Biology subjects

Chen, Y.-C.

Publications and source records attributed to Chen, Y.-C..

At least 19 recordsLinked to original sources

bioRxiv2026

Temporal regulation of a spatial patterning factor in Drosophila neurogenesis

A central question in neurobiology is how the transient programs that pattern neural progenitors are translated into the enormous, stable diversity of neuronal types. Spatial and temporal cues act only briefly, yet each neuron's identity is defined and maintained for life by terminal selector transcription factors (TFs). How a neuron's developmental origin is read out into a particular selector code remains poorly understood. Some current models propose that spatial and temporal origins are inherited independently through separate selectors. We show instead that, in the Drosophila optic lobe, the same selector can be activated by different patterning axes through physically distinct enhancers, even within the same lineage. Visual system homeobox (Vsx1) spatially patterns a central neuroepithelial domain and later acts as a terminal selector in dozens of neuronal types, most originating exclusively from that domain. However, in Dm2 neurons that are produced from every domain, it is regulated not by neuroepithelial Vsx1 but by the neuroblast temporal TF BarH1, through an enhancer distinct from its domain-specific ones. Combining in vivo reporters with sequence-to-accessibility deep-learning models, we identify and disrupt the key binding sites in this enhancer, impairing its Dm2-specific activity. Reciprocally, the temporal TF Homeobrain (Hbn) acts as a terminal selector in the related neuron Mi21 independently of its neuroblast temporal window: its expression in these late-born neurons is instead placed under dorsoventral spatial control. Patterning inputs therefore need not be partitioned across separate selectors but converge combinatorially on the modular enhancers of shared ones, revealing a cis-regulatory logic that re-encodes this limited set of inputs into vast neuronal diversity.

neuroscience↗

bioRxiv2026

Single-locus chromatin memory enables flexible spatial fate specification in the Drosophila visual system

Spatial patterning generates neuronal diversity by compartmentalizing progenitors into domains with distinct molecular identities. However, these patterning cues are often transient in neurogenic domains, raising the question of how spatial information can be preserved and how rigidly it constrains neuronal fates. Here we show that a single-locus chromatin memory in the Drosophila medulla enables spatial identity to be both faithfully executed and flexibly bypassed. Medulla progenitors are partitioned into three spatial domains marked by Vsx1, Optix and Bifid. Domain-resolved single-cell multiome profiling reveals that progenies from different neuroepithelial domains are nearly indistinguishable for both transcriptome and chromatin accessibility, although persistent, domain-specific accessibility is retained only at a single spatial-factor locus, either Vsx1/2 or Bifid. These same factors are absent when neuroepithelial cells are converted to neural stem cells but are re-expressed in postmitotic neurons to execute domain-specific fates. Because this bookmarking is so restricted, specific classes of neurons can skip the domain-specific re-expression program and default to a common ground state, adopting equivalent fates regardless of spatial origin. Other neurons reach the same domain-ignoring state by expressing Vsx1/2 through a program independent of their domain of origin. PRC2-mediated silencing restricts Vsx1 re-expression to its home domain, while temporal identity and Notch signaling in newborn neurons determine which neurons engage or bypass the spatial program. Thus, single-locus chromatin memory preserves spatial information without making it an obligatory determinant of every neuronal fate.

developmental biology↗

bioRxiv2026

An introgressed haplotype decouples phenotype from genome-wide ancestry

Introgression redistributes genetic variation among diverging lineages, shaping evolution-ary trajectories and contributing to phenotypic evolution. Yet how localized introgressed genomic regions persist despite extensive genomic homogenization remains poorly under-stood. Here, we investigate the evolutionary history of the northeastern Iranian great tit (Parus major intermedius), a grey-plumaged member of the great tit complex occurring at the eastern range margin of the green- and yellow-plumaged major lineage, adjacent to the grey-plumaged Central Asian bokharensis lineage, and long regarded as a putative hybrid. We find that P. m. intermedius retains predominantly major-derived genomic ancestry despite its grey plumage, revealing extensive genomic homogenization across the genome. Surprisingly, a single localized introgressed haplotype on chromosome 24 retains bokharensis-derived ancestry, exhibits elevated genomic differentiation relative to the genomic background, and overlaps the carotenoid-processing gene BCO2, a strong candidate underly-ing plumage pigmentation. Our findings provide a genomic explanation for the discordance between phenotype and genome-wide ancestry, demonstrating how localized introgression can preserve genomic regions associated with phenotypic divergence despite extensive genomic homogenization. This system illustrates how individual genomic regions can retain distinct evolutionary histories long after the surrounding genome has largely homogenized.

evolutionary biology↗

bioRxiv2026

Reduced LANCL1-AS1 in old human skeletal muscle diminishes mitochondrial activity, shortens mt-mRNA poly(A) tails, and suppresses myogenesis

Regeneration of skeletal muscle preserves muscle mass and function, which decline with age. Here, we sought to identify long noncoding (lnc)RNAs involved in skeletal muscle myogenesis and potentially relevant to muscle aging. Cross-sectional analysis of skeletal muscle transcriptomes from healthy 22-through 89-year-old individuals revealed lncRNA LANCL1-AS1 among the top declining transcripts. Conversely, LANCL1-AS1 increased robustly during skeletal myogenesis and promoted myogenic differentiation in culture. Affinity pulldown by ChIRP followed by mass spectrometry revealed that LANCL1-AS1 associated with the mitochondrial protein LRPPRC, enhancing the formation of the chaperone complex LRPPRC-SLIRP, which maintains longer poly(A) tails of mitochondrial (mt-)mRNAs and stabilizes mt-mRNAs. Importantly, while myoblasts from old rhesus monkey muscle expressed lower levels of LANCL1-AS1 and mt-mRNAs, and displayed lower mitochondrial activity than young monkey myoblasts, overexpressing LANCL1-AS1 in old myoblasts restored mitochondrial activity and myogenesis. We propose that the age-associated reduction in LANCL1-AS1 contributes to impaired mitochondrial function and reduced myogenic capacity in aging skeletal muscle.

molecular biology↗

bioRxiv2026

Structural and Functional Principles of Hcp-Mediated Antibacterial Toxin Delivery by the Type VI Secretion System

The type VI secretion system (T6SS) is a bacterial contractile nanomachine that translocates toxic effectors into neighboring cells, helping bacteria to survive and compete in polymicrobial environments. The core T6SS structural protein Hcp forms the inner tube and mediates the loading and delivery of diverse effectors. Yet, how Hcp selectively recruits structurally and functionally distinct effectors in the absence of recognizable secretion signals remains poorly understood. Here, using Pseudomonas aeruginosa H1-T6SS as a model, we combined competition-coupled deep mutational scanning with cryo-EM based structural analysis to determine how Hcp accommodates distinct effectors. The resulting mutational landscape distinguishes structurally constrained residues required for Hcp tube assembly from lumen-facing residues specialized for cargo engagement. Near-atomic-resolution structures of Hcp bound to Tse2 and Tse4, together with a high-confidence Hcp-Tse1 model, revealed that while effector-specific contacts exist, Hcp engages different cargos through largely shared, dispersed interfaces characterized by polar-biased and variation-tolerant interactions. Comparative structural analyses further showed that effector-interacting residues are not governed by conserved primary-sequence motifs, but by conserved lumen-facing geometry and permissive physicochemical properties across distantly related bacteria. Together, our findings support a model in which Hcp acts as a selective yet adaptable scaffold that accommodates diverse antibacterial effectors through conserved structural features and flexible interaction surfaces, providing a mechanistic framework for understanding cargo selection by the T6SS and explaining how a conserved secretion nanomachine can evolve to deliver diverse toxic payloads.

microbiology↗

bioRxiv2026

The missing part of the DMSP cycle in coral holobionts: Endozoicomonas exports acetate derived from DMSP degradation

Endozoicomonas, a dominant symbiotic bacterium in coral holobionts, is noted for its ability to degrade dimethylsulfoniopropionate (DMSP) so as to generate acetate. While acetate is a well-known short-chain fatty acid in metabolic cross-feeding relationships, it remains unclear whether acetate derived from bacterial DMSP degradation is available to corals and their other symbionts. In this study, we employed Endozoicomonas ruthgatesiae strain 8E (herein referred as 8E) as a model to examine availability of DMSP-derived acetate for other symbionts. Using gas chromatography-mass spectrometry (GC-MS), we observed a significant increase in acetate excretion in 8E upon exposure to DMSP. Stable isotope labeling further confirmed that this elevated acetate efflux originated directly from DMSP, suggesting a complete cycle of DMSP-derived carbon among coral symbionts. Transcriptomic analysis revealed that DMSP exposure upregulated dddD expression and triggered a systemic reconfiguration of metabolism, characterized by down-regulation of the TCA cycle and the Pta-AckA pathway, with carbon flux redirected to the glyoxylate shunt. These findings suggest that upon exposure to DMSP, metabolism of 8E shifts from biomass production to DMSP catabolism, resulting in acetate efflux. Notably, we found that elevated temperature diminishes DMSP cleavage activity of 8E, indicating thermal sensitivity of this bacterial metabolic activity. ImportanceEndozoicomonas is known for its dominance in coral holobionts and its ability to degrade DMSP, an important compound in the marine sulfur cycle. Acetate is one resulting product in microbial DMSP metabolism and a common cross-feeding molecule. Whether DMSP-derived acetate in coral-associated DMSP-degrading bacteria is employed for cross-feeding stands a critical step in making a complete carbon cycle of DMSP metabolism within coral holobionts. In this study, we employed GC-MS and RNA-sequencing techniques to offer the first evidence of acetate excretion in Endozoicomonas while metabolizing DMSP, as well as its underlying genetic mechanism. Furthermore, we demonstrate reduced genetic response and DMSP-degrading capability under an elevated temperature in Endozoicomonas ruthgatesiae strain 8E, the model bacterium employed in this study. These findings provide the missing puzzle of DMSP metabolism in coral holobionts and suggest a potential role of DMSP in modulating symbiotic interactions within coral holobionts.

microbiology↗

bioRxiv2026

A Lineage-Specific Peptide Suppresses Juvenile Hormone to Drive Reproductive and Longevity Reprogramming in Ants

In ants and other eusocial insects, reproductive division of labor is tightly regulated by juvenile hormone (JH), which suppresses reproduction in most individuals to maintain the worker caste. However, how social cues trigger systemic JH suppression to permit reproductive activation remains unclear. In the ant Harpegnathos saltator, workers respond to queen loss by engaging in sustained ritualistic dueling and transitioning into reproductive, long-lived pseudoqueens (gamergates). This provides a powerful model for investigating the molecular basis of socially induced plasticity. We examined the hemolymph proteome of transitioning ants and identified HCRG1, a lineage-restricted peptide upregulated during dueling, as a circulating factor that physically interacts with Hex70c, a broadly conserved JH-binding Hexamerin. HCRG1 promotes ovarian development by antagonizing JH signaling. Expression of ant HCRG1 in the heterologous solitary model Drosophila also extends lifespan. These findings identify an evolutionarily derived circulating factor that links social sensory perception to systemic JH suppression, enabling coordinated reproductive and longevity transitions in a social insect.

evolutionary biology↗

bioRxiv2026

Multiomic State-Transitions Reveal Post-Treatment Transcriptome Desynchronization in Acute Myeloid Leukemia

Temporal dynamics of the peripheral blood transcriptome are crucial for understanding leukemia evolution and response to therapy because they can reveal how gene expression programs drive abnormal cell states, disease heterogeneity, and treatment resistance. Using a mathematical model of state-transitions, we studied the temporal dynamics of peripheral blood messenger RNA (mRNA) and microRNA (miRNA) transcriptomes in a mouse model of acute myeloid leukemia (AML). In our state-transition model, mRNA and miRNA transcriptomes are represented as a particle undergoing Brownian motion in a two-dimensional multiomic potential landscape. Following chemotherapy, we observed a temporal desynchronization between mRNA and miRNA transcriptomic responses corresponding to an asymmetric shift in the landscape. Specifically, mRNA trajectories responded almost immediately post-treatment, whereas miRNA responses were delayed by approximately two weeks. Clustering analysis identified that the temporal delay is driven by a prominent cluster of miRNAs from the imprinted Dlk1-Dio3 region. Although previously implicated in acute promyelocytic leukemia, lymphomas, and metabolic dysregulation, this provides the first evidence linking the Dlk1-Dio3 locus to AML chemotherapy response and treatment-induced transcriptomic desynchronization. This framework offers an innovative dynamics-based strategy to identify biological drivers of therapeutic response and novel therapeutic targets across hematological malignancies. Key PointsO_LITreatment can induce desynchronization between messenger RNA and microRNA transcriptome dynamics in a murine model of AML C_LIO_LIMicroRNAs from the imprinted Dlk1-Dio3 locus are identified as key contributors to desynchronization and may serve as therapeutic targets C_LI

cancer biology↗

bioRxiv2026

A conserved transcriptomic model defines metabolic resilience and vulnerability in obesity

BackgroundObesity arises from a complex interplay of genetic and environmental factors, with alterations of transcriptional networks that integrate metabolic, immune, and regulatory pathways. Conventional measures such as body mass index (BMI) quantify body size but fail to capture the molecular heterogeneity underlying divergent metabolic outcomes. We therefore sought to construct a gene expression-based transcriptomic representation of obesity, using BMI as a practical training anchor, and to use this framework to delineate transcriptional programs associated with metabolically healthy and pathogenic obesity, with subsequent projection to mouse transcriptomic data for cross-species validation. MethodsTranscriptome data of human visceral adipose tissue (N= 1,298) were used to derive the transcriptomic BMI model, and genes contributing to the model were functionally annotated by gene set enrichment analysis. The human-trained model was subsequently applied to mouse selection lines (N = 18) with divergent obesity phenotypes. In the human cohort, post hoc stratification into metabolically healthy obesity (MHO) and metabolically unhealthy obesity (MUO) groups was performed using a downstream classification framework incorporating observed BMI together with predicted BMI, to assess whether model-derived predicted BMI reflected obesity-related pathophysiologic status. ResultsModel-selected genes were involved in coordinated regulation of lipid metabolism, immune activation, and growth signaling, extending to mitochondrial and translational pathways. Cross-species analyses uncovered conserved metabolic polarization: DU6 mice exhibited lipid-anabolic and inflammatory remodeling, whereas DU6P mice displayed oxidative, mitochondrial, and GH-axis-enriched transcriptional states. In human cohorts, MHO individuals showed upregulation of mitochondrial energetics and protein synthesis, while MUO individuals were characterized by increased autophagy, lipid catabolism, and stress-adaptive signaling on the transcriptional level. Together, these findings define a conserved molecular continuum linking oxidative efficiency to metabolic health and inflammation to metabolic vulnerability. ConclusionsThis integrative transcriptomic framework bridges human and mouse adipose biology to uncover conserved mechanisms underlying obesity phenotypes. By contrasting mitochondrial and translational programs with inflammatory and catabolic pathways, it provides mechanistic insight into metabolic resilience and a foundation for precision approaches to obesity management.

systems biology↗

bioRxiv2026

Mechanical licensing of functional dendritic cell states for enhanced T cell priming

The plasticity of dendritic cell (DC) functional state is a major hurdle in DC therapy, yet how DCs acquire distinct states independent of ontogeny remains poorly understood. Here, we demonstrate that changes in matrix stress relaxation mechanically educate DCs to adopt distinct, persistent functional states even after the removal of mechanical cues. Stem cell-derived DCs cultured in a fast-relaxing environment exhibited enhanced antigen presentation, faster migration, and higher expression of T cell-recruiting chemokines. Slow-relaxing DCs, biased towards pro-inflammatory cytokine secretion, were enriched for gene signatures associated with lipid accumulation and stress response. These mechanical responses were conserved across human and murine DCs. Using ovalbumin (OVA) as the model antigen, fast-relaxing DCs elicited a CD8+-biased response in vitro, with higher antigen-specific CD8+ T cell activation and proliferation. In vivo adoptive cell transfer of mechanically educated DCs demonstrated that the fast-relaxing matrix licensed DCs to induce a potent draining lymph node T cell response with more antigen-specific T cells and higher restimulation potential. We further showed that DCs sensed matrix stress relaxation through PI3K signaling and actin branching, mediated by the concerted signaling of IL-4 and GM-CSF. Together, these findings demonstrate the role of matrix stress relaxation on the functional state of DCs and suggest a novel approach to enhance ex vivo cellular engineering by targeting mechanical signaling. Graphical AbstractStem cell-derived dendritic cells (DCs) generated ex vivo are engineered using biomaterial platform with tunable matrix stress relaxation. Mechanical education of DCs is licensed by cytokine signaling, actin branching, and PI3K signaling. Fast-relaxing DCs exhibit higher antigen presentation and faster migration, which enhances their capacity to prime and activate antigen-specific CD8+ T cells. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/725170v2_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@19c68aaorg.highwire.dtl.DTLVardef@19ba1f0org.highwire.dtl.DTLVardef@a49ea5org.highwire.dtl.DTLVardef@1ab7153_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2026

Layered social competition coordinates reproductive hierarchy formation in ants

Social interactions establish reproductive hierarchies and regulate division of labor in eusocial insect colonies. In the ant Harpegnathos saltator, queen loss induces a subset of workers to transition into reproductive pseudo-queens, known as gamergates, through a ritualized antennal-dueling tournament that can last for more than a month. Gamergate transition is associated with sustained dueling engagement, yet the interaction networks and social dynamics that shape reproductive hierarchy formation remain unclear. Here, we combine long-term automated tracking with behavioral classifiers to systematically quantify social interactions, including antennal dueling and two distinct biting behaviors: aggressive grooming and mandible locking. We find that antennal dueling is organized into two activity states, an engaged state and a disengaged state, and that persistent maintenance of the engaged state, rather than transient entry into it, predicts successful transition to gamergate fate. Early access to abundant food shapes dueling activity and biases ants toward entry into the engaged state. Moreover, engaged-state individuals exhibit a strong assortative preference for dueling with one another and cluster spatially within the colony. We further show that mandible locking precedes transitions out of the engaged state, whereas aggressive grooming reinforces the disengaged state, together consistent with a role in stabilizing worker fate. Our findings reveal how structured social interactions organize reproductive hierarchy formation by regulating stable behavioral states associated with caste fate.

neuroscience↗

bioRxiv2026

Shared roles and team membership are reflected in functional connectome similarity: Neural evidence from real-world volleyball teams

In task-oriented teams, long-term coordination among specialized roles may contribute to shared patterns of cognition and behavior, yet little is known about how such experience is reflected in brain functional organization. Here, we examined whether cross-individual differences in whole-brain functional connectivity were associated with court position and team membership in professional volleyball players. In the resting-state and naturalistic volleyball game-viewing conditions, we analyzed dyadic functional connectivity differences to test whether effects of shared position and team were evident across intrinsic and contextually engaged brain states, controlling for differences in playing time and performance-related statistics. We found that same-position players showed smaller functional connectivity differences. These effects were most prominent and widespread across brain networks during game viewing, whereas at rest they were specific to the somatomotor network. Team membership was also associated with smaller functional connectivity differences during game viewing, although position x team interactions varied across networks after covariate adjustment. A complementary machine learning classifier further showed that shared position could be predicted from intersubject differences in functional connectivity with accuracy exceeding a frequency-based baseline. Together, these findings suggest that shared role-specific and team-based experience may contribute to structured similarity in functional brain organization within a real-world team setting.

neuroscience↗

bioRxiv2026

Endogenous network modeling reveals mechanisms of repair Schwann cell decline and potential recovery targets

Schwann cells, the principal glial cells of the peripheral nervous system, play a central role in nerve repair following injury. Upon injury, mature Schwann cells dedifferentiate into repair Schwann cells. These processes are governed by complex gene regulatory networks, yet the quantitative dynamics of these processes remain unclear. Here, using a bottom-up systems biology approach, we constructed an endogenous regulatory network model based on experimentally validated interactions, without relying on high-throughput data as input. The model captures Schwann cell dedifferentiation dynamics and reveals a potential landscape composed of stable states and intermediate transition states. Simulations recapitulate post-injury trajectories and confirm the role of c-Jun upregulation in maintaining repair capacity. Furthermore, the model predicts multiple potential therapeutic targets, including P53, JNK, and PTEN, for sustaining repair competence. We also identify intrinsic heterogeneity within repair Schwann cells and uncover key transition states that simultaneously connect repair-competent cells to both repair-deficient and apoptotic phenotypes, indicating that these intermediate states may represent critical regulatory bottlenecks and key cellular targets for improving the success of peripheral nerve regeneration. Overall, this work provides new insights into the precise regulation of Schwann cell fate and establishes a theoretical framework for regenerative medicine and clinical strategies in peripheral nerve repair.

neuroscience↗

bioRxiv2026

Autoimmune-like CD8⁺ T Cell Responses Drive Atherosclerotic Plaque Instability and Predict Cardiovascular Events

Background and aimsAtherosclerotic plaque rupture is a major cause of myocardial infarction and stroke. However, the precise drivers of plaque destabilisation remain elusive. We hypothesised that antigen-driven, autoimmune-like T cell responses are central to the destabilisation and rupture of atherosclerotic plaques. MethodsTo dissect T cell responses specifically in unstable compared to stable plaques, we leveraged near-infrared autofluorescence (NIRAF) imaging-guided dissection of human carotid plaques. We also used our tandem stenosis model reflecting plaque instability as seen in patients to differentiate between unstable and stable plaques in mice. To explore T cell involvement, we studied T cell differentiation states and T cell receptor (TCR) repertoires by single-cell multi-omics. Then, testing if antigen-driven CD8+ T cell responses drive plaque instability in mice, we applied a combination of AAV8-PCSK9-induced atherosclerosis, tandem stenosis and TCR transgenic mice. Finally, we leveraged data from the AtheroExpress Biobank Study to link T cell immunity to histology-defined instability and cardiovascular outcomes. ResultsT cell responses in unstable versus stable atherosclerosis were distinct. Unstable human plaques contained highly expanded, autoimmune-like CD8 T cells with markedly increased cytotoxic signatures, reduced exhaustion and distinct clonal repertoires compared to stable regions. Most plaque CD8 T cells exhibited a pronounced tissue-resident transcriptional program. Moreover, the transcriptional signature of these plaque resident T cells was distinct from multiple other human tissues. Autoimmune-like cytotoxic and tissue-resident CD8+ T cell responses were also evident in murine atherosclerosis, where restricting the activation of antigen-driven CD8+ T cells prevented plaque destabilisation. Importantly, analysis of carotid endarterectomy samples from >1000 patients identified that intraplaque cytotoxic CD8 T cell gene signatures strongly correlated with histological instability and predicted future strokes. ConclusionsIntegrated human, murine and clinical analyses demonstrate that autoimmune-like, cytotoxic CD8 T cell responses are central drivers of plaque instability and major cardiovascular events. Targeting pathogenic CD8 T cell responses may thus offer a compelling immunomodulatory strategy to stabilise plaques and reduce the risks of stroke and myocardial infarction. Graphical AbstractO_ST_ABSKey QuestionC_ST_ABSRupture of unstable atherosclerotic plaques is a typical cause of myocardial infarction and stroke. To understand the underlying cause and to prevent plaque rupture, we addressed the central hypothesis that autoimmune-like T cell responses drive plaque destabilisation and rupture. Key FindingsCD8+ T cells are clonally expanded with increased cytotoxic signatures in unstable versus stable plaques (mice and humans) and require antigen recognition to drive plaque instability. Cytotoxic CD8+ T cell signatures in excised plaques correlate with increased future cardiovascular events. Take Home MessageAutoimmune-like adaptive immune reactions, dominated by CD8+ T cells, are a major driver of plaque instability/rupture. Therefore, targeting pathogenic CD8 T cell responses offers a compelling immunomodulatory strategy to stabilise plaques and reduce the risk of myocardial infarction and stroke. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/720043v1_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@bd83dcorg.highwire.dtl.DTLVardef@1bee3borg.highwire.dtl.DTLVardef@1b56bc0org.highwire.dtl.DTLVardef@1b5176f_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2026

Therapeutic knockdown of MLKL reduces diet-induced obesity and improves insulin signalling in mature adipocytes

Obesity affects one in three adults and is complicated by adipose inflammation, lipotoxicity and cell death. We previously identified RIPK1 as a genetic determinant of human obesity risk and adipose inflammation. Because RIPK1 is the apical kinase in the necroptosis pathway upstream of RIPK3 and the executioner protein MLKL, and emerging evidence links MLKL to lipid metabolism, MLKL has surfaced as a potential metabolic regulator. However, conflicting findings in Mlkl knockout mice fed a high fat diet have left its therapeutic relevance unresolved. MLKL has not been previously targeted through therapeutic knockdown in vivo in the context of diet-induced obesity. Here, we evaluated two independent MLKL antisense oligonucleotides (ASOs) in high fat diet (HFD)-fed C57BL/6J mice. In a 24-week progression model, MLKL ASO markedly reduced body weight, fat mass and hepatic steatosis compared with controls, while preserving lean mass. MLKL knockdown also lowered the respiratory exchange ratio, indicating a shift toward increased fat oxidation. In the intervention model, once obesity was established after 12 weeks of HFD feeding, both MLKL ASOs, and similarly, two independent RIPK1 ASOs, reversed weight gain and improved systemic glucose control. In vitro, MLKL-CRISPR/Cas9 knockout blocked 3T3-L1 adipogenesis, indicating a requirement for MLKL during adipocyte differentiation. However, in mature adipocytes, MLKL siRNA reduced palmitic acid-induced lipid accumulation, increased isoprenaline-stimulated lipolysis, and prevented TNF-mediated suppression of insulin-mediated AKT signalling and glucose uptake. Collectively, these findings demonstrate that partial MLKL suppression reprograms whole-body energy metabolism, enhances insulin sensitivity and limits diet-induced adiposity. MLKL, therefore, represents a promising and mechanistically novel therapeutic target for obesity and insulin resistance.

physiology↗

bioRxiv2026

Engineering a performance-improved, axon-targeted kalium channelrhodopsin for optogenetic neuropathway inhibition

Optogenetic neuropathway inhibition is a powerful approach for dissecting circuit functions. This strategy, however, frequently encounters practical challenges due to insufficient expression or performance of the optogenetic silencer on axonal projections/terminals. HcKCR1, a light-gated potassium-selective channel from Hyphochytrium catenoides, has shown great promise for optogenetic inhibition. Unfortunately, the application of HcKCR1 in neuropathway manipulations is hindered by its unsatisfactory gating properties and poor axonal trafficking. To overcome these hurdles, we first engineered a performance-improved HcKCR1 (piKCR) that allowed more reliable neuronal inhibition at low intensities of green or red light. We next engineered an axon-targeted piKCR (piKCR.AT) that demonstrated long-range axonal trafficking and optical presynaptic inhibition in the mouse hippocampus. When piKCR.AT was expressed in the cerebellar Purkinje Cells (PCs), optical manipulation of PC outputs to the deep cerebellar nuclei robustly disrupted mouse movement on the balance beam. With enhanced performance and axonal distribution, piKCR.AT may provide new opportunities for elucidating neuropathway functions in health and diseases.

bioengineering↗

bioRxiv2026

Convergent Roles of Growth Differentiation Factor-15 (GDF-15) in Mechanotransduction, Vascular Disorganization, and Immune Suppression in Melanoma

Melanoma, particularly in its advanced forms, remains one of the most lethal skin cancers, with limited effective treatments for both common cutaneous subtypes and rarer variants such as acral melanoma. The effects of the extracellular matrix (ECM) and other cancer-cell extrinsic processes on melanoma development remain underexplored. This study identifies Growth Differentiation Factor-15 (GDF-15) as a novel mechanosensing-regulated driver of melanoma pathogenesis across melanoma types. GDF-15 is shown here to be mechanically induced by ECM rigidity and compressive forces occurring during metastatic progression, leading to significantly elevated levels in both cutaneous and acral melanoma cells. In this study, ECM rigidity was recapitulated using cell-adhesive gelatin methacryloyl (GelMA) hydrogel microparticles (microgels) with tunable stiffness, providing a biomimetic platform to investigate how mechanical cues in the tumor microenvironment regulate GDF-15 expression in melanoma. A previously unrecognized synergy between GDF-15 and inflammatory factors commonly present in tumors was identified and found to promote a disorganized, hyperpermeable vasculature, thereby facilitating tumor nutrient access and impeding effective immune cell infiltration. GDF-15 knockdown reduced the intratumoral hemorrhage phenotype, indicating a causal role. GDF-15 also functions by directly suppressing natural killer (NK) cell-mediated cytotoxicity, revealing a second cooperating mechanism of immune evasion. These effects position GDF-15 as a key node linking mechanical stress, co-operation with inflammatory factors, abnormal vascular development, and immune dysfunction, thereby converging on a pathways and processes not previously described in melanomas. TEASERUncovering GDF-15 as a central mediator at the intersection of mechanical rigidity and external force, disorganized vascular hemorrhagic remodeling, co-operation with inflammatory factors, and immune evasion, revealing a previously unrecognized therapeutic vulnerability across both common and rare melanoma subtypes

cancer biology↗

bioRxiv2025

A 3D Amphioxus Brain Atlas Illuminates the Blueprint of the Ancestral Chordate Brain

Comparative studies on highly complex vertebrate brains have provided insights into the evolutionary history of morphological diversity. However, a long-standing question in vertebrate brain evolution is how the fundamental blueprint emerged. To probe the cellular and molecular origins of brain architecture in the chordate lineage, we performed single-nucleus RNA-seq combined with spatial transcriptomics and generated a three-dimensional cell atlas of the basal chordate amphioxus central nervous system (CNS). This atlas reveals a tripartite organization along the anterior-posterior axis of the adult amphioxus brain, with a rostral retinal/hypothalamic region followed by a di-mesencephalon and caudally, the hindbrain and spinal cord. Notably, we show that the amphioxus brain contains cell clusters resembling the zona limitans intrathalamica and midbrain-hindbrain boundary, both of which demarcate the major brain compartments. Furthermore, expression profiling and gene ontology enrichment analyses support that the cell clusters located in the rostral part of the amphioxus forebrain correspond to vertebrate retinal primordium and hypothalamic cells. However, the absence of key telencephalic marker expression in the amphioxus anterior forebrain suggests that the telencephalon likely represents a vertebrate innovation. Together, our findings establish a spatial transcriptomic framework for the amphioxus CNS and provide a critical link for understanding the evolution of the complex vertebrate brain.

evolutionary biology↗