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Cheng, S.

Publications and source records attributed to Cheng, S..

At least 55 records · Page 3Linked to original sources

Comprehensive Transcriptome Annotation of Thousands of HIV-1 Genomes

Alternative splicing in HIV-1 has been a central focus of decades of research, uncovering key mechanisms of viral gene regulation, immune evasion, and therapeutic response - yet, no reference resource has existed to support transcriptome-wide analysis, limiting adoption of modern computational methods. We present HIV Atlas (https://ccb.jhu.edu/HIV_Atlas), the first reference-quality annotation of HIV-1 and SIV transcriptional diversity. We manually curated transcriptomes for HIV-1HXB2 and SIVmac239 and developed Vira, an automated annotation-transfer method specifically designed to address unique challenges of viral genome biology, to generate high-quality annotations for 2,077 complete HIV-1 genomes. Using the resources presented in our work, we evaluated conservation of splice sites, revealing near-perfect preservation of major donors and acceptors. Furthermore, using several public datasets, we demonstrate how HIV Atlas enhances methodology, improves the quality and novelty of results, and opens novel avenues for research, supporting more accurate and comprehensive analyses of bulk, single-cell, and spatial RNA-seq in HIV-1 studies.

genomics↗

Unifying spatial and episodic representations in the hippocampus through flexible memory use

A key question in neuroscience is why the hippocampus is essential for episodic memory in humans, while dominantly exhibiting spatial representations in a number of other species. Some accounts suggest that spatial representation is the primary hippocampal function. Here, we propose that the primary function is storing and retrieving episodic memories, and spatial representations emerge due to this memory function. To demonstrate this, we adopt a computational model that autonomously learns to store information in memory and retrieve it to solve a variety of tasks. In memory tasks, the model develops associations and categorical representations akin to concept cells. In navigation tasks, the model forms representations of the spatial structure, performs geometric computations, and even learns representations of unique events similar to recently discovered barcodes. Our model predicts that the hippocampus represents any task-relevant variable, if the animal learns the task, suggesting that space is not special for the hippocampus.

neuroscience↗

Bayesian inference of introgression between sister lineages using genomic data

Inference of interspecific gene flow using genomic data is important to reliable reconstruction of species phylogenies and to our understanding of the speciation process. Gene flow is harder to detect if it involves sister lineages than nonsisters; for example, most heuristic methods based on data summaries are unable to infer gene flow between sisters. Likelihood-based methods can identify introgression between sisters but the test exhibits several nonstandard features, including boundary problems, indeterminate parameters, and multiple routes from the alternative to the null hypotheses. In the Bayesian test, those irregularities pose challenges to the use of the Savage-Dickey (S-D) density ratio to calculate the Bayes factor. Here we develop a theory for applying the S-D approach under nonstandard conditions. We show that the Bayesian test of introgression between sister lineages has low false-positive rates and high power. We discuss issues surrounding the estimation of the rate of gene flow between sister lineages, especially at very low or very high rates, and suggest that evidence for gene flow between sisters be assessed via a Bayesian test. We find that the species split time has a major impact on the information content in the data, with more information at deeper divergence. We use a genomic dataset from Sceloporus lizards to illustrate the test of gene flow between sister lineages.

evolutionary biology↗

Single-objective lattice light sheet microscopy with microfluidics for single-molecule super-resolution imaging of mammalian cells

Single-molecule localization microscopy (SMLM) has redefined optical imaging by enabling imaging beyond the diffraction limit, allowing nanoscale investigation into cellular architecture and molecular dynamics. Light sheet illumination enhances SMLM through optical sectioning of the sample, which drastically improves the signal-to-background ratio and reduces photobleaching and photodamage. Lattice light sheet (LLS) microscopy, in which a 2D optical lattice is implemented for light sheet illumination, can provide exceptional sectioning and extended imaging depth when imaging in scattering samples. However, its conventional dual-objective design poses challenges for certain applications. Here, we present an imaging platform which implements LLS illumination with a reflective single-objective geometry (soLLS) inside a microfluidic chip, enabling the use of a single high numerical aperture objective for both illumination and detection, mitigating constraints of a dual-objective setup. We provide quantitative characterization of the propagation properties of the soLLS and demonstrate that it outperforms conventional Gaussian light sheets in terms of useful field of view and sectioning when propagating through scattering samples. Next, by combining soLLS with point spread function engineering, we demonstrate the platform for improved 3D single-molecule super-resolution imaging of multiple targets across multiple cells. The soLLS imaging platform thus expands investigations of nanoscale cellular and intercellular structures and mechanisms into more challenging samples for a wide range of applications in biology and biomedicine.

biophysics↗

Place cell activity and behaviour during task acquisition and extinction learning predict renewal outcome

Extinction learning (EL) and the subsequent renewal of learned behaviours are crucial for adaptive responding, yet the underlying neural mechanisms that differentiate successful renewal from its absence remain unclear. Here, we explored the behavioral and neurophysiological basis of spatial appetitive EL, as well as renewal failure and renewal success. We recorded place cell activity from hippocampal area CA1 in male rats that performed a context-dependent spatial appetitive learning task in a T-maze (rewarded context A), followed by EL (unrewarded context B), and subsequent renewal testing (unrewarded context A). Half of the animals exhibited significant renewal ("renewers") and the other half failed to renew ("non-renewers"). Our findings reveal fundamental differences in learning strategies between groups revealed by differences in both spatial behavior and in place cell activity during both initial acquisition and subsequent EL. Specifically, renewers exhibited a context-based EL strategy, whereas non-renewers followed a goal-directed strategy. The spatial distribution of hippocampal place cell activity differed significantly between groups, indicating the hippocampus role in the learning processes. Furthermore, renewers exhibited a greater extent of global remapping of place cells compared to non-renewers, consistent with predictions by our computational modeling. This suggests that global remapping serves as a key neural mechanism underlying effective renewal, allowing for the segregation of distinct memories and preventing the generalization of extinction. Our results highlight how hippocampal place cell dynamics during acquisition and EL predict later behavioral renewal outcomes, providing critical insights into the neural basis of memory updating and contextual control over learned behaviors. Significance StatementThis study reveals that individual differences in associative learning strategies determine the outcome of memory renewal/re-activation. After first learning, and then extinguishing, a spatial learning task in two different contexts, some animals renewed their behavior when returned to the acquisition context ("renewers"), while others did not ("non-renewers"). Intriguingly, hippocampal place cell activity during acquisition and extinction learning predicted the subsequent renewal efficacy in these distinct animal groups. In particular, renewers exhibited more global remapping than non-renewers, a neural mechanism that segregates memories from different contexts and prevents over-generalization of extinction. These findings provide critical insights into how the hippocampus supports context-dependent memory acquisition and updating, providing new insights into the physiological basis of individual differences in behavioral flexibility.

neuroscience↗

The microbial tryptophan metabolite indole acts on the gastrointestinal tract to improve glucose homeostasis by enhancing GLP-1 secretion and L-cell differentiation

Aims/hypothesisGrowing evidence implicates gut microbiota-derived metabolites in metabolic homeostasis. Indole, a microbial tryptophan metabolite, has been reported to enhance Glucagon-like peptide-1 (GLP-1) secretion in vitro, and its derivatives have been inversely associated with risk of type 2 diabetes (T2D). We hypothesised that indole acts via the gastrointestinal tract to modulate glucose homeostasis, and aimed to test this hypothesis using in vitro and in vivo models. MethodsThe acute effects of indole on GLP-1 secretion in vitro, and on glucose tolerance and hormone secretion in mice, were determined. Subsequently, the effects of indole on intestinal epithelial cell fate and L-cell differentiation in murine ileal organoids and in vivo were studied. Finally, the utility of chronic indole administration in a murine model of T2D was explored. ResultsIndole stimulated in vitro GLP-1 secretion in a concentration-dependent manner, and improved acute glucose control in vivo. Additionally, we demonstrate that indole drives enteroendocrine L-cell differentiation in murine ileal organoids, resulting in increased L-cell density and longer-term glucoregulatory benefits in vivo. Finally, sub-chronic indole administration improved glucose tolerance and insulin sensitivity in diabetic mice. Conclusions/interpretationOur findings identify indole as an anti-diabetic molecule that acts on the gut, and raise the possibility of incorporating indole into nutraceutical supplements to aid in the treatment or prevention of T2D. This highlights the importance of gut microbiota-derived metabolites in metabolic health and opens new avenues for developing novel strategies to combat T2D. Research in ContextO_ST_ABSWhat is already known about this subject?C_ST_ABSO_LIGut microbiota-derived metabolites play a role in metabolic homeostasis. C_LIO_LIIndole, a microbial tryptophan metabolite, enhances GLP-1 secretion in vitro. C_LIO_LIIndole derivatives are inversely associated with type 2 diabetes (T2D) risk. C_LI What is the key question?O_LIDoes indole act on the gut to modulate glucose homeostasis? C_LI What are the new findings?O_LIIndole stimulates GLP-1 secretion and improves acute glucose control in vivo. C_LIO_LIIndole drives enteroendocrine L-cell differentiation in murine ileal organoids, increasing L-cell density and long-term glucoregulatory benefits. C_LIO_LISub-chronic indole administration improves glucose tolerance and insulin sensitivity in mice with type 2 diabetes, showing the potential of gut microbiota-derived metabolites as therapeutic targets. C_LI How might this impact clinical practice in the foreseeable future?O_LIIndole could be incorporated into nutraceutical supplements for T2D prevention or treatment. C_LI

physiology↗

Arousal-Driven Serial Dependence: Internal States Modulate Perceived Duration

Emotional experiences shape not only how we perceive the present but also how recent experiences inform our current judgments. This study examined whether emotional arousal and valence modulate serial dependence in time perception--the tendency for prior stimuli to bias ongoing estimates. Participants viewed affective images that induced high-arousal (positive or negative) or low-arousal (neutral) states and then reproduced each images duration. High arousal reliably lengthened perceived durations. More critically, it strengthened serial dependence, with the strongest biases emerging when high-arousal trials followed other high-arousal trials, showing a state-dependent amplification of temporal integration. Emotional valence, by contrast, exerted no measurable influence on either temporal distortion or sequential bias. These findings show that emotional arousal tunes how the brain weighs past against present, highlighting internal emotional states as a key driver of temporal continuity in perception.

neuroscience↗

Notch as a Driver of Lineage Plasticity and Therapeutic Target in Enzalutamide-Resistant Prostate Cancer

Resistance to androgen receptor (AR)-targeted therapies, such as enzalutamide, in castration-resistant prostate cancer (CRPC) remains a significant clinical challenge, often driven by mechanisms including lineage plasticity. The precise molecular mechanisms driving this process, particularly downstream effectors, remain incompletely understood. Given its established roles in cell fate and stemness, alongside its complex functions in prostate cancer, the Notch signaling pathway presented a compelling focus for study. This study investigates the role of Notch signaling in mediating lineage plasticity and therapeutic resistance in CRPC. Employing transcriptomic analysis and functional assays, we identified Notch activity is elevated across prostate cancer progression resistance. Notably, both CRISPR-mediated knockout and targeted inhibition of Notch reversed enzalutamide resistance in vitro. Collectively, this study delineates dynamic alterations in Notch signaling activity during prostate cancer progression and establishes its function as a crucial and druggable driver of therapy resistance. These findings underscore Notch signaling as a promising therapeutic target to counteract resistance to AR-targeted therapies in advanced prostate cancer.

cancer biology↗

Metabolic and ribosomal dysregulation drive developmental arrest of Schistosoma japonicum in non-permissive rats

Parasitic flatworms of the genus Schistosoma infect a wide range of definitive hosts, which are categorized as permissive or non-permissive based on their capacity to support parasite development. Unlike permissive hosts such as mice, Schistosoma japonicum undergoes pronounced developmental arrest in non-permissive hosts like rats; however, the molecular mechanisms underlying this phenomenon remain largely unclear. In this study, we conducted a comprehensive morphological and transcriptomic comparison of S. japonicum derived from mouse and rat hosts at multiple time points post-infection, identifying the period between 12 and 24 days post-infection (dpi) as a critical window for developmental arrest in parasites from rats. Utilizing single-cell RNA sequencing, we constructed a high-resolution cellular atlas of S. japonicum at 14 and 24 dpi from both host species, revealing host-dependent alterations in cell composition and transcriptional programs during parasite development. Functional analyses further demonstrated that impairments in mitochondrial function and anaerobic glycolysis contribute to the developmental arrest observed in parasites from rats. Additionally, downregulation of ribosomal genes was associated with reduced protein synthesis and impaired cell proliferation. Together, these findings suggest that disruptions in energy metabolism and ribosomal function are key drivers of developmental arrest in non-permissive hosts. This study provides novel, parasite-centered insights into host permissiveness and identifies potential molecular targets for schistosomiasis control strategies.

developmental biology↗

NodoMap: a spatio-cellular map of the mouse nodose ganglia

The vagus nerve is a key component of the parasympathetic nervous system, innervating multiple abdominal organs to monitor and regulate their function. It forms the main neural pathway between the gastrointestinal tract and the brain, playing a major role in the regulation of energy homeostasis. The cell bodies for vagal sensory neurons reside in the nodose ganglia, with the left and right ganglia reported to have distinct roles in food intake and reward. Here, we have integrated our own single nucleus RNA sequencing data with multiple publicly available datasets to create a database of 108,482 nuclei and cells, and combined this with spatial transcriptomics to present a spatio-cellular transcriptional map of the mouse nodose ganglia, the NodoMap. Nodose ganglia neuronal cells clustered into twenty-two different subtypes, all found in both left and right nodose ganglia, but with significant differences in gene expression between left and right ganglia across multiple neuronal subtypes. Overnight fasting modulated gene expression across specific neuronal subtypes, including nutrient responsive pathways. Spatial transcriptomics showed that while vagal neuronal types were highly interspersed, patterns of organisation into cellular neighbourhoods could be observed, with neighbourhoods identified of predominantly non-neuronal cells and of different neuronal populations accompanied by glial-like cells. Thus, NodoMap provides a detailed atlas of the mouse nodose ganglia in a spatial context, providing a platform for vagovagal neurocircuit analysis, and serving as an important resource to identify targets for pharmacotherapies for metabolic disease.

physiology↗

Alternatively-Spliced CAMKK2 isoforms drive differential metabolic stress response and the regulation of ferroptosis

Calcium/Calmodulin-dependent protein kinase kinase 2 (CAMKK2) is a multifunctional kinase that regulates metabolic processes by phosphorylating downstream targets. CAMKK2 is expressed as several highly similar protein isoforms, although the specific functions of these individual isoforms remain largely unexplored. These isoforms have been shown to display tissue-specific expression patterns, suggesting unique roles in distinct cellular contexts. In this study, we investigated the biochemical and functional relevance of CAMKK2 isoforms, LF and SF, in the context of glucose metabolism. Co-immunoprecipitation experiments revealed that the LF isoform preferentially binds the adaptor protein 14-3-3, while the SF isoform interacts with Calmodulin. Furthermore, the interaction between SF and Calmodulin was enhanced upon glucose starvation, whereas this interaction was not observed for LF. To assess their functional significance, we generated doxycycline-inducible, isoform-specific HeLa cell lines. Under low glucose conditions, cells expressing the LF isoform failed to activate AMPK, while cells expressing the SF isoform exhibited robust increase in AMPK phosphorylation. Moreover, LF-expressing cells accumulated higher levels of reactive oxygen species, upregulated ferroptosis-related genes via BACH1/NRF2, and displayed increased cell death compared to SF-expressing cells. Collectively, these findings demonstrate that CAMKK2 isoforms exhibit differential selectivity for protein partners and mediate distinct downstream signaling pathways, impacting metabolism in cancer.

biochemistry↗

ZNF638 represses the transcription of HBV closed circular DNA involving HUSH complex-mediated histone modifications of epigenetic silencing

Hepatitis B virus (HBV) infection poses a critical threat to public health burden worldwide. As the major template of viral transcription, the covalently closed circular DNAs (cccDNAs) of HBV was known to form microchromosomes and interact with various host proteins. In the present study, ZNF638 was found to significantly reduce the transcription of HBV into pgRNAs, and subsequently reduce cccDNA formation and viral propagation. We discovered that ZNF638 was able to bind the preS and S gene regions of HBV, repressing the transcription of cccDNA upon increased modification of H3K9me3 mediated by SETDB1. This epigenetic silencing of cccDNA transcription was further demonstrated to involve the activity of HUSH, a multi-protein complex to mediate epigenetic modifications of histone into suppressed nucleosomes. In in vivo models, we evaluated the effects of ZNF638 deficiency on HBV-targeting siRNA therapy. A significant reduction of the efficacy was observed in animals with reduced ZNF638 expression. In summary, we report that ZNF638 is a potent host factor to repress the transcription of HBV DNAs and to attenuate HBV infection. The role of ZNF638 on HBV repression involves its binding to cccDNA at specific regions for recruiting HUSH complex to write H3K9me3 histone marks for epigenetic silencing. ZNF638 serves as a critical host factor to associate HBV infection and disease progression. Additionally, ZNF638 serves as a potential indicator to predict the outcome of HBV-targeting siRNA therapy.

biochemistry↗

Enteropancreatic neurons drive the glucoregulatory response to ingested lipid

Enteropancreatic neurons project from the small intestinal wall to the pancreas. Though well positioned to mediate the effects of ingested nutrients on pancreatic function, the metabolic role of these neurons is unclear. Diets rich in olive oil promote weight loss and improve remission rates in patients with T2DM. Here, we show that olive oil improves acute glucose tolerance by stimulating insulin release via neurotensin receptor type 1 (NTSR1)-expressing enteropancreatic neurons. These neurons are necessary for the effects of olive and neurotensin on glucose tolerance, and their activation is sufficient to improve glucose tolerance. These findings suggest a mechanism by which dietary olive oil regulates blood glucose levels and present a novel functional role for enteropancreatic neurons in regulating glucose homeostasis.

physiology↗

Pan-cancer Analysis Identified Ectopic RUNX1T1 Associated with Lineage Plasticity

Cancer remains a leading cause of death worldwide, with lineage plasticity emerging as a hallmark that drives therapy resistance and tumor progression, allowing cancer cells to rapidly alter their identity and evade targeted therapies. Although various genomic and transcriptomic aberrations correlate with lineage plasticity, the lack of pan-cancer gene markers quantifying lineage plasticity has limited its utility as a predictive biomarker. Homeobox (HOX) genes encode a family of transcription factors that play critical roles in embryonic development and tissue identity by establishing distinct expression patterns, known as HOX codes, in specific cell lineages. Through comprehensive bioinformatic analysis of multi-omics data--including expression profiles of 39 HOX genes from over 80,000 RNA sequencing samples across 114 cancer types--we first demonstrated that HOX codes effectively represent the lineages of cancer cells. We then identified multiple lineage-plastic cancer subtypes by applying the calculated HOX codes. Specifically, we identified lineage-plastic tumor subtypes in prostate cancer, lung cancer, and acute myeloid leukemia (AML), which exhibit altered HOX codes compared to non-plastic subtypes. Downstream differential expression analysis revealed significantly elevated RUNX1T1 levels across all three lineage-plastic cancer types, which was further validated through bulk and single-cell RNA sequencing data derived from preclinical and clinical samples. Together, our findings provide a novel strategy for characterizing lineage plasticity in pan-cancer cells and suggest ectopic RUNX1T1 expression as a pan-cancer marker and critical mediator of lineage plasticity.

cancer biology↗

Dopaminergic drugs modulate fear extinction related processes in humans, but effects are mild

The ability to extinguish learned fear responses is crucial for adaptive behavior. The mesolimbic dopaminergic system originating in the ventral tegmental area has been proposed to contribute to fear extinction learning because of its critical role in reward learning. The unexpected omission of aversive unconditioned stimuli (US) is considered as rewarding (outcome better than expected) and to drive extinction learning. We tested the hypothesis that extinction learning is facilitated by dopaminergic drugs and impeded by anti-dopaminergic drugs. The effects of dopamine agonists [levodopa (100 mg) and bromocriptine (1.25 mg)] and antagonists [tiapride (100 mg) and haloperidol (3 mg)] on fear extinction learning were compared to placebo in 146 young and healthy human participants. A three-day differential fear conditioning paradigm was performed with pupil size and skin conductance responses (SCRs) being recorded. Fear acquisition training was performed on day 1, extinction training on day 2, and recall was tested on day 3. The conditioned stimuli (CS+, CS-) consisted of two geometric figures. A short electrical stimulation was used as the aversive US. One of the four drugs or placebo was administered prior to the extinction phase on day 2. Overall, effects were small and seen only in the bromocriptine group. In line with our hypothesis, we measured reduced pupil dilation during late recall in the bromocriptine group compared to the placebo group, indicating faster re-extinction of spontaneously recovered fear reactions on the third day. Effects of levodopa and haloperidol were unspecific and related to generally increased SCR levels in the levodopa group (already prior to drug intake), and miotic side-effects of haloperidol. Findings provide additional support that the dopaminergic system contributes to extinction learning in humans, possibly by improving consolidation of fear extinction memory.

neuroscience↗

A heart releasing neuropeptide that synchronizes brain-heart regulation during courtship behavior

Distinct internal states drive varied animal behaviors, yet the mechanisms by which non-neuronal factors encode these states remain largely unknown. Here, we show that cardiac activity regulates internal mating states through a conserved brain-heart axis in male flies and mice. In Drosophila, a ppk23-P1 pathway triggers heart rate acceleration upon female perception via crustacean cardioactive peptide, while the heart secretes ion transport peptide that feeds back onto P1 neurons to enhance courtship. Ejaculation rapidly decreases heart rate via Corazonin, mitigating prolonged tachycardia. In mice, a conserved Substance P-TacR1 pathway modulates courtship. Finally, we developed a computational framework to decode internal mating states from cardiac physiology, revealing distinct cardiac signatures. Our findings unveil a novel role for heart-derived neuropeptides in internal state regulation, elucidate a positive feedback loop between the heart and brain, and demonstrate the evolutionary conservation of the brain-heart axis in orchestrating dynamic behavioral and physiological states.

neuroscience↗

Development and Clinical Evaluation of a Multiplexed Health Surveillance Panel Using Ultra High-Throughput PRM-MS in an Inflammatory Bowel Disease Cohort.

Despite advances in clinical proteomics, translating protein biomarker discoveries into clinical use remains challenging due to the technical complexity of the validation process. Targeted MS-based proteomics approaches such as parallel reaction monitoring (PRM) offer sensitive and specific assays for biomarker translation. In this study, we developed a multiplex PRM assay using the Stellar mass spectrometry platform to quantify 57 plasma proteins, including 21 FDA-approved proteins. Loading curves (11-points) were performed at 4 sample throughputs (100, 144, 180, and 300 samples per day) using independent, optimized, and scheduled PRM methods. Following optimization, an inflammatory bowel disease (IBD) cohort of plasma samples (493 IBD, 509 matched controls) was analyzed at a throughput of 180 SPD. To monitor system performance, the study also included 1,000 additional injections for system suitability tests, low-, middle-, and high-quality controls, washes, and blanks. Using this approach, we observed high quantifiability (linearity, sensitivity, reproducibility) in the PRM assay and consistent in data acquisition across a large cohort. We also validated the candidate IBD markers, C-reactive protein and orosomucoid protein, identified in a recent discovery experiment.

biochemistry↗

Wnt/Beta-Catenin Signaling Is Active in Neuroendocrine Prostate Cancer

Wnt/beta-Catenin signaling plays a critical role in prostate cancer (PCa) progression, yet its precise contributions in neuroendocrine prostate cancer (NEPCa) remain incompletely understood. In this study, we utilized TRAMP/Wnt-reporter mice to monitor Wnt/beta-Catenin activity and investigated transcriptional alterations associated with NEPCa development. RNA sequencing and pathway enrichment analyses identified neuroactive ligand-receptor interaction, MAPK, calcium, and cAMP signaling as key pathways enriched in NEPCa. Although Wnt signaling was not among the top-enriched pathways, elevated Axin2 expression and increased Wnt-reporter activity suggest its involvement in NEPCa progression. We observed upregulated expression of Wnt3, Wnt6, Dvl2, Dvl3, and Lef1 in NEPCa, coupled with reduced expression of Yap1 and Frat1, which are involved in beta-Catenin degradation. Pharmacological inhibition of Wnt/beta-Catenin signaling using FC101 significantly suppressed PCa growth, underscoring its potential as a therapeutic target. These findings reveal that Wnt/beta-Catenin signaling is active in NEPCa through multiple mechanisms and highlight the need for further investigation into the regulatory interplay between Wnt and YAP1 in prostate cancer.

cancer biology↗