) and at endpoint (CKD with weight loss or 12 weeks of age). The severity of CKD was confirmed by biochemical and histological analyses. Muscle atrophy was assessed via fiber cross-sectional area analysis, atrogene expression and transcriptomics. Adipose tissue wasting was assessed by measuring adipocyte area and proteins involved in lipid synthesis and breakdown. Liver acute phase response and systemic inflammation were evaluated by measuring circulating levels of key factors using ELISA. Results: Col4a3-/- animals developed CKD (decrease in mGFR: -85%, P<0.0001) and cachexia within 8-12 weeks of age. Cachexia was characterized by a progressive loss of body weight (-17.8% +/- 1.0, P<0.0001), lean (-8.2% +/- 2.0, P<0.0001) and fat mass (-66.5% +/- 4.7, P<0.0001) associated with reduced grip strength (-24.3% +/- 0.0, P=0.0002). At the tissue level, cachexia led to muscle atrophy and induction of atrogenes. Muscle transcriptomics further validated the cachectic phenotype of the Col4a3-/-, with 47% of genes altered in a similar manner with the well-established colon-C26 mouse model of cancer cachexia. It also revealed signatures that appeared more specific to renal cachexia. Adipose tissue wasting was characterized by a depletion in fat stores, consecutive to an imbalance between proteins involved in lipogenesis and lipolysis. Cachexia in this model was also associated with the induction of acute phase response in liver, elevated circulating levels of serum amyloid A and systemic inflammation, with the induction of established cachexia mediators (IL-6, GDF-15 P<0.0001). Both male and female mice developed cachexia. Conclusions: Our data highlight the potential of using the Col4a3-/- mouse model of CKD for the future study of renal cachexia, offering a more robust alternative to classically used models of partial nephrectomy or adenine-rich diet.

pathology↗

bioRxiv2026

Systematic Engineering of Loss-of-Function Alleles in the Zebrafish Mitochondrial Proteome

Pathogenic variants in the 13 protein-coding genes of the mitochondrial genome underlie clinically and biochemically heterogeneous disorders. Most mtDNA-encoded genes lack defined loss-of-function (LOF) models in vivo. To address this gap, we have generated Z-Terminator, a systematic in vivo atlas of loss-of-function alleles covering all the mtDNA-encoded OXPHOS subunits in zebrafish (Danio rerio). We used mitochondrial TALE base editors to introduce premature termination codon (PTC) alleles via C-to-T transitions across Complexes I, III, IV, and V. Larvae harboring PTC alleles displayed bioenergetic defects and elevated lactate. While mtDNA mutations are associated with sensorineural hearing loss, the cellular basis has remained unclear. We show that engineered mtDNA LOF alleles directly impair hair cell function in proportion to heteroplasmy in a living vertebrate. We investigated the germline transmission and tissue-specific heteroplasmy of these LOF alleles and observed that a subset of variants was transmitted to the F1 generation and displayed distinct mutant loads across organs. These findings establish Z-Terminator as a vertebrate platform for interrogating the role of mtDNA protein-coding genes in cellular dysfunction and for elucidating the pathophysiology of mitochondrial disorders.

genetics↗

bioRxiv2026

LRRC57/RABIN is a presynaptic inhibitor of Rab GTPases in glutamatergic neurons

Synaptic vesicle cycling, if not properly constrained, can result in excessive neurotransmitter release and subsequent neural pathology. Rab GTPases orchestrate synaptic vesicle trafficking through GTP-dependent interactions with effector proteins, but the restraining mechanism of these interactions is unknown. Here we identify LRRC57 (or RABIN for RAB INhibitor), a conserved brain-enriched protein in glutamatergic synapses that binds multiple GTP-loaded synaptic Rabs and competitively blocks access to their effectors. Loss of Rabin increased glutamate release, expanded vesicle pools, accelerated vesicle turnover, and produced circuit hyperexcitability with epileptiform activity, which was mitigated by an antiepileptic agent that targets presynaptic function. Conversely, overexpression of the Rabin gene suppressed neurotransmitter release and protected against induced seizures and persistent epileptiform discharges. Together, these findings define a noncanonical decoy-effector mechanism that constrains presynaptic Rab signaling to preserve excitatory circuit stability.

neuroscience↗

bioRxiv2026

Perturb-seq resolves physiologic programs and bidirectional regulation of non-canonical NF-κB signaling in epidermal organoids

Regulated keratinocyte differentiation is required for formation of the stratified epidermis and a functional barrier. Understanding genetic drivers of keratinocyte differentiation is crucial for understanding several skin diseases. Perturb-seq is a single-cell CRISPR screen that measures transcriptomic responses to perturbations. To date, Perturb-seq experiments have principally focused on 2-dimensional cell culture models lacking hallmarks of skin development - physiological desmosome formation and barrier function. Here, we leverage Perturb-seq in an epidermal organoid model that recapitulates physiologically relevant differentiation programs. We demonstrate that our perturbations significantly impact diverse differentiation programs and reveal bidirectional function of non-canonical NF-{kappa}B signaling in late keratinocyte differentiation.

genomics↗

bioRxiv2026

Nod factor signaling controlled genes in Medicago truncatula nodules

O_LILegume nodule formation is induced by rhizobia secreted Nod factors (NFs). It has been shown that NF receptors also accumulate in the apex of Medicago truncatula nodules. However, the NF signaling induced transcriptional changes in there have never been studied. C_LIO_LIHere, we studied this by using NF signaling mutant TE7, a weak allele of IPD3, blocked in rhizobial release. Nodule apices were isolated with laser microdissection and used for transcriptional analysis. C_LIO_LIWe identified 1655 NF signaling controlled genes in nodule apex. By comparing this with the transcriptome data from VAMP721d&e RNAi nodule apices, we identified a subset of 445 genes whose expression depends on NF signaling and rhizobial release. Further, we compared the set of genes controlled by NF signaling in nodule apices with that controlled in root epidermis, and these showed only a small overlap. NIN is induced by NF signaling both in the root epidermis and in the nodule. By overexpression of NIN in TE7 and knock down of NIN in wildtype nodules we showed that NF signaling controlled rhizobial release depends on NIN. C_LIO_LINF signaling controls a distinct set of genes in nodules, the function of which depends at least in part on NIN. C_LI

Developmental Biology↗

bioRxiv2026

Alternative organelle targeting of OPA1 mediates fatty acid release from lipid droplets

Mitochondria and lipid droplets (LDs) are functionally coupled to coordinate fatty acid utilization and storage. However, a comprehensive understanding of mitochondria-LD alliances remains elusive. We have identified a previously unrecognized role for optical atrophy 1 (OPA1), a mitochondrial fusion factor, in the regulation of fatty acid release from LDs. We demonstrated that OPA1s exon 4 adapts an amphipathic helix to target OPA1 to LDs. OPA1 localized to LDs promote fatty acid release by facilitating the recruitment of lipases to LDs. In addition, OPA1s residence on LDs competes with its mitochondrial entry, influencing mitochondria fusion and connectivity. Furthermore, the S158N polymorphism within OPA1s exon 4 exhibiting attenuated fatty acid release from LDs is associated with changes in metabolic traits in pediatric cancer survivors. Altogether, our findings reveal that OPA1 actively mediates fatty acid release from LDs and provide a mechanistic link between OPA1 and human metabolism.

cell biology↗

bioRxiv2026

Primary human dermal fibroblasts selectively sense microbial ligands and initiate immune response through chemokines secretion

Fibroblasts are traditionally considered structural cells that maintain tissue homeostasis and facilitate repair. However, accumulating evidence suggests they also participate in innate immunity, although their pattern recognition capabilities remain incompletely characterized. Here, we systematically assessed the innate immune responses of commercially available primary human dermal fibroblasts from a male and a female donor. Fibroblasts were stimulated with a panel of microbe-associated molecular patterns (MAMPs) targeting various pattern recognition receptors (PRRs), including Toll-like receptors (TLRs), NOD-like receptors (NODs), Alpha kinase 1 (ALPK1) and STING. Innate immune activation was quantified by measuring the nuclear translocation of NF-{kappa}B via high content microscopy and cytokines and chemokines secretion by ELISA; baseline PRRs expression was determined by quantitative PCR. Only a restricted subset of agonists, specifically E. coli LPS (TLR4), Poly I:C (TLR3 / RIG-I) and unexpectedly ADP heptose (ALPK1) induced robust NF-{kappa}B activation and secretion of the chemokines IL-8 and MCP-1. Apart from IL-6 and RANTES, which were produced exclusively following Poly I:C stimulation, pro-inflammatory cytokines (IL-1{beta}, TNF, IFN-{beta}) and the anti-inflammatory cytokine IL-10 remained undetectable. Consistent with this limited reactivity, qPCR of PRRs revealed basal expression of TLR4 and ALPK1, whereas most other receptors were expressed at very low or undetectable levels. Notably, NOD1 was highly expressed although no cell activation was observed with several NOD1 agonists. Dose-response analysis revealed surprisingly high sensitivity to LPS. In conclusion, primary human dermal fibroblasts exhibit a highly selective but sensitive innate immune response, largely restricted to chemokine production upon PRR activation. This unexpected dissociation between chemokine and cytokine responses suggests that fibroblasts function as sentinel cells in early skin defense, capable of detecting key microbial patterns at low concentrations, to orchestrate local immune surveillance. Further investigation into interindividual variability and context-dependent activation is needed.

immunology↗

bioRxiv2026

Spatiotemporal dynamics of ethylene biosynthesis shape infection and nodule initiation in Medicago truncatula

Ethylene is a well-established negative regulator of nodulation, yet how ethylene biosynthesis and perception are spatially coordinated during early symbiotic signalling remains unresolved. Here, we investigate the dynamics of ethylene responses in Medicago truncatula using transcriptomics, promoter-reporter analyses, loss-of-function approaches and a synthetic reporter. We show that the activity of the ethylene-responsive EBSn reporter shifts from inner root tissues under non-symbiotic conditions to the outer cortex and epidermis following rhizobial inoculation, revealing a spatial reprogramming of ethylene signalling. Among the eight Medicago 1-AMINOCYCLOPROPANE-1-CARBOXYLIC ACID SYNTHASE (ACS) genes, upon rhizobia application MtACS3 is induced in outer root cell layers, while MtACS10 is repressed in the inner cortex and pericycle, mirroring the shift in ethylene perception. Functional analysis demonstrates that MtACS10 restricts nodule initiation, whereas MtACS3 modulates infection thread number, prevents nodule clustering, and contributes to radial positioning of nodule primordia. Rhizobial induced ectopic ACS expression in the root interior counteracts MtACS10 repression and blocks nodulation, highlighting the requirement for spatially confined downregulation of ethylene biosynthesis. Together, these findings establish a framework in which localized shift in ethylene biosynthesis, mediated by distinct Medicago ACS genes, balances infection and organogenesis while co-defining the spatial limits of the root susceptible zone.

plant biology↗

bioRxiv2026

Fusion of lipid membranes: an alternative pathway

Membrane fusion is ubiquitous in myriad biological processes, including presynaptic neurotransmitter release, myoblast fusion, virus entry, and fertilization1-3. It is often considered in the presence of fusogenic proteins, which mediate the fusion by pulling the membranes into contact to overcome the high energy barrier imposed by hydration repulsion4-7. Here we uncover an alternative pathway - membrane fusion arising from electroporation induced by transmembrane potentials8,9 in absence of proteins. Using biased molecular dynamics simulations to carry out extensive potential-of-mean-force calculations10, we show how electroporation of opposing membranes promotes membrane fusion via formation of an intermembrane splayed lipid and peripore stalk, without any protein involvement. We validate our mechanism by demonstrating experimentally, via video microscopy and second harmonic generation imaging11 of interacting giant unilamellar vesicles (GUVs), that GUV fusion occurs in the presence of transmembrane potentials but not in their absence. The magnitude of these transmembrane potentials is biologically relevant, prevalent in transient states near the surfaces of cell membranes8,12, underscoring the potential importance of this mechanism in biological events.

biophysics↗

bioRxiv2026

Nematicidal indole oxazoles and chemoattractants from soil bacteria

Ecological interactions between bacteria and nematodes in many environments provide a basis for the prediction that diverse bacteria produce anti-nematode compounds. The discovery of microbial secondary metabolites with broad-spectrum nematostatic or nematicidal properties can be hastened by drug screening approaches that include several nematode species and phenotypes. We cultured a collection of 22 soil-derived bacterial isolates that carry in their genomes putative pathways for production of unknown secondary metabolites. Isolates were cultured in various media to enhance natural product diversity and yield, and we evaluated culture filtrates for activity against two evolutionarily distinct nematode species: Clade V free-living nematode Caenorhabditis elegans and Clade III mammalian parasitic nematodes in the genus Brugia. Partitioned extracts from Pseudomonas sp. strain TE4607 stunted C. elegans development and caused motility defects in both blood-circulating larval and adult stages of Brugia. The primary active compound was identified as labradorin 1, an indole with known antibacterial and anticancer properties that had not been previously described as affecting nematodes. Notably, filtrates of Pseudomonas sp. TE4607 cultures attracted free-living nematodes in sensory assays, adding to evidence that certain Pseudomonas species modulate the behavior of free-living nematodes. These findings underscore the need to further explore the link between nematode sensory responses and whole-organism effects of microbial metabolites, with potential applications in anthelmintic discovery. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/700618v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@1909e29org.highwire.dtl.DTLVardef@17f9badorg.highwire.dtl.DTLVardef@c59d79org.highwire.dtl.DTLVardef@1e5abbf_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

NEURO-IMMUNE CRYPT-ASSOCIATED CELLS DRIVE COLORECTAL CARCINOGENESIS VIA REST-MEDIATED PHENOTYPIC REPROGRAMMING: IMPLICATIONS FOR TUMORIGENESIS AND VIRAL SUSCEPTIBILITY

Colorectal cancer (CRC) pathogenesis remains linked to poorly defined cellular origins and microenvironmental drivers. We identify Neuro-Immune Crypt-Associated (NICA) cells as a privileged pathogen portal and a plausible epithelial cell of origin. During carcinogenesis, the repressor REST drives a neuroendocrine-to-epithelial transition by silencing NICA-associated neuroendocrine markers, a lineage loss reversible via epigenetic modulation or genetic ablation in CRC models. This landscape is further shaped by EBV-infected B-lineage cells (BLEICS), which transactivate HERV-H/F elements in CRC cells through paracrine signaling, establishing a niche-restricted viral scar. While tumor crypts sense this retroviral pressure, they exhibit an abortive antiviral signature marked by RNase L downregulation, creating a functional execution gap. We propose a pathogen-first model where chronic inflammatory pressure triggers mutation-silencing -the simultaneous genotoxic and epigenetic inactivation of tumor suppressors. Together, the convergence of NICA plasticity, BLEICS-mediated HERV induction, and compromised antiviral surveillance redefines CRC as a pathogen-driven disruption of the neuro-immune niche.

cancer biology↗

bioRxiv2025

Deciphering acquired resistance mechanisms to sustained auxin-inducible protein degradation in cells and mice

Targeted protein degradation is a favorable strategy for studying the immediate downstream effects of protein loss-of-function. An appealing platform among these technologies is the auxin-inducible degron (AID) system. Although this system has been applied extensively to cell and animal models, degradation resistance to long-term auxin treatment has not been studied. With the advent of the new AID2 system, cellular toxicity due to the high concentrations of auxin required in the original AID1 system is no longer a concern, making it possible to study protein degradation over extended periods. In this study, we derived multiple miniAID-tagged knock-in human cell lines and a Ctcf-miniAID knock-in mouse strain to investigate mechanisms of degradation resistance. We revealed four independent resistance mechanisms, including a nonsense mutation in the CTCF coding sequence that removed the miniAID peptide, a missense point mutation in the miniAID coding region that disrupted ubiquitin complex targeting, and silencing of the OsTIR1 adaptor protein. Resistance to auxin degradation was also acquired in mouse primary CtcfminiAID/miniAID knock-in B-ALL cells through missense mutations of the OsTIR1(F74G) protein in vivo and ex vivo. In summary, our innovative study expands our understanding of the AID system and cautions careful consideration of design for future applications in mammalian system.

cell biology↗

bioRxiv2025

Antiretroviral treatment does not prevent extrapulmonary tuberculosis during SIV/Mtb co-infection in macaques

Co-infection with both HIV and M. tuberculosis (Mtb) results in disseminated tuberculosis (TB) and accelerated progression of HIV. Despite greater access to antiretroviral treatment (ART), it remains unclear whether suppression of HIV replication protects against severe Mtb infection. Here, using a macaque model of SIV/Mtb coinfection, we investigated whether treatment of SIV infection with ART influenced control of a subsequent Mtb challenge compared to SIV infected macaques who were not treated with ART. Using a macaque model of simian immunodeficiency virus (SIV)-Mtb co-infection, macaques were first infected with SIVB670, SIVB670 with ART, or saline followed by a low-dose Mtb inoculation with serial clinical, microbiological, PET CT imaging, and immunologic assessments. At necropsy, gross pathology, viremia, bacterial burden, and immunologic parameters were compared. SIV-TB animals had greater gross pathology and total bacterial burden than TB only and SIV/ART/TB groups. However, despite normal blood CD4 counts and undetectable SIV RNA, SIV/ART/TB macaques showed similar clinical parameters and extrapulmonary involvement as SIV/TB animals. Analysis of barcoded-Mtb suggests ART control of SIV replication does not prevent Mtb extrapulmonary dissemination. These data indicate that people living with HIV on ART remain at high risk of bacterial dissemination and extrapulmonary TB disease, particularly when methods to identify extrapulmonary disease are inconsistent. This highlights the importance of understanding the mechanism of extrapulmonary spread and disease severity in HIV/TB co-infected individuals.

immunology↗

bioRxiv2025

Unraveling the Co-Morbidity between COVID-19 and Neurodegenerative Diseases Through Multi-scale Graph Analysis: A Systematic Investigation of Biological Databases and Text Mining

The COVID-19 pandemic has generated a vast volume of research, yet much of it focuses on individual diseases, overlooking complex comorbidity relationships. While extensive literature exists on both neurodegenerative diseases (NDDs), such as Alzheimers and Parkinsons, and COVID-19, their intersection remains underexplored. Co-morbidity modeling is crucial, particularly for hospitalized patients often presenting with multiple conditions. This study investigates the interplay between COVID-19 and NDDs by integrating knowledge graphs (KGs) built from curated biomedical datasets and text mining tools. We performed comprehensive analyses--including path analysis, phenotype coverage, and mapping of cellular and genetic factors--across multiple KGs, such as PrimeKG, DrugBank, OpenTargets, and those generated via natural language processing (NLP) methods. Our findings reveal notable variability in graph density and connectivity, with each KG offering unique insights into molecular and phenotypic links between COVID-19 and NDDs. Key genetic and inflammatory markers, especially immune response genes, consistently appeared across graphs, suggesting a shared pathogenic basis. By unifying structured biological data with unstructured textual evidence, we enhance co-morbidity modeling and improve recall in identifying mechanisms underlying COVID-19- NDD interactions. This integrative framework supports the development of a co-morbidity hypothesis database aimed at facilitating therapeutic target discovery. All data, methods, and instructions for accessing the co-morbidity hypothesis database are publicly available at: https://github.com/SCAI-BIO/covid-NDD-comorbidity-NLP.

bioinformatics↗

bioRxiv2025

ibaqpy: A scalable Python package for baseline quantification in proteomics leveraging SDRF metadata

Intensity-based absolute quantification (iBAQ) is essential in proteomics as it allows for the assessment of a proteins absolute abundance in various samples or conditions. However, the computation of these values for increasingly large-scale and high-throughput experiments, such as those using DIA, TMT, or LFQ workflows, poses significant challenges in scalability and reproducibility. Here, we present ibaqpy (https://github.com/bigbio/ibaqpy), a Python package designed to compute iBAQ values efficiently for experiments of any scale. ibaqpy leverages the Sample and Data Relationship Format (SDRF) metadata standard to incorporate experimental metadata into the quantification workflow. This allows for automatic normalization and batch correction while accounting for key aspects of the experimental design, such as technical and biological replicates, fractionation strategies, and sample conditions. Designed for large-scale proteomics datasets, ibaqpy can also recompute iBAQ values for existing experiments when an SDRF is available. We showcased ibaqpys capabilities by reanalyzing 17 public proteomics datasets from ProteomeXchange, covering HeLa cell lines with 4,921 samples and 5,766 MS runs, quantifying a total of 11,014 proteins. In our reanalysis, ibaqpy is a key component in automating reproducible quantification, reducing manual effort and making quantitative proteomics more accessible while supporting FAIR principles for data reuse.

bioinformatics↗

bioRxiv2024

A novel HLA Class II presentation prediction algorithm deciphers immunogenic CD4 epitopes specific to KRAS G12C

Accurate prediction of peptide presentation by HLA molecules is important for generation of effective individualized cancer vaccines and immunotherapies. While presentation prediction algorithms for HLA class I have been successfully applied in the context of such therapies, improved prediction algorithms for class II are needed. EDGE-II is a novel algorithm based on a protein large language model that has a learned allele deconvolution network trained on existing and new immunopeptidomics data. It delivers state-of-the-art performance on prediction of peptide presentation by HLA class II and immunogenicity elicited by CD4+ T-cell epitopes. In a patient with a KRAS G12C positive tumor treated with a KRAS G12C targeting immunotherapy, EDGE-II identified KRAS G12C class II neoantigens that elicited clonally expanded CD4+ T cells with cytotoxic transcriptional profiles post-vaccination. EDGE-II could play an important role in the development of effective cancer immunotherapies by elucidating an enriched understanding of the immunopeptidome.

bioinformatics↗

bioRxiv2022

Robust induction of functional astrocytes using NGN2 expression in human pluripotent stem cells

Astrocytes play essential roles in normal brain function, with dysfunction implicated in diverse developmental and degenerative disease processes. Emerging evidence of profound species divergent features of astrocytes coupled with the relative inaccessibility of human brain tissue underscore the utility of human pluripotent stem cell (hPSC) technologies for the generation and study of human astrocytes. However, existing approaches for hPSC-astrocyte generation are typically lengthy, incompletely characterized, or require intermediate purification steps, limiting their utility for multi-cell line, adequately powered functional studies. Here, we establish a rapid and highly scalable method for generating functional human induced astrocytes (hiAs) based upon transient Neurogenin 2 (NGN2) induction of neural progenitor-like cells followed by maturation in astrocyte media, which demonstrate remarkable homogeneity within the population and across 11 independent cell lines in the absence of additional purification steps. These hiAs express canonical astrocyte markers, respond to pro-inflammatory stimuli, exhibit ATP-induced calcium transients and support neuronal maturation in vitro. Moreover, single-cell transcriptomic analyses reveal the generation of highly reproducible cell populations across individual donors, most closely resembling human fetal astrocytes, and highly similar to hPSC-derived astrocytes generated using more complex approaches. Finally, the hiAs capture key molecular hallmarks in a trisomy 21 disease model. Thus, hiAs provide a valuable and practical resource well-suited for study of basic human astrocyte function and dysfunction in disease.

neuroscience↗