1
|
Bentzinger CF, Wang YX, von Maltzahn J, Soleimani VD, Yin H, Rudnicki MA. Fibronectin regulates Wnt7a signaling and satellite cell expansion. Cell Stem Cell 2013; 12:75-87. [PMID: 23290138 DOI: 10.1016/j.stem.2012.09.015] [Citation(s) in RCA: 272] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Revised: 06/07/2012] [Accepted: 09/14/2012] [Indexed: 01/07/2023]
Abstract
The influence of the extracellular matrix (ECM) within the stem cell niche remains poorly understood. We found that Syndecan-4 (Sdc4) and Frizzled-7 (Fzd7) form a coreceptor complex in satellite cells and that binding of the ECM glycoprotein Fibronectin (FN) to Sdc4 stimulates the ability of Wnt7a to induce the symmetric expansion of satellite stem cells. Newly activated satellite cells dynamically remodel their niche via transient high-level expression of FN. Knockdown of FN in prospectively isolated satellite cells severely impaired their ability to repopulate the satellite cell niche. Conversely, in vivo overexpression of FN with Wnt7a dramatically stimulated the expansion of satellite stem cells in regenerating muscle. Therefore, activating satellite cells remodel their niche through autologous expression of FN that provides feedback to stimulate Wnt7a signaling through the Fzd7/Sdc4 coreceptor complex. Thus, FN and Wnt7a together regulate the homeostatic levels of satellite stem cells and satellite myogenic cells during regenerative myogenesis.
Collapse
|
Research Support, U.S. Gov't, Non-P.H.S. |
12 |
272 |
2
|
Yin H, Pasut A, Soleimani VD, Bentzinger CF, Antoun G, Thorn S, Seale P, Fernando P, van Ijcken W, Grosveld F, Dekemp RA, Boushel R, Harper ME, Rudnicki MA. MicroRNA-133 controls brown adipose determination in skeletal muscle satellite cells by targeting Prdm16. Cell Metab 2013; 17:210-24. [PMID: 23395168 PMCID: PMC3641657 DOI: 10.1016/j.cmet.2013.01.004] [Citation(s) in RCA: 232] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 08/18/2012] [Accepted: 01/11/2013] [Indexed: 12/17/2022]
Abstract
Brown adipose tissue (BAT) is an energy-dispensing thermogenic tissue that plays an important role in balancing energy metabolism. Lineage-tracing experiments indicate that brown adipocytes are derived from myogenic progenitors during embryonic development. However, adult skeletal muscle stem cells (satellite cells) have long been considered uniformly determined toward the myogenic lineage. Here, we report that adult satellite cells give rise to brown adipocytes and that microRNA-133 regulates the choice between myogenic and brown adipose determination by targeting the 3'UTR of Prdm16. Antagonism of microRNA-133 during muscle regeneration increases uncoupled respiration, glucose uptake, and thermogenesis in local treated muscle and augments whole-body energy expenditure, improves glucose tolerance, and impedes the development of diet-induced obesity. Finally, we demonstrate that miR-133 levels are downregulated in mice exposed to cold, resulting in de novo generation of satellite cell-derived brown adipocytes. Therefore, microRNA-133 represents an important therapeutic target for the treatment of obesity.
Collapse
|
Research Support, N.I.H., Extramural |
12 |
232 |
3
|
Soleimani VD, Punch VG, Kawabe YI, Jones AE, Palidwor GA, Porter CJ, Cross JW, Carvajal JJ, Kockx CEM, van IJcken WFJ, Perkins TJ, Rigby PWJ, Grosveld F, Rudnicki MA. Transcriptional dominance of Pax7 in adult myogenesis is due to high-affinity recognition of homeodomain motifs. Dev Cell 2012; 22:1208-20. [PMID: 22609161 DOI: 10.1016/j.devcel.2012.03.014] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Revised: 01/20/2012] [Accepted: 03/28/2012] [Indexed: 01/08/2023]
Abstract
Pax3 and Pax7 regulate stem cell function in skeletal myogenesis. However, molecular insight into their distinct roles has remained elusive. Using gene expression data combined with genome-wide binding-site analysis, we show that both Pax3 and Pax7 bind identical DNA motifs and jointly activate a large panel of genes involved in muscle stem cell function. Surprisingly, in adult myoblasts Pax3 binds a subset (6.4%) of Pax7 targets. Despite a significant overlap in their transcriptional network, Pax7 regulates distinct panels of genes involved in the promotion of proliferation and inhibition of myogenic differentiation. We show that Pax7 has a higher binding affinity to the homeodomain-binding motif relative to Pax3, suggesting that intrinsic differences in DNA binding contribute to the observed functional difference between Pax3 and Pax7 binding in myogenesis. Together, our data demonstrate distinct attributes of Pax7 function and provide mechanistic insight into the nonredundancy of Pax3 and Pax7 in muscle development.
Collapse
|
Research Support, Non-U.S. Gov't |
13 |
127 |
4
|
Jones AE, Price FD, Le Grand F, Soleimani VD, Dick SA, Megeney LA, Rudnicki MA. Wnt/β-catenin controls follistatin signalling to regulate satellite cell myogenic potential. Skelet Muscle 2015; 5:14. [PMID: 25949788 PMCID: PMC4421991 DOI: 10.1186/s13395-015-0038-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 04/08/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Adult skeletal muscle regeneration is a highly orchestrated process involving the activation and proliferation of satellite cells, an adult skeletal muscle stem cell. Activated satellite cells generate a transient amplifying progenitor pool of myoblasts that commit to differentiation and fuse into multinucleated myotubes. During regeneration, canonical Wnt signalling is activated and has been implicated in regulating myogenic lineage progression and terminal differentiation. METHODS Here, we have undertaken a gene expression analysis of committed satellite cell-derived myoblasts to examine their ability to respond to canonical Wnt/β-catenin signalling. RESULTS We found that activation of canonical Wnt signalling induces follistatin expression in myoblasts and promotes myoblast fusion in a follistatin-dependent manner. In growth conditions, canonical Wnt/β-catenin signalling prime myoblasts for myogenic differentiation by stimulating myogenin and follistatin expression. We further found that myogenin binds elements in the follistatin promoter and thus acts downstream of myogenin during differentiation. Finally, ectopic activation of canonical Wnt signalling in vivo promoted premature differentiation during muscle regeneration following acute injury. CONCLUSIONS Together, these data reveal a novel mechanism by which myogenin mediates the canonical Wnt/β-catenin-dependent activation of follistatin and induction of the myogenic differentiation process.
Collapse
|
Journal Article |
10 |
63 |
5
|
Sharanek A, Burban A, Laaper M, Heckel E, Joyal JS, Soleimani VD, Jahani-Asl A. OSMR controls glioma stem cell respiration and confers resistance of glioblastoma to ionizing radiation. Nat Commun 2020; 11:4116. [PMID: 32807793 PMCID: PMC7431428 DOI: 10.1038/s41467-020-17885-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 07/22/2020] [Indexed: 12/13/2022] Open
Abstract
Glioblastoma contains a rare population of self-renewing brain tumor stem cells (BTSCs) which are endowed with properties to proliferate, spur the growth of new tumors, and at the same time, evade ionizing radiation (IR) and chemotherapy. However, the drivers of BTSC resistance to therapy remain unknown. The cytokine receptor for oncostatin M (OSMR) regulates BTSC proliferation and glioblastoma tumorigenesis. Here, we report our discovery of a mitochondrial OSMR that confers resistance to IR via regulation of oxidative phosphorylation, independent of its role in cell proliferation. Mechanistically, OSMR is targeted to the mitochondrial matrix via the presequence translocase-associated motor complex components, mtHSP70 and TIM44. OSMR interacts with NADH ubiquinone oxidoreductase 1/2 (NDUFS1/2) of complex I and promotes mitochondrial respiration. Deletion of OSMR impairs spare respiratory capacity, increases reactive oxygen species, and sensitizes BTSCs to IR-induced cell death. Importantly, suppression of OSMR improves glioblastoma response to IR and prolongs lifespan. The suppression of the receptor for oncostatin M (OSMR) can prevent glioblastoma cell growth. Here, the authors demonstrate a role for OSMR in modulating glioma stem cell respiration and its impact on resistance to ionizing radiation.
Collapse
|
Research Support, Non-U.S. Gov't |
5 |
54 |
6
|
Lazure F, Blackburn DM, Corchado AH, Sahinyan K, Karam N, Sharanek A, Nguyen D, Lepper C, Najafabadi HS, Perkins TJ, Jahani-Asl A, Soleimani VD. Myf6/MRF4 is a myogenic niche regulator required for the maintenance of the muscle stem cell pool. EMBO Rep 2020; 21:e49499. [PMID: 33047485 PMCID: PMC7726801 DOI: 10.15252/embr.201949499] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 12/16/2022] Open
Abstract
The function and maintenance of muscle stem cells (MuSCs) are tightly regulated by signals originating from their niche environment. Skeletal myofibers are a principle component of the MuSC niche and are in direct contact with the muscle stem cells. Here, we show that Myf6 establishes a ligand/receptor interaction between muscle stem cells and their associated muscle fibers. Our data show that Myf6 transcriptionally regulates a broad spectrum of myokines and muscle‐secreted proteins in skeletal myofibers, including EGF. EGFR signaling blocks p38 MAP kinase‐induced differentiation of muscle stem cells. Homozygous deletion of Myf6 causes a significant reduction in the ability of muscle to produce EGF, leading to a deregulation in EGFR signaling. Consequently, although Myf6‐knockout mice are born with a normal muscle stem cell compartment, they undergo a progressive reduction in their stem cell pool during postnatal life due to spontaneous exit from quiescence. Taken together, our data uncover a novel role for Myf6 in promoting the expression of key myokines, such as EGF, in the muscle fiber which prevents muscle stem cell exhaustion by blocking their premature differentiation.
Collapse
|
Research Support, Non-U.S. Gov't |
5 |
45 |
7
|
Soleimani VD, Baum BR, Johnson DA. Quantification of the retrotransposon BARE-1 reveals the dynamic nature of the barley genome. Genome 2006; 49:389-96. [PMID: 16699559 DOI: 10.1139/g05-119] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We used quantitative real-time PCR analysis to measure the copy number of the BARE-1 retrotransposon in 5 cultivars of barley (Hordeum vulgare), as well as in samples from its wild relative, Hordeum spontaneum. Two sets of PCR primers were used to amplify regions within the long terminal repeat (LTR) and the reverse transcriptase (RT) gene of BARE-1 (GenBank accession Z17327). The LTR primers detected an average of 2.148 x 105 +/- 0.012 x 105 copies per haploid genome among barley samples, whereas the RT primers detected an average of 1.588 x 104 +/- 0.085 x 104 copies. The average ratio of LTR:RT was estimated to be 13.5:1. This finding indicates that more than 7% of the barley genome is occupied by BARE-1 elements in the form of solo LTRs and another 2.6% of the genome is occupied by the full-length element. Taken together, BARE-1 sequences represent approximately 9.6% of the barley genome among the barley plants used in this study. For the above estimation, a genome size of 5.44 x 103 Mb for H. vulgare and 5.39 x 103 Mb for H. spontaneum were assumed. Our study on quantification results of the BARE-1 for a small group of barley cultivars showed that there are significant differences among cultivars in terms of BARE-1 copy number, providing further evidence that BARE-1 is active and has a major role in shaping the barley genome as a result of breeding and selection. Quantification results also showed that most of the elements (> 90%) are present as truncated copies (solo LTRs). These results show that there is a high level of recombination leading to the formation of truncated elements and a subsequent DNA loss from the genome. Taken together, our study provides a glimpse into a dynamic micro-evolutionary process that is the by-product of genome reshuffling and directional selection in barley breeding programs.
Collapse
|
Journal Article |
19 |
25 |
8
|
Blackburn DM, Lazure F, Corchado AH, Perkins TJ, Najafabadi HS, Soleimani VD. High-resolution genome-wide expression analysis of single myofibers using SMART-Seq. J Biol Chem 2019; 294:20097-20108. [PMID: 31753917 DOI: 10.1074/jbc.ra119.011506] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 11/15/2019] [Indexed: 12/26/2022] Open
Abstract
Skeletal muscle is a heterogeneous tissue. Individual myofibers that make up muscle tissue exhibit variation in their metabolic and contractile properties. Although biochemical and histological assays are available to study myofiber heterogeneity, efficient methods to analyze the whole transcriptome of individual myofibers are lacking. Here, we report on a single-myofiber RNA-sequencing (smfRNA-Seq) approach to analyze the whole transcriptome of individual myofibers by combining single-fiber isolation with Switching Mechanism at 5' end of RNA Template (SMART) technology. Using smfRNA-Seq, we first determined the genes that are expressed in the whole muscle, including in nonmyogenic cells. We also analyzed the differences in the transcriptome of myofibers from young and old mice to validate the effectiveness of this new method. Our results suggest that aging leads to significant changes in the expression of metabolic genes, such as Nos1, and structural genes, such as Myl1, in myofibers. We conclude that smfRNA-Seq is a powerful tool to study developmental, disease-related, and age-related changes in the gene expression profile of skeletal muscle.
Collapse
|
Research Support, Non-U.S. Gov't |
6 |
24 |
9
|
Sharanek A, Burban A, Hernandez-Corchado A, Madrigal A, Fatakdawala I, Najafabadi HS, Soleimani VD, Jahani-Asl A. Transcriptional control of brain tumor stem cells by a carbohydrate binding protein. Cell Rep 2021; 36:109647. [PMID: 34469737 DOI: 10.1016/j.celrep.2021.109647] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 06/29/2021] [Accepted: 08/09/2021] [Indexed: 12/12/2022] Open
Abstract
Brain tumor stem cells (BTSCs) and intratumoral 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 the mesenchymal subtype of glioblastoma. Using a combination of pharmacological and genetic approaches, we establish that inhibition of LGALS1 signaling in BTSCs impairs self-renewal, suppresses tumorigenesis, 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 the BTSC transcriptional landscape. Our data unravel an oncogenic signaling pathway by which the galectin1/HOXA5 complex maintains BTSCs and promotes glioblastoma.
Collapse
|
|
4 |
23 |
10
|
Scimè A, Soleimani VD, Bentzinger CF, Gillespie MA, Le Grand F, Grenier G, Bevilacqua L, Harper ME, Rudnicki MA. Oxidative status of muscle is determined by p107 regulation of PGC-1alpha. ACTA ACUST UNITED AC 2010; 190:651-62. [PMID: 20713602 PMCID: PMC2928004 DOI: 10.1083/jcb.201005076] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
p107, a member of the retinoblastoma susceptibility protein family, influences lipid metabolism in muscle and other tissues by repressing the PPAR-γ co-factor PGC-1α. Mice lacking p107 exhibit a white adipose deficiency yet do not manifest the metabolic changes typical for lipodystrophy, and instead exhibit low levels of serum triglycerides and a normal liver phenotype. When fed a high fat diet, p107-null mice still did not accumulate fat in the liver, and display markedly elevated energy expenditures together with an increased energy preference for lipids. Skeletal muscle was therefore examined, as this is normally the major tissue involved in whole body lipid metabolism. Notably, p107-deficient muscle express increased levels of peroxisome proliferator–activated receptor gamma co-activator-1α (PGC-1α) and contained increased numbers of the pro-oxidative type I and type IIa myofibers. Chromatin immunoprecipitation revealed binding of p107 and E2F4 to the PGC-1α proximal promoter, and this binding repressed promoter activity in transient transcription assays. Ectopic expression of p107 in muscle tissue in vivo results in a pronounced 20% decrease in the numbers of oxidative type IIa myofibers. Lastly, isolated p107-deficient muscle tissue display a threefold increase in lipid metabolism. Therefore, p107 determines the oxidative state of multiple tissues involved in whole body fat metabolism, including skeletal muscle.
Collapse
|
Research Support, Non-U.S. Gov't |
15 |
17 |
11
|
Abstract
In this issue of Cancer Cell, Rubin et al. (2011) describe using various conditional mouse models to trace the developmental origin and genetic basis of rhabdomyosarcomas. Their work provides a genetic dissection underlying rhabdomyosarcomas development and unveils unexpected relationship between various soft-tissue tumor types.
Collapse
|
Comment |
14 |
15 |
12
|
Lazure F, Farouni R, Sahinyan K, Blackburn DM, Hernández-Corchado A, Perron G, Lu T, Osakwe A, Ragoussis J, Crist C, Perkins TJ, Jahani-Asl A, Najafabadi HS, Soleimani VD. Transcriptional reprogramming of skeletal muscle stem cells by the niche environment. Nat Commun 2023; 14:535. [PMID: 36726011 PMCID: PMC9892560 DOI: 10.1038/s41467-023-36265-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 01/23/2023] [Indexed: 02/03/2023] Open
Abstract
Adult stem cells are indispensable for tissue regeneration, but their function declines with age. The niche environment in which the stem cells reside plays a critical role in their function. However, quantification of the niche effect on stem cell function is lacking. Using muscle stem cells (MuSC) as a model, we show that aging leads to a significant transcriptomic shift in their subpopulations accompanied by locus-specific gain and loss of chromatin accessibility and DNA methylation. By combining in vivo MuSC transplantation and computational methods, we show that the expression of approximately half of all age-altered genes in MuSCs from aged male mice can be restored by exposure to a young niche environment. While there is a correlation between gene reversibility and epigenetic alterations, restoration of gene expression occurs primarily at the level of transcription. The stem cell niche environment therefore represents an important therapeutic target to enhance tissue regeneration in aging.
Collapse
|
research-article |
2 |
13 |
13
|
Sahinyan K, Blackburn DM, Simon MM, Lazure F, Kwan T, Bourque G, Soleimani VD. Application of ATAC-Seq for genome-wide analysis of the chromatin state at single myofiber resolution. eLife 2022; 11:72792. [PMID: 35188098 PMCID: PMC8901173 DOI: 10.7554/elife.72792] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 02/09/2022] [Indexed: 12/11/2022] Open
Abstract
Myofibers are the main components of skeletal muscle, which is the largest tissue in the body. Myofibers are highly adaptive and can be altered under 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 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 allows for the sequencing of an individual myofiber at a depth sufficient for peak calling and for comparative analysis of chromatin accessibility under various physiological and disease conditions. Application of this technique revealed significant differences in chromatin accessibility between resting and regenerating myofibers, as well as between myofibers from a mouse model of Duchenne Muscular Dystrophy (mdx) and wild-type (WT) counterparts. This technique can lead to a wide application in the identification of chromatin regulatory elements and epigenetic mechanisms in muscle fibers during development and in muscle-wasting diseases.
Collapse
|
|
3 |
13 |
14
|
Soleimani VD, Nguyen D, Ramachandran P, Palidwor GA, Porter CJ, Yin H, Perkins TJ, Rudnicki MA. Cis-regulatory determinants of MyoD function. Nucleic Acids Res 2019; 46:7221-7235. [PMID: 30016497 PMCID: PMC6101602 DOI: 10.1093/nar/gky388] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 04/30/2018] [Indexed: 01/06/2023] Open
Abstract
Muscle-specific transcription factor MyoD orchestrates the myogenic gene expression program by binding to short DNA motifs called E-boxes within myogenic cis-regulatory elements (CREs). Genome-wide analyses of MyoD cistrome by chromatin immnunoprecipitation sequencing shows that MyoD-bound CREs contain multiple E-boxes of various sequences. However, how E-box numbers, sequences and their spatial arrangement within CREs collectively regulate the binding affinity and transcriptional activity of MyoD remain largely unknown. Here, by an integrative analysis of MyoD cistrome combined with genome-wide analysis of key regulatory histones and gene expression data we show that the affinity landscape of MyoD is driven by multiple E-boxes, and that the overall binding affinity—and associated nucleosome positioning and epigenetic features of the CREs—crucially depend on the variant sequences and positioning of the E-boxes within the CREs. By comparative genomic analysis of single nucleotide polymorphism (SNPs) across publicly available data from 17 strains of laboratory mice, we show that variant sequences within the MyoD-bound motifs, but not their genome-wide counterparts, are under selection. At last, we show that the quantitative regulatory effect of MyoD binding on the nearby genes can, in part, be predicted by the motif composition of the CREs to which it binds. Taken together, our data suggest that motif numbers, sequences and their spatial arrangement within the myogenic CREs are important determinants of the cis-regulatory code of myogenic CREs.
Collapse
|
Research Support, Non-U.S. Gov't |
6 |
9 |
15
|
Soleimani VD, Baum BR, Johnson DA. Genetic diversity among barley cultivars assessed by sequence-specific amplification polymorphism. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 110:1290-1300. [PMID: 15803291 DOI: 10.1007/s00122-005-1966-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2004] [Accepted: 02/14/2005] [Indexed: 05/24/2023]
Abstract
We analyzed the genetic structure and relationships among barley cultivars (Hordeum vulgare L.) with sequence-specific amplification polymorphisms (S-SAPs). Polymorphisms were identified in 824 individual barley plants representing 103 cultivars (eight plants per cultivar) widely grown in Canada and the United States, using PCR primers designed from the long terminal repeat of the barley retrotransposon BARE-1 and a subset of four selective MseI primers. From the 404 bands scored, 150 were polymorphic either within or between cultivars. Genetic structure assessed with analysis of molecular variance attributed the largest component of variation to the within groups of cultivars (69-86%). Within-cultivar genetic variation was estimated as average gene diversity over loci and ranged from 0 (completely homogenous) to 0.076 (most heterogeneous cultivar). Only 17 out of 103 cultivars (16%) were judged to be homogenous by this criterion. Relationships among cultivars were analyzed by cluster analysis using unweighted pair-groups using arithmetic averages and found groups similar to those determined by agriculturally significant phenotypic traits such as spike morphology (two-rowed or six-rowed), cultivar type (malting or feed), seed characteristic (hull-less or hulled), and growth habit (winter or spring), with minor overlaps. Discriminant analysis of groups determined by these phenotypic traits fully supported the different groups with minor overlaps between the malting/feed. S-SAP markers generated from retrotransposons such as BARE-1 are invaluable tools for the study of genetic diversity in organisms with a narrow genetic base such as barley. In this study, S-SAP analysis revealed significant amounts of cryptic variation in closely related cultivars including somaclonal variation, which could not be inferred by the pedigree analysis.
Collapse
|
Comparative Study |
20 |
8 |
16
|
Sahinyan K, Lazure F, Blackburn DM, Soleimani VD. Decline of regenerative potential of old muscle stem cells: contribution to muscle aging. FEBS J 2023; 290:1267-1289. [PMID: 35029021 DOI: 10.1111/febs.16352] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 12/23/2021] [Accepted: 01/11/2022] [Indexed: 01/01/2023]
Abstract
Muscle stem cells (MuSCs) are required for life-long muscle regeneration. In general, aging has been linked to a decline in the numbers and the regenerative potential of MuSCs. Muscle regeneration depends on the proper functioning of MuSCs, which is itself dependent on intricate interactions with its niche components. Aging is associated with both cell-intrinsic and niche-mediated changes, which can be the result of transcriptional, posttranscriptional, or posttranslational alterations in MuSCs or in the components of their niche. The interplay between cell intrinsic alterations in MuSCs and changes in the stem cell niche environment during aging and its impact on the number and the function of MuSCs is an important emerging area of research. In this review, we discuss whether the decline in the regenerative potential of MuSCs with age is the cause or the consequence of aging skeletal muscle. Understanding the effect of aging on MuSCs and the individual components of their niche is critical to develop effective therapeutic approaches to diminish or reverse the age-related defects in muscle regeneration.
Collapse
|
Review |
2 |
3 |
17
|
Sharp C, Soleimani V, Hannuna S, Camplani M, Damen D, Viner J, Mirmehdi M, Dodd J. P83 Remote pulmonary function testing – computer gaming in the respiratory world. Thorax 2015. [DOI: 10.1136/thoraxjnl-2015-207770.220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
|
10 |
2 |
18
|
Rasool D, Soleimani VD, Jahani-Asl A. Isolation of Adult Mouse Neural Stem Cells and Assessment of Self-Renewal by ELDA. Methods Mol Biol 2022; 2515:343-354. [PMID: 35776362 DOI: 10.1007/978-1-0716-2409-8_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The generation of new neurons in the adult brain throughout life is integral to brain plasticity and repair. Adult neural stem cells (aNSCs), present in the subventricular zone (SVZ) of the lateral ventricle wall and the subgranular zone (SGZ) of the hippocampal dentate gyrus, divide symmetrically or asymmetrically to maintain the stem cell pool or become committed progenitors and differentiate into various cell lineages. Depletion or dysregulation of aNSCs impairs proper brain connectivity and function and can contribute to several brain diseases including cognitive and neurodegenerative disorders and brain cancer. In this chapter, we present our optimized method to obtain and maintain reproducible neurosphere cultures from the adult mouse brain followed by evaluation of self-renewal using the extreme limiting dilution assay (ELDA) software. We use this assay routinely on aNSCs obtained from patient mouse models to generate log fraction plots and provide confidence intervals for all limiting dilution assay (LDA) data. At the same time, given the low number of NSCs required for the completion of the ELDA experiment, it is feasible to employ this approach to conduct high-content compound screening for therapeutic interventions aimed at enhancing the stem cell pool or combating a cohort of genetic and epigenetic disorders.
Collapse
|
|
3 |
1 |
19
|
Blackburn DM, Lazure F, Soleimani VD. SMART approaches for genome-wide analyses of skeletal muscle stem and niche cells. Crit Rev Biochem Mol Biol 2021; 56:284-300. [PMID: 33823731 DOI: 10.1080/10409238.2021.1908950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Muscle stem cells (MuSCs) also called satellite cells are the building blocks of skeletal muscle, the largest tissue in the human body which is formed primarily of myofibers. While MuSCs are the principal cells that directly contribute to the formation of the muscle fibers, their ability to do so depends on critical interactions with a vast array of nonmyogenic cells within their niche environment. Therefore, understanding the nature of communication between MuSCs and their niche is of key importance to understand how the skeletal muscle is maintained and regenerated after injury. MuSCs are rare and therefore difficult to study in vivo within the context of their niche environment. The advent of single-cell technologies, such as switching mechanism at 5' end of the RNA template (SMART) and tagmentation based technologies using hyperactive transposase, afford the unprecedented opportunity to perform whole transcriptome and epigenome studies on rare cells within their niche environment. In this review, we will delve into how single-cell technologies can be applied to the study of MuSCs and muscle-resident niche cells and the impact this can have on our understanding of MuSC biology and skeletal muscle regeneration.
Collapse
|
Journal Article |
4 |
0 |
20
|
Sharanek A, Raco L, Soleimani VD, Jahani-Asl A. In situ detection of protein-protein interaction by proximity ligation assay in patient derived brain tumor stem cells. STAR Protoc 2022; 3:101554. [PMID: 35880130 PMCID: PMC9307678 DOI: 10.1016/j.xpro.2022.101554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Improper or aberrant protein-protein interactions can lead to severe human diseases including cancer. Here, we describe an adapted proximity ligation assay (PLA) protocol for the assessment of galectin-1-HOXA5 interaction in brain tumor stem cells (BTSCs). We detail the steps for culturing and preparation of BTSCs followed by PLA and detection of protein interactions in situ using fluorescent microscopy. This PLA protocol is optimized specifically for BTSCs and includes key controls for effective result analysis. For complete details on the use and execution of this protocol, please refer to Sharanek et al. (2021).
Proximity ligation assay to detect protein-protein interaction in BTSCs Optimized plating conditions for BTSC preparation using minute starting material Inclusion of appropriate controls for the PLA to ensure specificity and precision Alternative reagents and buffers to allow user to adapt the protocol to their needs Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
Collapse
|
|
3 |
|
21
|
Scimè A, Soleimani VD, Bentzinger CF, Gillespie MA, Le Grand F, Grenier G, Bevilacqua L, Harper ME, Rudnicki MA. Oxidative status of muscle is determined by p107 regulation of PGC-1a. J Gen Physiol 2010. [DOI: 10.1085/jgp1364oia3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
|
15 |
|
22
|
Burban A, Sharanek A, Hernandez-Corchado A, Najafabadi HS, Soleimani VD, Jahani-Asl A. Targeting glioblastoma with a brain-penetrant drug that impairs brain tumor stem cells via NLE1-Notch1 complex. Stem Cell Reports 2024; 19:1534-1547. [PMID: 39423824 PMCID: PMC11589194 DOI: 10.1016/j.stemcr.2024.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 09/23/2024] [Accepted: 09/23/2024] [Indexed: 10/21/2024] Open
Abstract
Brain tumor stem cells (BTSCs) are a population of self-renewing malignant stem cells that play an important role in glioblastoma tumor hierarchy and contribute to tumor growth, therapeutic resistance, and tumor relapse. Thus, targeting of BTSCs within the bulk of tumors represents a crucial therapeutic strategy. Here, we report that edaravone is a potent drug that impairs BTSCs in glioblastoma. We show that edaravone inhibits the self-renewal and growth of BTSCs harboring a diverse range of oncogenic mutations without affecting non-oncogenic neural stem cells. Global gene expression analysis revealed that edaravone significantly alters BTSC transcriptome and attenuates the expression of a large panel of genes involved in cell cycle progression, stemness, and DNA repair mechanisms. Mechanistically, we discovered that edaravone directly targets Notchless homolog 1 (NLE1) and impairs Notch signaling pathway, alters the expression of stem cell markers, and sensitizes BTSC response to ionizing radiation (IR)-induced cell death. Importantly, we show that edaravone treatment in preclinical models delays glioblastoma tumorigenesis, sensitizes their response to IR, and prolongs the lifespan of animals. Our data suggest that repurposing of edaravone is a promising therapeutic strategy for patients with glioblastoma.
Collapse
|
research-article |
1 |
|
23
|
Soleimani V, Sudak L. Adaptive bone remodeling using orthotropic Cosserat elasticity. Comput Biol Med 2025; 190:110058. [PMID: 40184944 DOI: 10.1016/j.compbiomed.2025.110058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2025] [Revised: 03/09/2025] [Accepted: 03/19/2025] [Indexed: 04/07/2025]
Abstract
The mechanical properties of bone are essential for supporting movement and protecting vital organs. Computational modeling is a key method for studying these properties. While some models address the anisotropic adaptive remodeling of bone, they often rely on classical elasticity theory, which inadequately describes materials with complex microstructures like bone. This study introduces a novel approach by incorporating the Cosserat elasticity theory into the adaptive remodeling framework, overcoming the limitations of classical elasticity. By modeling a proximal femur bone segment as an orthotropic material, we explore how Cosserat elasticity influences bone mechanics. The study also considers the adaptive behavior of the Cosserat parameters in relation to the stiffness modulus, Poisson's ratio, and the internal length scale. Our results indicate that Cosserat elasticity predicts bone behavior with a maximum displacement deviation of 36.33%, showing lower displacements compared to classical elasticity models, particularly at higher internal length scales. Furthermore, the Cosserat model shows a similar but lower average density distribution in the proximal femur, aligning well with existing literature, and more noticeable in localized stress areas. The study extends its analysis to a finite element model of a proximal femur specimen and concludes that the application of the Cosserat theory of elasticity in the context of adaptive bone remodeling yields more accurate results compared to classical elasticity. These findings suggest that the Cosserat theory offers a more realistic approach to bone modeling, particularly for materials where deformation is significantly influenced by microstructure. This advancement has important implications for biomechanics and materials science.
Collapse
|
|
1 |
|
24
|
Sahinyan K, Blackburn DM, Soleimani VD. ATAC-Seq of a Single Myofiber from Mus musculus. Bio Protoc 2022; 12:e4452. [PMID: 35990589 PMCID: PMC9362843 DOI: 10.21769/bioprotoc.4452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/05/2022] [Accepted: 04/28/2022] [Indexed: 12/29/2022] Open
Abstract
Chromatin accessibility is a key determinant of gene expression that can be altered under different physiological and disease conditions. Skeletal muscle is made up of myofibers that are highly plastic and adaptive. Therefore, assessing the genome-wide chromatin state of myofibers under various conditions is very important to gain insight into the epigenetic state of myonuclei. The rigid nature of myofibers, as well as the low number of myonuclei that they contain, have rendered genome-wide studies with myofibers challenging. In recent years, ATAC-Seq from whole muscle and single nucleus ATAC-Seq have been performed. However, these techniques cannot distinguish between different fiber and cell types present in the muscle. In addition, due to the limited depth capacity obtained from single nucleus ATAC-Seq, an extensive comparative analysis cannot be performed. Here, we introduce a protocol where we combine the isolation of a single myofiber with OMNI ATAC-Seq. This protocol allows for genome-wide analysis of accessible chromatin regions of a selected single myofiber at a sufficient depth for comparative analysis under various physiological and disease conditions. This protocol can also allow for a specific myofiber to be selected, such as a regenerating myofiber. In the future, this protocol can help identify global changes in chromatin state under various conditions, as well as between different types of myofibers. Graphical abstract.
Collapse
|
methods-article |
3 |
|
25
|
Blackburn DM, Sahinyan K, Hernández-Corchado A, Lazure F, Richard V, Raco L, Perron G, Zahedi RP, Borchers CH, Lepper C, Kawabe H, Jahani-Asl A, Najafabadi HS, Soleimani VD. The E3 ubiquitin ligase Nedd4L preserves skeletal muscle stem cell quiescence by inhibiting their activation. iScience 2024; 27:110241. [PMID: 39015146 PMCID: PMC11250905 DOI: 10.1016/j.isci.2024.110241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/14/2023] [Accepted: 06/07/2024] [Indexed: 07/18/2024] Open
Abstract
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 panomics approach we show that the PAX7/NEDD4L axis acts against muscle stem cell activation in homeostatic skeletal muscle. Our findings suggest 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 doublecortin (DCX), which is exclusively expressed during their in vivo activation. Together, these data establish that the ubiquitin proteasome system, mediated by Nedd4L, is a key contributor to the muscle stem cell quiescent state in adult mice.
Collapse
|
research-article |
1 |
|