Biology subjects

Soleimani, V. D.

Publications and source records attributed to Soleimani, V. D..

7 recordsLinked to original sources

bioRxiv2026

TCF4 Mediates PHF6 Transcriptional Regulation of Neural Stem Cells in the Developing Brain, a Mechanism Disrupted in Börjeson Forssman Lehmann Syndrome (BFLS)

Transcriptional hierarchies govern neural stem cell (NSC) fate decisions during neurodevelopment, and disruption of these regulatory networks underlies neurodevelopmental disorders. Borjeson-Forssman-Lehmann syndrome (BFLS) is an X-linked intellectual disability (XLID) caused by mutations in a chromatin-associated transcriptional regulator, the plant homeodomain zinc finger protein 6 (PHF6). Although BFLS mouse models harboring PHF6 patient mutations recapitulate neurogenic and cognitive deficits, the molecular mechanisms linking PHF6 dysfunction to these phenotypes remain poorly understood. Here, we identify transcription factor 4 (TCF4), a basic helix-loop-helix transcription factor implicated in neurodevelopmental and psychiatric disorders, as a critical downstream effector of PHF6 in NSC fate regulation. Tcf4 expression is reduced in BFLS mouse models harbouring R342X and C99F-m mutations and in a conditional Phf6 knockout driven by Nestin-Cre. Mechanistically, PHF6 binds the Tcf4 gene regulatory element upstream of its transcriptional start site (TSS) and promotes Tcf4 expression. Tcf4 depletion in embryonic NSCs enhances self-renewal and stemness, increasing neurosphere formation and expression of stem cell markers, Nestin and Sox2. Conversely, TCF4 restoration rescues NSC defects caused by PHF6 loss of function in BFLS and Phf6/Nestin-Cre mice. This regulatory relationship persists in adult NSCs where TCF4 similarly restricts stem cell expansion. Importantly, restoration of TCF4 expression in embryonic brain ameliorates behavioral and cognitive deficits in BFLS mice. Together, these findings establish a PHF6-Tcf4 transcriptional pathway that restricts NSC self-renewal and links disrupted transcriptional control of NSC fate to the neurodevelopmental and behavioral abnormalities of BFLS.

neuroscience↗

bioRxiv2026

A Multiomic Analysis of Cachectic Mice Reveals Cancer Driven Suppression of Muscle Stem Cell Differentiation

Cancer cachexia affects a large proportion of cancer patients, inducing a rapid decline in muscle mass. Patients with cachexia have a worse prognosis and are less responsive to cancer therapies. The exact cause of cachexia remains unknown, nor are there any effective treatments for the condition. In this study, we use the C26 adenocarcinoma cell line to determine how cancer cells affect myofiber and muscle stem cell function. We determined that C26 cancer cells adapt to the host environment, in both male and female mice, greatly altering their transcriptome to promote their survival and growth. C26 cells directly communicate with muscle stem cells via GDF15 and MMP9. These circulatory factors cause the muscle stem cells to upregulate the EMT pathway and become less capable of undergoing differentiation and contributing to muscle regeneration. Muscle stem cells from tumor bearing mice are less proliferative and less prone to differentiation, Chromatin accessibility data shows that there are fewer accessible myogenic regulatory binding sites. Cytokine array determined that circulating GDF15 and MMP9 were highly upregulated and were derived form C26 tumor cells. However, blocking tumor derived GDF15 is not sufficient to prevent the onset of cachexia and rescue the loss of muscle stem cell function. Together, these findings establish a new conceptual paradigm in which cancer orchestrates muscle wasting through coordinated transcriptional, metabolic, and epigenetic suppression of muscle stem cell differentiation.

cell biology↗

bioRxiv2023

The E3 Ubiquitin Ligase Nedd4L Acts as a Checkpoint Against Activation in Quiescent Muscle Stem Cells

Adult stem cells play a critical role in tissue repair and maintenance. In tissues with slow turnover, including skeletal muscle, these cells are maintained in a mitotically quiescent state yet remain poised to re-enter the cell cycle to replenish themselves and regenerate the tissue. Using a multiomics approach we identify the PAX7/NEDD4L axis as a checkpoint against muscle stem cell activation in homeostatic skeletal muscle. Our findings demonstrate that PAX7 transcriptionally activates the E3 ubiquitin ligase Nedd4L and that the conditional genetic deletion of Nedd4L impairs muscle stem cell quiescence, with an upregulation of cell cycle and myogenic differentiation genes. Loss of Nedd4L in muscle stem cells results in the expression of DCX which is only expressed during their in vivo activation. Together, this data establishes that the ubiquitin proteasome system, mediated by Nedd4L, is a key regulator of the muscle stem cell quiescent state in non-injured skeletal muscle. Highlights- General inhibition of the ubiquitin proteasome system with MG132 results in muscle stem cells (MuSCs) breaking quiescence. - The E3 ubiquitin ligase Nedd4L is a transcriptional target of Pax7. - The Pax7/Nedd4l axis restricts MuSC activation in homeostatic skeletal muscle. - Genetic deletion of Nedd4L induces MuSCs transition towards activation.

cell biology↗

bioRxiv2021

Application of ATAC-Seq for genome-wide analysis of the chromatin state at single myofiber resolution

Skeletal myofibers are the main components of skeletal muscle which is the largest tissue in the body. Myofibers are highly adaptive in nature and they can vary in different biological and disease conditions. Therefore, transcriptional and epigenetic studies on myofibers are crucial to discover how chromatin alterations occur in the skeletal muscle under different conditions. However, due to the heterogenous nature of skeletal muscle, studying myofibers in isolation proves to be a challenging task. Single cell sequencing has permitted for the study of the epigenome of isolated myonuclei. While this provides sequencing with high dimensionality, the sequencing depth is lacking, which makes comparisons between different biological conditions difficult. Here we report the first implementation of single myofiber ATAC-Seq, which permits for the sequencing of an individual myofiber at a depth sufficient for peak calling and for comparative analysis of chromatin accessibility under various physiological, physical and disease conditions. Application of this technique revealed significant differences in chromatin accessibility between resting and regenerating myofibers. This technique can lead to wide application in identifying chromatin regulatory elements and epigenetic mechanisms in muscle fibers during development and in muscle-wasting diseases.

genetics↗

bioRxiv2021

Transcriptional Reprogramming of Skeletal Muscle Stem Cells by the Niche Environment

Adult stem cells are indispensable for tissue regeneration. Tissue-specific stem cells reside in a specialized location called their niche, where they are in constant cross talk with neighboring niche cells and circulatory signals from their environment. Aging has a detrimental effect on the number and the regenerative function of various stem cells. However, whether the loss of stem cell function is a cause or consequence of their aging niche is unclear. Using skeletal muscle stem cells (MuSCs) as a model, we decouple cell-intrinsic from niche-mediated extrinsic effects of aging on their transcriptome. By combining in vivo MuSC heterochronic transplantation models and computational methods, we show that on a genome-wide scale, age-related altered genes fall into two distinct categories regarding their response to the niche environment. Genes that are inelastic in their response to the niche exhibit altered chromatin accessibility and are associated with differentially methylated regions (DMRs) between young and aged cells. On the other hand, genes that are restorable by niche exposure exhibit altered transcriptome but show no change in chromatin accessibility or DMRs. Taken together, our data suggest that the niche environment plays a decisive role in controlling the transcriptional activity of MuSCs, and exposure to a young niche can reverse approximately half of all age-associated changes that are not epigenetically encoded. The muscle niche therefore serves as an important therapeutic venue to mitigate the negative consequence of aging on tissue regeneration.

genetics↗

bioRxiv2021

Transcriptional Control of Brain Tumour Stem Cell Fate by a Carbohydrate Binding Protein

Brain tumour stem cells (BTSCs) and intratumoural heterogeneity represent major challenges in glioblastoma therapy. Here, we report that the LGALS1 gene, encoding the carbohydrate binding protein, galectin1, is a key regulator of BTSCs and glioblastoma resistance to therapy. Genetic deletion of LGALS1 alters BTSC gene expression profiles and results in downregulation of gene sets associated with mesenchymal subtype of glioblastoma. Using a combination of pharmacological and genetic approaches, we establish that inhibition of LGALS1 signalling in BTSCs impairs self-renewal, suppresses tumourigenesis, prolongs lifespan, and improves glioblastoma response to ionizing radiation in preclinical animal models. Mechanistically, we show that LGALS1 is a direct transcriptional target of STAT3 with its expression robustly regulated by the ligand OSM. Importantly, we establish that galectin1 forms a complex with the transcription factor HOXA5 to reprogram BTSC transcriptional landscape. Our data unravel an oncogenic signalling pathway by which galectin1/HOXA5 complex maintains BTSCs and promotes glioblastoma.

cancer biology↗

bioRxiv2019

High Resolution Genome Wide Expression Analysis of Single Myofibers Using SMART-Seq

Skeletal muscle is a heterogeneous tissue. Individual myofibers that make up muscle tissue exhibit variation in their metabolic and contractile properties. Although there are biochemical and histological assays to study myofiber heterogeneity, efficient methods to analyze the whole transcriptome of individual myofibers are lacking. We have developed single myofiber RNA-Seq (smfRNA-Seq) to analyze the whole transcriptome of individual myofibers by combining single fiber isolation with Switching Mechanisms at 5 end of RNA Template (SMART) technology. Our method provides high-resolution genome wide expression profiles of single myofibers. Using smfRNA-Seq, we have analyzed the differences in the transcriptome of young and old myofibers to validate the effectiveness of this new method. Using smfRNA-Seq, we performed comparative gene expression analysis between single myofibers from young and old mice. Our data suggests that aging leads to significant changes in the expression of metabolic and structural genes in myofibers. Our data suggests that smfRNA-Seq is a powerful tool to study developmental, disease and age-related dynamics in the composition of skeletal muscle.

molecular biology↗