Biology subjects

Chen, S.

Publications and source records attributed to Chen, S..

At least 505 records · Page 28Linked to original sources

bioRxiv2023

Pathogenic variants in CRX have distinct cis-regulatory effects on enhancers and silencers in photoreceptors

Dozens of variants in the photoreceptor-specific transcription factor (TF) CRX are linked with human blinding diseases that vary in their severity and age of onset. It is unclear how different variants in this single TF alter its function in ways that lead to a range of phenotypes. We examined the effects of human disease-causing variants on CRX cis-regulatory function by deploying massively parallel reporter assays (MPRAs) in live mouse retinas carrying knock-ins of two variants, one in the DNA binding domain (p.R90W) and the other in the transcriptional effector domain (p.E168d2). The degree of reporter gene dysregulation caused by the variants corresponds with their phenotypic severity. The two variants affect similar sets of enhancers, while p.E168d2 has stronger effects on silencers. Cis-regulatory elements (CREs) near cone photoreceptor genes are enriched for silencers that are de-repressed in the presence of p.E168d2. Chromatin environments of CRX-bound loci were partially predictive of episomal MPRA activity, and silencers were notably enriched among distal elements whose accessibility increases later in retinal development. We identified a set of potentially pleiotropic regulatory elements that convert from silencers to enhancers in retinas that lack a functional CRX effector domain. Our findings show that phenotypically distinct variants in different domains of CRX have partially overlapping effects on its cis-regulatory function, leading to misregulation of similar sets of enhancers, while having a qualitatively different impact on silencers.

genomics↗

bioRxiv2023

Endogenous recapitulation of Alzheimers disease neuropathology through human 3D direct neuronal reprogramming

Alzheimers disease (AD) is a neurodegenerative disorder that primarily affects elderly individuals, and is characterized by hallmark neuronal pathologies including extracellular amyloid-{beta} (A{beta}) plaque deposition, intracellular tau tangles, and neuronal death. However, recapitulating these age-associated neuronal pathologies in patient-derived neurons has remained a significant challenge, especially for late-onset AD (LOAD), the most common form of the disorder. Here, we applied the high efficiency microRNA-mediated direct neuronal reprogramming of fibroblasts from AD patients to generate cortical neurons in three-dimensional (3D) Matrigel and self-assembled neuronal spheroids. Our findings indicate that neurons and spheroids reprogrammed from both autosomal dominant AD (ADAD) and LOAD patients exhibited AD-like phenotypes linked to neurons, including extracellular A{beta} deposition, dystrophic neurites with hyperphosphorylated, K63-ubiquitin-positive, seed-competent tau, and spontaneous neuronal death in culture. Moreover, treatment with {beta}- or {gamma}-secretase inhibitors in LOAD patient-derived neurons and spheroids before A{beta} deposit formation significantly lowered A{beta} deposition, as well as tauopathy and neurodegeneration. However, the same treatment after the cells already formed A{beta} deposits only had a mild effect. Additionally, inhibiting the synthesis of age-associated retrotransposable elements (RTEs) by treating LOAD neurons and spheroids with the reverse transcriptase inhibitor, lamivudine, alleviated AD neuropathology. Overall, our results demonstrate that direct neuronal reprogramming of AD patient fibroblasts in a 3D environment can capture age-related neuropathology and reflect the interplay between A{beta} accumulation, tau dysregulation, and neuronal death. Moreover, miRNA-based 3D neuronal conversion provides a human-relevant AD model that can be used to identify compounds that can potentially ameliorate AD-associated pathologies and neurodegeneration.

neuroscience↗

bioRxiv2023

Synergistic effects of multiple pesticides on the flight ability of honey bees (Apis cerana F.)

Pesticides cause risks in the environment for Asian honey bees (Apis cerana). Imidacloprid (I), chlorpyrifos (C) and glyphosate (G) are among the most-widely used pesticides in the world. It is not clear on how these pesticides and combination of them affect the flight ability of A. cerana. Here we utilized flight mills to show new results that acute treatment of individual pesticides, such as 0.2 ng/bees imidacloprid (20 L, 10 ng/g), 0.6 ng/bees chlorpyrifos (20 L, 30 ng/g) and 1.2 ng/bees glyphosate (20 L, 60 ng/g), had no effect on the flight ability of bees. However, forager bees showed a significantly decrease in the flying duration and flying distance when oral exposed to two or three these pesticides. This evidence indicated that two or three pesticides can produce synergistic changes in the flight ability and behavior of honeybees. Results showed a light on new understandings of complex effects and potential risks of these three pesticide on bee behavior including homing ability and food-collecting ability. Our results are key information to understand new synergistic potential among pesticide formulations and how they impair bee behavior. Table of Contents Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/541595v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@70e24dorg.highwire.dtl.DTLVardef@1195fb8org.highwire.dtl.DTLVardef@db5ad5org.highwire.dtl.DTLVardef@1287b51_HPS_FORMAT_FIGEXP M_FIG C_FIG

animal behavior and cognition↗

bioRxiv2023

Perception of Speech Turn Dynamics is preserved in Congenitally Deaf children with Cochlear Implants

Perceptual and speech production abilities of children with cochlear implants (CI) are usually tested by word and sentence repetition or naming tests. However, in their daily life they show very heterogeneous language skills. Here, we describe a way of increasing the ecological validity of language assessment, promoting the use of close to real-life listening situations. The setup consists in watching the audio-visual conversation of two individuals. Childrens gaze-switches from one speaker to the other serve as a proxy of their prediction abilities. Moreover, to better understand the basis and the impact of anticipatory behaviour, we also measured childrens ability to understand the dialogue content, their speech perception and memory skills as well as their rhythmic skills. Importantly, we compared children with CI performances with those of an age-matched group of children with NH. While children with CI revealed poorer speech perception and verbal working memory abilities than NH children, there was no difference in gaze anticipatory behaviour. Interestingly, in children with CI only, we found a significant correlation between dialogue comprehension, perceptive skills and gaze anticipatory behaviour. Our results confirm and extend to a conversational context previous findings showing an absence of predictive deficits in children with CI. The current design seems an interesting avenue to provide an accurate and objective estimate of anticipatory language behaviour in a rather ecological conversational context also with young children.

neuroscience↗

bioRxiv2023

Three-dimensional Shear Wave Elastography Using Acoustic Radiation Force and A 2-D Row-Column Addressing (RCA) Array

Acoustic radiation force (ARF)-based shear wave elastography (SWE) is a clinically available ultrasound imaging mode that noninvasively and quantitatively measures tissue stiffness. Current implementations of ARF-SWE are largely limited to 2-D imaging, which does not provide robust estimation of heterogeneous tissue mechanical properties. Existing 3-D ARF-SWE solutions that are clinically available are based on wobbler probes, which cannot provide true 3-D shear wave motion detection. Although 3-D ARF-SWE based on 2-D matrix arrays have been previously demonstrated, they do not provide a practical solution because of the need for a high channel-count ultrasound system (e.g., 1024-channel) to provide adequate volume rates and the delicate circuitries (e.g., multiplexers) that are vulnerable to the long-duration "push" pulses. To address these issues, here we propose a new 3-D ARF-SWE method based on the 2-D row-column addressing (RCA) array which has a much lower element count (e.g., 256), provides an ultrafast imaging volume rate (e.g., 2000 Hz), and can withstand the push pulses. In this study, we combined the comb-push shear elastography (CUSE) technique with 2-D RCA for enhanced SWE imaging field-of-view. In vitro phantom studies demonstrated that the proposed method had robust 3-D SWE performance in both homogenous and inclusion phantoms. An in vivo study on a breast cancer patient showed that the proposed method could reconstruct 3-D elasticity maps of the breast lesion, which was validated using a commercial ultrasound scanner. These results demonstrate strong potential for the proposed method to provide a viable and practical solution for clinical 3-D ARF-SWE.

bioengineering↗

bioRxiv2023

FAM210A Regulates Mitochondrial Translation and Maintains Cardiac Mitochondrial Homeostasis

AimsMitochondria play a vital role in cellular metabolism and energetics and support normal cardiac function. Disrupted mitochondrial function and homeostasis cause a variety of heart diseases. Fam210a (family with sequence similarity 210 member A), a novel mitochondrial gene, is identified as a hub gene in mouse cardiac remodeling by multi-omics studies. Human FAM210A mutations are associated with sarcopenia. However, the physiological role and molecular function of FAM210A remain elusive in the heart. We aim to determine the biological role and molecular mechanism of FAM210A in regulating mitochondrial function and cardiac health in vivo. Methods and ResultsTamoxifen-induced MHCMCM-driven conditional knockout of Fam210a in the mouse cardiomyocytes induced progressive dilated cardiomyopathy and heart failure, ultimately causing mortality. Fam210a deficient cardiomyocytes exhibit severe mitochondrial morphological disruption and functional decline accompanied by myofilament disarray at the late stage of cardiomyopathy. Furthermore, we observed increased mitochondrial reactive oxygen species production, disturbed mitochondrial membrane potential, and reduced respiratory activity in cardiomyocytes at the early stage before contractile dysfunction and heart failure. Multi-omics analyses indicate that FAM210A deficiency persistently activates integrated stress response (ISR), resulting in transcriptomic, translatomic, proteomic, and metabolomic reprogramming, ultimately leading to pathogenic progression of heart failure. Mechanistically, mitochondrial polysome profiling analysis shows that FAM210A loss of function compromises mitochondrial mRNA translation and leads to reduced mitochondrial encoded proteins, followed by disrupted proteostasis. We observed decreased FAM210A protein expression in human ischemic heart failure and mouse myocardial infarction tissue samples. To further corroborate FAM210A function in the heart, AAV9-mediated overexpression of FAM210A promotes mitochondrial-encoded protein expression, improves cardiac mitochondrial function, and partially rescues murine hearts from cardiac remodeling and damage in ischemia-induced heart failure. ConclusionThese results suggest that FAM210A is a mitochondrial translation regulator to maintain mitochondrial homeostasis and normal cardiomyocyte contractile function. This study also offers a new therapeutic target for treating ischemic heart disease. Translational PerspectiveMitochondrial homeostasis is critical for maintaining healthy cardiac function. Disruption of mitochondrial function causes severe cardiomyopathy and heart failure. In the present study, we show that FAM210A is a mitochondrial translation regulator required for maintaining cardiac mitochondrial homeostasis in vivo. Cardiomyocyte-specific FAM210A deficiency leads to mitochondrial dysfunction and spontaneous cardiomyopathy. Moreover, our results indicate that FAM210A is downregulated in human and mouse ischemic heart failure samples and overexpression of FAM210A protects hearts from myocardial infarction induced heart failure, suggesting that FAM210A mediated mitochondrial translation regulatory pathway can be a potential therapeutic target for ischemic heart disease.

pathology↗

bioRxiv2023

Co-engagement of TIGIT+ immune cells to PD-L1+ tumours by a bispecific antibody potentiates T-cell response and tumour control

Co-targeting PD-1/PD-L1 and TIGIT/CD226 is being pursued to broaden the efficacy of current immunotherapy. Here we demonstrate that a bispecific antibody (BsAb) targeting PD-L1 and TIGIT, HB0036, shows major advantages over the combination of the two parental monoclonal Abs (mAbs). We demonstrated that HB0036 co-engages PD-L1+ tumour cells and TIGIT+ T cells, and thereby upregulates CD226 on T cells and induces a greater T-cell proliferative response compared to the combination of the parental antibodies in vitro. In vivo, HB0036 recruits greater amounts of TIGIT antibody in PD-L1+ tumours but not in PD-L1- tumours, compared with therapy using the two parental antibodies. We also observed improved tumour control and favourable immunological signatures with HB0036 in syngeneic and xenograft tumour models. Collectively, these findings demonstrate that bispecific antibodies targeting PD-L1 and TIGIT offer superior benefits in cancer immunotherapy compared with therapy using the two parental antibodies. Based on these studies, a phase I clinical trial with HB0036 has been initiated in patients with solid tumours (NCT05417321).

immunology↗

bioRxiv2023

Phase transition of maternal RNAs during vertebrate oocyte-to-embryo transition

The oocyte-to-embryo transition (OET) is regulated by maternal products stored in the oocyte cytoplasm, independent of transcription. How maternal products are precisely remodeled to dictate the OET remains an open question. In this work, we discover the dynamic phase transition of maternal RNAs during Xenopus OET. We have identified 863 maternal transcripts that transition from a soluble state to a detergent-insoluble one after oocyte maturation. These RNAs are enriched in the animal hemisphere and many of them encode key cell cycle regulators. In contrast, 165 transcripts, including nearly all Xenopus germline RNAs and some vegetally localized somatic RNAs, undergo an insoluble-to-soluble phase transition. This phenomenon is conserved in zebrafish. Our results demonstrate that the phase transition of germline RNAs influences their susceptibility to RNA degradation machinery and is mediated by the remodeling of germ plasm. This work thus uncovers novel remodeling mechanisms that act on RNAs to regulate vertebrate OET.

developmental biology↗

bioRxiv2023

A deep catalog of protein-coding variation in 985,830 individuals

Coding variants that have significant impact on function can provide insights into the biology of a gene but are typically rare in the population. Identifying and ascertaining the frequency of such rare variants requires very large sample sizes. Here, we present the largest catalog of human protein-coding variation to date, derived from exome sequencing of 985,830 individuals of diverse ancestry to serve as a rich resource for studying rare coding variants. Individuals of African, Admixed American, East Asian, Middle Eastern, and South Asian ancestry account for 20% of this Exome dataset. Our catalog of variants includes approximately 10.5 million missense (54% novel) and 1.1 million predicted loss-of-function (pLOF) variants (65% novel, 53% observed only once). We identified individuals with rare homozygous pLOF variants in 4,874 genes, and for 1,838 of these this work is the first to document at least one pLOF homozygote. Additional insights from the RGC-ME dataset include 1) improved estimates of selection against heterozygous loss-of-function and identification of 3,459 genes intolerant to loss-of-function, 83 of which were previously assessed as tolerant to loss-of-function and 1,241 that lack disease annotations; 2) identification of regions depleted of missense variation in 457 genes that are tolerant to loss-of-function; 3) functional interpretation for 10,708 variants of unknown or conflicting significance reported in ClinVar as cryptic splice sites using splicing score thresholds based on empirical variant deleteriousness scores derived from RGC-ME; and 4) an observation that approximately 3% of sequenced individuals carry a clinically actionable genetic variant in the ACMG SF 3.1 list of genes. We make this important resource of coding variation available to the public through a variant allele frequency browser. We anticipate that this report and the RGC-ME dataset will serve as a valuable reference for understanding rare coding variation and help advance precision medicine efforts.

genetics↗

bioRxiv2023

Molecular mechanisms for activation of the 26S proteasome

Various hormones, kinases, and stressors (fasting, heat shock) stimulate 26S proteasome activity. To understand how its capacity to degrade ubiquitylated protein can increase, we studied ZFAND5, which promotes protein degradation during muscle atrophy. Cryo-electron microscopy showed that ZFAND5 induces large conformational changes in the 19S regulatory particle. ZFAND5s AN1 Zn finger interacts with the Rpt5 ATPase and its C-terminus with Rpt1 ATPase and Rpn1, a ubiquitin-binding subunit. Surprisingly, these C-terminal interactions are sufficient to activate proteolysis. With ZFAND5 bound, entry into the proteasomes protein translocation channel is wider, and ZFAND5 dissociation causes opening of the 20S gate for substrate entry. Using single-molecular microscopy, we showed that ZFAND5 binds ubiquitylated substrates, prolongs their association with proteasomes, and increases the likelihood that bound substrates undergo degradation, even though ZFAND5 dissociates before substrate deubiquitylation. These changes in proteasome conformation and reaction cycle can explain the accelerated degradation and suggest how other proteasome activators may stimulate proteolysis.

molecular biology↗

bioRxiv2023

A near-complete genome sequence of einkorn wheat provides insight into the evolution of wheat A subgenomes

Einkorn wheat (Triticum monococcum) is one of the oldest cereal crops to be domesticated by human beings, playing essential role in early agriculture development. Today, it is considered an important genomic resource for modern wheat improvement, especially for resistance against pests and diseases. However, the exploration and utilization of useful genes from T. monococcum is limited due to the lack of a reference genome and annotation for this species. Here, we report a near-complete genome assembly for T. monococcum with a total length of 5.11 Gb with a contig N50 of 131.2Mb and scaffold N50 of 728.66Mb, representing a genome assembly of highest quality for any wheat genome reported. Phylogenomic analysis confirmed T. monococcum is closely-related to T. urartu, the progenitor of wheat A subgenomes. A 4AL/5AL terminal translocation is present in the diploid species T. urartu and T. monococcum, taking place before wheat polyploidization. T. monococcum has significantly expanded and unique gene families involved in DNA damage repair and heat stress tolerance, reflecting its adaptive evolution to cope with historical harsh climate in its natural habitat, South East Turkey. The genome sequence confirmed the introgression of T. monococcum rust resistance genes at 5AmL into modern bread wheat varieties. This near-complete reference genome of T. monococcum will be an essential resource for wheat functional and evolutionary genomic studies and expedite the cloning of useful genes in T. monococcum for future wheat improvement.

genomics↗

bioRxiv2023

Functional interrogation of twenty type 2 diabetesassociated genes using isogenic hESC-derived β-like cells

Genetic studies have identified numerous loci associated with type 2 diabetes (T2D), but the functional role of many loci has remained unexplored. In this study, we engineered isogenic knockout human embryonic stem cell (hESC) lines for 20 genes associated with T2D risk. We systematically examined {beta}-cell differentiation, insulin production and secretion, and survival. We performed RNA-seq and ATAC-seq on hESC-{beta} cells from each knockout line. Analyses of T2D GWAS signals overlapping with HNF4A-dependent ATAC peaks identified a specific SNP as a likely causal variant. In addition, we performed integrative association analyses and identified four genes (CP, RNASE1, PCSK1N and GSTA2) associated with insulin production, and two genes (TAGLN3 and DHRS2) associated with sensitivity to lipotoxicity. Finally, we leveraged deep ATAC-seq read coverage to assess allele-specific imbalance at variants heterozygous in the parental hESC line, to identify a single likely functional variant at each of 23 T2D GWAS signals.

genetics↗

bioRxiv2023

Hypoxia-induced circSTT3A maintains Breast Cancer Stem Cell formation by Stabilizing PGK1 protein

BackgroundHypoxia is a key feature of tumor microenvironment that can cause fundamental changes in cancer cells, and may also lead to the development of breast cancer stem cells (BCSCs) with self-renewal ability. However, the mechanism of hypoxia in inducing BCSCs is not fully understood. MethodsPerforming RNA sequence and bioinformatics analysis, a hypoxia specific circular RNA (circRNA), named circSTT3A, was identified in hypoxic breast cancer cells and tissues. The clinical significance of circSTT3A was investigated in breast cancer (BC) tissues and tissue array. The loss and acquisition of circSTT3A were carried out in vivo and in vitro to confirm its functional roles in BCSC stemness maintenance. HIF1 droved circSTT3A expression was evaluated by chromatin immunoprecipitation and dual luciferase reporter assays. RNA pull-down, RNA immunoprecipitation, silver staining detection, mass spectrographic analysis, co-immunoprecipitation assays and western blotting were exerted to determine circSTT3A directly binding with HSP70 and PGK1 proteins. CircSTT3A-mediated serine metabolism was determined by UHPLC-QTRAP-MS system and ELISA kit. BC mouse model was used to assess the effects of circSTT3A/Hsp70/PGK1 on tumorigenesis and chemotherapy resistance in vivo. ResultsA novel hypoxia specific circSTT3A was significantly upregulated in clinical breast cancer tissues, and was related to the clinical stage and poor prognosis of BC patients. The hypoxia inducible factor 1 alpha (HIF1)-regulated circSTT3A has remarkable effect on mammosphere formation in breast cancer cells. Our work revealed that circSTT3A directly interacting with nucleotide-binding domain of heat shock protein 70 (HSP70) increases the ability of HSP70 to recruit phosphoglycerate kinase 1 (PGK1) via its substrate-binding domain, which reduces the ubiquitination of PGK1 and increases the stability of PGK1. The enhanced PGK1 catalyzes 1,3-diphosphoglycerate (1, 3-BPG) into 3-phosphoglycerate (3-PG) leading to 3-PG accumulation and increase of serine synthesis, thus to facilitate BCSC enrichment under hypoxic microenvironment. Loss of circSTT3A or PGK1 substantially induces suppression in tumor initiation and tumor growth, which dramatically increases tumor sensitivity to Doxorubicin treatment in mice. ConclusionsHypoxia induced circSTT3A/HSP70/PGK1 axis plays a critical role in maintaining BCSC properties and may be meaningful for treating patients with breast cancer.

cancer biology↗

bioRxiv2023

scEpiTools: a database to comprehensively interrogate analytic tools for single-cell epigenomic data

Single-cell sequencing technology has enabled the characterization of cellular heterogeneity at an unprecedented resolution. To analyze single-cell RNA-sequencing data, numerous tools have been proposed for various analytic tasks, which have been systematically summarized and concluded in a comprehensive database called scRNA-tools. Although single-cell epigenomic data can effectively reveal the chromatin regulatory landscape that governs transcription, the analysis of single-cell epigenomic data presents assay-specific challenges, and an abundance of tools with varying types and functionalities have thus been developed. Nevertheless, these tools have not been well summarized, hindering retrieval, selection, and utilization of appropriate tools for specific analyses. To address the issues, we here proposed scEpiTools database with a multi-functional platform (http://health.tsinghua.edu.cn/scepitools). Specifically, based on the comprehensive collection and detailed annotation of 553 articles, scEpiTools groups articles into 14 major categories and 90 subcategories, provides task-specific recommendation for different emphases, and offers intuitive trend analysis via directed graphs, word clouds, and statistical distributions. For single-cell chromatin accessibility data analysis, we proposed a novel ensemble method named scEpiEnsemble, which, along with multiple methods as built-in kernels, can be used for flexible and efficient online analysis via the scEpiTools platform. We envision that scEpiTools will guide tool usage and development for single-cell epigenomic data and provide valuable resources for understanding regulatory mechanisms and cellular identity. Author summaryCompared to single-cell RNA-sequencing data, single-cell epigenomic data can reflect a set of epigenetic modifications at the cellular level. In general, the analysis of these data is typically divided into several steps: 1) retrieving available tools based on the omics of data and tasks; 2) selecting appropriate tools manually; and 3) utilizing the chosen tools to analyze data. However, due to the rapid development of tools and the unique complexity of the data, each of the above steps is extremely challenging for researchers. To provide researchers with great convenience, we developed scEpiTools (http://health.tsinghua.edu.cn/scepitools), a database with multiple functionalities. For instance, given the omics type and the analytic task, researchers can easily browse all the available tools via the hierarchical categorization of scEpiTools, and get recommendation scores from multiple perspectives. Considering that researchers may encounter difficulties in hardware requirements or environment setup, we also provide online analysis with various commonly used tools, as well as a novel ensemble method named scEpiEnsemble. In summary, scEpiTools represents a valuable resource for the single-cell epigenomics community, facilitating retrieval, selection and utilization of appropriate tools for diverse analyses, and helping to drive future advancements in the field.

bioinformatics↗

bioRxiv2023

Discovery of microRNA-derived RNAs and proteins in human cells

MicroRNAs (miRNAs) are short noncoding RNAs that can regulate gene expression through the binding of their 5-ends to mRNAs. However, the biological effects of miRNA binding via their 3-ends remain unclear. Here, we discover that the exact reverse pairing of the 3-ends of miRNAs or miRNA-like RNAs, collectively termed microsized RNAs (msRNAs), with template RNAs can initiate the production of msRNA-derived RNAs (msdRs), which can subsequently be translated into polypeptides (msdPs). Using 2,632 human msRNAs from miRBase, 11,121 msdRs and 1,239 msdPs were predicted based on a 15-nucleotide pairing threshold, and the presence of representative msdRs and msdPs was confirmed in human cells. Of clinical relevance, msdP0188 is highly expressed in human lung and breast cancers, and its corresponding msRNAs and msdRs represent novel anti-cancer targets. Notably, inhibiting telomerase reverse transcriptase, a putative RNA-dependent RNA polymerase identified by bioinformatic screening, led to reduced levels of msdP0188 in human cancer cells. Our findings reveal a novel "msRNA [->] msdR [->] msdP" axis, expanding the classical central dogma and predicting many previously unrecognized RNAs and polypeptides with potential biological functions in human cells and other systems.

cell biology↗

bioRxiv2023

Assembly and Cation-selectivity Mechanisms of Neuronal Gap Junction Channel Connexin 36 Elucidated by Cryo-EM

Electrical synapses are essential components of neural circuits. Dysfunction of electrical synapses can lead to obstacles in learning and memory. Neural signal transduction across electrical synapses is primarily mediated by a gap junction channel, Connexin 36 (Cx36), the lack of which causes impaired electrical couplings in cortical interneurons and thalamic reticular nucleus (TRN) neurons. Unique characteristics of Cx36 gap junction channel include its insensitivity in transjunctional membrane potential, as well as its preference for homomeric assembly, prone to exclude other paralogous connexins from co-assembly. However, the structural basis underlying Cx36 function and assembly remains elusive. Here, we report the cryo-EM structure of human Cx36 at 2.67 [A] resolution and identified critical residues underpinning its obligatory homomeric assembly. In particular, we found non-canonical electrostatic interactions between protomers from opposing hemichannels and a steric complementary site between adjacent protomers within a hemichannel, which together offer a structural explanation for the assembly specificity in homomeric and heteromeric gap junction channels. Moreover, the narrowest restriction along the channel axis overlaps with an acidic patch, where Glu43, Asp47 and Asp48 may contribute to cation-selectivity. Also, the amino-terminal helix reported to be responsible for sensing membrane potential in other connexins was disordered in our Cx36 structure, in line with its channel activity independent of membrane potential. Together, this work elucidated the assembly mechanisms of the electrical synaptic gap junction channel, and offered possible explanations for sustained Cx36 activity upon membrane depolarization, which allows efficient action potential propagation across electrical synapses.

biophysics↗

bioRxiv2023

D-SPIN constructs gene regulatory network models from multiplexed scRNA-seq data revealing organizing principles of cellular perturbation response

Gene regulatory networks within cells modulate the expression of the genome in response to signals and changing environmental conditions. Reconstructions of gene regulatory networks can reveal the information processing and control principles used by cells to maintain homeostasis and execute cell-state transitions. Here, we introduce a computational framework, D-SPIN, that generates quantitative models of gene regulatory networks from single-cell mRNA-seq datasets collected across thousands of distinct perturbation conditions. D-SPIN constructs probabilistic models of regulatory interactions between genes or gene-expression programs to fit the cell state distributions under different perturbations. Using large Perturb-seq and drug-response datasets, we demonstrate that D-SPIN models reveal key regulators of cell fate decisions and the coordination of distant cellular pathways in response to gene knockdown perturbations. D-SPIN also dissects gene-level drug response mechanisms in heterogeneous cell populations, elucidating how combinations of immunomodulatory drugs acting on distinct regulators induce novel cell states through additive recruitment of gene expression programs. The D-SPIN model further predicts cell state distributions under drug dosage combinations beyond the training data. D-SPIN provides a computational framework for constructing interpretable models of gene regulatory networks to reveal principles of cellular information processing and physiological control.

bioinformatics↗

bioRxiv2023

Sentence superiority in the reading brain

When a sequence of written words is briefly presented and participants are asked to identify just one word at a post-cued location, then word identification accuracy is higher when the word is presented in a grammatically correct sequence compared with an ungrammatical sequence. This sentence superiority effect has been reported in several behavioral studies and two EEG investigations. Taken together, the results of these studies support the hypothesis that the sentence superiority effect is primarily driven by rapid access to a sentence-level representation via partial word identification processes that operate in parallel over several words. Here we used MEG to examine the neural structures involved in this early stage of written sentence processing, and to further specify the timing of the different processes involved. Source activities over time showed grammatical vs. ungrammatical differences first in the left inferior frontal gyrus (IFG: 325-400 ms), then the left anterior temporal lobe (ATL: 475-525 ms), and finally in both left IFG and left posterior superior temporal gyrus (pSTG: 550-600 ms). We interpret the early IFG activity as reflecting the rapid bottom-up activation of sentence-level representations, including syntax, enabled by partly parallel word processing. Subsequent activity in ATL and pSTG is thought to reflect the constraints imposed by such sentence-level representations on on-going word-based semantic activation (ATL), and the subsequent development of a more detailed sentence-level representation (pSTG). These results provide further support for a cascaded interactive-activation account of sentence reading.

neuroscience↗