Biology subjects

Yamazaki, M.

Publications and source records attributed to Yamazaki, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Comprehensive functional mapping of accessory chromosomes identifies a dominant virulence-regulator paralog in tomato wilt pathogen

Accessory chromosomes (ACs) serve as flexible genomic compartments that facilitate rapid adaptive evolution in eukaryotic microbes. In the tomato wilt pathogen Fusarium oxysporum f. sp. lycopersici, ACs are essential for virulence and host specificity; however, their structural complexity and functional redundancy have hindered a systematic characterization of their distinct roles. Here, we established a CRISPR/Cas9-based chromosomal dissection platform to generate a comprehensive functional map of pathogenicity determinants within ACs. Using this platform, we successfully generated a library of 36 large deletion mutants across the approximately 10 Mb putative AC region, enabling a chromosome-scale functional characterization of these compartments. A systematic screen of this library identified seven discrete AC segments that are indispensable for full virulence toward tomato. High-resolution chromosomal dissection of one virulence-associated segment through iterative subdivision and targeted gene disruption revealed that FTF1a-1, a single member of the Fusarium transcription factor 1 (FTF1) family that originated from the duplication of core-chromosomal virulence gene FTF2 into the AC region, functions as a dominant regulator of virulence. Given that the FTF1a-3 paralog contributes only marginally to virulence and the deletion of other paralogs does not markedly affect disease development, our findings demonstrate a functional hierarchy within the duplicated FTF1 gene family. These results imply that neofunctionalization of virulence genes within plastic fungal genomes promotes hyper-virulence and drives host-specific adaptation in F. oxysporum.

microbiology↗

bioRxiv2026

Transcriptome-based genome-wide analysis reveals hybridization dynamics and genetic structure of Japanese giant salamanders

AbstractsThe Japanese giant salamander (Andrias japonicus), an apex predator and a Special Natural Monument in Japan, is threatened by hybridization with introduced Chinese giant salamanders (Andrias davidianus). This hybridization has caused genetic introgression and expansion of hybrid populations, posing a serious conservation risk. Because morphological identification of hybrids is occasionally unreliable and current genetic methods rely on limited markers, a genome-wide approach is required. However, the extremely large genome ([~]50 Gb) of giant salamanders has hindered whole-genome analyses. In this study, we conducted transcriptome-based analyses of Japanese giant salamanders, Chinese giant salamanders, and their hybrids, generating RNA-seq data from 34 individuals. A total of over 419,000 SNP candidates were identified, from which 4,457 high-confidence SNPs in highly expressed genes were selected for analysis. Population structure analyses for Nabari colony revealed that hybrid individuals form two major groups, corresponding to different degrees of genetic contribution from Japanese and Chinese lineages. Most hybrids were inferred to be F2 or backcross individuals, while F1 hybrids were rare. Mitochondrial analysis indicated that all hybrids possessed Japanese-type mitochondrial genome, suggesting male-mediated introgression from Chinese salamanders. Differential expression analysis revealed enhanced stress-response pathways in hybrids and stronger antiviral responses in Japanese individuals. Using the axolotl genome as a reference, we constructed a virtual chromosomal map, identifying large haplotype blocks and supporting recent hybridization with limited recombination. This study provides a genome-wide framework for understanding hybridization dynamics and supports future conservation and evolutionary studies.

ecology↗

bioRxiv2026

Radicular and periodontal structural defects underlie refractory oral pathology in the adult Hyp mouse model of X-linked hypophosphatemia

ObjectiveX-linked Hypophosphatemia is associated with dental complications, including spontaneous endodontic infections (abscesses) in non-carious teeth and severe periodontal loss. Previous studies have mainly focused on dentin Hypomineralization; however, the structural basis underlying periodontal tissue failure remains unclear. We aimed to investigate histoanatomical abnormalities in the dentin and periodontium of Hyp mice to clarify structural consequences of Phex deficiency in adult molars. MethodsWe performed detailed histological and scanning electron microscopy analyses on the molar regions of untreated adult Hyp mice and wild-type littermates, with particular attention to the structural integrity of the root and periodontal ligament. Additionally, odontoblast process morphology and periodontal attachment abnormalities were evaluated. ResultsHyp molars exhibited marked root abnormalities, including radicular shunt-like defects and disorganized odontoblast processes, particularly in furcation and radicular dentin. Periodontal attachment showed characteristic asymmetry: detachment from the cementum surface was frequently observed, whereas attachment to the alveolar bone surface was relatively preserved. These changes were accompanied by thinning and discontinuity of Sharpeys fibers and increased vascularity in the periodontal ligament. ConclusionsThese findings provide a histoanatomical framework for understanding refractory dental complications in X-linked hypophosphatemia and support the importance of intervention during root development.

pathology↗

bioRxiv2026

Stereoselective methyl-swapping demonstrates target specificity of cognitive enhancer

The Integrated Stress Response (ISR) couples cellular stress sensing to translational control, playing a critical role in the homeostatic regulation of cell health. However, prolonged and unmitigated ISR activation becomes maladaptive and drives the progression of a wide range of pathologies, including cognitive decline. Pharmacological inhibition of the ISR with the small, drug-like molecule ISRIB has proven remarkably effective in reversing cognitive deficits and pathology in animal models, highlighting its potential for therapeutic intervention in humans. We engineered an allele-specific ISRIB analog (mISRIB) that selectively targets a mutant form of eIF2B, the molecular target of ISRIB, without affecting wild-type eIF2B. Notably, mISRIB treatment in mice homozygous for the eIF2B mutant allele enhances synaptic plasticity and long-term memory, confirming the on-target mechanism underlying ISRIBs cognitive benefits. Our results provide a framework for dissecting the ISRs contributions within complex cellular networks, such as those governing brain function, with precise temporal and spatial resolution.

biochemistry↗

bioRxiv2025

Arabidopsis epigenetic factor AS2 attenuates nucleolar stress by camptothecin and establishes leaf polarity by repressing a CDK inhibitor

The Arabidopsis thaliana leaf, exhibiting a symmetrically extended flat morphology, consists of two distinct cellular domains: adaxial and abaxial layers. The ASYMMETRIC LEAVES2 (AS2) gene is essential for specifying the adaxial domain, and its protein forms nucleolar structures, termed AS2 bodies, at ribosomal-DNA loci. Numerous nucleolus-related genes have been reported to be cooperatively involved in leaf adaxialization together with AS2. However, the molecular relationships between AS2 and these genes remain unclear. To identify chemical modulators of AS2 function, we screened a chemical library containing natural products and identified eight molecules, including camptothecin, that induced filamentous leaves in the as2 mutant. Camptothecin is an inhibitor of topoisomerase I, which is required for transcription of ribosomal-RNA genes, and induces nucleolar stress. Treatment with 10-hydroxy-camptothecin increased KIP-RELATED-PROTEIN5/INHIBITOR-OF-CYCLIN-DEPENDENT-KINASE3 (KRP5/ICK3) transcript levels, encoding a CDK inhibitor, and caused notable changes in the number and morphology of AS2 bodies. Given its role in leaf morphogenesis, our findings suggest that AS2 is a key factor in establishing leaf adaxial-abaxial polarity by regulating cell proliferation and protecting against nucleolar stress through coordinated interactions with nucleolar proteins.

developmental biology↗

bioRxiv2025

Lysine lactylation regulates ATF4-mediated stress responses under glucose starvation in canine hemangiosarcoma

Hemangiosarcoma (HSA) is a malignant endothelial tumor that occurs frequently in dogs but is rare in other species including humans. Due to its aggressive behavior and limited therapeutic options, patient prognosis is generally poor. Tumor cells produce excess lactate via anerobic glycolysis, and it regulate gene expressions through histone lactylation in response to cellular metabolic conditions. However, how histone lactylation affects biological behavior under glucose-limited conditions in HSA remains unknown. Here, we established canine HSA cell lines and patient-derived xenograft models and investigated the role of histone lactylation during glucose deprivation. HSA cells exhibited higher global histone lactylation levels than normal endothelial cells. Although glucose restriction reduced global histone lactylation levels, Cleavage Under Targets and Tagmentation (CUT&Tag) analysis revealed enrichment of lactylation peaks at transcription-start sites (TSSs) of ATF4-regulated stress-response, asparagine biosynthesis and immune-related genes. TSSs of stress-response genes were co-occupied with RNA polymerase II phosphorylated at serine 5 and showed increased gene expressions, suggesting that lactylation at TSSs activated transcription under glucose-deprived conditions. [U-13C]glutamine tracing indicated that HSA cells synthesized asparagine from glutamine when glucose was scarce. Asparagine supplementation modestly activated cell proliferation. In HSA patient tissues, H3K18la levels were heterogeneous, and M2-like macrophages preferentially infiltrated tumor regions showing low histone lactylation levels. Consistently, glucose-starved HSA cells attracted macrophages and induced M2-like polarization in vitro. These findings demonstrate that lysine lactylation, possibly histone lactylation, persists even under glucose-deprived conditions and regulate transcription that supports tumor cell survival and fosters a pro-tumor microenvironment. One Sentence SummaryLysine lactylation is enriched at TSSs of stress-response genes under glucose starvation and associated with their transcription in canine hemangiosarcoma.

cancer biology↗

bioRxiv2024

Antibiotics that Kill Gram-negative Bacteria by Restructuring the Outer Membrane Protein BamA

The essential outer membrane protein insertase BamA has recently emerged as a valid target for killing Gram-negative bacteria. Bamabactins, competitive inhibitors targeting the lateral gate of BamA, disrupt the substrate folding process, compromise the outer membrane integrity, and lead to bacterial cell death. Despite their promise, the full pharmacological potential of bamabactins remains underexploited. We applied phylogenetic genome mining and synthetic biology to identify xenorceptides which selectively kill Enterobacteriaceae. Mode of action studies show that xenorceptide A2 integrates itself into BamA as an additional {beta}-strand between {beta}1 and {beta}16 at the lateral gate, inducing a conformation of BamA that has not been observed before. Biological evaluation of xenorceptide A2 shows promising activity in vitro and in vivo, and limited resistance which differentiates it from other bamabactin antibiotics. Our data show that the chemical diversity of bamabactins is far greater than previously recognized and thus an attractive source for antibiotic discovery.

microbiology↗

bioRxiv2024

Extensive intrachromosomal duplications in a virulence-associated fungal accessory chromosome

Filamentous fungi have evolved compartmentalized genomes consisting of conserved core regions and dynamic accessory regions, which aid the adaptation to changing environments including the interaction with host organisms. In the Fusarium oxysporum species complex, accessory regions play an important role during infection and it has been reported that these regions undergo extensive duplications, however, it is currently unknown how such duplications shape accessory regions. Moreover, the function of accessory regions apart from encoding virulence effectors is not completely understood. Here we determined the karyotype of F. oxysporum Tropical Race 4 (TR4), which causes the ongoing pandemic of Fusarium wilt of banana (FWB). We show that the single accessory chromosome of TR4 isolate II5 has undergone extensive intrachromosomal duplications, resulting in triplication of the chromosome size compared to other closely related TR4 strains. By obtaining mutant strains that have lost the accessory chromosome, we demonstrate that this chromosome is dispensable for vegetative growth but is required for full virulence on banana. Lastly, we found that the loss of chromosome 12 co-occurs with structural rearrangements of core chromosomes, which are generally co-linear between members of the F. oxysporum species complex. Together, our results provide new insights into the chromosome dynamics of the banana infecting TR4 lineage of the F. oxysporum species complex. SignificanceFusarium oxysporum is a major fungal plant pathogen that causes vascular wilt disease on a wide variety of agronomically important crops. A current epidemic of Fusarium wilt of banana (FWB), caused by tropical race 4 (TR4), poses a major threat to global banana production and threatens food security in tropical and subtropical regions where banana is an important staple crop. Controlling TR4 requires a better understanding of the molecular mechanisms underlying pathogenicity, including the evolution of pathogenicity-related accessory regions. Here we demonstrate that intrachromosomal duplications are a key mechanism of accessory chromosome evolution in the F. oxysporum species complex. We identified a single accessory chromosome and show that TR4 mutants that lost this accessory chromosome display significantly reduced virulence on banana plants. Our results provide insight into the evolution of accessory chromosomes in the F. oxysporum species complex, underscore their importance in pathogenicity, and provide new clues for the development of resistant banana plants.

microbiology↗

bioRxiv2022

Genome-wide association study highlights escape from aphids by delayed growth in Arabidopsis thaliana

Field studies have shown that plant phenological and architectural traits often explain substantial variation in herbivory. Although plant genes involved in physical and chemical defense are well studied, less is known about the genetic basis underlying effects of plant growth traits on herbivory. Here, we conducted a genome-wide association study (GWAS) of aphid abundance in a field population of Arabidopsis thaliana. This field GWAS detected a significant peak on the third chromosome of A. thaliana. Out of candidate genes near this significant genomic region, a mutant of a ribosomal gene (AT3G13882) exhibited slower growth and later flowering than a wild type under laboratory conditions. A no-choice assay with the turnip aphid, Lipaphis erysimi, found that aphids were unable to successfully establish on the mutant. These findings suggest the potential role of growth-related genes in altering herbivore abundance.

ecology↗

bioRxiv2022

ROR1 plays a critical role in pancreatic tumor-initiating cells with a partial EMT signature.

Tumor-initiating cells are the major drivers of chemoresistance and relapse, making them attractive targets for cancer therapy. However, the identity of tumor- initiating cells in human pancreatic ductal adenocarcinoma (PDAC) and the key molecules underlying their traits remain poorly understood. Here, we show that a partial epithelial-mesenchymal transition (EMT)-like subpopulation marked by high expression of receptor tyrosine kinase-like orphan receptor 1 (ROR1) is the origin of heterogeneous tumor cells in PDAC. We demonstrate that ROR1 depletion suppresses tumor growth, recurrence after chemotherapy, and metastasis. Mechanistically, ROR1 induces the expression of AURKB by activating E2F to enhance PDAC proliferation. Furthermore, epigenomic analyses reveal that ROR1 is transcriptionally dependent on YAP/BRD4 binding at the enhancer region, and targeting this pathway reduces ROR1 expression and prevents PDAC growth. Collectively, our findings reveal a critical role of ROR1high cells as tumor-initiating cells and the functional importance of ROR1 in PDAC progression, thereby highlighting its therapeutic targetability. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=192 HEIGHT=200 SRC="FIGDIR/small/499868v2_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@167bf72org.highwire.dtl.DTLVardef@49df52org.highwire.dtl.DTLVardef@1e480a3org.highwire.dtl.DTLVardef@b987bf_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2022

Reproducible and sensitive micro-tissue RNA-sequencing from formalin-fixed paraffin-embedded tissue for spatial gene expression analysis

Spatial transcriptome analysis of formalin-fixed paraffin-embedded (FFPE) tissues using RNA-sequencing (RNA-seq) provides interactive information on morphology and gene expression, which is useful for clinical applications. However, despite the advantages of long-term storage at room temperature, FFPE tissues may be severely damaged by methylene crosslinking and provide less gene information than fresh-frozen tissues. In this study, we proposed a sensitive FFPE micro-tissue RNA-seq method that combines the punching of tissue sections (diameter: 100 m) and the direct construction of RNA-seq libraries. We evaluated a method using mouse liver tissues at 2 years after fixation and embedding and detected approximately 7,000 genes in micro-punched tissue-spots (thickness: 10 m), similar to that detected with purified total RNA (2.5 ng) equivalent to the several dozen cells in the spot. We applied this method to clinical FFPE specimens of lung cancer that had been fixed and embedded 6 years prior, and found that it was possible to determine characteristic gene expression in the microenvironment containing tumor and non-tumor cells of different morphologies. This result indicates that spatial gene expression analysis of the tumor microenvironment is feasible using FFPE tissue sections stored for extensive periods in medical facilities.

molecular biology↗

bioRxiv2021

The UV RESISTANCE LOCUS 8-Mediated UV-B Response Is Required Alongside CRYPTOCHROME1 For Plant Survival Under Sunlight In The Field

As sessile organisms, plants are subjected to fluctuating sunlight including potentially detrimental ultraviolet-B radiation (UV-B). In Arabidopsis thaliana, experiments under controlled conditions have shown that UV RESISTANCE LOCUS 8 (UVR8) controls photomorphogenic responses for acclimation and tolerance to UV-B; however, its long-term impacts on plant performance remain poorly understood in naturally fluctuating environments. Here we quantified the survival and reproduction of different Arabidopsis mutant genotypes in diverse field and laboratory conditions. We found that uvr8 mutants produced more fruits than wild type in growth chambers with artificial low UV-B conditions but not in natural field conditions. Importantly, independent double mutants of UVR8 and the blue-light photoreceptor gene CRYPTOCHROME 1 (CRY1) in two genetic backgrounds showed a drastic reduction in fitness in the field. UV-B attenuation experiments in field conditions and supplemental UV-B in growth chambers demonstrated that UV-B caused the conditional cry1 uvr8 lethality phenotype. RNA sequencing in different conditions revealed a large number of genes with statistical interaction of UVR8 and CRY1 mutations in the presence of UV-B in the field. Among them, Gene Ontology analysis identified enrichment of categories related to UV-B response, oxidative stress, photoprotection and DNA damage repair. Our study demonstrates the functional importance of the UVR8-mediated response across life stages in natura, which is partially redundant with CRY1, and provides an integral picture of gene expression associated with plant environmental responses under diverse environmental conditions.

plant biology↗

bioRxiv2021

Laboratory analysis of glucose, fructose, and sucrose contents in Japanese common beverages for the exact assessment of beverage-derived sugar intake

BackgroundThe adverse health effects of sugar-sweetened beverage consumption have been studied worldwide. There are several reports on actual sugar contents in sugar-sweetened beverages. However, there is no recent report on actual sugar contents in Japanese sugar-sweetened beverages. Therefore, we attempted to analyze glucose, fructose, and sucrose contents in Japanese common beverages. MethodsGlucose, fructose, and sucrose contents in 49 beverages including 8 energy drinks, 11 sodas, 4 fruit juices, 7 probiotic drinks, 4 sports drinks, 5 coffee drinks, 6 green tea drinks, and 4 tea drinks were determined using the enzymatic methods. ResultsTow zero calorie drinks, 2 sugarless coffee drinks, and 6 green tea drinks contained no sugar. Three coffee drinks contained only sucrose. The orders of median glucose, fructose, and sucrose contents in categorized beverages containing sugars were as follows: for glucose, fruit juice > energy drink [≥] soda >> probiotic drink > black tea drink > sports drink; for fructose, probiotic drink [≥] energy drink > fruit juice > soda >> sports drink > black tea drink; and for sucrose, black tea drink > energy drink [≥] probiotic drink > fruit juice > soda > coffee drink >> sports drink. The rate of total fructose content in total sugar content in 38 sugar-containing beverages was approximately 40-60%. The total sugar content analyzed was not always equivalent to carbohydrate content indicated on the nutrition label. ConclusionsThese results indicate that actual sugar content in Japanese common beverages is necessary for the exact assessment of beverage-derived sugar intake.

biochemistry↗

bioRxiv2020

Association between the extent of DNA methylation at the CpG sites of HIF3A and parameters of obesity in the general Japanese population

Obesity is a major public health problem worldwide owing to the substantial increase in risk of metabolic diseases. Hypoxia-inducible factors (HIFs) regulate transcriptional responses to hypoxic stress. DNA methylation in the CpG sites of intron 1 of HIF3A is associated with body mass index in the whole blood and adipose tissue. This study investigates the correlation between DNA methylation of HIF3A and parameters of obesity, including thickness of visceral (VAT) and subcutaneous adipose tissues, in the general Japanese population. Participants (220 men and 253 women) who underwent medical examination were enrolled in this cross-sectional study. We used pyrosequencing to quantify DNA methylation (CpG sites of cg16672562, cg22891070, and cg27146050) in HIF3A. DNA methylation of HIF3A was only different in women. Multiple regression analysis showed that DNA methylation level at cg27146050 was associated with thickness of VAT in women. DNA methylation level at cg27146050 also correlated with body mass index and percentage of body fat in women after excluding smokers and non-smokers who quit smoking with the last 5 years. DNA methylation in the CpG site (cg27146050) of HIF3A correlated with parameters of obesity in Japanese women.

biochemistry↗

bioRxiv2020

Neurexins play a crucial role in cerebellar granule cell survival by organizing autocrine machinery for neurotrophins

Neurexins (NRXNs) are among the key presynaptic cell adhesion molecules that regulate synapse function and formation via trans-synaptic interaction with postsynaptic ligands. Here, we generated cerebellar granule cell (CGC)-specific Nrxn triple-knockout (TKO) mice to allow the deletion of all NRXNs. Unexpectedly, most CGCs died in these mice. The requirement of NRNXs for cell survival was reproduced in cultured CGCs. We showed that the axons of cultured Nrxn TKO CGCs that were not in contact with the postsynaptic structure had defects in the formation of presynaptic protein cluster and action potential-induced Ca2+ influx. Additionally, these cells were impaired in the secretion from axons of depolarization-induced fluorescence-tagged brain-derived neurotrophic factor (BDNF), and the cell-survival defect was rescued by the application of BDNF. Our results suggest that CGC survival is maintained by autocrine neurotrophic factors, and that NRXNs organize the presynaptic protein clusters and the autocrine neurotrophic factor secretory machinery independent of contact with postsynaptic ligands.

neuroscience↗

bioRxiv2020

Reward-associated configural cues elicit theta oscillations of rat retrosplenial neurons phase-locked to LFP theta cycle

Previous behavioral studies implicated the retrosplenial cortex (RSC) in stimulus-stimulus associations, and also in retrieval of remote associative memory based on EEG theta oscillations. To investigate the neural mechanisms underlying these processes, RSC neurons and local field potentials (LFPs) were simultaneously recorded from well-trained rats performing a cue-reward association task. In the task, simultaneous presentation of two multimodal conditioned stimuli (configural CSs) predicted a reward outcome opposite to that associated with individual presentation of each elemental CS. Here, we show neurophysiological evidence that the RSC is involved in stimulus-stimulus association where configural CSs are discriminated from each elementary CS that is a constituent of the configural CSs, and that memory retrieval of rewarding CSs is associated with theta oscillation of RSC neurons during CS presentation, which is phase-locked to LFP theta cycles.

neuroscience↗

bioRxiv2020

Gene Deletion Studies Reveal A Critical Role For Prostamide/Prostaglandin F2α Synthase In Prostamide F2α Formation

Prostamide/prostaglandin F synthase (PM/PGFS) is an enzyme with very narrow substrate specificity and is dedicated to the biosynthesis of prostamide and prostaglandin F2. The importance of this enzyme, relative to the aldoketoreductase (AKR) series, in providing functional tissue prostamide F2 levels was determined by creating a line of PM/PGFS gene deleted mice. Deletion of the gene encoding PM/PGFS (fam213b) was accomplished by a two exon disruption. Prostamide F2 levels in WT and PM/PGFS KO mice were determined by LC/MS/MS. Intraocular pressure was measured by tonometry and outflow facility was measured by the iPerfusion method in enucleated mouse eyes. Deletion of fam213b had no observed effect on behavior, appetite, or fertility. Intraocular pressure was significantly elevated by approximately 4 mmHg in PM/PGFS KO mice compared to littermate WT mice. No effect on pressure dependent outflow facility occurred, which is consistent with the typically reported prostanoid effect of increasing outflow through the unconventional pathway. The elevation of intraocular pressure caused by deletion of the gene encoding the PM/PGFS enzyme likely results from a diversion of the endoperoxide precursor pathway to provide increased levels of those prostanoids that raise intraocular pressure, namely prostaglandin D2 (PGD2), thromboxane A2 (TxA2). It follows that PM/PGFS may serve an important regulatory role in the eye by providing PGF2 and prostamide F2 to constrain the influence of those prostanoids that raise intraocular pressure.

pharmacology and toxicology↗

bioRxiv2019

Elasticity and Topography-Controlled Collagen Hydrogels Mimicking Native Cellular Milieus

Accumulating evidence demonstrates that the elasticity and topography of a cell culture substrate influence cell behavior, in addition to its chemical composition. However, cellular responses to in vivo extracellular matrix (ECM), a hydrogel of proteins (mainly collagen) with various elasticity and a nanometer-to micrometer-scale topography, remain to be elucidated owing to a lack of substrate that provides such complex cues. This study introduces novel collagen hydrogels that can combine, for the first time, elastic, topographic, and compositional cues that recapitulate native ECM. A simple and reagent-free method based on radiation crosslinking alters ECM-derived collagen solutions into hydrogels with a well-defined and tunable elastic modulus covering the broad range of soft tissues (1-236 kPa) and microtopographies while ensuring intrinsic biological functionality of collagen. These collagen hydrogels enabled investigating cell responses to soft topographic cues such as those encountered in vivo, revealing that topography overrides the elasticity and structurally constrains cell morphology by controlling actin cytoskeleton organization. The collagen hydrogels not only reduce in vivo and in vitro behavioral disparity of cells by mimicking native ECM but also facilitate the design of artificial ECM to control cell function and fate in tissue engineering and regenerative medicine.

bioengineering↗