Biology subjects

Pan, A.

Publications and source records attributed to Pan, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Integrating Multisource Target Evidence with Machine-Learning Potency Prediction for Alzheimer's Disease Drug Discovery

Alzheimer's disease (AD) target evidence is distributed across biological, chemical, structural, regulatory, and trial-registry sources, complicating reproducible target evaluation and modeling. We developed a traceable data-to-model platform that integrates AGORA-centered evidence through Target Explorer, Drug-Target Lookup, and Model Portfolio workspaces. The resource contains 967 targets, 452,249 compounds, and 1,430,260 measurements. On a curated PIK3CA dataset, target-specific fine-tuning of the Boltz-2 affinity head increased Pearson r from 0.248 to 0.560 and reduced mean absolute error from 0.900 to 0.706 on 469 held-out compounds. Separately, we screened 42 regression models over 50 random splits for ten moderate-sized target datasets; a random forest model for XDH achieved the highest mean R^2 (0.815). The platform connects curated evidence, model-ready datasets, reproducible evaluation, and public results while clearly separating contextual evidence from therapeutic claims and random-split performance from generalization to unseen chemical scaffolds.

bioinformatics↗

bioRxiv2026

Towards Robust Automated Mouse Scratching Behavior Detection for Itch Research

Automated detection of mouse scratching behavior could reduce manual annotation and is essential for preclinical itch research. However, robust performance across laboratories remains a challenge for current methods. We present Scratch-AID+, a framework dedicated to automated mouse scratching detection, including a diverse and progressive set of approaches: classic ResNet-based detectors, task-adaptive fine-tuning of video foundation models, and in-context learning with advanced multimodal large language models. To simulate real-world use cases, we benchmark on a public dataset and utilize additional cross-laboratory video recordings for independent testing. We find that classic baselines suffered severe performance degradation on external data under the realistic setting with sparse scratching events. In contrast, fine-tuned video foundation models successfully bridged this generalizability gap, achieving significantly better detection performance. Furthermore, frozen multimodal large language models demonstrated promising out-of-the-box ability using only few-shot demonstrations. We also examined the effects of different video preprocessing strategies. Our findings highlight the improved performance and generalizability of the adapted foundation models for automated scratching behavior analysis and shed light on the real-world deployment of such detectors. Our code is publicly available at https://anonymous.4open.science/r/scratch aid-plus/.

bioinformatics↗

bioRxiv2026

Azacitidine Response in Myelodysplastic Syndromes is Marked by NK-like CD8 T-Cell Expansion and CXCL12+ Reticular Cell Remodeling

Myelodysplastic syndromes (MDS) are driven by somatic mutations in hematopoietic stem and progenitor cells (HSPCs), leading to clonal expansion and ineffective hematopoiesis. Hypomethylating agents (HMAs; azacitidine or decitabine) are the standard of care for higher-risk MDS. However, their effects on the bone marrow (BM) microenvironment, and the extent to which these changes correlate with clinical response, remain poorly understood. We performed longitudinal analyses of BM aspirates, trephine biopsies, and peripheral blood samples from MDS patients treated with azacitidine in a clinical trial (NCT03493646), integrating CyTOF, 5' single-cell RNA and TCR sequencing, plasma proteomics, and multiplex immunofluorescence microscopy to characterize changes associated with azacitidine response. Clinical responders showed expansion of GzmBCD56CD8 T cells together with increased type I and type II interferon signaling within the T-cell compartment. Responders also exhibited marked alterations in circulating platelet- and myeloid-derived factors with the potential to remodel the BM niche. Spatial analyses revealed expansion of "neighborhoods" enriched for CXCL12-abundant reticular cells and CD8 T cells in responders, whereas HSPC-enriched neighborhoods were largely unchanged. In contrast, several HSPC-enriched neighborhoods expanded in non-responders. These microenvironmental changes were accompanied by evidence of enhanced myelopoiesis in clinical responders. Our findings support a model in which azacitidine response extends beyond direct effects on malignant hematopoietic cells to involve coordinated remodeling of the BM microenvironment which may be reinforced by platelet- and myeloid-derived signals that establish a feed-forward circuit promoting productive hematopoiesis. One Sentence SummaryLongitudinal bone marrow profiling reveals stromal and immune correlates of azacitidine response in myelodysplastic syndrome.

cancer biology↗

bioRxiv2026

Galectin-3 is Necessary for Selective Cathartocytosis, which Expedites the Development of Proliferative Gastric SPEM

The expression and secretion of sulfated colonic-type mucins is a feature of high-risk metaplasias of the gastrointestinal foregut (Barretts esophagus, type III intestinal metaplasia of the stomach, and pancreatic intraepithelial neoplasia). Galectin-3 is a lectin that preferentially associates with galactose modified by a 3-O-sulfate relative to its unmodified counterparts and is upregulated as the tissue transitions to high-risk metaplasia, dysplasia, and cancer. Since both galectin-3 and sulfated glycotopes are aberrantly and concurrently overexpressed in high-risk premalignant and malignant tissue transformations, we sought to investigate the role of galectin-3 in the metaplastic reaction. We found that injury induces the expression of Lgals3 at the RNA and protein levels. Unlike cancer cell lines, we show that in vivo galectin-3 colocalized with sulfomucins in zymogenic granules of the gastric chief cell. Utilizing a synchronous, chemically-induced murine model that produces spasmolytic polypeptide expressing metaplasia, we found that galectin-3 facilitates cathartocytosis of the vesicles it resides in, but not organelles lacking LGALS3. Inhibition of cellular downscaling resulted in delayed expression of the metaplastic transcription factor Sox9 as well as proliferation. Here, we present a new role for galectin-3 in promoting the transition from normal, homeostatic tissue to metaplasia and our data suggest that cathartocytosis represents an unconventional secretory pathway for galectin-3, which has been a matter of controversy as galectins are not secreted via canonical pathways.

cancer biology↗

bioRxiv2026

Establishing the molecular basis for MDA5 mutation-linked autoimmunity

Melanoma differentiation-associated protein 5 (MDA5), a member of the RIG-I-like receptor family, is a cytoplasmic sensor essential for innate antiviral immunity. MDA5 distinguishes viral RNA from host RNA in part through its ATP hydrolysis activity, which promotes filament turnover on shorter endogenous dsRNAs. Here, we show that the gain-of-function T331I disease-linked mutation within the ATP binding pocket disrupts this balance, resulting in constitutive interferon signaling. Through a combination of cryo-electron microscopy (cryoEM), biochemical assays, and cellular analyses, we reveal the extensive network of interactions that precisely position ATP for catalysis in the wild-type MDA5 ATP binding pocket, and also demonstrate that the T331I mutation impairs ATPase activity, thereby stabilizing MDA5-dsRNA complexes and leading to aberrant immune activation. These findings elucidate how MDA5 ATPase activity regulates antiviral specificity and prevents autoimmunity by controlling filament stability and downstream signaling, offering a mechanistic molecular explanation for disease pathogenesis.

biochemistry↗

bioRxiv2025

Decreased endothelial cell retinoic acid signaling accelerates progression of single ventricle pulmonary arteriovenous malformations

BackgroundPulmonary arteriovenous malformations (PAVMs) are vascular complications that universally develop in patients with single ventricle congenital heart disease after Glenn surgery. However, the pathophysiological mechanisms underlying single ventricle PAVMs are poorly understood. To comprehensively evaluate molecular changes post-Glenn, we performed single-cell RNA sequencing (scRNAseq) on rat lung samples after Glenn surgery. MethodsUsing adult Sprague Dawley rats, we performed scRNAseq on unfiltered lung samples 3 weeks after left-sided Glenn or sham surgery. We compared endothelial cell (EC) differentially expressed genes (DEGs) in our model to two mouse models of hereditary hemorrhagic telangiectasia (HHT), a hereditary condition characterized by visceral AVMs. Finally, we modified the vitamin A (Vit A) content of Glenn and sham rat diets and re-assessed PAVM shunting and EC transcriptional differences. ResultsUsing scRNAseq (n=4 Glenn, n=4 sham), we identified 13 transcriptionally distinct lung cell clusters, including 3 EC clusters (general, capillary, lymphatic), with pronounced differences between Glenn and sham in the general EC cluster ([~]17% of genes). Comparison to HHT mouse models confirmed overlap of [~]18% of DEGs, including identification of significantly downregulated genes involved in and regulated by all-trans retinoic acid (ATRA) signaling in all 3 models. Dietary deficiency of Vit A intake, a precursor of ATRA, caused increased PAVM shunting (p<0.01) that was mitigated with excess dietary Vit A intake. Lastly, EC-specific RNAseq identified Vit A diet-induced gene expression differences, including regulation of PI3K signaling. ConclusionsIn this study, we report the novel application of scRNAseq to study mechanisms underlying single ventricle PAVMs in a surgical rat model. We identified multiple dysregulated biological processes in rat lung ECs post-Glenn, including decreased ATRA signaling and conserved gene expression patterns with HHT. Dietary modification of Vit A intake altered post-Glenn shunting and represents a novel potential therapeutic strategy for single ventricle PAVMs and HHT AVMs.

physiology↗

bioRxiv2025

Early-onset β-amyloidosis in human brains with hematological malignances and cardiovascular diseases: Revisiting injury/stress induced axonal pathology

{beta}-Amyloid (A{beta}) and tau pathologies are hallmarks of Alzheimers disease (AD) and they develop in human brain following differential spatiotemporal trajectories. As such, young/adult-onset tau-independent {beta}-amyloidosis is rare. We encountered four such cases among 397 banked brains, with the donors died of hematological malignances (blood cancers) or cardiovascular diseases. To explore the pathological implications, we examined 17 brains (10-87 year-old, y) from blood cancer patients and three (52-82 y) with cardiovascular diseases, focusing on vascular injury, axonal pathology and A{beta} formation. A{beta} plaques occurred in two adult brains (31 y, 63 y) with blood cancers and two (52 y, 65 y) with cardiovascular diseases in the absence of tau. In the blood cancer brains, 17/17 had vascular injuries seen in hematoxylin-eosin stained sections, 13/17 had iron leakage, and 13/17 had axonal pathology. Malignant cell infiltration was found in 5/14 brains with myeloid, lymphocytic and lymphoma malignances, with light chain infiltration in 3/3 brains with multiple myeloma. In the cardiovascular disease brains, A{beta} deposition primarily as diffuse plaques occurred in the cerebral cortex, with vascular and axonal pathologies in the white matter, striatum and internal capsule. Using a multi-labeling approach, the injury/stress induced axonal pathology was found to concur with {beta}-amyloid processor protein elevation and enhanced {beta}-secretase 1 processing but not intraneuronal A{beta} accumulation. The current findings suggest that hematological malignances and cardiovascular diseases are risk conditions for early-onset cerebral {beta}-amyloidosis, potentially attributable to vascular injury.

neuroscience↗

bioRxiv2025

Cross-ancestry information transfer framework improves protein abundance prediction and protein-trait association identification

Genetics-informed proteome-wide association studies (PWAS) provide an effective way to map the complex molecular landscape of biological mechanisms for complex diseases. PWAS relies on an ancestry-matched reference panel to model protein expression using genetic variants as features and determine the proteins impact on phenotype. However, reference panels from underrepresented populations remain relatively limited. In this study, we developed an analytic framework that borrows information from potentially multiple ancestries to boost the protein abundance prediction accuracy in an underrepresented population. We illustrate the frameworks utility and reproducibility through application to PWAS in East Asians: BioBank Japan (BBJ), Korean Genome and Epidemiology Study (KoGES), and Taiwan Biobank (TWB). An ensemble of information-sharing approaches was integrated to build the Multi-Ancestry-based Best-performing Model (MABM). MABM substantially improved the prediction performance with higher performance observed in both cross-validation and an external validation dataset (Tongji-Huaxi-Shuangliu Birth Cohort). Leveraging the BBJ, we identified three times as many significant PWAS associations with MABM as with the baseline Lasso model. Notably, 47.5% of the MABM specific associations were reproduced in independent East Asian datasets with concordant effect sizes. Furthermore, MABM enhanced gene/protein prioritization for downstream functional validation by (1) confirming a greater number of well-established gene/protein-trait associations and (2) identifying previously uncharacterized trait-associated genes. The benefits of MABM were further validated in additional ancestries and demonstrated in brain tissue-based PWAS, underscoring its broad applicability. Our findings close critical gaps in multi-omics research, develop a new reference resource of genetic models of protein abundance, and facilitate trait-relevant protein discovery in underrepresented populations.

genomics↗

bioRxiv2025

Putative long-range mossy fiber sprouting and regional hypermetabolic capacity in the hippocampus of patients with mesial temporal lobe epilepsy

Mesial temporal lobe epilepsy (MTLE) is pathologically characterized by neuronal loss in the dentate hilus, CA3 and CA1 regions, and mossy fiber (MF) sprouting into the inner molecular layer (iML). The latter forms aberrant excitatory circuities that are considered to facilitate recurrent seizures, with the subiculum also being related to epileptogenic activation. We recently identified a distinct expression of -smooth muscle actin (SMA) at the MF terminals in human hippocampus. This prompted us to explore MF sprouting in resected hippocampi (n=20) from patients with MTLE relative to postmortem control (n=20) using SMA along with reference markers for pathological cross-validation. Compared to control, neuronal loss assessed with neuron-specific nuclear antigen and sortilin immunolabeling reached CA1 in all resected hippocampi. SMA, zinc transporter 3 and {beta}-secretase 1 immunolabeling in the iML tended to be increased. The MF-related markers also revealed a preserved fibrous band extending across CA1 to subiculum. Cytochrome c oxidase immunolabeling also increased in iML and subiculum in the MTLE group. Taking together, the current findings point to the existence of long-range MF sprouting and a regional hypermetabolic compacity in the hippocampal formation of patients with drug resistant MTLE.

neuroscience↗

bioRxiv2025

Application of machine learning to discriminate photoreceptor cell species in xenotransplanted chimeric retinas

Photoreceptor transplantation is being studied to improve visual function in retinal diseases causing blindness, such as age-related macular degeneration, hereditary eye diseases, and traumatic retinopathy, among others. Preclinical studies often involve the delivery of exogenous human photoreceptor cells into the retinas of animal models. In such experiments, a key readout is the differential frequency of donor cell somatic integration versus artificial labeling secondary to material transfer of cytosolic or nuclear labels from donor to recipient cells. For this analysis, the ability to recognize photoreceptor nuclei as being of donor (human) versus animal is key, but purely immunohistology discrimination can be challenging because of antigenic species overlap or intercellular antigen transfer. To address this challenge, we sought to develop and validate a computational technique to discriminate between photoreceptor cells of different animal species based on machine learning of nuclear morphology. Here, we aimed to evaluate the feasibility of using computer-assisted detection of separate nuclei and employing random forest classification to automate the species differentiation, among DAPI-stained photoreceptors after xeno-transplantation of human photoreceptors into the retinas of mice and pigs. Our models were trained on single-species samples and validated with mixed-species samples. We then transplanted human embryonic stem cell-derived retinal organoid cells into rodent and pig retinal degeneration models. The random forest model accurately determined cell identity post-xenotransplantation, validated by histological assessment using an anti-human nuclear antibody. Our results support the potential efficacy of employing machine learning image analysis and classification techniques that may promote experimental rigor, minimize observer bias, and enable high throughput semi-automated workflows for transplantation outcomes analysis. The methodological framework reported here may enable a more nuanced and precise analysis of the behavior of transplanted photoreceptors for the purposes of human retinal regeneration.

neuroscience↗

bioRxiv2025

An integrated DNA interactome and transcriptome profiling reveals a PU.1/enhancer RNA-mediated Feed-forward Regulatory Loop Regulating monocyte/macrophage development and innate immune functions

High expression of the myeloid master ETS transcription factor PU.1 drives the development of monocyte/macrophage (Mono/M{Phi}), a crucial cellular component of the innate immune system. Disruptions in normal expression patterns of PU.1 are linked to a variety myeloid malignancy and immune diseases. It is evidenced that PU.1 binds to and modulates enhancers of several myeloid genes. While noncoding RNAs transcribed from noncoding genes at the enhancers are increasingly reported to be involved in enhancer regulation, the crosstalk between PU.1 and noncoding RNAs in enhancer-mediated myeloid gene regulation in Mono/M{Phi} differentiation and immune response has not been systematically investigated. In this study, we interrogated the PU.1-mediated transcriptome and cistrome with our comprehensive collection of putative and verified enhancers. Among a repertoire of noncoding genes present at PU.1-bound enhancers, we discovered that PU.1 acts as a potent transcription factor inducer of the noncoding RNA LOUP, which we previously identified as an RNA inducer of PU.1. The genomic region within the LOUP locus occupied by PU.1 is characterized by the epigenetic features of a myeloid-specific super-enhancer. Targeted disruption of the PU.1-binding motifs resulted in the downregulation of LOUP promoter activity. Depletion of LOUP reduced the expression of Mono/M{Phi} cell markers as well as the transcriptional program associated with Mono/M{Phi} differentiation Mono/M{Phi} innate defense mechanisms, including phagocytosis, antimicrobial activity, and chemoattractant cytokine production. LOUP induces Mono/M{Phi} phagocytic activities. Collectively, our findings indicate that PU.1 and enhancer RNA LOUP are biomolecular components of an unidentified feed-forward loop that promotes their mutual expression, contributing to Mono/M{Phi} differentiation and innate immune functions. The identification of the PU.1/LOUP regulatory circuit provides valuable insights into the mechanisms underlying cell-type and gene-specific enhancer activity and Mono/M{Phi} biology, as well as significant implications for advancing our understanding of immune diseases and myeloid malignancies.

molecular biology↗

bioRxiv2025

Clinico-genomic features predict distinct metastatic phenotypes in cutaneous melanoma

Metastasis drives mortality and morbidity in cancer. While some patients develop broad metastatic disease across multiple organs, others exhibit organ-specific spread. To identify mechanisms underlying metastatic organotropism, we analyzed clinico-genomic data from over 7,000 patients with metastatic cutaneous melanoma in three independent cohorts (one primary discovery and two validation cohorts including a nationwide electronic health record-derived deidentified database), leveraging machine learning approaches to clinical data. We found that female sex and increased tumor mutational burden associate with decreased metastatic potential, while older age associates with increased lung and adrenal metastases. Using unsupervised analyses, patients clustered into five metastatic patterns: a "highly metastatic" cluster characterized by involvement of many organs, a "low metastatic" cluster characterized by few metastatic sites (mostly lymph node metastases), and three additional clusters each characterized by metastasis to specific sites (brain, lung, liver). Mutations in B2M and PTEN associated with increased overall metastatic potential. PTEN mutations were also associated with brain metastases but were enriched only in the "highly metastatic" cluster and not the brain-specific cluster. Mutations in GNAQ or GNA11 (GNA) associated with increased liver metastasis. To validate this association, we tested and demonstrated liver tropism in two GNA-mutant genetically engineered cutaneous melanoma mouse models of metastasis. Overall, our study elucidates distinct phenotypes of metastasis in patients with melanoma and identifies novel clinical and genomic associations that illuminate the drivers of clinical metastatic organotropism.

cancer biology↗

bioRxiv2024

Sortilin C-terminal fragment deposition depicts tangle-related nonamyloid neuritic plaque growth in Alzheimers disease

Sortilin C-terminal fragments (sorfra) can co-deposit in {beta}-amyloid (A{beta}) plaques in human brain. However, sorfra plaques develop in the cerebrum with a spatiotemporal trajectory as of tauopathy. Here we examined sorfra pathogenesis relative to neuritic plaque evolution in the human brains with amyloid and tau pathologies converged in the neocortex and hippocampus. Sorfra plaques occurred in correlation with pTau/tangle, but not A{beta}, pathologies across cerebral regions, neighboring cortical/hippocampal areas, and along the sulcal valley to gyral hilltop transition. Sorfra plaques and neuritic plaques were matchable in location, shape and size between consecutive sections, and were colocalized in double-labeling preparations. Microscopical study and tissue clearance three-dimensional imaging revealed sorfra/A{beta} colocalized as well as independent plaques. Among the former, sorfra labeling correlated negatively to A{beta}/amyloid labeling and {beta}-secretase-1 labeling in dystrophic neurites. Sorfra plaques were depleted of microtubule-associated protein 2 (MAP2) labeled neuronal somata and dendrites, whereas normal looking MAP2/sortilin co-labeled profiles occurred nearby. Sorfra deposits were seen in astrocytes but not microglia around the plaques. Taken together, sorfra plaques are anatomically matchable to silver stained neuritic plaques. They develop with tangle-related somatodendritic degeneration, presenting as nonamyloid growth of the A{beta} plaques and formation of A{beta}-independent neuritic plaques during Alzheimers disease pathogenesis.

neuroscience↗

bioRxiv2024

SNRK regulates TGFbeta levels in atria to control cardiac fibrosis

Atrial fibrosis is central to the pathology of heart failure (HF) and atrial fibrillation (AF). Identifying precise mechanisms underlying atrial fibrosis will provide effective strategies for clinical intervention. This study investigates a metabolic serine threonine kinase gene, sucrose non-fermenting related kinase (SNRK), that we previously reported to control cardiac metabolism and function. Conditional knockout of Snrk in mouse cardiomyocytes (Snrk cmcKO) leads to atrial fibrosis and subsequently HF. The precise mechanism underlying cardiomyocyte SNRK-driven repression of fibrosis is not known. Here, using mouse, rat, and human tissues, we demonstrate that SNRK expression is high in atria, especially in atrial cardiomyocytes. SNRK expression correlates with lower levels of pro-fibrotic protein transforming growth factor-beta 1 (TGF{beta}1) in the atrial cardiomyocytes. In HL-1 adult immortalized mouse atrial cells, using siRNA approaches, we show that Snrk knockdown cells show more TGF{beta}1 secretion, which was also observed in heart lysates from Snrk cardiac-specific knockout mice in vivo. These effects were exacerbated upon infusion of Angiotensin II. Results from Snrk knockdown cardiomyocytes co-cultured with cardiac fibroblasts suggest that SNRK represses TGF{beta}1 signaling (Smad 2/3) in atrial CMs and prevents paracrine cardiac fibroblast activation (-SMA marker). In conclusion, high SNRK expression in atria regulates cardiac homeostasis, by preventing the release of TGF{beta}1 secretion to block cardiac fibrosis. These studies will assist in developing heart chamber-specific fibrosis therapy for non-ischemic HF and AF.

cell biology↗

bioRxiv2024

Testing the application of plasma glucocorticoids and their ratios as biomarkers of acute and chronic stress in rescued wild koala patients: a pilot study

Koalas (Phascolarctos cinereus) are one of the most iconic marsupial species endemic to Australia. However, their population is declining due to threats including habitat loss, disease, dog attacks, and vehicle collisions. These threats also serve as acute or chronic stressors that impact koala welfare and conservation. Cortisol is widely used as a biomarker to study stress in koalas. However, plasma cortisol concentration is less studied due to its limited ability to assess chronic stress and welfare concerns. Dehydroepiandrosterone sulphate (DHEAS) and dihydrotestosterone (DHT) are biomarkers that could potentially detect chronic stress due to their antagonising and inhibitory effects on cortisol. In this study, we used plasma cortisol and the ratio of DHEAS and DHT to cortisol to assess stress in rescued koalas (n = 10) admitted to RSPCA Queensland. Although no significant differences were found between koalas across all biomarkers and the ratios failed to detect chronic stressors, similar trends were found consistently, suggesting the potential use of the biomarkers to assess stress. Across all biomarkers, the highest medians were found in koalas with Chlamydia-related reproductive disease and oxalate nephrosis and the lowest medians were found in koalas with Chlamydia-related conjunctivitis. Higher medians were also found consistently in females (n = 3) and adult koalas. In addition, insignificant negative correlations were found across all biomarkers between age, weight, and body conditioning scores, except for the positive correlation between weight and cortisol and cortisol:DHT. Overall, the consistency of trends and the insignificant differences found across biomarkers in our study suggested that using a single biomarker to assess chronic stress is insufficient, especially for hospital-based studies limited by sample population. Thus, this pilot study provides first step towards developing a koala-specific allostatic load index based on multiple stress biomarkers to understand chronic stress in rescued koalas. Lay summaryStress in koalas can be challenging for their welfare and conservation. In this study, we tested plasma glucocorticoids and their ratios as biomarkers of acute and chronic stress. Our finding showed ratios of DHEAS and DHT to cortisol are comparable across stress parameters and animal demographic characteristics. This study serves as a foundational framework for developing a stress index based on multiple biomarkers that could be useful tool for koala welfare.

neuroscience↗

bioRxiv2024

Ellagic acid: a potential inhibitor of enhancer of zeste homolog-2 and protein arginine methyltransferase-5

Dysregulation of epigenetic processes, characterized by aberrant DNA methylation patterns and histone modifications, is a hallmark of cancer, driving its initiation, progression, and metastasis by silencing tumor suppressor genes or activating oncogenes. Perturbations in histone modifications such as H3K27me3 by EZH2 and H4R3me2s by PRMT5 play significant roles in these epigenetic alterations, disrupting normal gene expression and facilitating oncogene activation while suppressing tumor suppressor genes. Consequently, inhibitors targeting enzymes involved in DNA methylation, histone modification, or chromatin remodeling, such as PRMTs and PRC complexes, are promising anti-cancer agents, with several undergoing pre-clinical and clinical trials. Our screening of a phytochemical library revealed ellagic acid as an effective inhibitor of both EZH2 and PRMT5. Ellagic acid interacts strongly with the EZH2 and PRMT5:MEP50 complex, binding to their active sites through {pi}-cation interactions and hydrogen bonds. Surface Plasmon Resonance study confirmed potent binding affinities of ellagic acid, with KD values of 3.28E-06 and 6.54E-05 for EZH2 and PRMT5:MEP50 respectively. In-vitro assays validated inhibitory effects on EZH2 and PRMT5:MEP50 by reducing the levels of their catalytic products H3K27me3 and H4R3me2s respectively and induction of autophagy and apoptosis. Further In-vivo studies using mouse xenografts further demonstrated significant tumor size reductions upon oral administration of ellagic acid, with decreased expression of the proliferative marker ki67 and histone repressive marks. Taken together we showed that inhibition of EZH2 and PRMT5:MEP50 by ellagic acid could be used to develop breast cancer therapeutic drug.

cancer biology↗

bioRxiv2024

InstructPLM: Aligning Protein Language Models to Follow Protein Structure Instructions

Large language models are renowned for their efficacy in capturing intricate patterns, including co-evolutionary relationships, and underlying protein languages. However, current methodologies often fall short in illustrating the emergence of genomic insertions, duplications, and insertion/deletions (indels), which account for approximately 14% of human pathogenic mutations. Given that structure dictates function, mutated proteins with similar structures are more likely to persist throughout biological evolution. Motivated by this, we leverage crossmodality alignment and instruct fine-tuning techniques inspired by large language models to align a generative protein language model with protein structure instructions. Specifically, we present a method for generating variable-length and diverse proteins to explore and simulate the complex evolution of life, thereby expanding the repertoire of options for protein engineering. Our proposed protein LM-based approach, InstructPLM, demonstrates significant performance enhancements both in silico and in vitro. On native protein backbones, it achieves a perplexity of 2.68 and a sequence recovery rate of 57.51, surpassing Protein-MPNN by 39.2% and 25.1%, respectively. Furthermore, we validate the efficacy of our model by redesigning PETase and L-MDH. For PETase, all fifteen designed variable-length PETase exhibit depolymerization activity, with eleven surpassing the activity levels of the wild type. Regarding L-MDH, an enzyme lacking an experimentally determined structure, InstructPLM is able to design functional enzymes with an AF2-predicted structure. Code and model weights of InstructPLM are publicly available*.

bioinformatics↗

bioRxiv2024

TASOR expression in naive embryonic stem cells safeguards their developmental potential

The seamless transition through stages of pluripotency relies on a delicate balance between transcription factor networks and epigenetic silencing mechanisms that ensure proper regulation of the developmental program, critical for normal development. Here, we uncover the pivotal role of the transgene activation suppressor (TASOR), a component of the human silencing hub (HUSH) complex, in sustaining cell viability during the transition from naive to primed pluripotency, despite its rapid downregulation during this transition. Loss of TASOR in naive cells triggers replication stress, disrupts H3K9me3 heterochromatin formation, and compromise the transcriptional and post-transcriptional silencing of LINE-1 (L1) transposable elements (TEs), with these effects become more pronounced in primed cells. Remarkably, the survival of Tasor-knockout cells during naive to primed transition can be restored through the inhibition of cysteine-aspartic acid protease (Caspase) or deletion of mitochondrial antiviral signaling protein (MAVS). This suggests that unscheduled L1 expression activates an innate immune response, leading to programmed cell death, specifically in cells exiting naive pluripotency. Additionally, we propose that HUSH-promoted H3K9me3 in naive PSCs sets the stage for ensuing DNA methylation in primed cells, establishing long-term silencing during differentiation. Our findings shed insights on the crucial impact of epigenetic programs established in early developmental stages on subsequent phases, underscoring their significance in the developmental process.

developmental biology↗