Biology subjects

Kong, D.

Publications and source records attributed to Kong, D..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Rapamycin Immunomodulation Utilizes Time-Dependent Alterations of Lymph Node Architecture, Leukocyte Trafficking, and Gut Microbiome

Transplant recipients require lifelong, multimodal immunosuppression to prevent rejection by reducing alloreactive immunity. Rapamycin, a mechanistic target of rapamycin (mTOR) inhibitor, is known to modulate adaptive and innate immunity, while the full spectrum of its immunosuppressive mechanisms remains incompletely understood. Given the broad expression of mTOR, we investigated the understudied effects of rapamycin on lymph node (LN) architecture, leukocyte trafficking, and the gut microbiome and metabolism after 3, 7, and 30 days of rapamycin treatment, to characterize the early, intermediate, and late changes. Rapamycin significantly reduced CD4+ T cells, CD8+ T cells, and regulatory T (Treg) cells in peripheral LNs, mesenteric LNs, and the spleen over time. Rapamycin induced early pro-inflammation transition to pro-tolerogenic status, by modulating the LN laminin 4:5 expression ratios through LN stromal cells laminin 5 expression and by adjusting Treg numbers and distribution. Additionally, rapamycin significantly altered gut microbiota composition and metabolic functions, shifting the Bacteroides to Firmicutes ratio and increasing amino acid bioavailability in the gut lumen. These effects were evident by 7 days and became most pronounced by 30 days in naive mice, with notable changes as early as 3 days in allogeneic splenocyte-stimulated mice. These findings reveal a novel mechanism of rapamycins action through time-dependent modulation of LN architecture and gut microbiome, which orchestrates changes in immune cell trafficking, providing a new framework for understanding and optimizing immunosuppressive therapies.

immunology↗

bioRxiv2024

A sensitive red/far-red photoswitch for controllable gene therapy in mouse models of metabolic diseases

Red light optogenetic systems are in high demand for the precise control of gene expression for gene- and cell-based therapies. Here, we report a red/far-red light-inducible photoswitch (REDLIP) system based on the chimeric photosensory protein FnBphP (Fn-REDLIP) or PnBphP (Pn-REDLIP) and their interaction partner LDB3, which enables efficient dynamic regulation of gene expression with a timescale of seconds without exogenous administration of a chromophore in mammals. We used the REDLIP system to establish the REDLIP-mediated CRISPR-dCas9 (REDLIPcas) system, enabling optogenetic activation of endogenous target genes in mammalian cells and mice. The REDLIP system is small enough to support packaging into adeno-associated viruses (AAVs), facilitating its therapeutic application. Demonstrating its capacity to treat metabolic diseases, we show that an AAV-delivered Fn-REDLIP system achieved optogenetic control of insulin expression to effectively lower blood glucose levels in type 1 diabetes model mice and control an anti-obesity therapeutic protein (thymic stromal lymphopoietin, TSLP) to reduce body weight in obesity model mice. REDLIP is a compact and sensitive optogenetic tool for reversible and non-invasive control that can facilitate basic biological and biomedical research.

synthetic biology↗

bioRxiv2024

Efficient degradation of oxidized polyethylene containing ester bonds by cutinase or lipase in aqueous phase

Polyethylene (PE) plastics are extensively utilized across agricultural, industrial, and medical sectors owing to their favorable physicochemical properties. However, their chemical stability and escalating production have resulted in severe waste accumulation and environmental pollution. Conventional disposal methods are plagued by resource inefficiency and secondary pollution. While emerging strategies offer promise, physicochemical methods demand harsh operating conditions, and biological routes remain inefficient. This research presents an integrated "chemical pretreatment-biodegradation-upcycling" system that combines the efficiency of chemical catalysis with the sustainability of biological conversion. Ester bonds were introduced into PE via Baeyer-Villiger oxidation, followed by enzymatic hydrolysis using the cutinase from Thermobifida fusca WSH03-11 (TfCut). Specifically, machine learning-aided optimization of reaction conditions and computational redesign of TfCut enhanced degradation efficiency, yielding a maximum weight loss of approximately 71.19%. The degradation intermediates were bio-converted into poly(3-hydroxybutyrate) (PHB) by the wild-type strain LETBE-HOU, isolated in this study, achieving a concentration of 16.75 mg/L. Multi-omics analysis of LETBE-HOU further revealed the PHB biosynthesis pathway and fatty acid degradation regulation. This work breaks the long-standing reliance on physiochemically-derived degradation intermediates for microbial conversion of PE, establishing a fully circular system that opens new avenues for future research.

biochemistry↗

bioRxiv2024

Novel regulator Fpr2 controls immune homeostasis via CCL4-dependent neutrophils

Polymorphonuclear leukocytes (PMNs) in Fpr2-deficient mice have significantly impaired bactericidal activity, yet the precise mechanism remains elusive. Our research unveiled the cellular heterogeneity of peripheral blood PMNs through single-cell RNA-sequencing (scRNA-seq) and identified two new neutrophil clusters related to bacterial infection, including a sterilization cluster named Neu_CSTA and a regulation cluster named Neu_CCL4. The lack of Fpr2 leads to an immune regulation imbalance of Neu_CCL4 on other clusters in uninfected conditions, resulting in persistent instability of PMNs in peripheral blood, elevated inflammatory factors, and increased NOX2 expression. Furthermore, our findings corroborate that the regulatory function of Neu_CCL4 on PMNs immune balance is closely tied to its high expression of the anti-inflammatory ligand Anxa1. Regulon analysis inferred by scRNA-seq and ChIP-seq data suggested that a specific transcription factor Elf4, could modulate the expression of Anxa1, thereby facilitating its regulatory impact on other clusters. In the infection state, there was a noted increase in intercellular interactions across different clusters, leading to a general improvement in the bactericidal activity of PMNs. In summary, our research revealed distinct functional cellular sub-populations of PMNs, discovered the potential regulatory mechanisms, and elucidated the essential roles of Fpr2 in their ability to resist infection.

immunology↗

bioRxiv2024

TRPC3 suppression ameliorates synaptic dysfunctions and memory deficits in Alzheimer's disease

Transient receptor potential canonical (TRPC) channels are widely expressed in the brain; however, their precise roles in neurodegeneration, such as Alzheimers disease (AD) remain elusive. Bioinformatic analysis of the published single-cell RNA-seq data collected from AD patient cohorts indicates that the Trpc3 gene is uniquely upregulated in excitatory neurons. TRPC3 expression is also upregulated in post-mortem AD brains, and in both acute and chronic mouse models of AD. Functional screening of TRPC3 antagonists resulted in a lead inhibitor JW-65, which completely rescued A{beta}-induced neurotoxicity, impaired synaptic plasticity (e.g., LTP), and learning memory in acute and chronic experimental AD models. In cultured rat hippocampal neurons, we found that treatment with soluble {beta}-amyloid oligomers (A{beta}Os) induces rapid and sustained upregulation of the TRPC3 expression selectively in excitatory neurons. This aberrantly upregulated TRPC3 contributes to A{beta}Os-induced Ca2+ overload through the calcium entry and store-release mechanisms. The neuroprotective action of JW-65 is primarily mediated via restoring A{beta}Os-impaired Ca2+/calmodulin-mediated signaling pathways, including calmodulin kinases CaMKII/IV and calcineurin (CaN). The synaptic protective mechanism via TRPC3 inhibition was further supported by hippocampal RNA-seq data from the symptomatic 5xFAD mice after chronic treatment with JW-65. Overall, these findings not only validate TRPC3 as a novel therapeutic target for treating synaptic dysfunction of AD but most importantly, disclose a distinct role of upregulated TRPC3 in AD pathogenesis in mediating Ca2+ dyshomeostasis.

neuroscience↗

bioRxiv2024

Developmental control of E-cadherin junctions by mechanical contractility in Drosophila embryos

Adherens junctions are very plastic structures that change their composition and structure depending on the state of the epithelial tissue, involving mechanical stress and tissue dynamics. In Drosophila embryos, adherens junctions mature only during gastrulation following their formation a few minutes before during cellularization. Although the developmental maturation is obvious during gastrulation, the factors and conditions controlling it have remained unclear. Here, we assay the levels, distribution pattern, and mobility of E-cadherin during Drosophila gastrulation. Indicating a maturation, we find an increase in total levels at junctions and a drop in the mobile fraction of E-cadherin molecules. Both developmental changes depend on Myo-II contractility. Consistent with stereotypic Myo-II regulation, we find that interference with Rho signaling leads to corresponding changes in E-cadherin levels and mobility, at least in part. Besides Rho signaling, Src42A contributes to junction maturation, as tested by both loss-function and gain-of-function situations. Together, we demonstrate developmental maturation of adherens junctions and identify Rho signaling and Src42A as upstream regulatory pathways.

developmental biology↗

bioRxiv2024

Correlated spontaneous activity sets up multi-sensory integration in the developing higher-order cortex

To perceive and navigate complex sensory environments, animals combine sensory information from multiple modalities in specialized brain circuits. Known as multisensory integration, this process typically depends on the existence of co-aligned topographic connections from several sensory areas to downstream circuits exhibiting multimodal representations. How such topographically co-aligned connectivity necessary for multisensory integration gets set up in early stages of development is still unknown. Inspired by the role of spontaneous activity in refining topographic connectivity between early sensory circuits, here we investigated the potential of such spontaneous activity to also guide the co-alignment of multiple sensory modalities in RL, a higher-order associative cortical area rostro-lateral to V1. Analyzing spontaneous activity simultaneously recorded in primary visual and somatosensory cortex and area RL at different developmental ages before sensory experience, we identify candidate features of this activity to guide the emergence of co-aligned topographic multisensory projections with somatosensory leading the visual projection. We confirm this hypothesis using a computational model of activity-dependent circuit refinement, and show that the correlation of spontaneous activity between the visual and somatosensory primary cortex can establish an optimal fraction of multisensory neurons in RL for stimulus decoding. Our model provides an exciting new computational perspective of the role of spontaneous activity in the emergence of topographically co-aligned multimodal sensory representations in downstream circuits, specialized for the processing of rich sensory environments.

neuroscience↗

bioRxiv2024

Macrophages facilitate interclonal cooperation-induced tumor heterogeneity and malignancy by activating the innate immune signaling

Tumor heterogeneity is a common hallmark of cancer and is considered a major cause of treatment failure and relapse, yet it remains poorly understood how various types of cells communicate within the tumor microenvironment (TME) to regulate tumor progression in vivo. Here we establish a tumor heterogeneity model in Drosophila eye epithelium by mutating the tricellular junction protein M6 in cells surrounding RasV12benign tumors and dissect the in vivo mechanisms underlying interclonal cooperation-induced malignancy by utilizing sophisticated genetic techniques in conjunction with single-cell RNA sequencing (scRNA-seq). Our findings reveal that loss of M6 facilitates the malignant transformation of neighboring RasV12 tumors by activating the Toll signaling, the innate immune response pathway. Notably, inhibiting Toll signaling impedes tumor progression, whereas its activation synergistically promotes RasV12 tumor malignancy by inactivating the Hippo pathway. Mechanistically, RasV12 tumors surrounded by M6 mutant clones lead to increased recruitment of hemocytes, which are the equivalent of macrophages in Drosophila, in a JNK pathway-dependent manner. Consequently, these tumor-associated macrophages secrete the Spatzle (Spz) ligand, which subsequently activates the Toll receptor within the RasV12 tumors, thereby triggering tumorigenesis. In summary, our study elucidates the complex in vivo interactions between genetically distinct oncogenic cells and between tumors and macrophages, shedding light on how macrophages exploit the innate immune signaling within tumors to regulate tumor heterogeneity and promote tumor progression. Significance statementIntratumoral heterogeneity profoundly affects cancer development and treatment in human tumors. The intricate nature of tumor cells and the presence of diverse cell types pose challenges to uncovering in vivo mechanisms responsible for heterogeneity. Our Drosophila tumor heterogeneity model reveals that fruit fly macrophages promotes both tumor heterogeneity and malignancy. Following recruitment by tumor cells, these macrophages secrete the ligand Spz to activate the Toll signaling pathway within tumor cells, which subsequently inactivates the Hippo pathway to drive tumorigenesis. Our study highlights the crucial role of hemocytes as intermediaries in coordinating tumor heterogeneity and facilitating intercellular communication between different cells within the TME.

cancer biology↗

bioRxiv2024

Nuclear receptor E75/NR1D2 drives tumor malignant transformation by integrating Hippo and Notch pathways

Hormone therapy resistance and the ensuing aggressive progression of tumors present a significant clinical challenge. However, the mechanisms underlying the induction of tumor malignancy by hormone inhibition remain poorly understood. Here we show that Drosophila malignant epithelial tumors exhibit a comparable decrease in ecdysone signaling, the primary steroid hormone pathway in Drosophila. Furthermore, we find that ectopic expression of the nuclear receptor E75 partially mimics ecdysone signaling inhibition, specifically promoting the malignant transformation of benign tumors by integrating the Hippo and Notch signaling pathways. Genome-wide DNA binding profiles and biochemistry data reveal that E75 not only physically interacts with the transcription factors of both Hippo and Notch pathways, but also exhibits widespread co-binding to their target genes, thus contributing to tumor malignancy. Moreover, we validate these findings by demonstrating that depletion of NR1D2, the mammalian equivalent of E75, inhibits the activation of Hippo and Notch target genes, impeding glioblastoma progression in vivo. In summary, our study unveils a previously unrecognized mechanism by which hormone inhibition promotes tumor malignant transformation, while providing a conserved mechanistic understanding of how Hippo and Notch pathways are integrated by the oncogene E75/NR1D2 during tumor progression.

cancer biology↗

bioRxiv2024

Developmental maturation of millimeter-scale functional networks across brain areas

Interacting with the environment to process sensory information, generate perceptions, and shape behavior engages neural networks in brain areas with highly varied representations, ranging from unimodal sensory cortices to higher-order association areas. Recent work suggests a much greater degree of commonality across areas, with distributed and modular networks present in both sensory and non-sensory areas during early development. However, it is currently unknown whether this initially common modular structure undergoes an equally common developmental trajectory, or whether such a modular functional organization persists in some areas--such as primary visual cortex--but not others. Here we examine the development of network organization across diverse cortical regions in ferrets of both sexes using in vivo widefield calcium imaging of spontaneous activity. We find that all regions examined, including both primary sensory cortices (visual, auditory, and somatosensory--V1, A1, and S1, respectively) and higher order association areas (prefrontal and posterior parietal cortices) exhibit a largely similar pattern of changes over an approximately 3 week developmental period spanning eye opening and the transition to predominantly externally-driven sensory activity. We find that both a modular functional organization and millimeter-scale correlated networks remain present across all cortical areas examined. These networks weakened over development in most cortical areas, but strengthened in V1. Overall, the conserved maintenance of modular organization across different cortical areas suggests a common pathway of network refinement, and suggests that a modular organization--known to encode functional representations in visual areas--may be similarly engaged in highly diverse brain areas. SignificanceDifferent areas of the mature brain encode vastly different representations of the world. This study shows that a modular functional organization where nearby neurons participate in similar functional networks is shared across different brain areas not only during early development, but also as the brain matures where it remains a shared feature that shapes neural activity. The largely conserved trajectory of developmental changes across brain areas suggests that similar circuit mechanisms may drive this maturation. This implies that the large literature on developing cortical circuits, which is largely focused on sensory areas, may also apply more broadly, and that perturbations during development that impinge on any such shared mechanisms may produce deficits that extend across multiple brain systems.

neuroscience↗

bioRxiv2024

MAIA: An open-source, modular, bioreactor for cities

This work presents the design and fabrication of MAIA, an open-source, modular, low-cost, and portable bioreactor for democratizing the development of synthetic biology based projects for urban settings. The integration of open-source synthetic biology (synbio) tools in a citys infrastructure planning and design is crucial for addressing the great challenges related to urbanization. Synbio tools have great potential to help us complement our current sensing and actuating urban infrastructure. The MAIA reactor controls bacterial growth variables, making it suitable for cell-based experiments while reducing the need for expensive laboratory equipment. Its low-cost and open-source design allow for easy replication and modification, making it accessible to a broader audience. Its portability makes it suitable for use outside of traditional laboratory settings. We qualitatively and quantitatively validated the reactors capability to support cell growth, stimulate gene expression, and act as a creative tool for students and users.

synthetic biology↗

bioRxiv2024

Transcriptome-wide identification of 5-methylcytosine by deaminase and reader protein-assisted sequencing

5-Methylcytosine (m5C) is one of the post-transcriptional modifications in mRNA and is involved in the pathogenesis of various diseases. However, the capacity of existing assays for accurately and comprehensively transcriptome-wide m5C mapping still needs improvement. Here, we develop a detection method named DRAM (deaminase and reader protein assisted RNA methylation analysis), in which deaminases (APOBEC1 and TadA-8e) are fused with m5C reader proteins (ALYREF and YBX1) to identify the m5C sites through deamination events neighboring the methylation sites. This antibody-free and bisulfite-free approach provides transcriptome-wide editing regions which are highly overlapped with the publicly available BS-seq datasets and allows for a more stable and comprehensive identification of the m5C loci. In addition, DRAM system even supports ultra-low input RNA (10ng). We anticipate that the DRAM system could pave the way for uncovering further biological functions of m5C modifications.

biochemistry↗

bioRxiv2024

Astrocytic metabolic control of orexinergic activity in the lateral hypothalamus regulates sleep and wake architecture

Neuronal activity undergoes significant changes during vigilance states, accompanied by an accommodation of energy demands. While the astrocyte-neuron lactate shuttle has shown that lactate is the primary energy substrate for sustaining neuronal activity in multiple brain regions, its role in regulating sleep/wake architecture is not fully understood. We manipulated the cell-specific expression of monocarboxylate transporters (MCTs), the major lactate transporters, to examine the involvement of astrocytic lactate supply in maintaining consolidated wakefulness. Our results demonstrate that reduced expression of MCT4 in astrocytes disrupts lactate supply to orexin neurons in the lateral hypothalamus (LH), impairing wakefulness stability. We also show that MCT2-mediated lactate uptake is necessary for maintaining tonic firing of orexinergic neurons and stabilizing wakefulness. Our findings provide both in vivo and in vitro evidence supporting the critical role of astrocyte-to-orexinergic neuron lactate shuttle in regulating proper sleep/wake stability-- a crucial step for maintaining physiological functions and overall well-being.

neuroscience↗

bioRxiv2024

The structure and diversity of the bacterial community in the overlying water of the Yangzong Lake in Yunnan

Bacteria are critical components of lake ecosystems, and understanding the characteristics of bacterial community structure and diversity indices is of significant importance for the analysis and management of lake ecology. In this study, overlying water samples were collected from Yangzong Lake in May, June, and July 2021. High-throughput sequencing and statistical analysis were employed to investigate the relationships between physicochemical factors, bacterial community structure, and diversity in the overlying water of Yangzong Lake. The results showed significant differences in oxidation-reduction potential among the sampling points. The order of oxidation-reduction potential was as follows: Yangzong DAHE > Yangzong Lake South > Yangzong Lake Middle > Yangzong Lake North, while other physicochemical factors exhibited minor differences. The number of OTUs and bacterial alpha diversity index in the overlying water of Yangzong Lake Middle were higher than those in Yangzong Lake North, Yangzong Lake South, and Yangzong DAHE. The dominant bacterial phyla in the overlying water were Actinobacteriota, Bacteroidota, and Proteobacteria. Actinobacteriota had the highest relative abundance of 34.63% in Yangzong Lake North, while Bacteroidota had the highest relative abundance of 33.79% in Yangzong Lake South, and Proteobacteria had the highest relative abundance of 27.29% in Yangzong Lake Middle. The dominant genera were hgcI_clade, CL500-29_marine_group, and Flavobacterium. Among them, hgcI_clade had the highest relative abundance of 37.56% in Yangzong Lake North, CL500-29_marine_group had the highest relative abundance of 35.22% in Yangzong Lake South, and Flavobacterium had the highest relative abundance of 42.02% in Yangzong Lake Middle. Correlation analysis revealed significant correlations between Campilobacterota at the phylum level and dissolved oxygen (DO) and total phosphorus (TP). At the genus level, Flavobacterium, Limnohabitans, and Pseudarcicella showed significant correlations with DO and TP.

microbiology↗

bioRxiv2024

One signal activated TIL enable potent anti-tumor activity across diverse solid tumor types

Adoptive T cell therapy (ACT) is a promising therapeutic option that enhances the anti-cancer immune response to recognize and eliminate tumor burden. Recently, ACT modalities with autologous tumor-infiltrating lymphocytes (TILs) have shown robust anti-tumor efficacy in solid tumors. However, this therapeutic strategys application remains suboptimal in stability and faces critical challenges, primarily due to the lack of costimulatory signals. Here, we unveil a novel engineering strategy one-signal-activated TIL (OSAT), which integrates CD3{zeta} with secondary signaling domains, to bypass the classical dual-signal requirement for T cell activation. We demonstrate that OSAT molecules 2 (CD3{zeta}-CD28, M2) and 7 (CD3{zeta}-CD137-CD28, M7) mediate efficient mono-signal activation, and recapitulate both the activation signatures and functional markers of mock T cells stimulated with dual signals. Notably, OSAT exhibited enhanced cytotoxicity and in vivo anti-tumor activity across syngeneic tumor models, especially when combined with PD-1 blockade therapy. Mechanistically, OSAT can be fully activated by first signal stimulation, leading to upregulation of activation and metabolic reprogramming genes, production of IL-2/IFN-{gamma}/TNF-, initiation of cytotoxicity, and enhanced TIL antitumor efficacy. These findings unveil integrating CD3{zeta} with secondary signaling domains as a higher efficacy modification for TILs with therapeutic potential for clinical cancer immunotherapy.

immunology↗

bioRxiv2024

Genetic Modulation of Protein Expression in Rat Brain

Genetic variations in protein expression are implicated in a broad spectrum of common diseases and complex traits. However, the fundamental genetic architecture and variation of protein expression have received comparatively less attention than either mRNA or classical phenotypes. In this study, we systematically quantified proteins in the brains of a large family of rats using tandem mass tag (TMT)-based quantitative mass-spectrometry (MS) technology. We identified and quantified a comprehensive proteome of 8,119 proteins from Spontaneously Hypertensive (SHR/Olalpcv), Brown Norway with polydactyly-luxate (BN-Lx/Cub), and 29 of their fully inbred HXB/BXH progeny. Differential expression (DE) analysis identified 597 proteins with significant differences in expression between the parental strains (fold change > 2 and FDR < 0.01). We characterized 95 variant peptides by proteogenomics approach and discovered 464 proteins linked to strong cis-acting quantitative trait loci (pQTLs, FDR < 0.05). We also explored the linkage of pQTLs with behavioral phenotypes in rats and examined the sex-specific pQTLs to reveal both distinct and shared cis-pQTLs between sexes. Furthermore, by creating a novel view of the rat pangenome, we improved the ability to pinpoint candidate genes underlying pQTL. Finally, we explored the connection between the pQTLs in rat and human disorders, underscoring the translational potential of our findings. Collectively, this work demonstrates the value of large and systematic proteo-genetic datasets in understanding protein modulation in the brain and its functional linkage to complex central nervous system (CNS) traits.

genetics↗

bioRxiv2023

Structure of scavenger receptor SCARF1 and its interaction with lipoproteins

SCARF1 (Scavenger receptor class F member 1, SREC-1 or SR-F1) is a type I transmembrane protein that recognizes multiple endogenous and exogenous ligands such as modified low-density lipoproteins (LDL) and is important for maintaining homeostasis and immunity. But the structural information and the mechanisms of ligand recognition of SCARF1 are largely unavailable. Here we solve the crystal structures of the N-terminal fragments of human SCARF1, which show that SCARF1 forms homodimers and its epidermal growth factor (EGF)-like domains adopt a long-curved conformation. Then we examine the interactions of SCARF1 with lipoproteins and are able to identify a region on SCARF1 for recognizing modified LDLs. The mutagenesis data show that the positively charged residues in the region are crucial for the interaction of SCARF1 with modified LDLs, which is confirmed by making chimeric molecules of SCARF1 and SCARF2. In addition, teichoic acids, a cell wall polymer expressed on the surface of gram-positive bacteria, are able to inhibit the interactions of modified LDLs with SCARF1, suggesting the ligand binding sites of SCARF1 might be shared for some of its scavenging targets. Overall, these results provide mechanistic insights into SCARF1 and its interactions with the ligands, which are important for understanding its physiological roles in homeostasis and the related diseases.

biophysics↗

bioRxiv2023

Engineering Material Properties of Transcription Factor Condensates to Control Gene Expression in Mammalian Cells and Mice

Phase separation of biomolecules into condensates is a key mechanism in the spatiotemporal organization of biochemical processes in cells. However, the impact of the material properties of biomolecular condensates on important processes, such as the control of gene expression, remains largely elusive. Here, we systematically tune the material properties of optogenetically induced transcription factor condensates and probe their impact on the activation of target promoters. We demonstrate that transcription factors in rather liquid condensates correlate with increased gene expression levels, whereas stiffer transcription factor condensates correlate with the opposite effect, a reduced activation of gene expression. We demonstrate the broad nature of these findings in mammalian cells and mice, as well as by using different synthetic and natural transcription factors. We observe these effects for both transgenic and cell-endogenous promoters. Our findings provide a novel materials-based layer in the control of gene expression, which opens novel opportunities in optogenetic engineering and synthetic biology.

synthetic biology↗