Biology subjects

Li, T.

Publications and source records attributed to Li, T..

At least 181 records · Page 10Linked to original sources

bioRxiv2025

CASTOR1: A Novel Tumor Suppressor Linking mTORC1 and KRAS Pathways in Tumorigenesis and Resistance to KRAS-Targeted Therapies in Non-Small Cell Lung Cancer

Cytosolic arginine sensor for mTORC1 Subunit 1 (CASTOR1) functions as a key regulator of mechanistic target of rapamycin complex 1 (mTORC1) signaling. Despite its frequent dysregulation in cancers via mechanisms such as KSHV microRNA-mediated inhibition or AKT-driven phosphorylation and degradation, the impact of CASTOR1 loss on tumor initiation and progression remains poorly understood. Here, we identify CASTOR1 as a critical tumor suppressor in non-small cell lung cancer (NSCLC) by demonstrating that its genetic ablation amplifies tumorigenesis in a KRAS-driven genetically engineered mouse model (GEMM;LSL-KRASG12D). CASTOR1 deficiency markedly enhances lung tumor incidence, accelerates tumor progression, and increases proliferative indices in KRASG12D-driven tumors (KRASG12D;C1KO) compared to CASTOR1 wild type (WT) tumors (KRASG12D;C1WT). Advanced-stage tumors exhibit elevated phosphorylated CASTOR1 (pCASTOR1) and reduced total CASTOR1 levels, suggesting active degradation during tumorigenesis. Mechanistically, CASTOR1 loss amplifies mTORC1 signaling, as evidenced by heightened phosphorylation of downstream effectors 4EBP1 and S6, while also augmenting AKT and ERK activation, uncovering a crosstalk between the PI3K/AKT/mTORC1 and KRAS/ERK pathways. Furthermore, CASTOR1 ablation induces genome instability, which may contribute to enhanced tumor incidence and progression. Importantly, CASTOR1 deficiency confers resistance to KRASG12D-specific inhibitors, while over half of KRASG12D;C1WT tumors also display resistance. Organoids derived from KRASG12D;C1KO and KRASG12D;C1WT tumors reveal a correlation between KRAS inhibitor resistance and hyperactivation of mTORC1, with mTORC1 and PI3K inhibitors sensitizing resistant tumors to KRASG12D-targeted therapies. These findings position CASTOR1 as a novel tumor suppressor that modulates mTORC1 and KRAS signaling to constrain NSCLC progression. Our study further highlights the therapeutic potential of combining mTORC1 or ERK inhibitors with KRAS-targeted therapies for NSCLC characterized by hyperactive KRAS signaling and impaired CASTOR1 activity. HighlightsO_LICASTOR1 functions as a tumor suppressor in NSCLC by limiting KRAS-driven tumor initiation and progression. C_LIO_LICASTOR1 is frequently lost or inactivated in wild-type tumors during tumor progression, contributing to advanced-stage malignancies. C_LIO_LICASTOR1 deficiency amplifies mTORC1 signaling and enhances PI3K/AKT and KRAS/ERK crosstalk, driving tumorigenesis and resistance to KRAS-specific inhibitors. C_LIO_LICombining mTORC1 or PI3K inhibitors with KRAS-targeted therapies effectively overcomes resistance in KRAS-driven NSCLC. C_LI

cancer biology↗

bioRxiv2025

Evolution of a fuzzy ribonucleoprotein complex in viral assembly

Previously we showed that the genetic diversity of SARS-CoV-2 nucleocapsid (N) protein explores a wide range of biophysical properties facilitated by non-local impact of point mutations to its intrinsically disordered regions (Nguyen et al., 2024). This includes modulation of self-association, such as the creation of a de novo binding interface through the P13L mutation characteristic of Omicron variants. In the present work we focus on the key function of N condensing viral RNA into ribonucleoprotein particles (RNPs) for viral assembly. Lacking high-resolution structural information, biochemical and biophysical approaches have revealed architectural principles of RNPs, which involve cooperative interactions of several protein-protein and protein-RNA interfaces, initiated through oligomerization of conserved transient helices in the central disordered linker of N. Here we study the impact of defining N-protein mutations in variants of concern on RNP formation, using biophysical tools, a virus-like particle assay, and reverse genetics experiments. We find convergent evolution in repeated, independent introduction of amino acid substitutions strengthening existing binding interfaces, compensating for other substitutions that promote viral replication but decrease RNP stability. Furthermore, we show that the P13L mutation of Omicron variants enhances RNP assembly and increases viral fitness. Overall, our data reveal RNP complexes to be highly variable not only in sequence and conformations, but also in thermodynamic and kinetic stability, with its pleomorphism affecting basic architectural principles. We hypothesize that the formation of polydisperse, fuzzy N-RNA clusters with multiple distributed weak binding interfaces optimizes reversible RNA condensation, while supporting host adaptation and allowing for a large sequence space to be explored.

biophysics↗

bioRxiv2025

A novel transgenic reporter to study vertebrate epigenetics

Epigenetic reprogramming contributes to the generation of cellular diversity during vertebrate development but the mechanisms directing this are still not well understood. Large-scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies, but similar large-scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated "EpiTag" zebrafish transgenic reporter line that permits easy cellular-level visualization of epigenetic silencing or activation in living animals during development, gametogenesis, and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants, identifying relevant vertebrate tissue-specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction-associated fatty liver disease (MAFLD). The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue-specific epigenetic gene regulation in vertebrates. One Sentence SummaryEpiTag transgenic zebrafish provide a powerful new tool for visualizing and studying epigenetic regulation in living vertebrate animals.

genomics↗

bioRxiv2025

Thermal cycling resets the irreversible liquid-to-solid transition of peptide condensates during aging

The ability of biomolecular condensates to reversibly dissolve and reform is crucial for maintaining cellular stability and functions. In metabolically active cells, stress granules can rapidly assemble and disassemble in response to environmental changes. However, as metabolic rates decline with aging, stress granules persist longer, disrupting mRNA translation and stress responses. Temperature, as a physical stimulus, plays a key role in controlling condensate formation, dissolution, and material properties. In this study, we explore how the reversibility of the liquid-to-solid transition of biomolecular condensates can be modulated by temperature change. Our findings reveal that aged condensates exhibit reduced responsiveness to external temperature stimuli. By using thermal cycling experiments to simulate repeated heat stress, we found that the time taken for irreversible fiber formation could be delayed up to 4.7-fold compared to condensates without thermal cycles. We also found the dissolution rate of condensates progressively slows as they age but remain more stable with thermal cycles. Importantly, our results indicate that continuous cycles of liquid-liquid phase separation and dissolution act as a reset mechanism, preserving the biomolecular condensates from further liquid-to-solid transition. These findings provide valuable insights into how aging impacts condensate behavior and highlight potential strategies to preserve cellular function through controlled phase transitions.

bioengineering↗

bioRxiv2025

Anatomical and Molecular Characterization of the Zebrafish Meninges

The meninges are a set of connective tissue layers that surround the central nervous system, protecting the brain from mechanical shock, supporting its buoyancy, guarding it from infection and injury, and maintaining brain homeostasis. Despite their critical role, the molecular identity, developmental origins, and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here, we show that the zebrafish, a genetically and experimentally accessible vertebrate, possesses an easily imaged mammalian-like meninges. Anatomical and cellular characterization of its composition via histology, electron microscopy, and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double-layered dura mater and intricate leptomeningeal layers. Using single cell transcriptomics, we define the molecular identities of meningeal cell populations, including a unique ependymin (epd)-expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges, provide a foundational description for future zebrafish meningeal research, and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges.

developmental biology↗

bioRxiv2025

Functional landscape of circular RNAs in human cancer cells

Circular RNAs (circRNAs) constitute a novel class of noncoding RNAs showcasing distinct tissue- and cell-specific expression patterns. Despite the extensive profiling of circRNAs, their individual functions remain poorly understood. To fill this gap, we designed a genome-wide library of 65,300 shRNAs, targeting 9,663 clinically relevant circRNAs and 3,981 of their linear parental genes, and conducted functional screening in seven types of human cancer. We identified a total of 1,342 essential circRNAs (13.9% screened) that impact cell proliferation in at least one cell line, and in 96.5% of the cases, the linear counterparts are not essential. While a shared common subset emerges as functional regulators across all examined cell lines, the majority of circRNAs are functional in a cell type-specific manner. For a comprehensive presentation of the functional circRNA landscape in cancer, we introduce FunCirc, an online database encompassing functional circRNAs across cancer cell lines, coupled with circRNA expression profiles from diverse cancer and tissue types. Our work enhances the understanding of circRNA functions in cancer and provides the scientific community with a resource to further investigate their intricate roles.

cancer biology↗

bioRxiv2025

Circular RNA profiling and functional screening in breast cancer identify circNSD1 as a suppressor of tumor autophagy

Circular RNAs (circRNAs) have emerged as critical regulators of cell biology. However, their function in breast cancer remains elusive. Herein, through circRNA profiling of 38 breast tumors and 10 benign breast tissues, we identified 509 of differentially expressed circRNAs. Integration with transcriptome-wide functional screening of approximately 10,000 circRNAs pinpointed circNSD1(6) as a top ranked tumor suppressor in breast cancer. circNSD1(6) is downregulated in tumors and suppression of the circular form, but not the linear form, promotes breast cancer proliferation and tumor growth. Mechanistically, circNSD1(6) interacts with autophagy receptor SQSTM1/p62 and inhibits the oligomerization of p62, thereby suppressing p62 body formation and p62-dependent autophagy. Furthermore, circNSD1(6) ameliorates p62-mediated Keap1 sequestration, hence suppresses the Nrf2 pathway and oxidative stress tolerance. Our study provides a landscape view of the transcription and function of circRNA in breast cancer, and uncovers the crucial role of circNSD1(6) in autophagy and antioxidant stress.

cancer biology↗

bioRxiv2025

Acute high-dose irradiation of human primary ovarian cells reveals a shift in transcriptomics profile and impairment in cell-cell adhesion

STUDY QUESTIONHow do human cortical (cPOCs) and medullary (mPOCs) primary ovarian cells respond to acute X-ray exposure? SUMMARY ANSWERAcute high-dose X-ray exposure causes a shift in cPOCs and mPOCs transcriptomic profiles and impairs significantly their cell-cell adhesion ability. WHAT IS KNOWN ALREADYRadiotherapy is a leading cancer treatment, due to its effectiveness in targeting malignant cells. However, it can also affect healthy cells, potentially causing organ dysfunction, among which ovaries. When targeted radiotherapy is not feasible, fertility preservation is recommended to avoid premature ovarian insufficiency. In addition, the effects of irradiation on ovarian somatic cells remain poorly understood. STUDY DESIGN, SIZE, DURATIONOvarian tissue was obtained from patients undergoing gender-affirming surgery at Karolinska University Hospital Huddinge, Sweden. The ovarian tissue was separated into cortex and medulla, then individually dissociated into single-cell suspensions using mechanical and enzymatic methods. Monolayer cultures from cPOCs and mPOCs were exposed to a single dose of 10 Gy X-ray irradiation or left unexposed as paired controls. Following irradiation, the cells were cultured at various time-points for further molecular and morphological evaluation. PARTICIPANTS/MATERIALS, SETTING, METHODSOvarian tissue from 8 patients (age 23-36 years) was used. Dissociated cPOCs and mPOCs were cultured to 80% confluence and irradiated with 10 Gy (1.33 Gy/min), with non-irradiated controls. Cellular ATP and mitochondrial activity were assessed, followed by immunofluorescence staining for canonical irradiation-induced effects in cells: DNA damage, apoptosis and cell cycle progression. Bulk RNA-sequencing was performed on controls and irradiated samples. Libraries were prepared using the Illumina Stranded mRNA Prep Ligation protocol and sequenced on Illumina NovaSeq6000 platform. Genes were considered to be differentially expressed under the cut-off of false discovery rate (FDR) < 0.05. Subsequently, affected biological pathway was predicted using all expressed genes ranked by log2 fold change again hallmark gene sets. To further investigate the potential upstream regulators, transcription factor enrichment analysis were performed based on DEGs. To assess changes at protein level, we mapped the proteomic profile using liquid chromatography-tandem mass spectrometry. Peptides were considered to be differentially expressed (DEPs) under the cut-off of p-value < 0.01. Finally, we measured the ability of cPOCs and mPOCs to form 3D aggregates after seeding irradiated and non-irradiated cells on Biosilk scaffolds. MAIN RESULTS AND THE ROLE OF CHANCEFollowing irradiation, ATP levels and mitochondrial activity in cPOCs and mPOCs were comparable to controls, indicating minimal irradiation impact on cell viability and proliferation. Immunofluorescence analysis confirmed the modulation of canonical pathways, such as DNA damage, apoptosis and cell cycle in both cPOCs and mPOCs. Transcriptomic analysis showed that cPOCs and mPOCs at 1 h post-irradiation clustered together with the related 1 h control. However, a shift in transcriptomic profile was observed after 4 h and even more after 24 h post-irradiation in both cPOCs and mPOCs. Gene set enrichment analysis (GSEA) indicated upregulation of the p53 pathway at 4 h and 24 h post-irradiation, alongside downregulation of MYC targets, E2F targets, the G2/M checkpoint and mTORC1 pathway. Gene pattern analysis showed irradiation-dependent trends related to extracellular matrix (ECM) organisation, p53-mediated apoptotic mechanisms and chromosome segregation during the 24 h period following irradiation. Additionally, transcription factor enrichment analysis based on DEGs suggested p53 and MYC as potential upstream regulators. On a proteomic level, DEPs associated with ECM organisation and cytoskeleton formation were detected at 4 and 24 h post-irradiation. Finally, X-ray exposure hindered the cell-cell adhesion ability of both cPOCs and mPOCs, leading to impaired formation of Silk-Ovarioids. LARGE SCALE DATAThe RNA sequencing count matrix is deposited in Gene Expression Omnibus (GEO) with accession number GSE291604. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD061796. The code used for the analysis can be found at https://github.com/tialiv/X-Ovary. LIMITATIONS, REASONS FOR CAUTIONThe ovarian tissue was obtained from gender-affirming surgery patients who received androgen treatment before removal. Even though unlikely, this hormonal treatment might influence ovarian environment and alter cellular response to irradiation. Additionally, in this study the impact of X-ray exposure was assessed on a monolayer cell model, thus limiting the extrapolation power of our results to ovary in vivo. Lastly, the impact of irradiation was focused on the somatic cell populations that are essential for ovarian function. Further studies are needed to investigate the effects of X-ray exposure on ovarian follicles and their function. WIDER IMPLICATIONS OF THE FINDINGSUnderstanding the roles of MYC, p53 and cell adhesion factors in response to irradiation could guide the development of future ovarian protective strategies. These findings lay the foundation for further studies on ovarian tissue protection and fertility preservation in cancer patients. STUDY FUNDING/COMPETING INTEREST(S)This work was funded by the European Unions HORIZON 2020 research and innovation programme (MATER) under the Marie Skodowska-Curie Actions (grant agreement No: 813707), the Estonian Research Council (grants PRG1076 and PSG608), the Orion Research Foundation sr personal grant, the Research grant from the Center for Innovative Medicine (CIMED) and the Karolinska Institutet Consolidator Grant.

cell biology↗

bioRxiv2025

De Novo Negatively Charged Binders Targeting MMLVRT Nucleic Acid Binding Sites Overcome Stability-Activity Trade-offs

The limited thermostability and storage-induced inactivation of Moloney murine leukemia virus reverse transcriptase (MMLV RT) have constrained its applications. In this study, a high-stability mutant, MMLV RT-SV, was generated through a multi-site mutagenesis strategy targeting the nucleic acid-binding pocket. Through de novo protein design, three highly negatively charged binders with affinities of 45 nM, 362 nM, and 829 nM were developed to specifically target the positively charged nucleic acid-binding region on the surface of MMLV RT-SV. Experimental results demonstrated that these binders formed complexes with the enzyme via electrostatic interaction, significantly enhancing the thermostability and long-term storage stability of MMLV RT-SV while not affecting its RNA- dependent DNA polymerase function. This work pioneers the rational design of negatively charged binders targeting strongly positively charged nucleic acid-binding sites, overcoming the traditional stability-activity trade-off inherent in site-directed mutagenesis and directed evolution. The proposed strategy not only provides an innovative solution to address the thermal sensitivity and storage instability of reverse transcriptase but also establishes a novel paradigm for De Novo-based precision engineering of enzyme functions, demonstrating significant potential in molecular diagnostics, gene editing, and related fields.

bioengineering↗

bioRxiv2025

Endothelial Cept1 Promotes Post-Ischemic Angiogenesis in a Pparα-Dependent Fashion

BackgroundCept1 is essential for de novo phopholipogenesis and is impacted by diabetes. We previously demonstrated that conditional knockdown of Cept1 in the endothelium leads to reduced hindlimb angiogenesis and tissue recovery. We hypothesized that Cept1 may also be sufficient in promoting post-ischemic angiogenesis and recovery in the setting of diabetes. MethodsCEPT1 content was evaluated in peripheral arteries of patients with peripheral arterial disease (PAD), and with or without diabetes. An endothelial cell (EC)-specific Cept1 overexpression mouse model was developed (Cept1fl/flCre+) in adult C57BL6 mice. Murine aortae were harvested, for single-cell RNA sequencing (scRNA-seq), and unilateral hindlimb ischemia was used to evaluate angiogenesis in Cept1fl/flCre+ mice. Primary ECs were isolated and HUVECs transduced with Cept1 cDNA were developed, and evaluated using molecular assays, in vitro functional assays, and mass spectrometry. ResultsIn humans, arterial intima CEPT1 was elevated in the setting of PAD and diabetes, along with ACOX1, VEGF2R, p-Akt, and p-eNOS. In mice, scRNA-seq demonstrated that ECs with Cept1 overexpression were enriched with wound healing, angiogenesis, sprouting, and cell migration pathways. Diabetic Cept1fl/flCre+ mice had improved hind-limb perfusion and angiogenesis, and their aortic rings had increased ex vivo capillary sprouting. Cept1 overexpression in ECs significantly increased migration, tubule formation, and proliferation as predicted by scRNA-seq. Cept1 overexpression in ECs led to increased Ppar, Acox1, Vegfa, and Vegf2r. Similarly, treatment with siPpar, and inhibitors for PPAR (GW6471), VEGFR2 (ZM323881), Akt (LY294002), and eNOS (L-NAME) abrogated CEPT1-induced EC migration. ConclusionsCept1 overexpression promotes EC function and post-ischemic recovery. The impact of CEPT1 on ECs is at least in part dependent on p-Akt/p-eNOS angiogenic signaling and PPAR. Since CEPT1 is elevated in diseased human peripheral arterial tissue, these findings suggest that CEPT1 may be playing an important compensatory role in vascular recovery and reperfusion following ischemic injury in the setting diabetes. HighlightsO_LICEPT1 content is higher in the peripheral arteries of individuals with peripheral arterial disease (PAD) and type 2 diabetes. C_LIO_LICept1 over expression induces endothelial cell activation and function and enhances post-ischemia angiogenesis in vivo. C_LIO_LICEPT1 induces endothelial pAkt/p-eNOS signaling and VEGF-A production in a PPAR dependent fashion. C_LIO_LICEPT1 may be an important regenerative signal that is increased in the peripheral arteries in the setting of PAD. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=124 SRC="FIGDIR/small/642511v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@dde6ecorg.highwire.dtl.DTLVardef@63c6c4org.highwire.dtl.DTLVardef@8e753dorg.highwire.dtl.DTLVardef@b314cd_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

Temporal variation in the acoustic dynamic range is a confounding factor in EEG-based tracking of absolute auditory attention to speech

Many studies have demonstrated that auditory attention to natural speech can be decoded from EEG data. However, most studies focus on selective auditory attention decoding (sAAD) with competing speakers, while the dynamics of absolute auditory attention decoding (aAAD) to a single target remains underexplored. The goal of aAAD is to measure the degree of attention to a single speaker, and it has applications for objective measurements of attention in psychological and educational contexts. To investigate this aAAD paradigm, we designed an experiment where subjects listened to a video lecture under varying attentive conditions. We trained neural decoders to reconstruct the speech envelope from EEG in the baseline attentive condition and use the correlation coefficient between the decoded and real speech envelope as a metric for attention to the speech. Our analysis shows that the envelope standard deviation (SD) of the speech envelope in the 1-4 Hz band strongly correlates with this metric across different segments of the speech stimulus. However, this correlation weakens in the 0.1-4 Hz band, where the degree of separation between the attentive and inattentive state becomes more pronounced. This highlights the unique contribution of the 0.1-1 Hz range, which enhances the distinction of attentional states and remains less affected by confounding factors such as the time-varying dynamic range of the speech envelope.

neuroscience↗

bioRxiv2025

Accurate prediction of multiple RNA modifications from nanopore direct RNA sequencing data with RNANO

Various types of RNA modifications exert vital regulatory functions across a broad array of biological processes. Nanopore direct RNA sequencing (DRS) has emerged as a promising technique holding the unique potential to capture signals from multiple types of RNA modifications in a single sequencing run. However, high-performance computational methods are demanded to recognize multiple modification types from complicated native DRS data from human cells. To this end, we developed RNANO, a deep learning-based method for predicting potential RNA modification sites and their modification states. This approach leverages an attention-enhanced multi-instance learning framework with the dynamic time warping algorithm to fine-tune the alignment between electrical signal events and reference sequences. RNANO efficiently detects seven common RNA modification types (m6A, m5C, {Psi}, m1A, Nm, ac4C, and m7G) in DRS data, exhibiting superior performance on both held-out testing samples and cross-cell-line independent benchmarks. A case study focusing on a cancer cell line also indicates that RNANO can pinpoint RNA modifications within key oncogenic pathways. In summary, RNANO enables accurate and efficient identification of multiple RNA modifications in human cell lines, offering useful clues for disease researches and therapeutic development related to RNA modifications.

bioinformatics↗

bioRxiv2025

Construction of a Heterologous Pathway in Escherichia coli for Terephthalate Assimilation

Polyethylene terephthalate (PET) is extensively used in products such as packaging and textiles, and it remains a significant contributor to plastic and microplastic pollution. Effective valorization of PET waste requires not only depolymerizing it into its monomers but also utilizing the resulting products, ethylene glycol (EG) and terephthalic acid (TPA). While prior research has demonstrated that Escherichia coli can convert TPA into value-added compounds for PET upcycling, limited work has focused on its assimilation for cell growth. This study focuses on constructing a complete TPA metabolic pathway in E. coli comprising TPA uptake and its conversion to protocatechuate (PCA). We engineered E. coli JME3, which already possesses PCA catabolism, to utilize TPA as a sole carbon source by introducing a heterologous transporter TpaK and a PCA-synthesizing enzyme cascade. The strain next underwent adaptive laboratory evolution (ALE) and expression tuning to improve growth performance. The final strain achieved a maximum growth rate of 0.25 h-{superscript 1}, demonstrating efficient TPA assimilation. These results expand the range of value-added compounds derived from PET upcycling and establish E. coli as a platform for coupling PET depolymerization with microbial growth, enabling high-throughput optimization of enzyme activity and PET biodegradation conditions.

bioengineering↗

bioRxiv2025

Surface Expansion Regionalization of the Hippocampus in Early Brain Development

The hippocampal formation is implicated in a myriad of crucial functions, particularly centered around memory and emotion, with distinct subdivisions fulfilling specific roles. However, there is no consensus on the spatial organization of these subdivisions, given that the functional connectivity and gene expression-based parcellation along its longitudinal axis differs from the histology-based parcellation along its medial-lateral axis. The dynamic nonuniform surface expansion of the hippocampus during early development reflects the underlying changes of microstructure and functional connectivity, providing important clues on hippocampal subdivisions. Moreover, the thin and convoluted properties bring out the hippocampal maturity largely in the form of expanding surface area. We thus unprecedentedly explore the development-based surface area regionalization and patterns of the hippocampus by leveraging 513 high-quality longitudinal MRI scans during the first two postnatal years. Our findings imply two discrete hippocampal developmental patterns, featuring one pattern of subdivisions along the anterior-posterior axis (head, regions 1 and 5; body, regions 2, 4, 6, and 7; tail, region 3) and the other one along the medial-lateral axis (subiculum, regions 4, 5, and 6; CA fields, regions 1, 2, and 7). Most of the resulting 7 subdivisions exhibit region-specific and nonlinear spatiotemporal surface area expansion patterns with an initial high growth, followed by a transition to low increase. Each subregion displays bilaterally symmetric pattern. The medial portion of the hippocampal head experiences the most rapid surface area expansion. These results provide important references for exploring the fine-grained organization and development of the hippocampus and its intricate cognitions.

neuroscience↗

bioRxiv2025

China Autism Brain Imaging Consortium: Charting Brain Growth in Chinese Children with Autism

Autism Spectrum Disorder (ASD) is a lifelong neurodevelopmental condition characterized by atypical brain growth. While advances in neuroimaging and openly sharing large-sample datasets such as the Autism Brain Imaging Data Exchange (ABIDE) have improved understanding of ASD, most studies focus on adolescents and adults, with early brain development-critical for diagnosis and intervention-remaining underexplored. Existing research predominantly involves Western samples, offering limited insight and generalizability into non-Caucasian populations. We introduce the China Autism Brain Imaging Consortium (CABIC) (https://php.bdnilab.com/resources/), a grassroots effort by researchers across the country to aggregate previously collected multi-site structural MRI datasets and phenotypic information from 1,451 autistic children and 1,119 typically developing children, covering an age range from early childhood to school age (1.0 - 12.92 years). Here, we present this resource and depict brain growth charts to push forward a more comprehensive understanding of the brain development in Chinese autism children. We constructed brain growth charts that reveal a developmental shift in autistic children, transitioning from early overgrowth to delayed maturation. Regional analyses identified distinct atypical trajectories across specific brain regions. Individual deviation scores quantified inter-subject variability, characterizing the heterogeneity of brain development in ASD. Comparative analyses between CABIC and ABIDE highlighted differences potentially attributable to ethnicity and culture, advancing our understanding of cross-population neurodevelopmental diversity. CABIC MRI datasets will be shared publicly to foster investigation of the potential neural mechanisms underlying ASD in non-Western populations and support efforts toward precision medicine for autistic individuals across diverse backgrounds.

neuroscience↗

bioRxiv2025

The impact of ambient contamination on demultiplexing methods for single-nucleus multiome experiments

Sample multiplexing has become an increasingly common design choice in droplet-based single-nucleus multi-omic sequencing experiments to reduce costs and remove technical variation. Genotype-based demultiplexing is one popular class of methods that was originally developed for single-cell RNA-seq, but has not been rigorously benchmarked in other assays, such as snATAC-seq and joint snRNA/snATAC assays, especially in the context of variable ambient RNA/DNA contamination. To address this, we develop ambisim, a genotype-aware read-level simulator that can flexibly control ambient molecule proportions and generate realistic joint snRNA/snATAC data. We use ambisim to evaluate demultiplexing methods across several important parameters: doublet rate, number of multiplexed donors, and coverage levels. Our simulations reveal that methods are variably impacted by ambient contamination in both modalities. We then applied the demultiplexing methods to two joint snRNA/snATAC datasets and found highly variable concordance between methods in both modalities. Finally, we develop a new metric, variant consistency, which we show is correlated with cell-level ambient molecule fractions in singlets. Applying our metric to two multiplexed joint snRNA/snATAC datasets reveals variable ambient contamination across experiments and modalities. We conclude that improved modelling of ambient material in demultiplexing algorithms will increase both sensitivity and specificity.

bioinformatics↗

bioRxiv2025

Functional Interrogation of Neuronal Subtypes via Intersectional Expression of Optogenetic Actuator Reveals Non-linear Components in a Linear Circuit

Investigating signal integration in a neural circuit is oftentimes challenging when the circuit contains neuronal subtypes that are transcriptomically similar, due to the lack of tools to express optogenetic actuators with high cellular specificity and to deliver light with high spatiotemporal accuracy. Here, we demonstrate the use of a split GAL4-based genetic "AND" gate to express Chrimson in specific touch receptor neuron (TRN) subtypes in the C. elegans touch response circuit. Combining this intersectional strategy for transgene expression with high-throughput optical targeting and behavioral quantification, we optogenetically interrogated the role of each TRN subtype in mediating the mechanosensor-induced escape response and in integrating signals that trigger the opposite motor output. Surprisingly, we found that although the response of the overall circuit linearly combines the competing anterior and posterior stimuli, this linearity is comprised of antagonistic non-linear contributions from the anterior and posterior sensors, which conspire to generate a linear response.

neuroscience↗

bioRxiv2025

Fluctuations in arousal reflect latent state transitions that facilitate behavioral optimization

People are often faced with surprising events that defy expectations. Such events elicit transient activity in the locus coeruleus/norepinephrine system and elevation of peripheral arousal markers including pupil dilation and the EEG P300, but the function of these signals remains unclear. We propose that they reflect latent state transitions that dynamically control the mental context governing learning and perception. We tested and confirmed five preregistered predictions of this theory using EEG and pupil measurements collected from people performing a color prediction and reproduction task. Task latent state transitions elicited pupil dilation and amplified event-related potentials including the P300. These EEG and pupil measures related to behavioral signatures of latent state updating, including reduced bias and bidirectional adjustment of learning, both across trials and individuals. Our findings support the theory that LC/NE-linked arousal systems optimize behavior by signaling environmental transitions to facilitate rapid adjustments of mental context.

neuroscience↗