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  1. Article: Oncogenes and cancer associated thrombosis: what can we learn from single cell genomics about risks and mechanisms?

    Tawil, Nadim / Mohammadnia, Abdulshakour / Rak, Janusz

    Frontiers in medicine

    2023  Volume 10, Page(s) 1252417

    Abstract: Single cell analysis of cancer cell transcriptome may shed a completely new light on cancer-associated thrombosis (CAT). CAT causes morbid, and sometimes lethal complications in certain human cancers known to be associated with high risk of venous ... ...

    Abstract Single cell analysis of cancer cell transcriptome may shed a completely new light on cancer-associated thrombosis (CAT). CAT causes morbid, and sometimes lethal complications in certain human cancers known to be associated with high risk of venous thromboembolism (VTE), pulmonary embolism (PE) or arterial thromboembolism (ATE), all of which worsen patients' prognosis. How active cancers drive these processes has long evaded scrutiny. While "unspecific" microenvironmental effects and consequences of patient care (e.g., chemotherapy) have been implicated in pathogenesis of CAT, it has also been suggested that oncogenic pathways driven by either genetic (mutations), or epigenetic (methylation) events may influence the coagulant phenotype of cancer cells and stroma, and thereby modulate the VTE/PE risk. Consequently, the spectrum of driver events and their downstream effector mechanisms may, to some extent, explain the heterogeneity of CAT manifestations between cancer types, molecular subtypes, and individual cases, with thrombosis-promoting, or -protective mutations. Understanding this molecular causation is important if rationally designed countermeasures were to be deployed to mitigate the clinical impact of CAT in individual cancer patients. In this regard, multi-omic analysis of human cancers, especially at a single cell level, has brought a new meaning to concepts of cellular heterogeneity, plasticity, and multicellular complexity of the tumour microenvironment, with profound and still relatively unexplored implications for the pathogenesis of CAT. Indeed, cancers may contain molecularly distinct cellular subpopulations, or dynamic epigenetic states associated with different profiles of coagulant activity. In this article we discuss some of the relevant lessons from the single cell "omics" and how they could unlock new potential mechanisms through which cancer driving oncogenic lesions may modulate CAT, with possible consequences for patient stratification, care, and outcomes.
    Language English
    Publishing date 2023-12-20
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2775999-4
    ISSN 2296-858X
    ISSN 2296-858X
    DOI 10.3389/fmed.2023.1252417
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Unraveling molecular mechanism underlying biomaterial and stem cells interaction during cell fate commitment using high throughput data analysis

    Sharifi, Erfan / Khazaei, Niusha / Kieran, Nicholas W. / Esfahani, Sahel Jahangiri / Mohammadnia, Abdulshakour / Yaqubi, Moein

    Gene. 2022 Feb. 20, v. 812

    2022  

    Abstract: Stem cell differentiation towards various somatic cells and body organs has proven to be an effective technique in the understanding and progression of regenerative medicine. Despite the advances made, concerns regarding the low efficiency of ... ...

    Abstract Stem cell differentiation towards various somatic cells and body organs has proven to be an effective technique in the understanding and progression of regenerative medicine. Despite the advances made, concerns regarding the low efficiency of differentiation and the remaining differences between stem cell products and their in vivo counterparts must be addressed. Biomaterials that mimic endogenous growth conditions represent one recent method used to improve the quality and efficiency of stem cell differentiation, though the mechanisms of this improvement remain to be completely understood. The effectiveness of various biomaterials can be analyzed through a multidisciplinary approach involving bioinformatics and systems biology tools. Here, we aim to use bioinformatics to accomplish two aims: 1) determine the effect of different biomaterials on stem cell growth and differentiation, and 2) understand the effect of cell of origin on the differentiation potential of multipotent stem cells. First, we demonstrate that the dimensionality (2D versus 3D) and the degradability of biomaterials affects the way that the cells are able to grow and differentiate at the transcriptional level. Additionally, according to transcriptional state of the cells, the particular cell of origin is an important factor in determining the response of stem cells to same biomaterial. Our data demonstrates the ability of bioinformatics to understand novel molecular mechanisms and context by which stem cells are most efficiently able to differentiate. These results and strategies can be used to suggest proper combinations of biomaterials and stem cells to achieve high differentiation efficiency and functionality of desired cell types.
    Keywords biocompatible materials ; cell differentiation ; cell growth ; genes ; medicine ; stem cells ; transcription (genetics)
    Language English
    Dates of publication 2022-0220
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 391792-7
    ISSN 1879-0038 ; 0378-1119
    ISSN (online) 1879-0038
    ISSN 0378-1119
    DOI 10.1016/j.gene.2021.146111
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: Age-dependent effects of metformin on human oligodendrocyte lineage cell ensheathment capacity.

    Mohammadnia, Abdulshakour / Cui, Qiao-Ling / Weng, Chao / Yaqubi, Moein / Fernandes, Milton G F / Hall, Jeffery A / Dudley, Roy / Srour, Myriam / Kennedy, Timothy E / Stratton, Jo Anne / Antel, Jack P

    Brain communications

    2024  Volume 6, Issue 2, Page(s) fcae109

    Abstract: Metformin restores the myelination potential of aged rat A2B5+ oligodendrocyte progenitor cells and may enhance recovery in children with post-radiation brain injury. Human late progenitor cells (O4+A2B5+) have a superior capacity to ensheath nanofibres ... ...

    Abstract Metformin restores the myelination potential of aged rat A2B5+ oligodendrocyte progenitor cells and may enhance recovery in children with post-radiation brain injury. Human late progenitor cells (O4+A2B5+) have a superior capacity to ensheath nanofibres compared to mature oligodendrocytes, with cells from paediatric sources exceeding adults. In this study, we assessed the effects of metformin on ensheathment capacity of human adult and paediatric progenitors and mature oligodendrocytes and related differences to transcriptional changes. A2B5+ progenitors and mature cells, derived from surgical tissues by immune-magnetic separation, were assessed for ensheathment capacity in nanofibre plates over 2 weeks. Metformin (10 µM every other day) was added to selected cultures. RNA was extracted from treated and control cultures after 2 days. For all ages, ensheathment by progenitors exceeded mature oligodendrocytes. Metformin enhanced ensheathment by adult donor cells but reduced ensheathment by paediatric cells. Metformin marginally increased cell death in paediatric progenitors. Metformin-induced changes in gene expression are distinct for each cell type. Adult progenitors showed up-regulation of pathways involved in the process of outgrowth and promoting lipid biosynthesis. Paediatric progenitors showed a relatively greater proportion of down- versus up-regulated pathways, these involved cell morphology, development and synaptic transmission. Metformin-induced AMP-activated protein kinase activation in all cell types; AMP-activated protein kinase inhibitor BML-275 reduced functional metformin effects only with adult cells. Our results indicate age and differentiation stage-related differences in human oligodendroglia lineage cells in response to metformin. Clinical trials for demyelinating conditions will indicate how these differences translate
    Language English
    Publishing date 2024-03-28
    Publishing country England
    Document type Journal Article
    ISSN 2632-1297
    ISSN (online) 2632-1297
    DOI 10.1093/braincomms/fcae109
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Unraveling molecular mechanism underlying biomaterial and stem cells interaction during cell fate commitment using high throughput data analysis.

    Sharifi, Erfan / Khazaei, Niusha / Kieran, Nicholas W / Esfahani, Sahel Jahangiri / Mohammadnia, Abdulshakour / Yaqubi, Moein

    Gene

    2021  Volume 812, Page(s) 146111

    Abstract: Stem cell differentiation towards various somatic cells and body organs has proven to be an effective technique in the understanding and progression of regenerative medicine. Despite the advances made, concerns regarding the low efficiency of ... ...

    Abstract Stem cell differentiation towards various somatic cells and body organs has proven to be an effective technique in the understanding and progression of regenerative medicine. Despite the advances made, concerns regarding the low efficiency of differentiation and the remaining differences between stem cell products and their in vivo counterparts must be addressed. Biomaterials that mimic endogenous growth conditions represent one recent method used to improve the quality and efficiency of stem cell differentiation, though the mechanisms of this improvement remain to be completely understood. The effectiveness of various biomaterials can be analyzed through a multidisciplinary approach involving bioinformatics and systems biology tools. Here, we aim to use bioinformatics to accomplish two aims: 1) determine the effect of different biomaterials on stem cell growth and differentiation, and 2) understand the effect of cell of origin on the differentiation potential of multipotent stem cells. First, we demonstrate that the dimensionality (2D versus 3D) and the degradability of biomaterials affects the way that the cells are able to grow and differentiate at the transcriptional level. Additionally, according to transcriptional state of the cells, the particular cell of origin is an important factor in determining the response of stem cells to same biomaterial. Our data demonstrates the ability of bioinformatics to understand novel molecular mechanisms and context by which stem cells are most efficiently able to differentiate. These results and strategies can be used to suggest proper combinations of biomaterials and stem cells to achieve high differentiation efficiency and functionality of desired cell types.
    MeSH term(s) Biocompatible Materials/pharmacology ; Cell Communication ; Cell Differentiation/drug effects ; Cell Proliferation/drug effects ; Gene Expression Profiling/methods ; Gene Expression Regulation/drug effects ; High-Throughput Nucleotide Sequencing ; Humans ; Regenerative Medicine ; Sequence Analysis, RNA ; Stem Cells/chemistry ; Stem Cells/cytology ; Stem Cells/drug effects
    Chemical Substances Biocompatible Materials
    Language English
    Publishing date 2021-12-11
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 391792-7
    ISSN 1879-0038 ; 0378-1119
    ISSN (online) 1879-0038
    ISSN 0378-1119
    DOI 10.1016/j.gene.2021.146111
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Transcription Factors in Regulatory and Protein Subnetworks during Generation of Neural Stem Cells and Neurons from Direct Reprogramming of Non-fibroblastic Cell Sources.

    Omrani, Mohammad Reza / Yaqubi, Moein / Mohammadnia, Abdulshakour

    Neuroscience

    2018  Volume 380, Page(s) 63–77

    Abstract: Direct reprogramming of non-fibroblastic cells to the neuronal cell types including induced neurons (iNs) and induced neural stem cells (iNSCs) has provided an alternative approach for the direct reprogramming of fibroblasts to those cells. However, to ... ...

    Abstract Direct reprogramming of non-fibroblastic cells to the neuronal cell types including induced neurons (iNs) and induced neural stem cells (iNSCs) has provided an alternative approach for the direct reprogramming of fibroblasts to those cells. However, to increase the efficiency of the reprogramming process the underlying mechanisms should be clarified. In the current study, we analyzed the gene expression profiles of five different cellular conversions to understand the most significant molecular mechanisms and transcription factors (TFs) underlying each conversion. For each conversion, we found the list of differentially expressed genes (DEGs) and the list of differentially expressed TFs (DE-TFs) which regulate expression of DEGs. Moreover, we constructed gene regulatory networks based on the TF-binding sites' data and found the most central regulators and the most active part of the networks. Furthermore, protein complexes were identified from constructed protein-protein interaction networks for DE-TFs. Finally, we proposed a list of main regulators for each conversion; for example, in the direct conversion of epithelial-like cells (ECs) to iNSCs, combination of centrality with active modules or protein complex analyses highlighted the role of POU3F2, BACH1, AR, PBX1, SOX2 and NANOG genes in this conversion. To the best of our knowledge, this study is the first one that analyzed the direct conversion of non-fibroblastic cells toward iNs and iNSCs and we believe that the expression manipulation of identified genes may increase efficiency of these processes.
    MeSH term(s) Cellular Reprogramming/genetics ; Datasets as Topic ; Gene Regulatory Networks/genetics ; Humans ; Neural Stem Cells/cytology ; Neurons/cytology ; Transcription Factors
    Chemical Substances Transcription Factors
    Language English
    Publishing date 2018-04-11
    Publishing country United States
    Document type Journal Article
    ZDB-ID 196739-3
    ISSN 1873-7544 ; 0306-4522
    ISSN (online) 1873-7544
    ISSN 0306-4522
    DOI 10.1016/j.neuroscience.2018.03.033
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Regulation of stress granule formation in human oligodendrocytes.

    Pernin, Florian / Cui, Qiao-Ling / Mohammadnia, Abdulshakour / Fernandes, Milton G F / Hall, Jeffery A / Srour, Myriam / Dudley, Roy W R / Zandee, Stephanie E J / Klement, Wendy / Prat, Alexandre / Salapa, Hannah E / Levin, Michael C / Moore, G R Wayne / Kennedy, Timothy E / Vande Velde, Christine / Antel, Jack P

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 1524

    Abstract: Oligodendrocyte (OL) injury and subsequent loss is a pathologic hallmark of multiple sclerosis (MS). Stress granules (SGs) are membrane-less organelles containing mRNAs stalled in translation and considered as participants of the cellular response to ... ...

    Abstract Oligodendrocyte (OL) injury and subsequent loss is a pathologic hallmark of multiple sclerosis (MS). Stress granules (SGs) are membrane-less organelles containing mRNAs stalled in translation and considered as participants of the cellular response to stress. Here we show SGs in OLs in active and inactive areas of MS lesions as well as in normal-appearing white matter. In cultures of primary human adult brain derived OLs, metabolic stress conditions induce transient SG formation in these cells. Combining pro-inflammatory cytokines, which alone do not induce SG formation, with metabolic stress results in persistence of SGs. Unlike sodium arsenite, metabolic stress induced SG formation is not blocked by the integrated stress response inhibitor. Glycolytic inhibition also induces persistent SGs indicating the dependence of SG formation and disassembly on the energetic glycolytic properties of human OLs. We conclude that SG persistence in OLs in MS reflects their response to a combination of metabolic stress and pro-inflammatory conditions.
    MeSH term(s) Humans ; Cytoplasmic Granules/metabolism ; Stress Granules ; Oligodendroglia ; Cytokines/metabolism ; Stress, Physiological ; Multiple Sclerosis/metabolism
    Chemical Substances Cytokines
    Language English
    Publishing date 2024-02-19
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-45746-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Comprehensive transcriptome mining of the direct conversion of mesodermal cells.

    Akbari, Bijan / Wee, Ping / Yaqubi, Moein / Mohammadnia, Abdulshakour

    Scientific reports

    2017  Volume 7, Issue 1, Page(s) 10427

    Abstract: The direct reprogramming of somatic cells is a promising approach for regenerative medicine, especially in the production of mesoderm layer-derived cells. Meta-analysis studies provide precise insight into the undergoing processes and help increase the ... ...

    Abstract The direct reprogramming of somatic cells is a promising approach for regenerative medicine, especially in the production of mesoderm layer-derived cells. Meta-analysis studies provide precise insight into the undergoing processes and help increase the efficiency of reprogramming. Here, using 27 high-throughput expression data sets, we analyzed the direct reprogramming of mesodermal cells in humans and mice. Fibroblast-derived cells showed a common expression pattern of up- and down-regulated genes that were mainly involved in the suppression of the fibroblast-specific gene expression program, and may be used as markers of the initiation of reprogramming. Furthermore, we found a specific gene expression profile for each fibroblast-derived cell studied, and each gene set appeared to play specific functional roles in its cell type, suggesting their use as markers for their mature state. Furthermore, using data from protein-DNA interactions, we identified the main transcription factors (TFs) involved in the conversion process and ranked them based on their importance in their gene regulatory networks. In summary, our meta-analysis approach provides new insights on the direct conversion of mesodermal somatic cells, introduces a list of genes as markers for initiation and maturation, and identifies TFs for which manipulating their expression may increase the efficiency of direct conversion.
    MeSH term(s) Cellular Reprogramming/genetics ; Computational Biology/methods ; Data Mining ; Fibroblasts/cytology ; Fibroblasts/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Humans ; Mesoderm/cytology ; Mesoderm/metabolism ; Molecular Sequence Annotation ; Transcriptome
    Language English
    Publishing date 2017-09-05
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-017-10903-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Concerns on "Dissection of Regulatory Elements During Direct Conversion of Somatic Cells Into Neurons" Paper.

    Yaqubi, Moein / Mohammadnia, Abdulshakour / Wee, Ping

    Journal of cellular biochemistry

    2017  

    Language English
    Publishing date 2017-06-06
    Publishing country United States
    Document type Letter
    ZDB-ID 392402-6
    ISSN 1097-4644 ; 0730-2312
    ISSN (online) 1097-4644
    ISSN 0730-2312
    DOI 10.1002/jcb.26187
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Cellular rejuvenation protects neurons from inflammation mediated cell death.

    Drake, Sienna S / Mohammadnia, Abdulshakour / Heale, Kali / Groh, Adam M R / Hua, Elizabeth M-L / Zaman, Aliyah / Hintermayer, Matthew A / Zandee, Stephanie / Gosselin, David / Stratton, Jo Anne / Sinclair, David A / Fournier, Alyson E

    bioRxiv : the preprint server for biology

    2023  

    Abstract: In multiple sclerosis (MS), the invasion of the central nervous system by peripheral immune cells is followed by the activation of resident microglia and astrocytes. This cascade of events results in demyelination, which triggers neuronal damage and ... ...

    Abstract In multiple sclerosis (MS), the invasion of the central nervous system by peripheral immune cells is followed by the activation of resident microglia and astrocytes. This cascade of events results in demyelination, which triggers neuronal damage and death. The molecular signals in neurons responsible for this damage are not yet fully characterized. In MS, retinal ganglion cell neurons (RGCs) of the central nervous system (CNS) undergo axonal injury and cell death. This phenomenon is mirrored in the experimental autoimmune encephalomyelitis (EAE) mouse model of MS. To understand the molecular landscape, we isolated RGCs from mice subjected to the EAE protocol. RNA-sequencing and ATAC-sequencing analyses were performed. Pathway analysis of the RNA-sequencing data revealed that RGCs displayed a molecular signature, similar to aged neurons, showcasing features of senescence. Single-nucleus RNA-sequencing analysis of neurons from human MS patients revealed a comparable senescence-like phenotype., which was supported by immunostaining RGCs in EAE mice. These changes include alterations to the nuclear envelope, modifications in chromatin marks, and accumulation of DNA damage. Transduction of RGCs with an
    Language English
    Publishing date 2023-10-02
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.09.30.560301
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Common Gene Expression Patterns in the Generation of Induced Neurons From Fibroblasts.

    Mohammadnia, Abdulshakour / Yaqubi, Moein / Wee, Ping

    Journal of cellular biochemistry

    2017  

    Abstract: In the current study, we analyzed ten gene expression data sets including RNA-sequencing and microarray experiment data during the direct reprogramming of mouse and human fibroblasts to induced neurons and found common gene expression pattern across all ... ...

    Abstract In the current study, we analyzed ten gene expression data sets including RNA-sequencing and microarray experiment data during the direct reprogramming of mouse and human fibroblasts to induced neurons and found common gene expression pattern across all data sets for this conversion.
    Language English
    Publishing date 2017-05-03
    Publishing country United States
    Document type Journal Article
    ZDB-ID 392402-6
    ISSN 1097-4644 ; 0730-2312
    ISSN (online) 1097-4644
    ISSN 0730-2312
    DOI 10.1002/jcb.26110
    Database MEDical Literature Analysis and Retrieval System OnLINE

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