scholarly journals CRISPR Therapeutics: New Emerging Developments and Clinical Applications

2021 ◽  
Vol 11 (5) ◽  
pp. 193-195
Author(s):  
Kaiser Jay Aziz-Andersen

CRISPR gene editing is a genetic engineering technique applied in clinical applications in which the genomes of living organisms may be modified. It is based on the principles of the CRISPR-Cas9 antiviral defense system. It is based on delivering the Cas9 nuclease complexed with a synthetic guide RNA into a living organism cell and that organisms’s genome can be “cut” and –“paste” at a desired location, allowing existing genes to be modified for desired outcome (i.e., CRISPR for Precision Medicine). CRISPR gene editing harnesses the natural defense mechanisms of some bacteria to cut human DNA strands. Then the DNA strand either heals itself or injects a new piece of DNA to mend the gap. Studies have been reported in Lung Cancer diagnosis and treatments. CRISPR-based engineering techniques have been developed for T Cells and Stem cells applications (i.e. Gene Corrections in Hematopoietic Stem Cells for the Treatment of Blood and Immune System Diseases). Even though earlier CRISPR methodologies were used for performing simple DNA edits, recent applications include the ability to delete genes or insert genes, and edit regulatory regions in a wide range of cell types. The role of CRISPR in human therapeutics is currently focused on utilizing CRISPR techniques to perform either in vivo editing of human cells–everything from the head, eye all the way to neurons and liver cells--or performing ex vivo therapies. The FDA’s new genomic CRISPR technology based products approval process begins with review and evaluation of preclinical studies in order to establish and characterize the proposed product’s safety profile. New genomic products must be shown to be safe and effective for the FDA approval process. The sponsor of the new genomic product must show that the product is safe and effective in human subjects.1

Author(s):  
Fatima Aerts-Kaya

: In contrast to their almost unlimited potential for expansion in vivo and despite years of dedicated research and optimization of expansion protocols, the expansion of Hematopoietic Stem Cells (HSCs) in vitro remains remarkably limited. Increased understanding of the mechanisms that are involved in maintenance, expansion and differentiation of HSCs will enable the development of better protocols for expansion of HSCs. This will allow procurement of HSCs with long-term engraftment potential and a better understanding of the effects of the external influences in and on the hematopoietic niche that may affect HSC function. During collection and culture of HSCs, the cells are exposed to suboptimal conditions that may induce different levels of stress and ultimately affect their self-renewal, differentiation and long-term engraftment potential. Some of these stress factors include normoxia, oxidative stress, extra-physiologic oxygen shock/stress (EPHOSS), endoplasmic reticulum (ER) stress, replicative stress, and stress related to DNA damage. Coping with these stress factors may help reduce the negative effects of cell culture on HSC potential, provide a better understanding of the true impact of certain treatments in the absence of confounding stress factors. This may facilitate the development of better ex vivo expansion protocols of HSCs with long-term engraftment potential without induction of stem cell exhaustion by cellular senescence or loss of cell viability. This review summarizes some of available strategies that may be used to protect HSCs from culture-induced stress conditions.


Blood ◽  
2012 ◽  
Vol 119 (1) ◽  
pp. 83-94 ◽  
Author(s):  
Terumasa Umemoto ◽  
Masayuki Yamato ◽  
Jun Ishihara ◽  
Yoshiko Shiratsuchi ◽  
Mika Utsumi ◽  
...  

AbstractThroughout life, one's blood supply depends on sustained division of hematopoietic stem cells (HSCs) for self-renewal and differentiation. Within the bone marrow microenvironment, an adhesion-dependent or -independent niche system regulates HSC function. Here we show that a novel adhesion-dependent mechanism via integrin-β3 signaling contributes to HSC maintenance. Specific ligation of β3-integrin on HSCs using an antibody or extracellular matrix protein prevented loss of long-term repopulating (LTR) activity during ex vivo culture. The actions required activation of αvβ3-integrin “inside-out” signaling, which is dependent on thrombopoietin (TPO), an essential cytokine for activation of dormant HSCs. Subsequent “outside-in” signaling via phosphorylation of Tyr747 in the β3-subunit cytoplasmic domain was indispensable for TPO-dependent, but not stem cell factor-dependent, LTR activity in HSCs in vivo. This was accompanied with enhanced expression of Vps72, Mll1, and Runx1, 3 factors known to be critical for maintaining HSC activity. Thus, our findings demonstrate a mechanistic link between β3-integrin and TPO in HSCs, which may contribute to maintenance of LTR activity in vivo as well as during ex vivo culture.


Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 4147-4147
Author(s):  
Sonja Loges ◽  
Martin Butzal ◽  
Uta Fischer ◽  
Ursula M. Gehling ◽  
Dieter K. Hossfeld ◽  
...  

Abstract The rare CD133+ stem cell population contains both hematopoietic and endothelial progenitors. Successful ex-vivo expansion of this multipotent population would therefore be of great benefit in many clinical settings including stem cell transplantation and gene therapy. We developed a cell culture system containing the recombinant human cytokines vascular endothelial growth factor (VEGF), FLT3 ligand (FLT3L) and stem cell growth factor (SCGF) for ex-vivo expansion of purified human CD133+ stem cells obtained from leukapheresis products from patients pre-treated with G-CSF. FACS analysis, colony assays and NOD-SCID transplantation studies were performed to monitor stem cell and endothelial phenotype in-vitro and in-vivo. Cultivation with VEGF, FLT3L and SCGF induced a mean 2200-fold increase of total cell counts in 5 weeks. FACS analysis revealed persistence of 6–15% CD133+ stem cells indicating proliferation and survival of primitive hematopoietic stem cells. 5–6% of the proliferating cells expressed the endothelial markers CD144 (VE-Cadherin) and von-Willebrand factor (vWF). Ex-vivo expanded stem cells could be differentiated into adherent endothelial cells after withdrawal of SCGF and FLT3L allowing generation of large numbers of endothelial cells. Colony-assays showed an increase of hematopoietic and endothelial colonies after 5 weeks of ex-vivo expansion indicating simultaneous proliferation of hematopoietic and endothelial precursors under the established culture conditions (CFU-E 60-fold, CFU-GEMM 48-fold, CFU-GM 59-fold, CFU-G 99-fold, CFU-M 1356-fold and CFU-EC 1843-fold). To assess in-vivo functionality, hematopoietic stem cells expanded ex-vivo for 7, 14, 21 and 32 days were transplanted into sublethally irradiated NOD-SCID mice. For each expansion period, the mean percentage of anti-human CD45 positive bone marrow cells 3 months post-transplantation was 11, 3, 3 and 1%, respectively. Human CD45+ cells for each set of experiments contained a mean of 15, 26, 8 and 32% T-cells (CD3+), 9, 0, 7 and 21% B-cells (CD19+), 24, 2, 2 and 11% monocytes (CD14+), 21, 3, 1 and 12% granulocytes (CD33+) and 19, 37, 44 and 24% stem cells (CD34+) (d7 (n=5), d14 (n=4), d21 (n=7) and d32 (n=6) respectively). Our experiments showed multilineage engraftment of human stem cells expanded for more than 4 weeks ex-vivo. Therefore our culture system provides a tool to generate large numbers of human stem and endothelial cells for clinical purposes.


Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 779-779
Author(s):  
Maegan L. Capitano ◽  
Nirit Mor-Vaknin ◽  
Maureen Legendre ◽  
Scott Cooper ◽  
David Markovitz ◽  
...  

Abstract DEK is a nuclear DNA-binding protein that has been implicated in the regulation of transcription, chromatin remodeling, and mRNA processing. Endogenous DEK regulates hematopoiesis, as BM from DEK-/- mice manifest increased hematopoietic progenitor cell (HPC) numbers and cycling status and decreased long-term and secondary hematopoietic stem cell (HSC) engrafting capability (Broxmeyer et al., 2012, Stem Cells Dev., 21: 1449; 2013, Stem Cells, 31: 1447). Moreover, recombinant mouse (rm) DEK inhibits HPC colony formation in vitro. We now show that rmDEK is myelosuppressive in vitro in an S-phase specific manner and reversibly decreases numbers (~2 fold) and cycling status of CFU-GM, BFU-E, and CFU-GEMM in vivo, with DEK-/- mice being more sensitive than control mice to this suppression. In contrast, in vivo administration of rmDEK to wild type and DEK-/- mice enhanced numbers of phenotypic LT-HSC. This suggests that DEK may enhance HSC numbers by blocking production of HPCs. We thus assessed effects of DEK on ex vivo expansion of human CD34+ cord blood (CB) and mouse Lin- BM cells stimulated with SCF, Flt3 ligand, and TPO. DEK significantly enhanced ex vivo expansion of rigorously-defined HSC by ~3 fold both on day 4 (~15 fold increase from day 0) and 7 (~29 fold increase from day 0) when compared to cells expanded without DEK. Expanding HSC with DEK also resulted in a decrease in the percentage of apoptotic HSC. Further studies were done to better define how DEK works on HSC and HPC. As extracellular DEK can bind to heparan sulfate proteoglycans (HSPG), become internalized, and then remodel chromatin in non-hematopoietic cells in vitro (Kappes et al., 2011, Genes Dev., 673; Saha et al., 2013, PNAS, 110: 6847), we assessed effects of DEK on the heterochromatin marker H3K9He3 in the nucleus of purified mouse lineage negative, Sca-1 positive, c-Kit positive (LSK) BM cells by imaging flow cytometry. DEK enhanced the presence of H3K9Me3 in the nucleus of DEK-/- LSK cells, indicating that rmDEK can be internalized by LSK cells and mediate heterochromatin formation. We also investigated whether inhibiting DEK's ability to bind to HSPG would block the inhibitory function of DEK in HPC. Blocking the synthesis of, the surface expression of, and the binding capability of HSPG blocked the inhibitory effect of DEK on colony formation. Blocking the ability of DEK to bind to HSPG also blocks the expansion of HSC in ex vivo expansion assays, suggesting that DEK mediates its function in both HSC and HPC by binding to HSPG but with opposing effects. To further evaluate the biological role of rmDEK, we utilized single-stranded anti-DEK aptamers that inactivate its function. These aptamers, but not their control, neutralized the inhibitory effect of rmDEK on HPC colony formation. Moreover, treating BM cells in vitro with truncated rmDEK created by incubating DEK with the enzyme DPP4 (DEK has targeted truncation sites for DPP4) eliminated the inhibitory effects of DEK, suggesting that DEK must be in its full- length form in order to perform its function. Upon finding that DEK has a Glu-Leu-Arg (ELR) motif, similar to that of CXC chemokines such as IL-8, and as DEK is a chemoattractant for mature white blood cells, we hypothesized that DEK may manifest at least some of its actions through CXCR2, the receptor known to bind and mediate the actions of IL-8 and MIP-2. In order to examine if this is indeed the case, we first confirmed expression of CXCR2 on the surface of HSC and HPC and then determined if neutralizing CXCR2 could block DEK's inhibitory function in HPC. BM treated in vitro with rmDEK, rhIL-8, or rmMIP-2 inhibited colony formation; pretreating BM with neutralizing CXCR2 antibodies blocked the inhibitory effect of these proteins. DEK inhibition of CFU-GM colony formation is dependent on Gai-protein-coupled receptor signaling as determined through the use of pertussis toxin, which is a mechanism unique to DEK, as we have previously reported that IL-8 and MIP-1a are insensitive to the inhibitory effects of pertussis toxin. Blocking the ability of DEK to bind to CXCR2 also inhibited the expansion of HSC in an ex vivo expansion assay. This suggests that DEK binds to CXCR2, HSPG or both to mediate its function on HPC and HSC, enhancing HSC but decreasing HPC numbers. Therefore, DEK may be a crucial regulatory determinant of HSC/HPC function and fate decision that is utilized to enhance ex vivo expansion of HSC. Disclosures No relevant conflicts of interest to declare.


2018 ◽  
Vol 2018 ◽  
pp. 1-16 ◽  
Author(s):  
Ross E. B. Fitzsimmons ◽  
Matthew S. Mazurek ◽  
Agnes Soos ◽  
Craig A. Simmons

As a result of over five decades of investigation, mesenchymal stromal/stem cells (MSCs) have emerged as a versatile and frequently utilized cell source in the fields of regenerative medicine and tissue engineering. In this review, we summarize the history of MSC research from the initial discovery of their multipotency to the more recent recognition of their perivascular identity in vivo and their extraordinary capacity for immunomodulation and angiogenic signaling. As well, we discuss long-standing questions regarding their developmental origins and their capacity for differentiation toward a range of cell lineages. We also highlight important considerations and potential risks involved with their isolation, ex vivo expansion, and clinical use. Overall, this review aims to serve as an overview of the breadth of research that has demonstrated the utility of MSCs in a wide range of clinical contexts and continues to unravel the mechanisms by which these cells exert their therapeutic effects.


Blood ◽  
2017 ◽  
Vol 130 (Suppl_1) ◽  
pp. 95-95
Author(s):  
Corey M Hoffman ◽  
Sarah E Latchney ◽  
Mark LaMere ◽  
Jason R Myers ◽  
John M Ashton ◽  
...  

Abstract While hematopoietic stem cells (HSCs)-intrinsic effects of aging have been explored, less is known about how HSC support is altered by the aged bone marrow microenvironment (BMME). To assess the role of the BMME in HSC aging, we compared the BMME in young (6-12 weeks) and aged (20-24 months) male mice and young (<50 years old; YO) and aged (>50 YO) human volunteers. Aged mice had remodeling of the BMME, with expansion of the marrow cavity and vascular volume compared to young mice. BMME constituents were redistributed within two distinct anatomic regions, namely endosteal bone-associated (BA) and marrow-associated (MA) cells. BA cells in aged mice contained fewer phenotypic mesenchymal/osteoblastic progenitors, with reduction in their ability to constitute colony forming units (CFUs). CFU loss was also observed in aged human volunteers. Aged murine MA had significant expansion of dysfunctional mesenchymal stem cells (MSCs) and activated macrophages (MΦ). Increased MΦ were also detected in aged human marrows. Following this in vivo characterization, we developed an ex vivo co-culture system to determine if aged murine BMME cells could impart aging characteristics to young HSCs. Young murine HSCs co-cultured with aged MA cells acquired phenotypic properties of aged HSCs, including increased CD41+ expression. Single cell RNA sequencing of Long Term-HSCs (LT-HSCs) from young and aged mice also identified upregulation of integrin-β3 (CD61) as a novel marker of aged LT-HSCs. Subsequent flow cytometry analysis confirmed the increase in CD61+ expression in vivo in aged HSCs. Importantly, aged MA - but not BA cells - also increased CD61+ expression in young HSCs ex vivo, highlighting the region-specific remodeling of the BMME that occurs with age. We then used a reductionist approach to identify targetable cellular and molecular regulators of the region-specific BMME-induced HSC aging. CD45+ and Ter119+ depletion in aged MA cells did not induce CD41+ expression in young HSCs, suggesting that a critical BMME component responsible for non-cell-autonomous HSC aging is present within the hematopoietic pool. Since marrow MΦ can regulate HSCs, we co-cultured aged MA MΦ with young MA and found that aged MΦ were sufficient to increase CD41+ expression in young HSCs. The addition of aged MΦ also expanded young MSCs, demonstrating that MΦ orchestrate both BMME remodeling and HSC aging. We next aimed to explore mechanisms by which aged MA MΦ impart aging characteristics to HSCs. Transcriptional analysis of murine MA MΦ demonstrated an increase in inflammatory activation in aged mice compared to young mice. This finding was also present in aged human MΦs. Among the inflammatory signals, interleukin-1β (IL-1β) was identified to be necessary and sufficient to mediate the aging effect of aged MA MΦ on young HSCs. Transcriptional analysis also revealed downregulation of phagocytic programs in aged MA MΦ compared to young MA MΦ. Supporting the transcriptional data, aged MA MΦs cultured in vitro demonstrated impaired ability to engulf senescent neutrophils compared to young MA MΦ. Bone marrow MΦ continuously remove large quantities of senescent neutrophils through phagocytosis, a process also known as efferocytosis. Complementing the in vitro findings, in vivo testing demonstrated that young MA MΦ are primarily responsible for engulfing senescent neutrophils and that aged MA MΦ had reduced engulfment of senescent neutrophils. No phagocytic defect was identified in aged BA MΦ, highlighting the regionalization of MΦ function within the BMME that is differentially impacted with age. Consistent with the systemic impact of the efferocytic defect of aged MA MΦ, aged mice had increased levels of circulating senescent neutrophils and. Moreover, neutrophils from aged mice had increased caspase-1 activity, a signal required for IL-1β activation. Together, these data provide evidence that aging differentially remodels two anatomically distinct BMMEs. Regional specialization of marrow MΦ was differentially impacted by aging and induced aging characteristics in HSCs. We propose that impaired removal of senescent neutrophils by aged MA MΦ increases IL-1β production, leading to local inflammation and disrupted BMME and HSC function in aged mice. Strategies aimed at restoring healthy efferocytic activity as well as diminishing IL-1β production or function could therefore reduce the aging effect on HSCs by rejuvenating the BMME. Disclosures Liesveld: Onconova: Honoraria; Seattle Genetics: Honoraria.


Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 722-722
Author(s):  
Tasleem Arif ◽  
Raymond Liang ◽  
Maio Lin ◽  
Svetlana Kalmikova ◽  
Artem Kasianov ◽  
...  

Despite their immense in vivo repopulating capacity, hematopoietic stem cells (HSCs) are largely quiescent at the steady-state. However, mechanisms that regulate HSC quiescence/cycling remain incompletely understood. Using mitochondrial membrane potential (MMP) to dissect the heterogeneity of HSCs (LSKCD150+CD48-), we find that HSCs within 25% lowest MMP (MMP-low) fractions are almost entirely (~95% ±2.65) in G0 as measured by Pyronin Y/Hoechst staining (p<0.05, n=3). In contrast, HSCs within 25% highest MMP (MMP-high HSCs) are in majority in cycling (see abstract 129099). To elucidate mechanisms implicated in the regulation of HSC cycling at the single cell level in quiescent MMP-low versus primed MMP-high HSCs we used single-cell RNA-Seq (scRNA-Seq) analysis. Cycling analysis in silico in each cell by CYCLONE further confirmed that over 80% of MMP-low HSCs are within G0/G1, as compared to less than 40% of MMP-high HSCs that are mostly in the S/G2/M phase. Notably, GO enrichment analysis related to protein degradation through lysosomal- and proteasomal-mediated pathways were significantly enriched in MMP-low HSCs (p=0.002). Strikingly, and in agreement with our scRNA-seq analysis, a greater abundance of lysosomes was observed in MMP-low relative to -high HSCs (p=0.002). Higher expression of lysosomal genes was further confirmed by qRT-PCR in MMP-low relative to -high HSCs. Analysis of lysosomal content by immunofluorescence staining showed that while the lysosomal specific marker LAMP2 was barely detectable in MMP-high HSCs, LAMP2 was readily found in MMP-low HSCs, results further confirmed by additional markers LAMP1 and LysoTracker Green. Lysosomes are, among others, a major component of organelle degradation through autophagy, which is required for the maintenance of HSCs however, whether lysosomes are implicated in regulating HSC beyond autophagy is unknown. To address this we examined the effect of the suppression (and not activation that is required for autophagy) of lysosomal activation on in vitro HSC maintenance. Treatment with concanamycin-A (ConA), a specific inhibitor of lysosomal acidification via inhibition of the vacuolar H+ -adenosine triphosphatase ATPase (v-ATPase) led to 3 fold improved frequency of phenotypically defined HSCs from optimally cultured lineage-negative cells in 24 hours (p<0.05, n=4). This was associated with 4-fold greater retention of the MMP-low HSC fraction (p<0.05, n=4). Cell divisions of single MMP-low and -high GFP+ HSCs treated with ConA or vehicle control was tracked up to 60 hours in culture. Over 70% of control treated MMP-low GFP+ HSCs did not divide during this time, whereas the majority (>85%) of MMP-high GFP+ HSCs divided at least once (p=0.001, n=5). While ConA treatment had only a slight effect on non-dividing MMP-low HSCs in culture, it significantly increased the frequency of non-dividing MMP-high GFP+ HSCs (p=0.007). Priming of MMP-low to -high HSCs was associated with lysosomal recruitment, and activation of mTOR signaling in MMP-high HSCs (p=0.001, n=5). Importantly, ConA-treatment led to the repression of mTOR expression and activity in MMP-high HSCs (p<0.001). In addition, a 48-hours ConA treatment led to enhanced frequency of LTC-ICs recovered in limiting dilution analysis of both MMP-low (p=0.023) and -high (p=0.004) HSCs ex vivo. To further investigate the role of suppression of lysosomal activation in vivo, FACS-purified MMP-low and -high HSCs were treated with vehicle control or ConA ex vivo for 4 days before 50 ConA- or control-treated MMP-low or -high HSCs were mixed with CD45.2 (2x105) competitor cells and injected into lethally irradiated mice (n=7) in a competitive repopulation assay. Reconstitution levels were consistently more robust in ConA-treated populations of MMP-low (p= 0.001) and -high (p=0.001) HSCs after 18 weeks as compared to control. Importantly, HSC-derived lineage output was balanced in its composition up to 18 weeks in recipients of MMP-low HSC regardless of ConA treatment as well as in ConA-treated MMP-high HSCs, while control MMP-high HSC was myeloid-biased. Overall our results, based on HSC mitochondrial heterogeneity, suggest that lysosomal -content and activity participate in the maintenance of HSC quiescence. Based on these findings, we propose a model that stipulates that lysosomal activation primes HSCs (G0⇒G1) while lysosomal suppression maintains HSC quiescence. Disclosures Ghaffari: Rubius Therapeutics: Consultancy.


Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 182-182 ◽  
Author(s):  
D. Wade Clapp

Abstract Fanconi anemia (FA) is characterized by bone marrow aplasia and myeloid leukemia. The identification of FA genes raises the potential of using gene transfer technology to introduce cDNAs into autologous HSCs. Current strategies using Moloney retroviruses require a 2–4 day ex vivo culture of HSC to facilitate stable integration of the transgene. However, ex vivo culture results in a time-dependent increase in apoptosis of Fancc−/− primitive HSC and mice reconstituted with the surviving cells have an increased risk of acquiring myeloid malignancies. Therefore we examined the potential of a recombinant foamy virus construct (MD9-FANCC-EGFP) to transduce murine Fancc −/− HSC in the absence of prestimulation. Forty-80% of progenitors that were in G0 – G1 at the time of transduction were transduced following a single 10–14 hr transduction. Aliquots of MD9-FANCC-EGFP transduced BM cells or cells encoding the EGFP transgene only were transplanted into irradiated recipient mice or recipients treated with IFN-g only. Four-six months following transplantation, recipient BM cells were isolated and clonogenic assays were established in a range of mitomycin c (MMC) concentrations. Fancc−/− progenitors encoding recombinant FANCC were found to have a similar resistance to MMC as wildtype (WT) controls while Fancc−/− progenitors encoding the reporter construct only retained a high sensitivity to MMC. To assess the potential of MD9-FANCC-EGFP to correct stem cell repopulating ability, we next utilized the competitive repopulating assay. The repopulating activity of MD9-FANCC-EGFP-transduced Fancc−/− stem cells was comparable to WT controls 18–24 months following transplantation in primary and secondary recipients. Additionally, while mice reconstituted with Fancc−/− cells transduced with the reporter construct had reduced repopulating ability as compared to the other groups, none of these recipients acquired myeloid malignancies. Collectively, these data provide in vivo evidence that an abbreviated transduction protocol utilizing a foamy-viral based vector allows efficient transduction of Fancc−/− HSC, and diminishes the selection pressure that occurs during ex vivo culture of Fancc−/− HSCs.


2018 ◽  
Vol 115 (36) ◽  
pp. E8368-E8377 ◽  
Author(s):  
Max Darnell ◽  
Alison O’Neil ◽  
Angelo Mao ◽  
Luo Gu ◽  
Lee L. Rubin ◽  
...  

Variations in a multitude of material microenvironmental properties have been observed across tissues in vivo, and these have profound effects on cell phenotype. Phenomenological experiments have suggested that certain of these features of the physical microenvironment, such as stiffness, could sensitize cells to other features; meanwhile, mechanistic studies have detailed a number of biophysical mechanisms for this sensing. However, the broad molecular consequences of these potentially complex and nonlinear interactions bridging from biophysical sensing to phenotype have not been systematically characterized, limiting the overall understanding and rational deployment of these biophysical cues. Here, we explore these interactions by employing a 3D cell culture system that allows for the independent control of culture substrate stiffness, stress relaxation, and adhesion ligand density to systematically explore the transcriptional programs affected by distinct combinations of biophysical parameters using RNA-seq. In mouse mesenchymal stem cells and human cortical neuron progenitors, we find dramatic coupling among these substrate properties, and that the relative contribution of each property to changes in gene expression varies with cell type. Motivated by the bioinformatic analysis, the stiffness of hydrogels encapsulating mouse mesenchymal stem cells was found to regulate the secretion of a wide range of cytokines, and to accordingly influence hematopoietic stem cell differentiation in a Transwell coculture model. These results give insights into how biophysical features are integrated by cells across distinct tissues and offer strategies to synthetic biologists and bioengineers for designing responses to a cell’s biophysical environment.


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