Biology subjects

Pahlevan Kakhki, M.

Publications and source records attributed to Pahlevan Kakhki, M..

4 recordsLinked to original sources

bioRxiv2026

Epigenomic profiling of cerebrospinal fluid cells identifies immune regulatory alterations and implicates protocadherins in multiple sclerosis

Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system (CNS), where DNA methylation may play a role by connecting genetic and environmental risk factors. We performed whole-genome DNA methylation profiling of cerebrospinal fluid (CSF) cells from relapsing-remitting MS patients and matched controls, identifying 2,710 differentially methylated positions (DMPs) and 4,330 regions (DMRs). These changes were enriched in immune signaling, adhesion and migration processes, and were accompanied by corresponding RNA expression changes. MS-associated methylation changes enriched in the cohesin chromatin regulation pathway mapped to enhancers of T helper 17 (Th17) cells, whereas in other T cell types they were mapping to bivalent enhancers and repressed chromatin. Notably, this pathway comprised multiple Protocadherin (PCDH) genes, typically expressed in neuronal cells, that displayed consistent methylation and expression changes in CSF cells. Expression of shared intracellular domain of PCDH{gamma} cluster proteins was confirmed in peripheral blood T cells by flow cytometry as well as expression of PCDH{gamma} cluster genes in memory CD4+ T cell subsets. Moreover, co-expression analysis suggests a role of PCDH genes in aryl hydrocarbon receptor (AHR) signaling. In summary, DNA methylation changes in CSF resident cells reflect dysregulated T cell activation and migration in MS and suggest a novel role of protocadherin molecules in MS pathogenesis.

immunology↗

bioRxiv2026

Targeted DNA methylation editing in vivo

The number of epigenome-wide association studies linking CpG DNA methylation with disease, traits and exposures, continues to rise. Despite the rapid development of epigenome editing tools, establishing causation remains challenging, particularly in vivo. In this study, we developed and characterized three Cre-dependent CRISPR-based mouse lines that enable locus-specific DNA methylation deposition by either constitutive or inducible dCas9-DNMT3A expression. We demonstrate robust highly locus-specific DNA methylation deposition at MHC class II (H2-Ab1) and interleukin 6 (Il6) genes in bone marrow-derived myeloid cells ex vivo. Moreover, neuron-specific methylation targeting resulted in reduced cannabinoid receptor 1 (Cnr1) expression in striatal neurons in vivo. Notably, we demonstrate that the causal effect of DNA methylation on gene expression is locus-dependent, reinforcing the necessity of such editing tools for detailed understanding of the role of DNA methylation and for addressing the causality of disease-associated CpGs.

molecular biology↗

bioRxiv2025

Oligodendroglia as functional effectors of Multiple Sclerosis risk variants

Multiple sclerosis (MS) is a neuroinflammatory disease for which a large number of non-coding single nucleotide polymorphisms (SNPs) have been associated with disease risk/susceptibility. Immune cells have been suggested as the principal functional effector cell types of these common variants. Here, we identify 76 MS-associated SNPs whose loci present accessible chromatin in homeostatic and diseased oligodendroglia (OLG), including both oligodendrocyte precursor cells (OPCs) and mature oligodendrocytes (MOLs). By applying high-throughput functional genomics, we found that a subset of these SNPs led to variant- and cell-specific regulatory effects in human induced pluripotent stem cell-derived oligodendroglia. Phenotypic profiling of these variants indicated that rs483180:PHGDH interfered with human OPC proliferation via long-range chromatin interactions with the S100A6 locus, while variants at rs2248137:CYP24A1 impaired oligodendrocyte differentiation by regulating BCAS1 expression. In addition, variants at rs1415069:DIPK1A enhanced secretion of the cytokine CCL2 by oligodendroglia, suggesting that these variants might be implicated in OLG-driven immune cell recruitment in MS. These findings position oligodendroglia as important drivers of MS pathogenesis through modulation of both their cell-intrinsic oligodendroglial function and intercellular communication by non-coding MS risk variants.

cell biology↗

bioRxiv2025

Systematic comparison of dCas9-based DNA methylation epimodifiers over time indicates efficient on-target and widespread off-target effects

CRISPR/dCas9-based epigenome editing systems, including DNA methylation epimodifiers, have greatly advanced molecular functional studies revolutionizing their precision and applicability. Despite their promise, challenges such as the magnitude and stability of the on-target editing and unwanted off-target effects underscore the need for improved tool characterization and design. We systematically compared specific targeting of the BACH2 gene promoter and genome-wide off-target effects of available and novel dCas9-based DNA methylation editing tools over time. We demonstrate that multimerization of the catalytic domain of DNA methyltransferase 3A enhances editing potency but also induces widespread, early methylation deposition at low-to-medium methylated promoter-related regions with specific gRNAs and, interestingly, also with non-targeting gRNAs. A small fraction of the methylation changes associated with transcriptional dysregulation and mapped predominantly to bivalent chromatin associating both with transcriptional repression and activation. Additionally, specific non-targeting control gRNA caused pervasive and long-lasting methylation-independent transcriptional alterations particularly in genes linked to RNA and energy metabolism. CRISPRoff emerged as the most efficient tool for stable targeting of the BACH2 promoter, with fewer and less stable off-target effects compared to other epimodifiers but with persistent transcriptome alterations. Our findings highlight the delicate balance between potency and specificity of epigenome editing and provide critical insights into the design and application of future tools to improve their precision and minimize unintended consequences.

molecular biology↗