Biology subjects

Haidar, M.

Publications and source records attributed to Haidar, M..

8 recordsLinked to original sources

bioRxiv2025

Identification and Implications for Tumor Heterogeneity of a DNA Methylation-Based Signature Classifying Pancreatic Ductal Adenocarcinoma Based on their Cellular Origin

BackgroundPancreatic ductal adenocarcinoma (PDAC) arises from distinct cellular origins, yet the extent to which DNA methylation patterns from normal pancreatic cells are preserved in tumor cells remains unclear. Identifying cell-of-origin signatures may enhance PDAC classification and therapeutic stratification. ObjectiveTo determine whether DNA methylation signatures in normal acinar and ductal pancreatic cells are retained in PDAC cell lines and to develop a robust classifier for distinguishing tumor origins. DesignWe performed DNA methylation profiling using the Illumina Infinium Mouse MethylationEPIC array on normal acinar and ductal cells and their PDAC derivatives in genetically engineered mouse models (GEMMs). Differential methylation analysis, and hierarchical clustering were used to identify and validate a conserved cell-of-origin DNA methylation signature. A logistic regression model was developed for classification. ResultsWe identified 178 CpG sites that remain preserved during tumorigenesis and effectively distinguished acinar- and ductal-derived PDAC cell lines. This signature was validated across independent sample sets, primary tumors, and orthotopic allografts. It successfully classified cell lines of unknown origin, including PDAC samples from KPC mice, and revealed the impact of oncogenic mutations on tumor fate. A logistic regression model supported these findings, confirming the robustness of the classification approach. Furthermore, the cell of origin influenced key PDAC characteristics, including treatment response, highlighting its potential role in molecular subtyping and patient stratification. ConclusionA preserved DNA methylation signature during pancreatic carcinogenesis distinguishes PDAC origins and influences tumor behavior. These results highlight the potential of DNA methylation profiling for tumor classification and personalized treatment strategies. They also raise important questions about the relevance of KPC mice as a preclinical model and the mechanisms driving PDAC heterogeneity. What is already known on this topicO_LIHuman PDAC exhibits significant heterogeneity, with molecular subtyping (classical vs basal-like) providing some insights into tumor behavior and clinical outcomes. C_LIO_LIMouse acinar and ductal cells can give rise to PDAC, influencing tumor characteristics and survival outcomes. C_LIO_LIDNA methylation is a powerful tool for tracing cellular identity and distinguishing cancer subtypes based on epigenetic profiles. C_LI What this study addsO_LIA cell-of-origin methylation signature is preserved during mouse carcinogenesis and across diverse experimental settings, providing a reliable tool for tumor classification. C_LIO_LIA DNA methylation-based classification system reliably distinguishes between acinar- and ductal-origin PDAC, filling a critical gap in methods to trace tumor lineage. C_LIO_LIAcinar- and ductal-derived PDACs exhibit distinct methylation patterns that correlate with differences in tumor behavior, such as chemoresistance, highlighting the biological relevance of cellular origin in PDAC. C_LIO_LIThe study provides new insights into how cell-of-origin influences PDAC heterogeneity and could lead to more precise therapeutic strategies tailored to the tumors lineage. C_LI How this study might affect research, practice or policyO_LIThis study provides a new, reliable method for classifying PDAC based on its cellular origin, which could significantly improve tumor classification in both preclinical and clinical settings, aiding in more accurate diagnoses and prognostic predictions. C_LIO_LIThe identification of distinct methylation patterns linked to tumor behavior offers valuable insights for developing personalized treatment strategies, as therapies could be tailored based on the tumors cellular origin and associated molecular characteristics. C_LIO_LIThe preservation of cell-of-origin methylation signature suggests the potential for developing a universal biomarker for PDAC classification, which could guide future clinical trials, therapeutic targeting, and patient stratification in PDAC care. C_LI

cancer biology↗

bioRxiv2022

Extracellular vesicle-associated cholesterol dictates the regenerative functions of macrophages in the brain

Macrophages play major roles in the pathophysiology of various neurological disorders, being involved in seemingly opposing processes such as lesion progression and resolution. Yet, the molecular mechanisms that drive their harmful and benign effector functions remain poorly understood. Here, we demonstrate that extracellular vesicles (EVs) secreted by repair-associated macrophages (RAMs) enhance remyelination ex vivo and in vivo by promoting the differentiation of oligodendrocyte precursor cells (OPCs). Guided by lipidomic analysis and applying cholesterol depletion and enrichment strategies, we find that EVs released by RAMs show markedly elevated cholesterol levels and that cholestserol abundance controls their reparative impact on OPC maturation and remyelination. Mechanistically, EV-associated cholesterol was found to promote OPC differentiation through direct membrane fusion. Collectively, our findings highlight that EVs are essential for cholesterol trafficking in the brain and that changes in cholesterol abundance dictate the reparative impact of EVs released by macrophages in the brain, potentially having broad implications for therapeutic strategies aimed at promoting repair in neurodegenerative disorders.

neuroscience↗

bioRxiv2022

Fatty acid desaturation by stearoyl-CoA desaturase-1 controls regulatory T cell differentiation and autoimmunity

The imbalance between pathogenic and protective T cell subsets is a cardinal feature of autoimmune disorders such as multiple sclerosis (MS). Emerging evidence indicates that endogenous and dietary-induced changes in fatty acid metabolism have a major impact on both T cell fate and autoimmunity. To date, however, the molecular mechanisms that underlie the impact of fatty acid metabolism on T cell physiology and autoimmunity remain poorly understood. Here, we report that stearoyl-CoA desaturase-1 (SCD1), an enzyme essential for the desaturation of fatty acids and highly regulated by dietary factors, acts as an endogenous brake on regulatory T cell (Treg) differentiation and augments autoimmunity in an animal model of MS. Guided by RNA sequencing and lipidomics analysis, we found that absence of Scd1 promotes hydrolysis of triglycerides and phosphatidylcholine through adipose triglyceride lipase (ATGL). ATGL-dependent release of docosahexaenoic acid enhanced Treg differentiation by activating the nuclear receptor peroxisome proliferator-activated receptor gamma. Our findings identify fatty acid desaturation by SCD1 as an essential determinant of Treg differentiation and autoimmunity, with potentially broad implications for the development of novel therapeutic strategies and dietary interventions for autoimmune disorders.

immunology↗

bioRxiv2021

Cortical hyperexcitability drives dying forward ALS symptoms and pathology in mice

Amyotrophic lateral sclerosis (ALS) is a progressive fatal disorder caused by degeneration of motor neurons in the cortex and spinal cord. The origin of ALS in the central nervous system is unclear, however cortical hyperexcitability appears as an early and intrinsic feature of ALS and has been linked to degeneration of spinal motor neurons via a dying-forward mechanism. Here, we implement chemogenetics to validate the dying forward hypothesis of ALS in mice. We show that chronic hyperexcitability of corticomotoneurons induced by excitatory chemogenetics results in motor symptoms and core neuropathological hallmarks of ALS, including corticomotoneuron loss, corticospinal tract degeneration and reactive gliosis. Importantly, corticomotoneuron loss was sufficient to drive degeneration of spinal motor neurons and neuromuscular junctions (NMJs), associated with cytoplasmic TAR DNA binding protein 43 (TDP-43) pathology. These findings establish a cortical origin of ALS mediated by neuronal hyperexcitability, consistent with a dying forward mechanism of neurodegeneration.

neuroscience↗

bioRxiv2020

miR-34c-3p regulates PKA activity independent of cAMP via ablation of PRKAR2B in Theileria annulata-infected leukocytes and Plasmodium falciparum-infected erythrocytes

MicroRNAs (miRNAs) are small non-coding RNAs that can play critical roles in regulating various cellular processes including during many parasitic infections. Here, we report a regulatory role for miR-34c-3p in cAMP-independent regulation of PKA activity in Theileria annulata infection of bovine leukocytes. We identified prkar2b (cAMP-dependent protein kinase A type II-beta regulatory subunit), as a novel miR-34c-3p target gene and demonstrated how infection-induced up-regulation of miR-34c-3p in leukocytes repressed PRKAR2B expression to increase PKA activity and promote the virulent disseminating tumour phenotype of T. annulata-transformed macrophages. Finally, we demonstrate that miR-34c-3p regulation of prkar2b expression is generalizable, by confirming that Plasmodium falciparum infection of red blood cells also raises intracellular levels of miR-34c-3p and show that this negatively regulates host prkar2b expression so increasing PKA activity. Infection-induced increase in miR-34c-3p levels, therefore, represents a novel cAMP-independent way of regulating host cell PKA activity in infections by Theileria and Plasmodium parasites. Abstract ImportanceTheileria and Plasmodium infections of leukocytes and erythrocytes; respectively, lead to an increase in host cell miR-34c-3p levels and we identified prkar2b (cAMP-dependent protein kinase A type II-beta regulatory subunit), as a specific miR-34c-3p target gene. We demonstrate how infection-induced up-regulation of miR-34c-3p repressed PRKAR2B expression to increase PKA activity independent of fluxes in cAMP. Thus, in two different host-parasite combinations infection-induced increase in miR-34c-3p represents a novel epigenetic way of increasing in host PKA activity that contributes to the pathology of disease.

cell biology↗

bioRxiv2018

TGF-b2, catalase activity, H2O2 output and metastatic potential of diverse types of tumour

Theileria annulata is a protozoan parasite that infects and transforms bovine macrophages causing a myeloid-leukaemia-like disease called tropical theileriosis. TGF-{beta}2 is highly expressed in many cancer cells and is significantly increased in Theileria-transformed macrophages, as are levels of Reactive Oxygen Species (ROS), notably H2O2. Here, we describe the interplay between TGF-{beta}2 and ROS in cellular transformation. We show that TGF-{beta}2 drives expression of catalase to reduce the amount of H2O2 produced by T. annulata-transformed bovine macrophages, as well as by human lung (A549) and colon cancer (HT-29) cell lines. Theileria-transformed macrophages attenuated for dissemination express less catalase and produce more H2O2, but regain both virulent migratory and matrigel traversal phenotypes when stimulated with TGF-{beta}2, or catalase that reduce H2O2 output. Increased H2O2 output therefore, underpins the aggressive dissemination phenotype of diverse tumour cell types, but in contrast, too much H2O2 can dampen dissemination.

cancer biology↗

bioRxiv2018

Theileria highjacks JNK2 into a complex with the macroschizont GPI-anchored surface protein p104

Theileria is a unique apicomplexan parasite capable of transforming its host cell into a disseminating tumour. Constitutive JNK activity characterizes bovine T and B cells infected with T. parva, and B cells and macrophages infected with T. annulata. Here, we show that T. annulata manipulates JNK activation by recruiting JNK2, and not JNK1, to the parasite surface, whereas JNK1 is found predominantly in the host cell nucleus. In silico analysis identified 3 potential JNK-binding motifs in the previously characterized GPI-anchored macroschizont surface protein (p104), and we demonstrate here that JNK2 is recruited to the parasite via physical interaction with p104. A cell penetrating peptide harbouring a p104 JNK-binding motif also conserved in T. parva p104 competitively ablated binding, whereupon liberated JNK2 became ubiquitinated and degraded. Sequestration of JNK2 depended on PKA-mediated phosphorylation of the conserved JNK-binding motif and upon disruption of the p104/JNK2 complex loss of JNK2 resulted in diminished matrigel traversal of T. annulata-transformed macrophages. Loss of JNK2 also resulted in upregulation of small mitochondrial ARF that promoted autophagy consistent with cytosolic sequestration of JNK2 sustaininf not only JNK2, but also nuclear JNK1 levels that combined contribute to both survival and dissemination of Theileria-transformed macrophages.\n\nAuthor SummaryTheileria annulata parasites infect and transform their host bovine leukocytes into tumourlike cells that disseminate throughout infected animals causing a widespread disease called tropical theileriosis. Virulence has been ascribed to the parasites ability to constitutively activate leukocyte c-Jun N-terminal Kinase (JNK) leading to permanent induction of Matrix Metallo-Proteinase 9 (MMP9) that promotes transformed macrophage dissemination. In attenuated live vaccines JNK-mediated AP-1-driven transcriptional activity is reduced so dampening dissemination. However, in leukocytes JNK exists as two isoforms JNK1 and JNK2 and here, we show for the first time that in T. annulata-transformed macrophages they have different subcellular localisations and perform separate functions. Surprisingly, JNK2 associates with the parasite and is not in the nucleus like JNK1. JNK2 is hijacked by the parasite and sequestered in a complex with a macroschizont surface protein called p104. Upon forced complex dissociation JNK2 gets degraded and its loss negatively affects infected macrophage survival and ability to disseminate.

microbiology↗

bioRxiv2018

GZMA and RASGRP1 are novel tumor suppressors that counter dissemination of Theileria annulata-transformed macrophages

Theileria annulata is a tick-transmitted apicomplexan parasite that infects and transforms bovine leukocytes into disseminating tumors that cause a disease called tropical theileriosis. Using comparative transcriptomics we identified genes transcriptionally perturbed during Theileria-induced transformation. Dataset comparisons highlighted a small set of genes associated with Theileria-transformed leukocyte dissemination. The roles of Granzyme A (GZMA) and RAS guanyl-releasing protein 1 (RASGRP1) were verified by CRISPR/Cas9-mediated knock-down. Knocking down of GZMA and RASGRP1 in attenuated macrophages led to a regain in their dissemination in Rag2/{gamma}C mice confirming their role as dissemination suppressors in vivo. We further evaluated the roles of GZMA and RASGRP1 in human B-lymphoma cells by comparing the transcriptome of 934 human cancer cell lines to that of Theileria-transformed bovine host cells. We confirmed dampened dissemination potential of human B-lymphoma cells that overexpress GZMA and RASGRP1. Our results provide evidence that GZMA and RASGRP1 have a novel tumor suppressor function in both T. annulata-infected bovine host cells and in human B-lymphomas.\n\nSummaryWe compared the transcriptomes of Theileria annulata transformed B-lymphocytes to 934 human cancer cell lines and provide functional evidence for shared tumor suppressor roles for GZMA and RASGRP1 in controlling the dissemination phenotype of both human B lymphomas and Theileria-transformed leukocytes.

molecular biology↗