Biology subjects

Hong, C.

Publications and source records attributed to Hong, C..

At least 19 recordsLinked to original sources

bioRxiv2026

TRIM21 licenses pancreatic acinar fate by modulating BiP phase state through VCP-dependent retrotranslocation

The endoplasmic reticulum (ER) chaperone BiP/GRP78 sits at the center of the proteostasis network, coordinating unfolded protein response (UPR) signaling and supporting oncogenic programs of plasticity, metastasis, immune evasion, and chemoresistance. While BiP undergoes liquid-liquid phase separation in vitro, whether mammalian cells dynamically tune this physicochemical behavior to prevent functional exhaustion or pathological condensation under sustained ER stress has remained unclear. Here, we identify the E3 ubiquitin ligase TRIM21 as a phase-state regulator that suppresses BiP's liquid-to-solid phase separation, clearing, and preventing insoluble aggregates-thereby controlling BiP's localization and availability to sustain the adaptive UPR under ER stress. We found that during ER stress, BiP is prone to liquid-to-solid phase separation, a transition that renders the chaperone dysfunctional. TRIM21 is recruited to BiP, where it directly polyubiquitinates BiP at specific K547/553/554/556 sites with K6-, K27-, K33-, and K63-linked chains; VCP recognizes these marks and extracts BiP from the ER lumen via ER-associated degradation (ERAD), coupling ubiquitin tagging to retrotranslocation. This preserves chaperone availability and sustains adaptive UPR-a homeostatic mechanism broadly relevant to UPR-driven diseases. In vivo, genetic ablation of Trim21 in KrasG12D/+; Pdx1Cre/+ mice triggers aberrant BiP solidification while curtailing acinar-to-ductal transdifferentiation and tumorigenesis; notably, TRIM21 co-localizes with BiP condensates in pre-malignant human pancreatic lesions, underscoring the clinical relevance of this regulatory axis. Our findings define the TRIM21-BiP axis as a phase-control system at the interface of proteostasis and stress adaptation, offering a new framework with translational potential.

cell biology↗

bioRxiv2026

Tumor context determines ARID1A effects on gastric cancer immunity

The role of ARID1A in cancer immune evasion remains uncertain, with prior studies reaching opposing conclusions. In addition, previous work has shown that the role of ARID1A in cell-autonomous tumorigenesis is context-dependent. Using isogenic murine gastric cancer models, we found that in vivo Arid1a loss in an autochthonous genetically engineered mouse model of gastric cancer conferred T cell-dependent immune evasion, while in vitro deletion did not. Mechanistically, tumor Arid1a loss reprogrammed the tumor microenvironment into an immune desert through suppression of GM-CSF secretion and interferon-{gamma} responsiveness. These changes were not observed when Arid1a was deleted in vitro. In human gastric cancer, an immune-cold phenotype was restricted to ARID1A mutants in the genomically stable subtype, while ARID1A loss in the chromosomal instability subtype was associated with variable immune profiles. These results demonstrate that tumor ARID1A loss does not intrinsically confer pro- or anti-tumor immune properties and instead is determined by tissue context.

cancer biology↗

bioRxiv2026

Prospective pan-cancer phosphoproteomics at clinical scale extends therapeutic options in precision oncology

Genomics-guided precision oncology has improved survival in cancer entities with actionable mutations but cannot capture oncogenic signaling that manifests at the protein level. Here, we report a prospective, real-world pan-cancer study profiling proteomes and phosphoproteomes of 1,998 tumor samples from adults and children with rare or advanced cancers enrolled in the German precision oncology programs DKFZ/NCT/DKTK MASTER, CATCH and INFORM and their molecular tumor boards (MTBs). We developed tumor proteome activity status (TOPAS) scores for 46 clinically relevant kinases, an immune activity score capturing antigen presentation and T-cell activation and identified therapeutically targetable cell-surface proteins for 94% of patients. These readouts enhance MTB recommendations by exposing actionable non-genomic kinase activity, refining interpretation of oncogenic genome alterations, and highlighting cell-surface treatment options. Three proof-of-concept analyses indicate clinical utility including kinase activity-stratified pazopanib response in sarcoma, immune activity score-tracked checkpoint-inhibitor outcomes pan-cancer, and a phosphoproteomic biomarker distinguishing EGFR-inhibitor response in chordoma.

cancer biology↗

bioRxiv2026

Top2a-dependent neuronal regulation of social behavior and persistent rescue of social deficit through PRC2-mediated epigenetic reprogramming

Disruption of social behavior is a core feature of autism spectrum disorder (ASD), yet the molecular and cellular mechanisms governing social behavior development are not well understood. We previously identified topoisomerase II (Top2a) as a critical regulator of social behavior and restricted and repetitive behavior through antagonism of polycomb repressive complex 2 (PRC2)-mediated H3K27 trimethylation (H3K27me3), based mainly on pharmacological perturbations during embryogenesis in zebrafish and mouse. However, whether neuronal Top2a is genetically required for social behavior in mammals, and whether PRC2 inhibition can rescue genetically induced social deficits, remain untested. Here, we establish a neuron-specific Top2a conditional knockout mouse model and demonstrate that neuronal Top2a haploinsufficiency selectively impairs social interaction without inducing restricted and repetitive behaviors or cognitive deficits. Pharmacological inhibition of PRC2 using the EZH2 inhibitor tazemetostat, combined with elacridar to facilitated blood-brain barrier penetration, robustly rescues social deficits in Top2a conditional knockout mice. Strikingly, a one-week oral dosing regimen produced a rescue effect that persisted for up to two months after treatment cessation, far exceeding the temporal window typically observed for neuromodulatory drugs targeting neurotransmitter systems. These results showcase the unique capability of epigenetic modulatory therapy to induce durable behavioral improvements and their therapeutic potential for treating social dysfunction in neuropsychiatric disorders. Together, our results provide direct genetic evidence that neuronal Top2a governs social behavior in mice and establish the neuronal Top2a-PRC2 axis as a conserved, targetable epigenetic pathway regulating social behavior.

neuroscience↗

bioRxiv2026

YY1-Mediated Polycomb Group Function Safeguards Hematopoietic Stem Cells from Premature Aging

Hematopoietic stem cells (HSCs) undergo functional decline with age, characterized by myeloid-biased differentiation, loss of quiescence, and altered metabolic homeostasis. The molecular mechanisms driving these changes remain incompletely understood. Yin Yang 1 (YY1) is a multifunctional transcription factor and mammalian Polycomb group (PcG) protein that recruits PcG complexes to specific genomic loci via its 26-amino acid REPO (Recruitment of Polycomb) domain. To define the role of YY1 PcG function in adult HSCs, we generated a conditional YY1 REPO domain knockout mouse model (Yy1-/{Delta}REPO). Deletion of the REPO domain led to premature HSC aging, with expansion of immunophenotypic HSCs but loss of long-term self-renewal capacity. Yy1-/{Delta}REPO HSCs exhibited myeloid-biased output, expansion of myeloid-primed multipotent progenitors, increased myeloid colony formation, and an elevated myeloid-to-lymphoid ratio in peripheral blood. These cells displayed reduced quiescence, elevated reactive oxygen species, increased mitochondrial oxidative capacity, and enhanced {beta}-galactosidase activity--hallmarks of cellular aging. RNA-seq demonstrated dysregulation of gene networks governing HSC metabolism. Together, these findings establish YY1 PcG activity as a key epigenetic mechanism that preserves metabolic quiescence, sustains long-term self-renewal, and delays HSC aging. Our studies reveal a fundamental PcG-dependent epigenetic mechanism that dictate cell fate decisions and function decline during HSC aging.

molecular biology↗

bioRxiv2025

Comparative analysis of the chloroplast genome of Paeonia suffruticosa 'Cun Song Ying reveals plastid characteristics and phylogenetic relationships

Chloroplast genomes provide valuable insights into plant evolution, phylogeny, and molecular breeding. Here, we present the first complete chloroplast genome of Paeonia suffruticosa Cun Song Ying. Using high-throughput sequencing combined with multiple bioinformatics approaches, we comprehensively characterized its chloroplast genome and compared it with those of closely related taxa. The chloroplast genome of Cun Song Ying is 152,704 bp in length and exhibits the typical quadripartite structure, comprising a large single-copy region (LSC), a small single-copy region (SSC), and two inverted repeat regions (IRa and IRb). A total of 138 genes were annotated, including 4 pseudogenes and 134 functional genes, which consist of 87 protein-coding genes, 39 tRNAs, and 8 rRNAs. Phylogenetic analysis revealed that Cun Song Ying shares the closest relationship with P. suffruticosa Luo Yang Hong. These findings provide new insights into the evolutionary history of peony plastids, and the identified highly variable regions may serve as potential DNA barcodes for cultivar identification.

genomics↗

bioRxiv2025

NQO1 phase condensation promotes stress granule assembly to facilitate pancreatic carcinogenesis

G3BP1 promotes pancreatic ductal adenocarcinoma (PDAC) tumorigenesis driven by oncogenic KRAS mutations through liquid-liquid phase separation (LLPS)-mediated assembly of stress granules (SGs). However, the regulatory mechanisms remain elusive. We identify the antioxidant enzyme NAD(P)H quinone dehydrogenase 1 (NQO1) as a novel SG regulator that enhances SG assembly in pancreatic cancer cells independently of reactive oxygen species (ROS). Mechanistic studies reveal that NQO1 does not regulate the expression of G3BP1 or other SG-associated genes. Instead, NQO1 undergoes LLPS dependent on its RNA-binding K homology (KH) like domain. Further analysis demonstrates that residues 121-131 of NQO1 directly interact with G3BP1s RNA-binding domain (RBD), enhancing the multivalency of G3BP1 complexes to potentiate LLPS-driven SG assembly. This interaction accelerates cell proliferation, KRAS mutation-induced acinar-to-ductal metaplasia (ADM), and pancreatic carcinogenesis. Notably, the interaction between NQO1 residues 121-131 and G3BP1s RBD is essential for NQO1 phase condensation under stress condition. Integrative analysis of human PDAC transcriptomic datasets reveals a weak association between NQO1 and G3BP1 levels. Importantly, both NQO1 and G3BP1 formed biological condensates and co-localized in the lesions of human PDAC tissue sections. Our study uncovers a novel KRAS mutation-driven mechanism of pancreatic carcinogenesis through the lens of phase separation, transcending conventional gene expression regulation and offering new insights into non-canonical KRAS-NQO1-G3BP1-SG regulatory networks in PDAC initiation.

cancer biology↗

bioRxiv2025

Increased activity of PRMT5-MEP50 complex improves survival of chromosomally unstable cancer cells by increasing tolerance to protein aggregation and proteotoxicity

Most cancers display chromosomal instability (CIN), a condition that leads to increased rates of chromosome missegregation and thus yields aneuploidy. CIN and aneuploidy are detrimental to healthy cells and therefore, aneuploid cells rely on aneuploidy-tolerating mechanisms to adopt a malignant fate. We previously found PRMT5 to be frequently amplified in a mouse model for aneuploid T cell lymphoblastic lymphoma. In this study, we investigated a possible role of PRMT5 as an aneuploidy tolerating gene. We report that PRMT5 is prone to aggregation when expressed at supra-stoichiometric levels compared to its obligate partner protein MEP50 (methylosome protein 50, WDR77). Intriguingly, we also find that protein aggregation, induced by CIN, is mitigated by jointly increased expression of PRMT5 and MEP50. Accordingly, concomitant PRMT5:MEP50 expression renders cancer cells less sensitive to proteasome inhibitors and CIN while inhibition sensitizes cells to CIN. Our findings provide a possible explanation for why PRMT5 and MEP50 display increased expression, particularly in aneuploid cancers and might reveal a targetable vulnerability of aneuploid cancer.

cancer biology↗

bioRxiv2025

Tumor-initiating genetics and therapy drive divergent molecular evolution in IDH-mutant gliomas

Astrocytomas and oligodendrogliomas are slow-growing and treatment-sensitive IDH-mutant gliomas diagnosed at ages 30-50. Local tumor regrowth and treatment resistance is inevitable resulting in 3-10 year astrocytoma and up to >20 years oligodendroglioma survival. We sought to identify genetic changes associated with tumor evolution in response to therapy through multi-timepoint whole-genome/whole-exome sequencing of 206 IDH-mutant glioma patient samples collected through the Glioma Longitudinal Analysis (GLASS) Consortium. We validated known genomic markers of tumor progression, including hypermutation and CDKN2A homozygous deletion, and discovered novel genetic alterations that distinguish the response to treatment in astrocytomas compared to oligodendrogliomas. Point mutations in PIK3CA, PIK3R1, and NOTCH1 were newly acquired in recurrent oligodendrogliomas and associated with increased mutation rates. Focal oncogene amplifications, together with CDKN2A homozygous deletions, were associated with an increase in recurrence-specific chromosomal imbalances in astrocytomas. Mutational signature analysis revealed additional differences and detected enrichment for the SBS11, and SBS119 mutational signatures after temozolomide treatment in both IDH-glioma subtypes, whereas astrocytomas showed increased ID8 signatures after radiotherapy. These signatures suggest that the genomes of oligodendroglioma and astrocytoma adapt to the selective pressures of tumor progression and treatment in different ways. However, in both IDH-mutant glioma subtypes we observed a convergence of acquired driver gene alterations with genome-wide changes and worse patient outcomes, signaling selection of treatment-refractory clones. By identifying new prognostic markers and delineating the genomic divergence of oligodendrogliomas and astrocytomas after diagnosis, our results suggest that different DNA damage response mechanisms are engaged following chemo- and radiation therapy.

cancer biology↗

bioRxiv2025

AAV NRF2 Gene Therapy Preserves Retinal Structure and Function in Rodent Models of Oxidative Damage

Dry age-related macular degeneration is the most frequent cause of visual impairment in individuals over age 50 in developed countries. It is characterized by subretinal deposits of oxidized proteins and lipids and results in progressive loss of high acuity vision. One major risk factor is smoking, which causes oxidative stress in many tissues, including the eye. We previously showed that an adeno-associated viral vector expressing human NRF2 (AAV8/Best1-Nrf2), a transcription factor that regulates responses to oxidative damage, slowed degeneration in mouse models of another blinding disorder, retinitis pigmentosa, which also includes oxidative stress. Here, our AAV8/Best1-Nrf2 vector was tested in a model of oxidative stress wherein sodium iodate was injected systemically, as this is often used to model dry age-related macular degeneration. Sodium iodate causes acute oxidative damage to supporting cells of the retina, the retinal pigment epithelial cells, and ultimately leads to photoreceptor death. Subretinal injection of AAV8/Best1-Nrf2 led to protection of the retinal pigment epithelium and photoreceptors, as well as preservation of visual function, in rat and mouse sodium iodate models. AAV8/Best1-Nrf2 may serve as an effective gene-agnostic therapy for diseases with oxidative stress, including dry age-related macular degeneration. ETOCOxidative stress occurs in diseases that lead to vision loss, including age-related macular degeneration (AMD). AMD is commonly modeled by injection of sodium iodate (S.I.), an oxidizing agent. AAV-mediated delivery of Nrf2, a transcription factor that regulates oxidative stress, protects the eye from S.I. damage in rat and mouse models. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC="FIGDIR/small/663952v1_ufig1.gif" ALT="Figure 1"> View larger version (67K): org.highwire.dtl.DTLVardef@357e57org.highwire.dtl.DTLVardef@1f9986dorg.highwire.dtl.DTLVardef@186537corg.highwire.dtl.DTLVardef@1d31aad_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2025

Inferring Spatially Varying Bending Stiffness of Biopolymers with Deep-Learning Approach

The bendability of biopolymers, including DNA, actin filaments, and microtubules, is crucial to diverse biological processes, such as cell motility and cytoskeletal organization. While conventional polymer models like the worm-like chain model assume uniform bending stiffness along the contour, biopolymers in reality often attain spatially varying bending stiffness as a result of complex cellular interactions. For instance, the bending stiffness of actin filaments and microtubules varies in response to associated binding proteins or chemical modifications. Despite its biological implications, measuring the position-dependent persistence length along polymer contours remains challenging. Here, we present a deep-learning-based method that quantitatively predicts spatially varying bending stiffness of biopolymers. Our framework segments a polymer chain into short over-lapping fragments, predicts local persistence lengths using a deep-learning model, and reconstructs full profiles. Using simulated data, we demonstrate that our approach achieves high accuracy and robustness even under data-scarce conditions. Applied to various biological systems, our method reveals a spatially varying stiffness from tip to base in filopodia as well as spatially heterogeneous stiffness in microtubules. Additionally, we investigate the internal mechanism of our deep-learning model and show that the model utilizes multiple physics-related features for persistence length estimation while adaptively adjusting its attention based on polymer stiffness.

biophysics↗

bioRxiv2025

Ancient DNA Reveals Hominoid Evolution: Intermediate DNA Sequences and Advances in Molecular Paleontology

AbstractFossils and ancient crude pottery vessels function as physical "DNA containers," preserving oriDNA (original, in situ DNA) and accumulating eDNA (environmental DNA) over time. Ancient DNA (aDNA) serves as molecular fossils, chronicling evolutionaryhistory. Using "nano-affinitybead technology", we extracted and sequenced DNAfrom Lycoptera fossils in the Jehol region and a "round-bellied jar (Jar)" from the Erlitou period in Guangwu Town, yielding 236,545 primate sequences from the fossils and 86,908 from the pottery. We observed that the AFF value of DNA sequences negatively corre lates with species divergence time1, offering a quantitative measure of DNA preservation and host divergence. Some fragments distinct from modern genomic sequences, termed "intermediate DNAsequences" (IDS), have been identified. Many IDS exhibit an upper age limit, preserving characteristics of the last common ancestor (LCA) of the Hominidae and offering molecular insights into "Darwins puzzle". Among IDS, the SRRA subtype (Sequence Reversal and Rearrangement), identified in mRNA-coding exonic sequences, arises from the incorporation of a complementary antisense strand upstream of the sense strand, either adjacent to it or separated bya sequence interval. This introduces a novel post-transcriptional regulatory mechanism at the mRNA level, driven by SRRA, which presets hairpin structures and Indels in the UTR or CDS of exonic sequences, modulating gene variation. We propose: "SRRAs played a critical trial-and-error role in early Hominidae evolution, facilitating adaptive genomic changes, with some SRRA sequences later excised from exons", positioning SRRAas an evolutionary "genetic switch". Additionally, seven species -specific fragments (SSFs) of non-human primates (NHPs) linked to Asian Homo erectus were identified in the fossils, and pottery DNA reveale d sequences from tropical species (e.g., zebrass, oil palms), providing evidence of climate-driven local extinction and supporting paleo-ecological and paleo-environmental reconstruction. This method of analyzing aDNA from non-skeletal materials opens new avenues in paleontology, archaeology, and geology, guiding the tracing of ancient migration patterns and fossil searches. DNAfragments preserved within "DNA containers " exhibit an "old-few, new-many" turnover pattern, with many aDNA fragments displaying non-deamination. This evidence challenges prevailing perspectives, the authenticity criteria for aDNA, and the capabilities and scope of the traditional research method, necessitating a thorough reevaluation of the relevant knowledge framework. Furthermore, this study opens new opportunities for frontier research.

paleontology↗

bioRxiv2025

Glioma-induced DNMT3A-dependent reduction of DNA methylation in microglia promotes a transient anti-tumoral phenotype.

Glioblastoma, aggressive primary brain tumors with a dismal prognosis, promote the recruitment of microglia, brain resident innate immune cells, and ultimately their activation toward a tumor-supportive phenotype that increases gliomal proliferation and invasion capability. Here, we report that upon stimulation by glioma cells, microglia transit via a reactive state holding anti-tumoral properties coupled to reduced DNMT3A chromatin occupancy and DNA demethylation that promote microglial pro-inflammatory gene expressions. We find that upon repression of Dnmt3a expression in microglia, those cells maintain anti-tumoral attributes in vitro and in vivo. In a syngeneic immunocompetent glioblastoma mouse model, brain delivery of antisense oligonucleotide targeting Dnmt3a expression led to reduced tumor growth. Taken together, our results reveal the involvement of DNA demethylation in the control of glioma cells-induced microglia activation and indicate that microglial DNMT3A is a potentially therapeutic target to treat brain neoplasms such as glioblastoma that include a microglial component.

immunology↗

bioRxiv2025

Few-shot in-context learning with large language models for antibody characterization

Large language models (LLMs) can learn new tasks by in-context learning (ICL), but it is unknown whether this ability reliably transfers to biological sequence classification. Here, we systematically evaluate how demonstration selection, shot count, and prompting strategies affect performance across 20 general-purpose LLMs. Using antibody characterization as a representative test case, we compare zero-shot, few-shot, and chain-of-thought (CoT) ICL on three classification tasks: humanness, antigen specificity, and isotype. Our results reveal a clear performance hierarchy: while zero-shot prompting performs near chance, few-shot prompting with randomly selected demonstrations improves performance, showing that LLMs can perform ICL using biological sequences from minimal supervision. However, matching protein-language model (pLM)-based classifier accuracy is only achieved when using label-diverse demonstrations drawn from antibodies similar to the query sequence. To leverage this insight, we introduce Sim-ICL, a framework that automatically retrieves such demonstrations. Using only 32-shot prompting, Sim-ICL achieves performance competitive with pLM-based classifiers, matching or outperforming them in two of the three tasks. Furthermore, reasoning-oriented prompts yield marginal gains and often produce fluent but biologically incorrect rationales, suggesting that current CoT explanations function as after-the-fact rationalizations rather than capturing mechanistic determinants of antibody properties. From these experiments, we derive practical design principles for ICL on biological sequences: use similarity-based, label-diverse demonstrations and modest shot counts, and treat reasoning prompts primarily as post hoc narratives rather than drivers of performance. Sim-ICL implements these principles in a streamlined, prompt-based framework for antibody sequence classification and, in principle, could be adapted to other biological sequence tasks.

bioinformatics↗

bioRxiv2024

Adrenocortical Cancer Cell uptake of Iron Oxide Nanoparticles

Adrenocortical carcinoma (ACC) is a rare cancer with poor prognosis, treated primarily through surgery and chemotherapy. Other treatments like radiation or thermal ablation for metastases have limited success, and recurrence is common. More effective management options are needed. Magnetic iron oxide nanoparticles (IONP) show promise in cancer treatment due to their ability to be modified for selective uptake by cancer cells. This study investigated IONP uptake in ACC cell lines (H295R, HAC-15, MUC-1) using a multicellular model with endothelial cells (HUVEC) and monocytes. IONP uptake was concentration- and time-dependent, with optimal uptake at 10 {micro}g/mL. IONP were found in the cytoplasm and intracellular vesicles of ACC cells. However, endothelial cells and monocytes also absorbed IONP, reducing uptake by ACC cells. These findings suggest ACC cells actively take up IONP, but better targeting is needed to enhance uptake specificity and efficiency.

pharmacology and toxicology↗

bioRxiv2024

Mechanisms driving epigenetic and transcriptional responses of microglia in a neurodegenerative lysosomal storage disorder model

Lysosomal dysfunction is causally linked to neurodegeneration in many lysosomal storage disorders (LSDs) and is associated with various age-related neurodegenerative diseases1,2, but there is limited understanding of the mechanisms by which altered lysosomal function leads to changes in gene expression that drive pathogenic cellular phenotypes. To investigate this question, we performed systematic imaging, transcriptomic, and epigenetic studies of major brain cell types in Sgsh null (KO) mice, a preclinical mouse model for Sanfilippo syndrome (Mucopolysaccharidosis Type IIIA, MPS-IIIA)3,4. MPS-IIIA is a neurodegenerative LSD caused by homozygous loss-of-function (LoF) mutations in SGSH which results in severe early-onset developmental, behavioral, and neurocognitive impairment5-15. Electron microscopy, immunohistochemistry, and single-nucleus RNA-sequencing analysis revealed microglia as the cell type exhibiting the most dramatic phenotypic alterations in Sgsh KO mice. Further temporal analysis of microglia gene expression showed dysregulation of genes associated with lysosomal function and immune signaling pathways beginning early in the course of the disease. Sgsh deficiency similarly resulted in increases in open chromatin and histone acetylation at thousands of putative microglia-specific enhancers associated with upregulated genes but had much less impact on the epigenetic landscapes of neurons or oligodendrocytes. We provide evidence for dominant and context-dependent roles of members of the MITF/TFE family as major drivers of microglia-specific epigenetic and transcriptional changes resulting from lysosomal stress that are dependent on collaborative interactions with PU.1/ETS and C/EBP transcription factors. Lastly, we show that features of the transcriptomic and epigenetic alterations observed in murine Sgsh deficiency are also observed in microglia derived from mouse models of age-related neurodegeneration and in human Alzheimers disease patients, revealing common and disease-specific transcriptional mechanisms associated with disease-associated microglia phenotypes.

neuroscience↗

bioRxiv2024

Identifying, Prioritizing, and Visualizing Functional Promoter SNVs with the Recurrence-agnostic REMIND-Cancer Pipeline and pSNV Hunter

Cancer is a heterogeneous disease that arises due to mutations that drive cancer progression. However, the identification of these functional mutations has typically focused only on protein-coding DNA. Among non-coding mutations, only a few have been clearly associated with cancer. We hypothesize that this gap in discovery is partly due to the limitations of current methods requiring high recurrence of mutations. To support candidate selection for experimental validation of lowly recurrent and singleton promoter mutations, new computational approaches for the integrated analysis of multi-omics data are required. To address this challenge, the REMIND-Cancer Pipeline leverages whole-genome sequencing and RNA-Seq data to extract and prioritize functional promoter mutations, regardless of their recurrence status. Subsequently, pSNV Hunter aggregates and visualizes comprehensive information for each candidate. We demonstrate the functionality of both tools by applying it to the PCAWG dataset. This workflow successfully identified and prioritized known highly-recurrent mutations, as well as, novel singletons and lowly recurrent candidates. Hence, the output of our workflow directly supports hypothesis generation for subsequent experimental validation to overcome limitations of recurrence-based approaches.

cancer biology↗

bioRxiv2024

The promoter mutation paucity as part of the dark matter of the cancer genome

Cancer is a heterogeneous disease caused by genetic alterations. Computational analysis of cancer genomes led to the expansion of the catalog of driver mutations. While individual high-impact mutations have been discovered also in gene promoters, frequency-based approaches have only characterized a few novel candidates. To investigate the promoter mutation paucity in cancer, we developed the REMIND-Cancer workflow to predict activating promoter mutations in silico, irrespective of their recurrence frequency, and applied it to the PCAWG dataset. We positively validated 7 candidates by luciferase assay including mutations within the promoters of ANKRD53 and MYB. Our analysis indicates that particular mutational signatures and necessary co-alterations constrain the creation and positive selection of functional promoter mutations. We conclude that activating promoter mutations are more frequent in the PCAWG dataset than previously observed, which has potential implications for personalized oncology.

bioinformatics↗