The stiffness-sensitive transcriptome of human tendon stromal cells

Matrix stiffness and its effects on tensional homeostasis act as major regulators of cellular states in health and disease. Stiffness-sensing studies are typically performed using cells that have acquired "mechanical memory" through prolonged propagation in rigid mechanical environments, e.g. tissue culture plastic (TCP). This may potentially mask the full extent of the stiffness-driven mechanosensing programs. To address this, we developed a biomaterial system composed of two-dimensional mechano-variant silicone substrates that is permissive to large-scale cell culture expansion processes. We broadly mapped the stiffness-mediated mechano-responses by performing RNA sequencing on human tendon-derived stromal cells. We find that matrix rigidities approximating tendon microscale stiffness range (E. ~35 kPa) distinctly favor programs related to chromatin remodeling and Hippo signaling; whereas more compliant stiffnesses (E. 2 kPa) were enriched in responses related to pluripotency, synapse assembly and angiogenesis. We also find that tendon stromal cells undergo dramatic phenotypic drift on conventional TCP, with near-complete suppression of tendon-related genes and emergence of expression signatures skewed towards fibro-inflammatory and metabolic activation. Strikingly, mechano-variant substrates abrogate fibroblasts activation, with tenogenic stiffnesses inducing a transcriptional program that strongly correlate with established tendon tissue-specific signatures. Computational inference predicted that AKT1 and ERK1/2 are major signaling hubs mediating stiffness-sensing in tendon cells. Together, our findings highlight how the underlying biophysical cues may dictate the transcriptional identity of resident cells, and how matrix mechano-reciprocity regulates diverse sets of previously underappreciated mechanosensitive processes in tendon stromal fibroblasts.

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Alterations of mesenchymal stromal cells in cerebrospinal fluid: insights from transcriptomics and an ALS clinical trial

Stem Cell Research & Therapy ◽

10.1186/s13287-021-02241-9 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Ashley A. Krull ◽

Deborah O. Setter ◽

Tania F. Gendron ◽

Sybil C. L. Hrstka ◽

Michael J. Polzin ◽

...

Keyword(s):

Gene Expression ◽

Cerebrospinal Fluid ◽

Growth Factors ◽

Mesenchymal Stromal Cells ◽

Stromal Cells ◽

Large Scale ◽

Therapeutic Benefit ◽

Protein Levels ◽

Genes Encoding ◽

Intrathecal Space

Abstract Background Mesenchymal stromal cells (MSCs) have been studied with increasing intensity as clinicians and researchers strive to understand the ability of MSCs to modulate disease progression and promote tissue regeneration. As MSCs are used for diverse applications, it is important to appreciate how specific physiological environments may stimulate changes that alter the phenotype of the cells. One need for neuroregenerative applications is to characterize the spectrum of MSC responses to the cerebrospinal fluid (CSF) environment after their injection into the intrathecal space. Mechanistic understanding of cellular biology in response to the CSF environment may predict the ability of MSCs to promote injury repair or provide neuroprotection in neurodegenerative diseases. Methods In this study, we characterized changes in morphology, metabolism, and gene expression occurring in human adipose-derived MSCs cultured in human (hCSF) or artificial CSF (aCSF) as well as examined relevant protein levels in the CSF of subjects treated with MSCs for amyotrophic lateral sclerosis (ALS). Results Our results demonstrated that, under intrathecal-like conditions, MSCs retained their morphology, though they became quiescent. Large-scale transcriptomic analysis of MSCs revealed a distinct gene expression profile for cells cultured in aCSF. The aCSF culture environment induced expression of genes related to angiogenesis and immunomodulation. In addition, MSCs in aCSF expressed genes encoding nutritional growth factors to expression levels at or above those of control cells. Furthermore, we observed a dose-dependent increase in growth factors and immunomodulatory cytokines in CSF from subjects with ALS treated intrathecally with autologous MSCs. Conclusions Overall, our results suggest that MSCs injected into the intrathecal space in ongoing clinical trials remain viable and may provide a therapeutic benefit to patients.

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ENIGMA and Global Neuroscience: A Decade of Large-Scale Studies of the Brain in Health and Disease Across More Than 40 Countries

Biological Psychiatry ◽

10.1016/j.biopsych.2020.02.167 ◽

2020 ◽

Vol 87 (9) ◽

pp. S56 ◽

Cited By ~ 4

Author(s):

Paul Thompson

Keyword(s):

Large Scale ◽

Health And Disease ◽

The Brain

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A Method for Measurement of Drug Sensitivity of Myeloma Cells Co-Cultured with Bone Marrow Stromal Cells

CrossRef Listing of Deleted DOIs ◽

10.1177/1087057113478168 ◽

2013 ◽

Vol 18 (6) ◽

pp. 637-646 ◽

Cited By ~ 18

Author(s):

Kristine Misund ◽

Katarzyna A. Baranowska ◽

Toril Holien ◽

Christoph Rampa ◽

Dionne C. G. Klein ◽

...

Keyword(s):

Bone Marrow ◽

Cell Survival ◽

Stromal Cells ◽

Bone Marrow Stromal Cells ◽

Large Scale ◽

Stromal Cell ◽

Marrow Stromal Cells ◽

Cell Nuclei ◽

Myeloma Cells

The tumor microenvironment can profoundly affect tumor cell survival as well as alter antitumor drug activity. However, conventional anticancer drug screening typically is performed in the absence of stromal cells. Here, we analyzed survival of myeloma cells co-cultured with bone marrow stromal cells (BMSC) using an automated fluorescence microscope platform, ScanR. By staining the cell nuclei with DRAQ5, we could distinguish between BMSC and myeloma cells, based on their staining intensity and nuclear shape. Using the apoptotic marker YO-PRO-1, the effects of drug treatment on the viability of the myeloma cells in the presence of stromal cells could be measured. The method does not require cell staining before incubation with drugs, and less than 5000 cells are required per condition. The method can be used for large-scale screening of anticancer drugs on primary myeloma cells. This study shows the importance of stromal cell support for primary myeloma cell survival in vitro, as half of the cell samples had a marked increase in their viability when cultured in the presence of BMSC. Stromal cell–induced protection against common myeloma drugs is also observed with this method.

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Stromal cells in health and disease

Cytometry Part A ◽

10.1002/cyto.a.23600 ◽

2018 ◽

Vol 93 (9) ◽

pp. 871-875 ◽

Cited By ~ 3

Author(s):

Frank A. Schildberg ◽

Vera S. Donnenberg

Keyword(s):

Stromal Cells ◽

Health And Disease

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A Potential of microRNAs for High-Content Screening

Journal of Nucleic Acids ◽

10.4061/2011/870903 ◽

2011 ◽

Vol 2011 ◽

pp. 1-15 ◽

Cited By ~ 9

Author(s):

Andrius Serva ◽

Christoph Claas ◽

Vytaute Starkuviene

Keyword(s):

Large Scale ◽

Cellular Processes ◽

Comprehensive Knowledge ◽

Functional Models ◽

Rapid Accumulation ◽

Health And Disease ◽

Temporal And Spatial ◽

And Function ◽

Functional Analyses ◽

Immense Potential

In the last years miRNAs have increasingly been recognised as potent posttranscriptional regulators of gene expression. Possibly, miRNAs exert their action on virtually any biological process by simultaneous regulation of numerous genes. The importance of miRNA-based regulation in health and disease has inspired research to investigate diverse aspects of miRNA origin, biogenesis, and function. Despite the recent rapid accumulation of experimental data, and the emergence of functional models, the complexity of miRNA-based regulation is still far from being well understood. In particular, we lack comprehensive knowledge as to which cellular processes are regulated by which miRNAs, and, furthermore, how temporal and spatial interactions of miRNAs to their targets occur. Results from large-scale functional analyses have immense potential to address these questions. In this review, we discuss the latest progress in application of high-content and high-throughput functional analysis for the systematic elucidation of the biological roles of miRNAs.

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Hidden in plain sight: What remains to be discovered in the eukaryotic proteome?

10.1101/469569 ◽

2018 ◽

Author(s):

Valerie Wood ◽

Antonia Lock ◽

Midori A. Harris ◽

Kim Rutherford ◽

Jürg Bähler ◽

...

Keyword(s):

Gene Ontology ◽

Fission Yeast ◽

Genome Sequencing ◽

Large Scale ◽

Biological Process ◽

Blind Spot ◽

Model Organisms ◽

Biological Processes ◽

Health And Disease

AbstractThe first decade of genome sequencing stimulated an explosion in the characterization of unknown proteins. More recently, the pace of functional discovery has slowed, leaving around 20% of the proteins even in well-studied model organisms without informative descriptions of their biological roles. Remarkably, many uncharacterized proteins are conserved from yeasts to human, suggesting that they contribute to fundamental biological processes. To fully understand biological systems in health and disease, we need to account for every part of the system. Unstudied proteins thus represent a collective blind spot that limits the progress of both basic and applied biosciences.We use a simple yet powerful metric based on Gene Ontology (GO) biological process terms to define characterized and uncharacterized proteins for human, budding yeast, and fission yeast. We then identify a set of conserved but unstudied proteins in S. pombe, and classify them based on a combination of orthogonal attributes determined by large-scale experimental and comparative methods. Finally, we explore possible reasons why these proteins remain neglected, and propose courses of action to raise their profile and thereby reap the benefits of completing the catalog of proteins’ biological roles.

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ENIGMA and Global Neuroscience: A Decade of Large-Scale Studies of the Brain in Health and Disease across more than 40 Countries

10.31234/osf.io/qnsh7 ◽

2019 ◽

Cited By ~ 3

Author(s):

Paul Thompson ◽

Neda Jahanshad ◽

Christopher R. K. Ching ◽

Lauren Salminen ◽

Sophia I Thomopoulos ◽

...

Keyword(s):

Large Scale ◽

Meta Analysis ◽

22Q11.2 Deletion Syndrome ◽

Autism Spectrum ◽

Deletion Syndrome ◽

Sex And Gender ◽

Post Traumatic Stress ◽

Global Alliance ◽

Compulsive Disorder ◽

Health And Disease

This review summarizes the last decade of work by the ENIGMA (Enhancing NeuroImaging Genetics through Meta Analysis) Consortium, a global alliance of over 1,400 scientists across 43 countries, studying the human brain in health and disease. Building on large-scale genetic studies that discovered the first robustly replicated genetic loci associated with brain metrics, ENIGMA has diversified into over 50 working groups (WGs), pooling worldwide data and expertise to answer fundamental questions in neuroscience, psychiatry, neurology, and genetics. Most ENIGMA WGs focus on specific psychiatric and neurological conditions, other WGs study normal variation due to sex and gender differences, or development and aging; still other WGs develop methodological pipelines and tools to facilitate harmonized analyses of “big data” (i.e., genetic and epigenetic data, multimodal MRI, and electroencephalography data). These international efforts have yielded the largest neuroimaging studies to date in schizophrenia, bipolar disorder, major depressive disorder, post-traumatic stress disorder, substance use disorders, obsessive-compulsive disorder, attention-deficit/hyperactivity disorder, autism spectrum disorders, epilepsy, and 22q11.2 deletion syndrome. More recent ENIGMA WGs have formed to study anxiety disorders, suicidal thoughts and behavior, sleep and insomnia, eating disorders, irritability, brain injury, antisocial personality and conduct disorder, and dissociative identity disorder. Here, we summarize the first decade of ENIGMA’s activities and ongoing projects, and describe the successes and challenges encountered along the way. We highlight the advantages of collaborative large-scale coordinated data analyses for testing reproducibility and robustness of findings, offering the opportunity to identify brain systems involved in clinical syndromes across diverse samples and associated genetic, environmental, demographic, cognitive and psychosocial factors.

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CrosstalkNet: mining large-scale bipartite co-expression networks to characterize epi-stroma crosstalk

10.1101/102848 ◽

2017 ◽

Author(s):

Venkata Manem ◽

George Adam ◽

Tina Gruosso ◽

Mathieu Gigoux ◽

Nicholas Bertos ◽

...

Keyword(s):

Stromal Cells ◽

Large Scale ◽

Network Visualization ◽

Visualization Tool ◽

Biological Processes ◽

Web Based ◽

Link Type ◽

A Cell ◽

Large Scale Networks ◽

User Friendly

ABSTRACTBackground:Over the last several years, we have witnessed the metamorphosis of network biology from being a mere representation of molecular interactions to models enabling inference of complex biological processes. Networks provide promising tools to elucidate intercellular interactions that contribute to the functioning of key biological pathways in a cell. However, the exploration of these large-scale networks remains a challenge due to their high-dimensionality.Results:CrosstalkNet is a user friendly, web-based network visualization tool to retrieve and mine interactions in large-scale bipartite co-expression networks. In this study, we discuss the use of gene co-expression networks to explore the rewiring of interactions between tumor epithelial and stromal cells. We show how CrosstalkNet can be used to efficiently visualize, mine, and interpret large co-expression networks representing the crosstalk occurring between the tumour and its microenvironment.Conclusion:CrosstalkNet serves as a tool to assist biologists and clinicians in exploring complex, large interaction graphs to obtain insights into the biological processes that govern the tumor epithelial-stromal crosstalk. A comprehensive tutorial along with case studies are provided with the application.Availability:The web-based application is available at the following location: http://epistroma.pmgenomics.ca/app/. The code is open-source and freely available from http://github.com/bhklab/EpiStroma-webapp.Contact:[email protected]

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Reproducible Large-Scale Isolation of Exosomes from Adipose Tissue-Derived Mesenchymal Stem/Stromal Cells and Their Application in Acute Kidney Injury

International Journal of Molecular Sciences ◽

10.3390/ijms21134774 ◽

2020 ◽

Vol 21 (13) ◽

pp. 4774 ◽

Cited By ~ 4

Author(s):

Jun Ho Lee ◽

Dae Hyun Ha ◽

Hyeon-kyu Go ◽

Jinkwon Youn ◽

Hyun-keun Kim ◽

...

Keyword(s):

Acute Kidney Injury ◽

Adipose Tissue ◽

Stromal Cells ◽

Large Scale ◽

Kidney Diseases ◽

Kidney Injury ◽

Preclinical Studies ◽

Scale Production ◽

Positive Effects ◽

Large Scale Production

Acute kidney injury (AKI) is a fatal medical episode caused by sudden kidney damage or failure, leading to the death of patients within a few hours or days. Previous studies demonstrated that exosomes derived from various mesenchymal stem/stromal cells (MSC-exosomes) have positive effects on renal injuries in multiple experimental animal models of kidney diseases including AKI. However, the mass production of exosomes is a challenge not only in preclinical studies with large animals but also for successful clinical applications. In this respect, tangential flow filtration (TFF) is suitable for good manufacturing practice (GMP)-compliant large-scale production of high-quality exosomes. Until now, no studies have been reported on the use of TFF, but rather ultracentrifugation has been almost exclusively used, to isolate exosomes for AKI therapeutic application in preclinical studies. Here, we demonstrated the reproducible large-scale production of exosomes derived from adipose tissue-derived MSC (ASC-exosomes) using TFF and the lifesaving effect of the ASC-exosomes in a lethal model of cisplatin-induced rat AKI. Our results suggest the possibility of large-scale stable production of ASC-exosomes without loss of function and their successful application in life-threatening diseases.

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