Biology subjects

Shi, A.

Publications and source records attributed to Shi, A..

At least 19 recordsLinked to original sources

bioRxiv2026

RNA-seq meta-analysis and machine learning identify stress-responsive genes and improve genomic prediction in common bean (Phaseolus vulgaris L.) with cross-species application in cowpea (Vigna unguiculata L.)

Common bean (Phaseolus vulgaris L.) is exposed to a broad spectrum of abiotic and biotic stresses that impose severe constraints on productivity, yet the molecular basis of stress tolerance remains poorly resolved, with independent studies yielding inconsistent and incomplete conclusions. To establish a comprehensive picture of the common bean stress transcriptome, we conducted a systematic meta-analysis of publicly available RNA-sequencing datasets spanning abiotic and biotic stress conditions across leaf and root tissues. Integrating statistical meta-analysis with machine-learning approaches, we identified stress-responsive gene sets whose robustness was verified through rigorous statistical approaches including independent dataset validation. Beyond confirming established stress-responsive genes, the machine-learning framework uncovered candidates overlooked by standard significance thresholds in individual studies yet carrying consistent transcriptional signals across studies. Co-expression and protein-protein network analyses further resolved these candidates into functionally coherent modules linked to specific stress-response programs. Notably, ethylene-responsive transcription factors were identified as hub genes in three of four stress-tissue groups, with NAC domain transcription factors emerging as additional hub genes in biotic stress contexts. Importantly, the biological significance of the identified gene sets was validated genomically: marker panels targeting consensus meta-analysis-derived and machine-learning-discovered gene regions improved genomic prediction accuracy for disease resistance traits in common bean and abiotic stress tolerance traits in cowpea relative to a baseline model with equivalent-sized random marker sets. Overall, these findings revealed conserved stress transcriptome signatures in common bean and provided a cross-species, evidence-based framework for prioritizing candidate genes and constructing biologically informed genomic selection tools to advance stress-resilient legume breeding.

genetics↗

bioRxiv2026

Multiscale learning and topological analysis across complex postures enable robust nematode size quantification in pharmacological assays

Body size is an important trait that reflects animal development and physiology. In nematodes, precise measurement is valuable for linking variation in body dimensions to biological questions such as developmental timing, genetic regulation, and drug responses. However, robust size measurements can be difficult to obtain because nematodes can vary in curvature, have self-intersecting postures, and overlap with neighboring animals. Current image analysis software, such as CellProfiler, can measure isolated animals in straight postures but struggles with curly or overlapping animals. Here, we present NemaSize, an artificial intelligence (AI)-aided pipeline to measure Caenorhabditis nematode body sizes across complex postures using multi-scale learning and topology-aware skeletonization. Using You Only Look Once (YOLO) models trained at different spatial scales, NemaSize first identifies individual animals in a large field of view (FOV; 6.75 x 6.75 mm) and then performs high-resolution body segmentation in the region of interest (ROI). Next, NemaSize converts segmented body masks into topological graph representations, allowing curly and overlapping animals to be classified and skeletonized according to the body topology. NemaSize achieved less than 4% overall error in length and width measurements across all posture classes. Compared to CellProfiler, NemaSize demonstrated higher robustness for complex postures, including a 48% error reduction in length measurements for curly or self-overlapping animals. Application of NemaSize in high-throughput imaging assays further shows that NemaSize provides accurate quantification of Caenorhabditis briggsae larval development in response to the anthelmintic drug ivermectin, a task that was difficult for CellProfiler because of curly animal postures. Together, NemaSize provides a robust approach for automated body size quantification for Caenorhabditis nematodes and will support broad applications in high-throughput pharmacological and genetic screens. Beyond nematodes, NemaSize introduces a multiscale computational framework for analyzing elongated biological objects with complex topologies.

pharmacology and toxicology↗

bioRxiv2026

Persistent Post-Inflammatory Matrix Stiffening Defines a Premalignant Mechanical Niche in Ulcerative Colitis-Associated Neoplasia

Patients with long-standing ulcerative colitis (UC) remain at risk for colorectal neoplasia even after overt inflammatory activity improves, suggesting that repaired mucosa may retain residual tissue-level abnormalities. Whether extracellular matrix remodeling leaves a persistent mechanical cue that contributes to early neoplastic remodeling is unknown. Here we identify post-inflammatory matrix stiffening as a premalignant mechanical niche in UC-associated neoplasia. In human colonic biopsies, collagen remodeling and atomic-force-microscopy-based mucosal stiffness increased from non-UC controls to UC and UC-associated dysplasia. A stiffness-associated transcriptional program was also enriched in histologically non-dysplastic mucosa from patients with UC-associated neoplasia. In mouse models, colonic stiffness increased along the colitis-to-tumorigenesis axis and remained elevated during apparent recovery, when epithelial permeability, junctional protein loss, crypt proliferation and nuclear {beta}-catenin accumulation persisted despite reduced disease activity. Stiffness-controlled intestinal epithelial cultures showed that stiff substrates were sufficient to disrupt ZO-1 organization and enhance {beta}-catenin redistribution, particularly under TNF- stimulation. Pharmacological matrix normalization with {beta}-aminopropionitrile partially restored barrier organization and attenuated early epithelial remodeling in vivo. Single-cell profiling identified a stiffness-associated MMP7-positive/YAP-active epithelial state that was enriched in collagen-rich regions and reduced after matrix softening. Inhibition of YAP or MMP7 attenuated stiffness-associated junctional disruption and {beta}-catenin redistribution. These findings suggest that inflammatory recovery and mechanical recovery can be uncoupled, and that persistent mucosal stiffening provides a tissue-level mechanism by which chronically injured UC mucosa may remain biologically vulnerable to premalignant epithelial remodeling.

Cancer Biology↗

bioRxiv2026

Why diabetes matters in dementia studies. Excluding diabetes status masks regional mitochondrial DNA copy number changes in human hippocampus, amygdala, and cerebellum in Alzheimers disease

STRUCTURED ABSTRACTO_ST_ABSINTRODUCTIONC_ST_ABSDiabetes is a major risk factor for Alzheimers disease (AD), and both diseases involve mitochondrial dysfunction. We hypothesised that AD is associated with reduced mitochondrial DNA copy number (mtDNA-CN) in vulnerable brain regions, and that diabetes modifies these changes. METHODSPost-mortem hippocampus, amygdala, and cerebellum samples (N=66-77) from non-cognitively impaired (NCI) and AD donors, with and without diabetes, were analysed. mtDNA-CN was quantified by absolute quantification. RESULTSOverall, mtDNA-CN was lower in AD. However, stratification by diabetes revealed opposite changes: non-diabetic AD cases showed reduced mtDNA-CN, whereas diabetic cases showed higher mtDNA-CN across all regions irrespective of cognitive status. DISCUSSIONThese findings confirm multiregional loss of mtDNA-CN in the AD brain, most evident in the absence of diabetes. The functional significance of higher mtDNA-CN in the diabetic brain remains unclear, but evidence that diabetes can mask effects has important implications for dementia studies.

neuroscience↗

bioRxiv2026

Accurate quantification of canine mitochondrial DNA copy number and its evaluation as a biomarker of brain injury

Acute brain injury is challenging to manage in veterinary medicine, with limited validated means of prognostication currently available. The brain is rich in mitochondrial content and contains thousands of copies of mitochondrial DNA (mtDNA) per cell. We hypothesized that brain cell loss following acute brain injury may result in release of mtDNA into the systemic circulation. To investigate this, mtDNA-CN was measured in blood (n=4-6/group) and cerebral cortex (n=1/group) samples from dogs with and without brain injury using absolute quantification by real-time qPCR. By filtering out regions with homology to nuclear mitochondrial insertion sequences (NumtS) and repetitive regions, oligonucleotide primers were designed to the canine mitochondrial and nuclear genomes. In controls, blood mtDNA-CN ranged from 98 to 288 (mean 193{+/-}72), in cases of brain injury, there was a non-significant trend for higher mtDNA-CN, ranging from 163-453 (mean 244{+/-}106). As expected, cerebral cortex contained higher mtDNA-CN than the blood. In a single case with serial sampling, mtDNA-CN increased five days post-injury. We present for the first time an assay to accurately quantify mtDNA-CN in canine samples, with potential as a biomarker for acute brain injury in veterinary practice. Simple SummaryThis work describes a novel assay to accurately measure absolute levels of canine mitochondrial DNA copy number (mtDNA-CN) in biological samples. We describe the range of mtDNA-CN in canine blood and show pilot data suggesting that blood mtDNA-CN should be evaluated as a potential biomarker of acute brain injury.

molecular biology↗

bioRxiv2025

Repurposed endogenous virus-like vesicles mediate dendritic cell long-range antigen presentation and T cell activation for enhanced cancer vaccination

Dendritic cells (DCs) release extracellular vesicles (DEVs) that amplify antigen presentation while incorporating patient-derived, rapidly evolving antigens. By enriching peptide-MHC and co-stimulatory ligands orders-of-magnitude above donor-cell levels, DEVs emerge as potent vesicle-vaccines, although efficacy remains limited by unclear mechanisms. We show that DCs repurpose viral components to generate endogenous virus-like vesicles (VLVs) that preferentially carry peptide-MHC and high-density co-stimulatory ligands, intensifying and extending antigen presentation. Upon antigen exposure, Arc partners with endogenous envelope proteins to assemble VLVs that directly engage T cells and trigger intrinsic adjuvanticity via viral mimicry. Arc-/- DEVs failed to prime antigen-specific T cell responses, whereas Arc overexpression with its 5'-UTR stem-loop shifted DEVs toward VLVs that trafficked to lymphoid organs, drove rapid CD4-assisted priming and durable CD8-biased memory, suppressed melanoma, and prolonged survival. These reveal a viral-mimicry mechanism enabling long-range immune activation and support Arc+ VLVs as an antigen-agnostic vaccine for cancer immunotherapy. HighlightsO_LIArc+ VLVs intensify and extend DC antigen presentation in vivo C_LIO_LIArc+ VLVs directly engage T cells and trigger viral-mimic adjuvanticity C_LIO_LIArc-/- DEVs fail to prime antigen-specific T cell responses C_LIO_LIEngineered Arc+ VLVs drive durable CD8-biased memory and tumor control C_LIO_LIArc+ VLV vaccination provides long-range and cross-tumor protection in vivo C_LI

bioengineering↗

bioRxiv2025

A Minimally Invasive, Scalable and Reproducible Neonatal Rat Model of Severe Focal Brain Injury

BackgroundNeonatal brain injuries such as stroke cause focal ischemic lesions that often result in lifelong neurological disabilities, as treatment options are limited. To speed up the discovery of potential therapies, early-phase screening with models that reliably reproduce brain injury, with scalable injury volume and minimal confounders, such as varying anaesthesia duration and painful procedures, is essential. MethodsPostnatal day 10 Sprague-Dawley rats of both sexes, with four litters per group and timepoint, were randomly allocated to delivery of intraperitoneal Rose Bengal (25, 40, or 60 mg/kg) and 10 minutes of light-emitting diode illumination through the intact scalp and skull. Infarct progression and reproducibility were assessed at 24 hours, 7 days, and 14 days post-injury. Outcomes included infarct volume and sensorimotor function, and cleaved caspase-3, glial fibrillary acidic protein (GFAP), and ionised calcium-binding adaptor molecule 1 (Iba1) immunoreactivity, with analysis of sex differences. Data were analysed using one-way or two-way ANOVA with Sidaks post-hoc tests. ResultsThere was no mortality due to the infarct, and procedure time was approximately 19 minutes across all groups; the lesion was consistent and supported scalability. The 25 mg/kg dose produced a reproducible cortical infarct (3.74 {+/-} 0.58 mm3; CV = 31%). Lesion size increased with dose and decreased over time (11.15 {+/-} 0.63 mm3 at 60 mg/kg versus 0.05 {+/-} 0.007 mm3 at 14 days; p < 0.0001). Cleaved caspase-3 and glial activation persisted for 14 days, indicating ongoing apoptosis and gliosis. No sex-dependent effects were observed in lesion volume, behaviour, or gliosis. ConclusionsThis refined neonatal photothrombotic ischaemia model is reproducible, scalable, and ethically improved, requiring no skin incision. Its minimal surgical burden, absence of mortality, consistent histopathology, and measurable functional outcomes make it an ideal platform for preclinical screening of neuroprotective and reparative interventions in the developing brain.

developmental biology↗

bioRxiv2025

The genomic basis of local adaptation in the white x Engelmann spruce hybrid zone

Hybridization between species can occur along repeated zones of contact, providing a natural laboratory for studying the interplay between migration and selection, and identifying loci involved in adaptation and reproductive isolation. However, interpreting how evolutionary processes shape genomic patterns can be challenging: repeatability of genotype-environment association alone is not strong evidence for selection, as hybrid zones derived from the same parental species are not evolutionarily independent. Conversely, processes that operate within the middle of each hybrid zone, such as selection driving directional introgression, may be more evolutionarily independent, and therefore provide stronger evidence of selection. Here we compared hybridization and local adaptation patterns between two replicated regions within the western Canada interior spruce hybrid zone: a broad latitudinal transect with gradual environmental variation and a narrow elevational transect with substantial topographical and environmental variation. We discovered a complex pattern of introgression, with strong differences in ancestry maintained even across small spatial scales at several locations along the elevational transect. Despite differences in their spatial scales, the elevational and latitudinal transects revealed strikingly similar genome-wide patterns of differentiation and adaptation, and consistent patterns of directional introgression. We explore the extent to which the evolutionary non-independence of these hybrid zones allows inferences about the role of natural selection and drift in shaping these patterns. Consistent with theory, we found longer genomic tracts in the elevational transect, likely because the steeper environmental gradients over shorter distances limit the rate of mixing by migration and recombination relative to drift and selection.

evolutionary biology↗

bioRxiv2025

Cell-type-selective synaptogenesis during the development of excitatory connectivity in the mammalian neocortex

The function of mammalian neocortex relies on the timing of axon extension and establishment of cell-type-biased patterns of excitatory synaptic connections. A subtype of excitatory neurons, layer 6 corticothalamic neurons (L6CThNs), ultimately exhibit a marked preference for synapsing onto parvalbumin-positive (PV) inhibitory interneurons over more common excitatory cells in layers 6 and 4 (L6, L4). We show that the intracortical axons of L6CThNs develop in phases, elongating within L6, then pausing before extending translaminar branches into L4. Decreasing L6CThN excitability selectively enhanced axon growth in L6 but not later elaboration in L4. For both layers, we tested whether preferential synaptogenesis onto rarer PV interneurons, or promiscuous synapse formation followed by selective pruning, generated adult connectivity. We found that L6CThNs formed functional AMPA-receptor-containing synapses preferentially onto PV interneurons. Silent L6CThN synapses were not detected. Our findings show that cell-type-biased synaptogenesis underlies the formation of functional cell-type-specific excitatory connections in the neocortex.

neuroscience↗

bioRxiv2025

The abscisic acid could reverse the cuproptosis in sepsis-associated acute kidney injury through the inhibition of ferredoxin-1

Sepsis-associated acute kidney injury (S-AKI) is a grave clinical condition with a poor prognosis. Prior studies have observed a potential correlation between copper (Cu) and S-AKI, though the underlying mechanisms remain to be fully elucidated. The present study aims to investigate the underlying mechanism between Cu and renal dysfunction under sepsis conditions. Utilizing a cecal ligation and puncture (CLP) murine model, we observed a substantial upregulation of inflammatory factors and deteriorated renal function (p<0.05), concomitant with an augmented mortality rate (p<0..05). Concurrently, the renal tissue exhibited a series of pathological manifestations, including fibrosis and cell death. Concurrently, the expression of the cuproptosis-regulating protein FDX-1 (p<0.05) was found to be elevated in CLP mice. Collectively, these data indicated the activation of cuproptosis in CLP-induced S-AKI. Intriguingly, the application of abscisic acid (ABA), a FDX-1 inhibitor, led to a substantial alleviation of mortality rate and inflammatory factor level (p<0.05). Furthermore, a significant alleviation was observed in renal pathology and biofunction (p<0.05). Collectively, these observations suggest that ABA exerts a protective effect on renal function during cuproptosis promoted S-AKI. Consequently, it can be concluded that ABA has the potential to reverse cuproptosis in S-AKI by inhibiting FDX-1.

molecular biology↗

bioRxiv2025

CSLAN: Cross-Species Latent Alignment Network for Trauma-Related Cell-Type Classification

Understanding cellular identity and function across species is fundamental to deciphering conserved biological principles and translating insights from model organisms to human health. However, integrating single-cell transcriptomic data, particularly from resource-limited human studies, with comprehensive datasets from model organisms like mice remains a significant challenge due to evolutionary divergence and technical variability. Here, we introduce the Cross-Species Latent Alignment Network (CSLAN), a transfer learning framework that effectively bridges this gap for robust cell type classification. CSLAN employs a novel strategy involving focused feature selection on source (mouse) data followed by pretraining an encoder-decoder architecture. Crucially, for transfer to human data, only the encoder is fine-tuned while the latent space processor and the decoder, which encapsulate learned, conserved cell type signatures, remains fixed. This targeted adaptation mechanism allows CSLAN to achieve exceptional accuracy (e.g., 96.67% for human immune cells in a trauma context) by efficiently aligning human gene expression profiles to a biologically informed latent space derived from mouse data. Our findings establish a powerful and broadly applicable paradigm for cross-species knowledge transfer, enabling deeper biological insights from limited human scRNA-seq data by leveraging the wealth of information from model systems, with significant implications for translational research and the construction of comprehensive, cross-species cell atlases.

bioinformatics↗

bioRxiv2025

EssentCell: Discovering Essential Evolutionary Relations in Noisy Single-Cell Data

Single-cell sequencing (SCS) enables investigating tumor evolution at a single cell resolution. A common type of analysis to investigate evolutionary structure from an SCS experiment is to determine a phylogenetic tree structure from the data. This problem has been well-studied under the assumption that mutations only accumulate in the evolution of cancer and there is a simple characterization of when the data is compatible with a perfect phylogeny based on the absence of a special "conflict" submatrix. SCS data can be represented as a binary matrix, where the ij-th entry indicates whether cell i has mutation j. In practice, SCS data is noisy, so a natural question is what is the minimum number of entries to flip in the data matrix, in order that the matrix becomes "conflict-free" and thus compatible with a perfect phylogeny. Furthermore, the false positive rate is orders of magnitude smaller than the false negative rate, so that at most a few false positives occur with high probability. We consider a variation of the minimum-flip problem in which the number of false positives in the solution is a parameter. Often, there can be multiple optimal solutions, so a natural question is what relations are true among all optimal solutions for a small range of possible false positives values; we call such relations essential. In this work, we propose an efficient algorithm based on integer linear programming to determine all essential relations in the data. We test our software tool, EssentCell, on several data sets and discuss the results found.

cancer biology↗

bioRxiv2024

Clathrin-associated carriers enable recycling through a kiss-and-run mechanism

Endocytosis and recycling control the uptake and retrieval of various materials, including membrane proteins and lipids, in all eukaryotic cells. These processes are crucial for cell growth, organization, function, and environmental communication. However, the mechanisms underlying efficient, fast endocytic recycling remain poorly understood. Here, by utilizing a biosensor and imaged-based screening, we uncover a novel recycling mechanism that couples endocytosis and fast recycling, which we name the clathrin-associated fast endosomal recycling pathway (CARP). Clathrin-associated tubulovesicular carriers containing clathrin, AP1, Arf1, Rab1, and Rab11, while lacking the multimeric retrieval complexes, are generated at subdomains of early endosomes, and then transported along actin to cell surfaces. Unexpectedly, the clathrin-associated recycling carriers undergo partial fusion with the plasma membrane. Subsequently, they are released from the membrane by dynamin and reenter cells. Multiple receptors utilize and modulate CARP for fast recycling following endocytosis. Thus, CARP represents a novel endocytic recycling mechanism with kiss-and-run membrane fusion.

cell biology↗

bioRxiv2024

Characterization of the SARS-CoV-2 BA.5 Variants in H11-K18-hACE2 Hamsters

This study aims to comprehensively characterize the SARS-CoV-2 BA.5 variants using K18 hACE2 transgenic mice and golden hamsters as model organisms. Previous research on SARS-CoV-2 has utilized both mouse and hamster models, leading to conflicting results concerning the viruss lethality. In our study, the finding suggests that H11-K18 hACE2 golden hamsters closely mimic the disease progression observed in human COVID-19 cases caused by BA.5 variants, demonstrating consistent severity and symptoms comparable to severe infections. Additionally, hamsters exhibit heightened respiratory viral replication, accurately reflecting the clinical viral kinetics observed in humans. The study emphasizes the critical importance of selecting an appropriate animal model for SARS-CoV-2 research, while also providing robust support for the hypothesis that BA.5 variants contribute to fatal outcomes in COVID-19 cases. These findings highlight the pivotal role of the golden hamster model in advancing our understanding of the pathogenic mechanisms underlying SARS-CoV-2 variants, as well as in the development of targeted therapeutic strategies. Significance StatementOur research work explores groundbreaking insights that could reshape our understanding of COVID-19 and pave the way for targeted therapies. We use golden hamster models to express the possibility of different animal models could contribute to human diseases. We hope this finding could clarify some conflicts existed, and help further development of medication for COVID.

immunology↗

bioRxiv2023

Skeletal Muscle Phenotype-Specific Effects of ACVR1B and TGFBR1 Receptor Signalling on Muscle Transcriptome, Force generation and Metabolism

Transforming growth factor-{beta} (TGF-{beta}) signaling is associated with progressive skeletal muscle wasting and fibrosis, while double knockout of TGF-{beta} type I receptors Acvr1b and Tgfbr1 results in hypertrophy. Gaining insights in how myofibre-specific knockout of these receptors affects muscle transcriptome, strength and mitochondrial activity could aid in the development of therapeutic interventions to improve muscle function. Here, we show that 3 months of myofibre-specific knockout of both receptors (dKO) in mice induced a 1.6-fold increase in gastrocnemius medialis mass and a 1.3-fold increase in maximal force. Soleus muscle mass and maximal force both increased 1.2-fold in dKO mice. Muscle hypertrophy in dKO mice was accompanied by a proportional increase in succinate dehydrogenase enzyme activity. Single receptor knockout caused minor phenotypical alterations. Transcriptome analyses revealed that gastrocnemius medialis had 1811 and soleus had 295 differentially expressed genes, mainly related to muscle contraction, hypertrophy, filament organization and oxidative metabolism. Hgf and Sln genes were strongly upregulated in both muscles of dKO mice, while Sntb1 was downregulated. This in combination of transcriptional changes are associated with muscle hypertrophy and increased mitochondrial biosynthesis. Our study highlights that myofibre-specific interference with both TGF-{beta} type I receptors concurrently stimulates myofibre hypertrophy and mitochondrial activity.

physiology↗

bioRxiv2023

GWAS and genomic selection for marker-assisted development of sucrose enriched soybean cultivars

Sucrose concentration in soy-derived foods is becoming a seminal trait for the production of food-grade soybeans. However, limited scientific knowledge is reported on this increasingly important breeding objective. In this study, 473 genetically diverse soybean germplasm accessions and 8,477 high-quality single nucleotide polymorphisms (SNPs) markers were utilized to pinpoint genomic regions associated with seed sucrose contents through a genome-wide association study (GWAS). A total of 75 significant SNPs (LOD [≥]6.0) were identified across GLM, FarmCPU and BLINK models, including four stable and novel SNPs (Gm03_45385087_ss715586641, Gm06_10919443_ss715592728, Gm09_45335932_ss715604570 and Gm14_10470463_ss715617454). Gene mining near 20 kb flanking genomic regions of four stable SNPs identified 23 candidate genes with the majority of them highly expressed in soybean seeds and pod shells. A sugar transporter encoding major facilitator superfamily gene (Glyma.06G132500) showing the highest expression in pod shells was also identified. Moreover, selection accuracy, efficiency and favorable alleles of 75 significantly associated SNPs were estimated for their utilization in soybean breeding programs. Furthermore, genomic predictions with three different scenarios revealed better feasibility of GWAS-derived SNPs for selection and improvement of seed sucrose concentration. These results could facilitate plant breeders in marker-assisted breeding and genomic selection of sucrose-enriched food-grade soybean cultivars for the global soy-food industry.

genomics↗

bioRxiv2022

Enhancer Reprogramming in Melanoma Immune Checkpoint Therapy Resistance

Immune checkpoint blockade (ICB) therapy has improved long-term survival for patients with advanced melanoma. However, there is critical need to identify potential biomarkers of response and actionable strategies to improve response rates. Through generation and analysis of 148 chromatin modification maps for 36 melanoma samples from patients treated with anti-PD- 1, we identified significant enrichment of active enhancer states in non-responders at baseline. Analysis of an independent cohort of 20 samples identified a set of 437 enhancers that predicted response to anti-PD-1 therapy (Area Under the Curve of 0.8417). The activated non-responder enhancers marked a group of key regulators of several pathways in melanoma cells (including c- MET, TGF{beta}, EMT and AKT) that are known to mediate resistance to ICB therapy and several checkpoint receptors in T cells. Epigenetic editing experiments implicated involvement of c-MET enhancers in the modulation of immune response. Finally, inhibition of enhancers and repression of these pathways using bromodomain inhibitors along with anti-PD-1 therapy significantly decreased melanoma tumor burden and increased T-cell infiltration. Together, these findings identify a potential enhancer-based biomarker of resistance to anti-PD-1 and suggest enhancer blockade in combination with ICB as a potential strategy to improve responses.

cancer biology↗

bioRxiv2022

Single cell RNA sequencing reveals mechanisms underlying a senescence-like phenotype of Alveolar Macrophages during Aging

Alveolar Macrophages (AMs) are unique innate immune cells that reside in the alveolar space and accommodate the ever-changing needs of the lungs against internal and external challenges. During homeostasis, AMs maintain themselves through self-renewal without input from adult hematopoietic stem cells. Currently, little is known regarding the influence of aging on AM dynamics, heterogeneity and transcriptional profiles. Here, we identified CBF{beta} as an indispensable transcription factor that ensures AM self-renewal. Deficiency in CBF{beta} led to decreased proliferation and self-renewal ability of AMs. Moreover, with single cell RNA sequencing analysis of AMs from young and aged mice, we discovered that despite similarities in the transcriptome of proliferating cells, AMs from the aged mice exhibited reduced embryotic stem cell-like features. Aged AMs also showed diminished capacity for DNA repair, potentially contributing to impaired cell cycle progression and elevation of senescence markers. In accordance with the analysis, we observed reduced number of AMs in aged mice, which had defective self-renewal ability and were more sensitive to the reduction of GM-CSF. Interestingly, decreased CBF{beta} was observed in the cytosol of AMs from aged mice. A similar senescence-like phenotype was also found in human AMs. Taken together, we conclude that AMs in the aged host harbor a senescence-like phenotype, potentially mediated by the activity of CBF{beta}. HighlightsO_LIscRNAseq revealed Alveolar Macrophage (AM) heterogeneity and self-renewal C_LIO_LICBF{beta} is associated with AM cell cycle and facilitate AM self-renewal C_LIO_LIAMs displayed a senescence-like phenotype during physiological Aging C_LIO_LIAging impairs CBF{beta} expression in mouse and human AMs C_LI

immunology↗