Mechanosensitive genomic enhancers potentiate the cellular response to matrix stiffness.
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| Title: | Mechanosensitive genomic enhancers potentiate the cellular response to matrix stiffness. |
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| Authors: | Cosgrove, Brian D. (AUTHOR), Bounds, Lexi R. (AUTHOR), Taylor, Carson Key (AUTHOR), Su, Alan L. (AUTHOR), Rizzo, Anthony J. (AUTHOR), Barrera, Alejandro (AUTHOR), Sun, Tongyu (AUTHOR), Safi, Alexias (AUTHOR), Song, Lingyun (AUTHOR), Whitlow, Thomas (AUTHOR), Tata, Aleksandra (AUTHOR), Iglesias, Nahid (AUTHOR), Diao, Yarui (AUTHOR), Tata, Purushothama Rao (AUTHOR), Hoffman, Brenton D. (AUTHOR), Crawford, Gregory E. (AUTHOR), Gersbach, Charles A. (AUTHOR) |
| Source: | Science. 12/11/2025, Vol. 390 Issue 6778, p1-21. 21p. |
| Subjects: | Epigenetics, Gene expression, Cell communication, Stiffness (Engineering), Gene enhancers, Extracellular matrix |
| Abstract: | Epigenetic control of gene expression and cellular phenotype is influenced by changes in the local microenvironment, yet how mechanical cues precisely influence epigenetic state to regulate transcription remains largely unmapped. In this study, we combined genome-wide epigenome profiling, epigenome editing, and phenotypic and single-cell RNA sequencing CRISPR screening to identify a class of genomic enhancers that responds to the mechanical microenvironment. These "mechanoenhancers" can be preferentially activated on either soft or stiff extracellular matrix contexts and regulate transcription to influence critical cell functions including apoptosis, adhesion, proliferation, and migration. Epigenetic editing of mechanoenhancers reprograms the cellular response to the mechanical microenvironment and modulates the activation of disease-related genes in lung fibroblasts from healthy and fibrotic donors. Epigenetic editing of mechanoenhancers holds potential for precise targeting of mechanically driven diseases. Editor's summary: Cells sense and respond to the stiffness of their surrounding environment, which can influence health or disease states such as fibrosis. Cosgrove et al. investigated how mechanical signals from the extracellular matrix (ECM) regulate gene activity through noncoding regions of DNA called mechanoenhancers. Using advanced genome editing and single-cell screening, the authors discovered that these DNA elements control cell behaviors such as growth, migration, and programmed cell death in response to ECM stiffness. Precise editing of mechanoenhancers can reprogram cell responses and may prevent disease-associated changes, highlighting their potential as therapeutic targets for mechanically driven diseases. —Di Jiang INTRODUCTION: Cellular behaviors are heavily influenced by the mechanical properties of their microenvironments, such as extracellular matrix stiffness and applied external forces. These mechanical stimuli are known to influence fundamental cellular functions such as growth, apoptosis, differentiation, and migration. Moreover, they play a key role in tissue development, regeneration, aging, and mechanically sensitive disease processes such as fibrosis, tumor growth, and atherosclerosis. Despite the role of mechanical inputs in these important functions, the influence of mechanical cues on the epigenome that regulates the downstream changes in gene expression that govern these behaviors remains largely unexplored. RATIONALE: Understanding how and where mechanical cues shape gene expression and genome structure could reveal how cells adapt to different physical environments and provide insights into mechanisms driving diseases such as fibrosis and cancer, where altered tissue stiffness is implicated in disease progression. This study aimed to identify regulatory regions of the noncoding genome that respond to changes in the mechanical environment and influence transcription of nearby genes. We refer to these mechanically sensitive genomic regulatory elements as "mechanoenhancers." Using a combination of genome-wide chromatin accessibility profiling, epigenetic editing, high-throughput CRISPR screening on cell functions including growth and migration, and CRISPR-based epigenetic editing paired with single-cell RNA sequencing (RNA-seq), we investigated how cells sense mechanical cues and convert that information into changes in genome structure, gene expression, and behavior. RESULTS: Human fibroblasts and A549 lung adenocarcinoma cells grown on soft (1 kPa) or stiff (50 kPa) hydrogels showed widespread differences in gene expression and chromatin accessibility by RNA-seq and ATAC-seq (assay for transposase-accessible chromatin with high-throughput sequencing). CRISPR interference (CRISPRi) was used to perturb differentially accessible regions surrounding stiffness-responsive genes such as MYH9, BMF, and FZD2 and identify distal mechanoenhancers that influence gene expression. Functional high-throughput CRISPRi screening was performed to discover ~100 putative regulatory regions that influenced cell growth or migration. CRISPRi screening with single-cell RNA-seq identified 201 functional connections of these mechanoenhancers to their gene targets, including CTGF, CYR61, NF2, RFLNB, RANGAP1, SKP2, and others. Epigenetic editing of mechanoenhancers with CRISPRi in cells cultured on stiff substrates, including activated human donor–derived fibroblasts from healthy and idiopathic pulmonary fibrosis lung tissue, resulted in gene expression patterns similar to those observed on soft substrates. Epigenetic modulation of these mechanoenhancers also resulted in functional changes in mechanosensing, migration, growth, and apoptosis. CONCLUSION: This study identifies mechanoenhancers as key regulators of how cells translate mechanical cues into gene activity and functional behaviors. Epigenetic repression of stiffness-activated mechanoenhancers resulted in marked reductions in target gene expression, even in the continued presence of strong mechanical cues. Epigenetic editing of these enhancers can reprogram the cellular response to material stiffness without disrupting normal gene function, highlighting mechanoenhancers as a promising potential therapeutic target in diseases characterized by abnormal tissue stiffness. Mechanoenhancers control gene expression responses in environments of pathological tissue stiffness.: (Left) Soft tissue matrix representative of the normal physiologic microenvironment leads to moderate gene expression levels. (Middle) Stiff matrix typical of some pathogenic environments can activate distal mechanoenhancers that promote target gene expression. (Right) Epigenetic editing of mechanoenhancers on stiff matrix can block responses to these cues, thereby reverting transcription levels and cell functions to those seen on softer tissue. prom, promoter; RE, regulatory element; Mech Enh, mechanoenhancer. [ABSTRACT FROM AUTHOR] |
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| Database: | Psychology and Behavioral Sciences Collection |
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| Abstract: | Epigenetic control of gene expression and cellular phenotype is influenced by changes in the local microenvironment, yet how mechanical cues precisely influence epigenetic state to regulate transcription remains largely unmapped. In this study, we combined genome-wide epigenome profiling, epigenome editing, and phenotypic and single-cell RNA sequencing CRISPR screening to identify a class of genomic enhancers that responds to the mechanical microenvironment. These "mechanoenhancers" can be preferentially activated on either soft or stiff extracellular matrix contexts and regulate transcription to influence critical cell functions including apoptosis, adhesion, proliferation, and migration. Epigenetic editing of mechanoenhancers reprograms the cellular response to the mechanical microenvironment and modulates the activation of disease-related genes in lung fibroblasts from healthy and fibrotic donors. Epigenetic editing of mechanoenhancers holds potential for precise targeting of mechanically driven diseases. Editor's summary: Cells sense and respond to the stiffness of their surrounding environment, which can influence health or disease states such as fibrosis. Cosgrove et al. investigated how mechanical signals from the extracellular matrix (ECM) regulate gene activity through noncoding regions of DNA called mechanoenhancers. Using advanced genome editing and single-cell screening, the authors discovered that these DNA elements control cell behaviors such as growth, migration, and programmed cell death in response to ECM stiffness. Precise editing of mechanoenhancers can reprogram cell responses and may prevent disease-associated changes, highlighting their potential as therapeutic targets for mechanically driven diseases. —Di Jiang INTRODUCTION: Cellular behaviors are heavily influenced by the mechanical properties of their microenvironments, such as extracellular matrix stiffness and applied external forces. These mechanical stimuli are known to influence fundamental cellular functions such as growth, apoptosis, differentiation, and migration. Moreover, they play a key role in tissue development, regeneration, aging, and mechanically sensitive disease processes such as fibrosis, tumor growth, and atherosclerosis. Despite the role of mechanical inputs in these important functions, the influence of mechanical cues on the epigenome that regulates the downstream changes in gene expression that govern these behaviors remains largely unexplored. RATIONALE: Understanding how and where mechanical cues shape gene expression and genome structure could reveal how cells adapt to different physical environments and provide insights into mechanisms driving diseases such as fibrosis and cancer, where altered tissue stiffness is implicated in disease progression. This study aimed to identify regulatory regions of the noncoding genome that respond to changes in the mechanical environment and influence transcription of nearby genes. We refer to these mechanically sensitive genomic regulatory elements as "mechanoenhancers." Using a combination of genome-wide chromatin accessibility profiling, epigenetic editing, high-throughput CRISPR screening on cell functions including growth and migration, and CRISPR-based epigenetic editing paired with single-cell RNA sequencing (RNA-seq), we investigated how cells sense mechanical cues and convert that information into changes in genome structure, gene expression, and behavior. RESULTS: Human fibroblasts and A549 lung adenocarcinoma cells grown on soft (1 kPa) or stiff (50 kPa) hydrogels showed widespread differences in gene expression and chromatin accessibility by RNA-seq and ATAC-seq (assay for transposase-accessible chromatin with high-throughput sequencing). CRISPR interference (CRISPRi) was used to perturb differentially accessible regions surrounding stiffness-responsive genes such as MYH9, BMF, and FZD2 and identify distal mechanoenhancers that influence gene expression. Functional high-throughput CRISPRi screening was performed to discover ~100 putative regulatory regions that influenced cell growth or migration. CRISPRi screening with single-cell RNA-seq identified 201 functional connections of these mechanoenhancers to their gene targets, including CTGF, CYR61, NF2, RFLNB, RANGAP1, SKP2, and others. Epigenetic editing of mechanoenhancers with CRISPRi in cells cultured on stiff substrates, including activated human donor–derived fibroblasts from healthy and idiopathic pulmonary fibrosis lung tissue, resulted in gene expression patterns similar to those observed on soft substrates. Epigenetic modulation of these mechanoenhancers also resulted in functional changes in mechanosensing, migration, growth, and apoptosis. CONCLUSION: This study identifies mechanoenhancers as key regulators of how cells translate mechanical cues into gene activity and functional behaviors. Epigenetic repression of stiffness-activated mechanoenhancers resulted in marked reductions in target gene expression, even in the continued presence of strong mechanical cues. Epigenetic editing of these enhancers can reprogram the cellular response to material stiffness without disrupting normal gene function, highlighting mechanoenhancers as a promising potential therapeutic target in diseases characterized by abnormal tissue stiffness. Mechanoenhancers control gene expression responses in environments of pathological tissue stiffness.: (Left) Soft tissue matrix representative of the normal physiologic microenvironment leads to moderate gene expression levels. (Middle) Stiff matrix typical of some pathogenic environments can activate distal mechanoenhancers that promote target gene expression. (Right) Epigenetic editing of mechanoenhancers on stiff matrix can block responses to these cues, thereby reverting transcription levels and cell functions to those seen on softer tissue. prom, promoter; RE, regulatory element; Mech Enh, mechanoenhancer. [ABSTRACT FROM AUTHOR] |
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| ISSN: | 00368075 |
| DOI: | 10.1126/science.adl1988 |
