Biology subjects

Yousefi, M.

Publications and source records attributed to Yousefi, M..

11 recordsLinked to original sources

bioRxiv2026

Increased Expression and Altered Functional Activities of Immune Receptors TREM1, PD-L1, and Others on Hematopoietic Progenitor Cells in a Mouse Model of Rheumatoid Arthritis

Hematopoietic stem and progenitor cells (HSPCs) sustain the production of hundreds of billions of new cells per day to maintain our blood and immune system. In this process, HSPCs regulate the hematopoietic output by sensing and integrating diverse physiological cues. Thus, HSPCs express many receptors traditionally studied for their functions in the immune system, and this allows HSPCs to directly detect microbial compounds, endogenous danger signals, cytokines, and other inflammatory mediators. However, how the expression levels of such receptors on HSPCs change under chronic inflammation and how such changes alter HSPC functions and immune cell production remains unexplored. Working in a murine model of rheumatoid arthritis, we demonstrate the induction of microbial sensors TLR2 and CD14, orphan inflammatory receptor TREM1, and checkpoint receptor PD-L1 on HSPCs and particularly the myeloid progenitor cells in the arthritis-afflicted mice. Furthermore, we demonstrate that the stimulation of HSPCs through these receptors in culture can significantly alter the dynamics of cell expansion and differentiation, with distinct responses from HSPCs of arthritis-afflicted versus healthy control mice. We hypothesize that the induction and stimulation of HSPCs through these immune receptors under chronic inflammation may impact the output and functional properties of their immune cell progeny, positing HSPCs as central players in the pathogenic inflammatory responses of rheumatoid arthritis and potentially other chronic inflammatory diseases. HIGHLIGHTSO_LIHematopoietic progenitor cells in murine models of rheumatoid arthritis show an upregulation of immune receptors TREM1, PD-L1, TLR2, and CD14. C_LIO_LIStimulation of murine hematopoietic stem and progenitor cells through these receptors in culture alters the dynamics of their expansion and differentiation. C_LIO_LIIn such cultures, hematopoietic stem and progenitor cells from mice afflicted with rheumatoid arthritis show altered responses to stimulation as compared to healthy controls. C_LI

immunology↗

bioRxiv2025

Identifying the Levant as a potential contact and interbreeding zone for Neanderthals and modern humans

Timing of interbreeding between modern humans and Neanderthals has been subject of numerous studies but its geography remains largely unknown. Genetic evidence suggests three different interbreeding events: first in the Marine Isotope Stage (MIS) 7 ([~]250 to 200 ka), then in the MIS5 ([~]100 to 120 ka) and the final event in the MIS3 ([~]60 to 50 ka). Here, we used all known archaeological sites between 60-50 ka associated with Neanderthals and modern human presence and a set of paleoenvironmental data to reconstruct Neanderthals and modern humans habitat suitability using the Species Distribution Modeling (SDM) techniques. Assessing geographical overlap between the two species, we identify potential interbreeding zone. We found that the Levant was main potential interbreeding area of the third event. Previous research has identified the Zagros Mountains in Iran as a potential interbreeding zone during the second interbreeding event MIS5 ([~]100 to 120 ka). Compiling the results of this study to previous research can help us to better understand the dynamics of modern humans and Neanderthals interbreeding over both time and space. The two potential interbreeding areas have high priority for future research.

evolutionary biology↗

bioRxiv2025

Trained Immunity Affecting Dendritic Cell Differentiation and Function in Rheumatoid Arthritis

Rheumatoid arthritis affects [~]0.5-1% of the adult population and results in joint inflammation, chronic pain, and many systemic comorbidities. Immune and inflammatory tissue damage is the main pathogenic mechanism in rheumatoid arthritis, and involves the hyperactivation of both innate and adaptive immune systems. Trained immunity has become well established as an important feature of the innate immune system that allows the host to mount functionally altered immune responses based on their previous history of immune exposures, independently of the classical adaptive immunological memory. However, the role of trained immunity in systemic autoimmune and inflammatory disorders remains poorly understood. In the current work, we demonstrate that emergency myelopoiesis is induced in chronic rheumatoid arthritis in murine models and acts not only to enhance innate immune cell numbers but also to produce functionally altered innate immune cells. Such effects are cell-intrinsic to hematopoietic stem and progenitor cells (HSPCs) and persist independently of the inflammatory disease milieu. Importantly, these trained immunity mechanisms impact not only macrophages but also dendritic cells, which are the major antigen presenting cells that bridge the innate and adaptive immune responses. Trained dendritic cells show changes in global gene expression profiles, and significantly altered responses to recall immune stimulation and capacity for T cell activation. This study therefore represents the first demonstration of dendritic cell trained immunity in rheumatoid arthritis.

immunology↗

bioRxiv2024

Modeling vehicle collision risk for the jungle cat in the Hyrcanian forests of Iran: A guide for vehicle collision prevention

Wildlife-vehicle collisions are an important wildlife conservation challenge, especially for carnivores. As in other countries, vehicle collisions pose a major threat to carnivores in Iran. The jungle cat (Felis chaus) is a small carnivore species facing multiple threats, including habitat destruction, land use changes, and particularly vehicle collisions. We collected data on jungle cat collisions to model jungle cat-vehicle collision risk in the Hyrcanian forests of northern Iran. We also modeled the jungle cat vehicle collision risk in the study area but by creating 1 km and 5 km buffers around the roads and identified high vehicle collision risk areas within the 1 km and 5 km butters. We used the Maxent model to identify most important predictors of collision risk. Our models showed that areas in west of Golestan province, east of Mazandaran province, and in central parts of Gilan province faced highest vehicle collision risk for the jungle cat in the Hyrcanian forests. Human footprint and slope were the most important predictors of the jungle cat vehicle collision, with 48.3% and 17.2% contribution and with positive and negative correlation respectively. Results of variable importance were similar when modeling area was limited to a 5 km buffer zone around the roads. But when modeling area was limited to a 1 km buffer zone around the roads, slope became insignificant. Collisions more likely occur where vegetation grows immediately adjacent to roads, so clearing a roadside strip would reduce potential collisions. We recommend that high collision-risk areas we identified for jungle cat in the Hyrcanian forests be a focus for future monitoring and conservation planning.

ecology↗

bioRxiv2024

A Novel Mouse Model Demonstrates In Vivo Replenishment of Central Nervous System Pericytes After Successful Acute Ablation

Central nervous system (CNS) pericytes play crucial roles in vascular development and blood-brain barrier maturation during prenatal development, as well as in regulating cerebral blood flow in adults. They have also been implicated in the pathogenesis of numerous neurological disorders. However, the behavior of pericytes in the adult brain after injury remains poorly understood, partly due to limitations in existing pericyte ablation models. To investigate pericyte responses following acute ablation, we developed a tamoxifen-inducible pericyte ablation model by crossing PDGFR{beta}-P2A-CreERT2 and Rosa26-DTA176 transgenic mouse lines. Using this model, we studied the effects of different tamoxifen doses and conducted histological examinations 15 and 60 days post-injection to assess both short- and long-term impacts of pericyte ablation. Our results demonstrate that a low dose of tamoxifen effectively ablates CNS pericytes in mice without reducing survival or causing significant systemic side effects, such as weight loss. Additionally, we found that the extent of pericyte depletion varies between the cortex and the spinal cords gray and white matter regions. Importantly, both pericyte coverage and numbers increased in the weeks following acute ablation, indicating the regenerative capacity of CNS pericytes in vivo. This model offers a valuable tool for future studies on the role of pericytes in neurological disorders, overcoming the limitations of constitutive pericyte ablation models.

neuroscience↗

bioRxiv2024

Variability in HIV-1 Transmitted/Founder Virus Susceptibility to Combined APOBEC3F and APOBEC3G Host Restriction

Several APOBEC3 enzymes restrict HIV-1 replication by deaminating cytosine to form uracil in single-stranded proviral (-)DNA. However, HIV-1 Vif binds to APOBEC3 enzymes and counteracts their activity by inducing their proteosomal degradation. This counteraction by Vif is not complete as evidenced by footprints of APOBEC3-mediated mutations within integrated proviral genomes of people living with HIV-1. The APOBEC3 enzymes are co-ordinately expressed in CD4+T cells and relative contributions of APOBEC3s in HIV-1 restriction is not fully understood. In this study, we investigated the activity of co-expressed APOBEC3F and APOBEC3G against HIV-1 Subtype B and Subtype C Transmitted/Founder viruses. APOBEC3F and APOBEC3G when co-expressed were previously determined to form a hetero-oligomer that enables partial resistance of APOBEC3F to Vif-mediated degradation. Here, we determined that that APOBEC3F interacts with APOBEC3G through its N-terminal domain. We provide evidence that this results in protection from Vif-mediated degradation because the APOBEC3F N-terminal domain contains residues required for recognition by Vif. We also found subtype specific differences in activity of Transmitted/Founder Vifs against APOBEC3G and the APOBEC3F/APOBEC3G hetero-oligomer. HIV-1 Subtype C Vifs were more active in counteracting APOBEC3G compared to HIV-1 Subtype B Vifs when APOBEC3G was expressed alone. However, HIV-1 Subtype C Vifs were less active against APOBEC3G when APOBEC3F and APOBEC3G were co-expressed. Consequently, when APOBEC3F and APOBEC3G were expressed together HIV-1 Subtype C viruses showed a decrease in relative infectivity compared to that when APOBEC3G was expressed alone. Inspection of Vif amino acid sequences revealed that that differences in amino acids adjacent to conserved sequences influenced the Vif-mediated APOBEC3 degradation ability. Altogether, the data provide a possible mechanism for how combined expression of APOBEC3F and APOBEC3G could contribute to mutagenesis of HIV-1 proviral genomes in the presence of Vif and provide evidence for variability in the Vif-mediated degradation ability of Transmitted/Founder viruses. Author SummaryAPOBEC3 enzymes act as barriers to HIV infection by inducing cytosine deamination in proviral DNA, but their effectiveness is hindered by their counteraction by HIV Vif, which leads to APOBEC3 proteasomal degradation. The APOBEC3-Vif interaction has largely been determined using lab adapted HIV-1 Subtype B viruses and with singular APOBEC3 enzymes. Here we examined how primary isolates of HIV-1 replicated in the presence of APOBEC3F and APOBEC3G. APOBEC3F and APOBEC3G interact and this imparts partial resistance to Vif-mediated degradation. We determined that APOBEC3F interacts with APOBEC3G through its N terminal domain, and that APOBEC3F, like APOBEC3G has Vif-mediated degradation determinants in the N-terminal domain, providing a rational for protection from Vif-mediated degradation. We also demonstrate subtype-specific differences in the activity of Transmitted/Founder Vifs against APOBEC3G and the APOBEC3F/APOBEC3G hetero-oligomer. Through an analysis of Vif amino acid sequences, we identified variations influencing the Vif-mediated APOBEC3 degradation ability. This research uncovers previously unidentified mechanisms by which combined expression of APOBEC3F and APOBEC3G may contribute to HIV-1 proviral genome mutagenesis in the presence of Vif and emphasizes the contribution of amino acid variation outside of previously identified conserved regions in Vif-mediating APOBEC3 degradation.

microbiology↗

bioRxiv2023

Fully accessible fitness landscape of oncogene-negative lung adenocarcinoma

Cancer genomes are almost invariably complex with genomic alterations cooperating during each step of carcinogenesis. In cancers that lack a single dominant oncogene mutation, cooperation between the inactivation of multiple tumor suppressor genes can drive tumor initiation and growth. Here, we shed light on how the sequential acquisition of genomic alterations generates oncogene-negative lung tumors. We couple tumor barcoding with combinatorial and multiplexed somatic genome editing to characterize the fitness landscapes of three tumor suppressor genes NF1, RASA1, and PTEN, the inactivation of which jointly drives oncogene-negative lung adenocarcinoma initiation and growth. The fitness landscape was surprisingly accessible, with each additional mutation leading to growth advantage. Furthermore, the fitness landscapes remained fully accessible across backgrounds with additional tumor suppressor mutations. These results suggest that while predicting cancer evolution will be challenging, acquiring the multiple alterations required for the growth of oncogene-negative tumors can be facilitated by the lack of constraints on mutational order.

cancer biology↗

bioRxiv2021

Combinatorial tumor suppressor inactivation efficiently initiates lung adenocarcinoma with therapeutic vulnerabilities

Lung cancer is the leading cause of cancer death worldwide, with lung adenocarcinoma being the most common subtype. Many oncogenes and tumor suppressor genes are altered in this cancer type and the discovery of oncogene mutations has led to the development of targeted therapies that have improved clinical outcomes. However, a large fraction of lung adenocarcinomas lacks mutations in known oncogenes, and the genesis and treatment of these oncogene-negative tumors remain enigmatic. Here, we perform iterative in vivo functional screens using quantitative autochthonous mouse model systems to uncover the genetic and biochemical changes that enable efficient lung tumor initiation in the absence of oncogene alterations. Through the generation of hundreds of diverse combinations of tumor suppressor alterations, we demonstrate that the inactivation of suppressors of the RAS and PI3K pathways drive the development of oncogene-negative lung adenocarcinoma. Human genomic data and histology identified RAS/MAPK and PI3K pathway activation as a common event in oncogene- negative human lung adenocarcinomas. We demonstrate that these Onc-negativeRAS/PI3K tumors and related cell lines are vulnerable to pharmacological inhibition of these signaling axes. These results transform our understanding of this prevalent yet understudied subtype of lung adenocarcinoma.

cancer biology↗

bioRxiv2021

A Mediterranean-like fat blend protects against the development of severe colitis in the mucin-2 deficient murine model

The Mediterranean diet (MD) is a health-promoting, moderate fat diet (~ 40% energy). It is not known if the blend of fats found in the MD contribute to the beneficial protective effects. We compared the MD fat blend (high monounsaturated, 2:1 n-6:n-3 polyunsaturated and moderate saturated fat) to isocaloric diets composed with corn oil (CO, n-6 polyunsaturated-rich), olive oil (high monounsaturated-rich) or milk fat (MF, saturated-rich) on spontaneous colitis development in Muc2-/- mice. The MD resulted in lower clinical and histopathological scores, and induced tolerogenic CD103+CD11b+ dendritic, Th22 and IL-17+IL-22+ cells important for intestinal barrier repair. MD also reduced attendant insulin resistance and a shift to a higher health-promoting gut microbes including Lactobacillus B. animalis and Muribaculaceae, whereas CO showed higher prevalence of mucin-degraders (Akkermansia muciniphila) and colitis promoters (Enterobacteriaceae). Our findings suggest that the MD fat blend could be recommended as a maintenance diet for colitis.

immunology↗

bioRxiv2020

Developing snakebite risk model using venomous snake habitat suitability as an indicating factor: An application of species distribution models in public health research

Snakebite envenoming is an important public health problem in Iran, despite its risk not being quantified. This study aims to use venomous snakes habitat suitability as an indicator of snakebite risk, to identify high-priority areas for snakebite management across the country. Thus, an ensemble approach using five distribution modeling methods: Generalized Boosted Models, Generalized Additive Models, Maximum Entropy Modeling Generalized Linear Models, and Random Forest was applied to produce a spatial snakebite risk model for Iran. To achieve this, four venomous snakes habitat suitability (Macrovipera lebetina, Echis carinatus, Pseudocerastes persicus and Naja oxiana) were modeled and then multiplied. These medically important snakes are responsible for the most snakebite incidents in Iran. Multiplying habitat suitability models of the four snakes showed that the northeast of Iran (west of Khorasan-e-Razavi province) has the highest snakebite risk in the country. In addition, villages that were at risk of envenoming from the four snakes were identified. Results revealed that 51,112 villages are at risk of envenoming from M. lebetina, 30,339 from E. carinatus, 51,657 from P. persicus and 12,124 from N. oxiana. This paper demonstrates application of species distribution modeling in public health research and identified potential snakebite risk areas in Iran by using venomous snakes habitat suitability models as an indicating factor. Results of this study can be used in snakebite and human-snake conflict management in Iran. We recommend increasing public awareness of snakebite envenoming and education of local people in areas which identified with the highest snakebite risk.

ecology↗

bioRxiv2020

Quantitative in vivo analyses reveal a complex pharmacogenomic landscape in lung adenocarcinoma

AbstractThe lack of knowledge about the relationship between tumor genotypes and therapeutic responses remains one of the most important gaps in enabling the effective use of cancer therapies. Here, we couple a multiplexed and quantitative platform with robust statistical methods to enable pharmacogenomic mapping of lung cancer treatment responses in vivo. We uncover a surprisingly complex map of genotype-specific therapeutic responses, with over 20% of possible interactions showing significant resistance or sensitivity. We validate one of these interactions - the resistance of Keap1 mutant tumors to platinum therapy - using a large patient response dataset. Our results highlight the importance of understanding the genetic determinants of treatment responses in the development of precision therapies and define a strategy to identify such determinants.

cancer biology↗