Biology subjects

Sacan, A.

Publications and source records attributed to Sacan, A..

6 recordsLinked to original sources

bioRxiv2026

Microglial epigenetic memory is associated with accelerated resolution of inflammatory pain induced by prophylactic macrophage-derived small extracellular vesicles

Small extracellular vesicles (sEVs) including exosomes play an important role in intercellular communication and can exert immunomodulatory effects in recipient cells. We have shown that a single prophylactic intrathecal injection of sEVs from RAW 264.7 macrophages two weeks prior, promotes faster resolution of mechanical and thermal hypersensitivity in the complete Freunds adjuvant (CFA) mouse model of inflammatory pain. How this long-term memory develops, and how sEVs regulate immune responses are unknown. Recent studies have shown that priming microglia with inflammatory stimuli can enhance or suppress responses to a delayed secondary insult via epigenetic modifications. We hypothesized that prophylactic intrathecal administration of macrophage-derived sEVs confers accelerated resolution of inflammatory pain by reprogramming epigenetic memory in spinal microglia in recipient CFA model mice. To determine whether prophylactic sEVs could attenuate pain in the absence of microglia when administering sEVs, we ablated microglia using a colony-stimulating factor 1 receptor (CSF1R) inhibitor, PLX5622. sEV-induced pain prophylaxis was completely abolished in PLX5622-fed mice, indicating that microglia are required to be present during sEV administration to confer early resolution of inflammatory pain hypersensitivity. ChIP-seq analysis in spinal microglia 14 days after sEV administration (prior to CFA) revealed an increased number of gene loci enriched for H3K4me1, a hallmark of innate immune memory. Furthermore, inhibiting the H3K4 mono-methyltransferase SETD7 abolished sEV-induced pain attenuation. Our findings indicate that both microglia and its epigenetic reprogramming contribute to pain prophylaxis induced by macrophage-derived sEVs, providing novel insights into the development of non-addictive preventive analgesia.

neuroscience↗

bioRxiv2025

Azurify integrates cancer genomics with machine learning to classify the clinical significance of somatic variants

Accurate classification of somatic variations from high-throughput sequencing data has become integral to diagnostics and prognostics across various cancers. However, the classification of these variations remains highly manual, inherently variable, and largely inaccessible outside specialized laboratories. Here, we introduce Azurify - a computational tool that integrates machine learning, public resources recommended by professional societies, and clinically annotated data to classify the pathogenicity of variations in precision cancer medicine. Trained on over 15,000 clinically classified variants from 8,202 patients across 138 cancer phenotypes, Azurify achieves 99.1% classification accuracy for concordant pathogenic variants in data from two external clinical laboratories. Additionally, Azurify reliably performs precise molecular profiling in leukemia cases. Azurifys unified, scalable, and modular framework can be easily deployed within bioinformatics pipelines and retrained as new data emerges. In addition to supporting clinical workflows, Azurify offers a high-throughput screening solution for research, enabling genomic studies to identify meaningful variant-disease associations with greater efficiency and consistency.

genomics↗

bioRxiv2024

Morphine-induced hyperalgesia impacts small extracellular vesicle miRNA composition and function

Morphine and other synthetic opioids are widely prescribed to treat pain. Prolonged morphine exposure can paradoxically enhance pain sensitivity in humans and nociceptive behavior in rodents. To better understand the molecular mechanisms underlying opioid-induced hyperalgesia, we investigated changes in miRNA composition of small extracellular vesicles (sEVs) from the serum of mice after a morphine treatment paradigm that induces hyperalgesia. We observed significant differential expression of 18 miRNAs in sEVs from morphine-treated mice of both sexes compared to controls. Several of these miRNAs were bioinformatically predicted to regulate cyclic AMP response element binding protein (CREB), a well-characterized transcription factor implicated in pain and drug addiction. We confirmed the binding and repression of Creb mRNA by miR-155 and miR-10a. We tested if serum-derived sEVs from morphine-treated mice could elicit nociceptive behavior in naive recipient mice. Intrathecal injection of 1 g sEVs did not significantly impact basal mechanical and thermal threshold in naive recipient mice. However, prophylactic 1 g sEV administration in recipient mice resulted in faster resolution of complete Freunds adjuvant-induced mechanical and thermal inflammatory hypersensitivity. Other behaviors assayed following administration of these sEVs were not impacted including sEV conditioned place preference and locomotor sensitization. These results indicate that morphine regulation of serum sEV composition can contribute to analgesia and suggest a potential for sEVs to be a non-opioid therapeutic intervention strategy to treat pain.

neuroscience↗

bioRxiv2024

Environmentally-mediated selection parallels population divergence across a chimpanzee subspecies contact zone

Species evolve from populations with ancestor-descendant relationships in a bifurcating process shaped by geography, gene flow, genetic drift, and natural selection leading to local adaptation to prevailing environmental and ecological conditions. Building on this foundational understanding, we explored local adaptation in chimpanzees (Pan troglodytes) at a key geographical intersection in Cameroon where the two main chimpanzee phylogenetic lineages converge. The Nigeria-Cameroon chimpanzee (P. t. ellioti) and central chimpanzee (P. t. troglodytes) last shared a common ancestor about 500 thousand years ago, with occasional gene flow between them. The evolutionary processes driving their prolonged separation are not fully understood, but neutral evolutionary mechanisms alone cannot account for the observed divergence pattern. Cameroon is often referred to as Africa in miniature because the Gulf of Guinea Forest, Congo Basin Forest, and savanna converge there, forming an ecotone. Thus, this contact zone between subspecies in Cameroon provides a unique natural laboratory that enabled us to investigate how environmental variation and natural selection shape divergence in chimpanzees. We developed a genome-wide panel of single-nucleotide polymorphisms (SNPs) in 112 wild chimpanzees sampled in multiple habitats across this contact zone. We augmented SNP discovery by sequencing eight new chimpanzee genomes from Cameroon and analyzing them with previously published chimpanzee genomes. We found that P. t. ellioti and P. t. troglodytes diverged from one another around 478,000 years ago and occasionally exchange migrants. We identified 1,690 unique SNPs across 905 genes associated with 31 environmental variables that describe the habitat. These genes are involved in essential biological processes, including immune response, neurological development, behavior, and dietary adaptations. This study highlights the importance of understanding the geographical context of natural selection, paving the way for future studies to interpret evidence for genetic variation with phenotypic traits and deepening our understanding of how populations diverge in response to environmental pressures. Author SummaryWe investigated how local adaptation contributes to shaping the diversification of chimpanzee subspecies at the geographical convergence point for the two major branches of the chimpanzee phylogenetic tree. We analyzed genome-wide SNP genotypes of 112 chimpanzees sampled from natural communities located in this understudied area. We used tiered methods that identified 905 genes subject to selection, each associated with one or more of 31 environmental predictors describing the habitat. We found strong signals of selection in immune response genes that separate P. t. troglodytes from P. t. ellioti, highlighting the important role of different pathogen histories in their evolution. We also found evidence of selection in genes associated with neurological development, behavior, and diet, that separate both the subspecies and populations of P. t. ellioti that occupy different niches. These findings suggest that ecological and cultural factors may also contribute to shaping the diversification of chimpanzees across the contact zone.

genomics↗

bioRxiv2024

IMMUNOTAR - Integrative prioritization of cell surface targets for cancer immunotherapy

Cancer remains a leading cause of mortality globally. Recent improvements in survival have been facilitated by the development of less toxic immunotherapies; however, identifying targets for immunotherapies remains a challenge in the field. To address this challenge, we developed IMMUNOTAR, a computational tool that systematically prioritizes and identifies candidate immunotherapeutic targets. IMMUNOTAR integrates user-provided RNA-sequencing or proteomics data with quantitative features extracted from publicly available databases based on predefined optimal immunotherapeutic target criteria and quantitatively prioritizes potential surface protein targets. We demonstrate the utility and flexibility of IMMUNOTAR using three distinct datasets, validating its effectiveness in identifying both known and new potential immunotherapeutic targets within the analyzed cancer phenotypes. Overall, IMMUNOTAR enables the compilation of data from multiple sources into a unified platform, allowing users to simultaneously evaluate surface proteins across diverse criteria. By streamlining target identification, IMMUNOTAR empowers researchers to efficiently allocate resources and accelerate immunotherapy development.

bioinformatics↗

bioRxiv2024

Inflammatory pain resolution by mouse serum-derived small extracellular vesicles

Chronic pain is a significant public health issue. Current treatments have limited efficacy and significant side effects, warranting research on alternative strategies for pain management. One approach involves using small extracellular vesicles (sEVs) to transport beneficial biomolecular cargo to aid pain resolution. Exosomes are 30-150 nm sEVs that can carry RNAs, proteins, and lipid mediators to recipient cells via circulation. Exosomes can be beneficial or harmful depending on their source and contents. To investigate the short and long-term effects of mouse serum-derived sEVs in pain modulation, sEVs from naive control or spared nerve injury (SNI) model donor mice were injected intrathecally into naive recipient mice. Basal mechanical thresholds transiently increased in recipient mice. This effect was mediated by opioid signaling as this outcome was blocked by naltrexone. Mass Spectrometry of sEVs detected endogenous opioid peptide leu-enkephalin. A single prophylactic intrathecal injection of sEVs two weeks prior to induction of the pain model in recipient mice delayed mechanical allodynia in SNI model mice and accelerated recovery from inflammatory pain after complete Freunds adjuvant (CFA) injection. ChipCytometry of spinal cord and dorsal root ganglion (DRG) from sEV treated mice showed that prophylactic sEV treatment reduced the number of natural killer (NK) and NKT cells in spinal cord and increased CD206+ anti-inflammatory macrophages in (DRG) after CFA injection. Further characterization of sEVs showed the presence of immune markers suggesting that sEVs can exert immunomodulatory effects in recipient mice to promote the resolution of inflammatory pain. Collectively, these studies demonstrate multiple mechanisms by which sEVs can attenuate pain.

neuroscience↗