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Choi, J.

Publications and source records attributed to Choi, J..

At least 91 records · Page 5Linked to original sources

Large Impact of Genetic Data Processing Steps on Stability and Reproducibility of Set-Based Analyses in Genome-Wide Association Studies

Genome-wide association studies (GWAS) are crucial to human genetics research, yet their stability and reproducibility are often questioned. This work describes, analyzes, and provides tools for overcoming reproducibility challenges in two highly popular components of GWAS: set-based (a) hypothesis testing and (b) effect size estimation. Specifically, we focus on how the set-based natures of (a) and (b) often fuel non-reproducible results due to differences in data processing pipelines that are rarely discussed. First, we describe the processing challenges in a statistical model misspecification framework. Second, we analytically calculate the differences in power and amounts of bias that can arise in (a) and (b), respectively, due to small data processing choices. Third, we provide tools for quantifying and avoiding the data processing obstacles in GWAS. We validate our analytical calculations through a simulation study, and we demonstrate the aforementioned challenges empirically through analysis of a whole-exome sequencing study of pancreatic cancer. Author SummaryThe lack of reproducibility and stability in genome-wide association studies (GWAS) have been widely reported. Here, we demonstrate how such reproducibility challenges arise in a common component of GWAS, set-based hypothesis testing and estimation studies. Specifically, we show how minor, seemingly harmless decisions in how scientists prepare their data can lead to major differences in the final conclusions. These data processing steps are rarely reported in detail, further obscuring their importance. Our work precisely measures the impact of data processing steps on power and bias of common modeling approaches. As a partial solution for future GWAS, we also provide an R software package to interact with our results, which can be used to assess the impact of choices at the design stage of GWAS studies. We further analyze a pancreatic cancer dataset using two modern pipelines and show how the pipelines produce very different results for ATM, a gene that has been previously linked with pancreatic cancer. Using the tools provided by this work can help significantly improve the reproducibility and stability of set-based results, enhancing the translational potential of GWAS investigations.

genetics↗

Multilayered molecular and cellular mechanisms underlying intestinal epithelial regeneration

Intestinal epithelial cells (IECs) are replenished by intestinal stem cells (ISCs) residing in the intestinal crypts and isthmus. Under homeostatic conditions, Lgr5+ crypt base columnar cells (CBCs) are considered the primary ISCs1,2. The supply of IECs, however, remains continuous even in the absence of Lgr5+ CBCs3, implying the existence of alternative ISC populations. Over the past decade, two contrasting models have emerged to explain the identities of these compensatory cells. The distinct cell population model proposes that slow-cycling, quiescent cells near the +4 position, act as reserve stem cells (rISCs)3-10. The cellular plasticity model suggests a broad spectrum of IECs can dedifferentiate into intermediate fetal-like states, thereby acquiring stemness11,12. It is unclear which of these models is correct because the signaling mechanisms governing crypt regenerative responses remain poorly understood. Here, we demonstrate that Hedgehog (Hh) signaling orchestrates intestinal regeneration following Lgr5+ CBC loss by uniquely driving the emergence of de novo Lgr5+ CBCs from non-Lgr5+ CBCs clones. This regenerative mechanism is fundamentally distinct from both classical self-renewal of existing Lgr5+ CBCs and fetal-like dedifferentiation in intestinal villi. By accelerating the cell cycle and driving clonal competition among stem cell pools, Hh signaling leaves rare dormant stem cells in the crypt and isthmus regions. These rare cells act as damage-resistant "seeds" that can promote damage recovery, thereby conferring damage resistance on the tissue as a whole. Collectively, our findings identify novel molecular and cellular mechanisms underlying ISC regeneration and suggest potential therapeutic strategies for various intestinal epithelial diseases.

cell biology↗

A T-cell Intrinsic Role for APOL1 Risk Alleles in Allograft Rejection

African Americans have an increased risk of kidney disease due to exonic variants in Apolipoprotein-L1 (G1 and G2). These prevalent variants have also been linked with kidney rejection, but outside of association with African ancestry, underpinning causal mechanisms are unknown. We investigated T-cell function using transgenic mice with physiologic expression of wild type (G0-), G1-, or G2-APOL1. Mice with variant APOL1 showed greater CD8+T-cell activation with expansion of a central memory (TCM) subset. Stimulated G1-CD8+T-cells showed enhanced proliferation and cytokine production, which reversed with APOL1 inhibition. In MHC-mismatched cardiac transplants, G1-mice demonstrated greater CD8+T-cell infiltration and reduced survival. Bulk transcriptome of G1-CD8+T-cells, and single-cell transcriptome of graft infiltrating TCMs, showed enrichment of canonical T-cell receptor (TCR) pathways including Ca2+-signaling. G1-CD8+T-cells demonstrated baseline ER-Ca2+ depletion followed by sustained increases in cytosolic-Ca2+ upon TCR stimulation. G1-CD8+T-cells were more sensitive to Ca2+ chelation, or store-operated Ca2+ entry inhibition, and relatively resistant to calcineurin antagonism vs. G0-CD8+T-cells. Analogously, in a kidney transplant cohort, APOL1-variant recipients developed rejection when they had elevated peripheral TCMs before transplantation and despite significantly higher tacrolimus levels vs G0/G0-AAs with rejection. In summary, we unravel an excitatory T-cell intrinsic mechanism for APOL1 exonic variants, causally linking them with kidney rejection.

immunology↗

Dichotomous transcriptome divergence at the cell-type level between the Drosophila male and female germlines

Gene expression evolution in reproductive organs plays a central role in species divergence, yet cell-type-resolved patterns in invertebrates remain poorly understood. We used single-nucleus RNA-sequencing to profile testis and ovary transcriptomes from the sibling species Drosophila melanogaster and D. simulans. Despite conserved cellular composition, we observed highly cell-type-specific expression and coexpression network divergence between species. In the testis, mitotic cells were conserved across species, mirroring patterns in mammals, while divergence peaked in late spermatocytes. In the ovary, divergence was less pronounced, peaking in early germline and late-stage follicle cells, and enriched on the X chromosome, consistent with a faster-X effect driven by positive selection. Genes expressed in these cell types exhibited narrower expression breadth, younger phylogenetic age, and elevated rates of protein evolution in both tissues. Our findings reveal contrasting evolutionary regimes in male and female germlines, shaped by adaptive and non-adaptive mechanisms, contingent on cell type and chromosomal context.

evolutionary biology↗

A deep population stratification and ongoing local adaptations of the range-expanding lovebug Plecia longiforceps

Rapidly range-expanding species provide a superb opportunity to study dynamic demography and ongoing adaptations to novel environments. Plecia longiforceps, a species of lovebug flies native to southeast China and Taiwan, has recently been expanding in Okinawa in Japan and Seoul in South Korea, where massive outbreaks are garnering public attention. Here we analyzed whole-genome sequences of 150 individuals across China, Korea, Okinawa, and Taiwan, including a newly identified northern Chinese population from Qingdao. We found a deep divergence between continental (Korea-China) and insular (Okinawa-Taiwan) populations and specify northern China and Taiwan as sources for Korea and Okinawa, respectively. Severely reduced genetic diversity in Korea and Qingdao suggests serial founder events during their northward expansion. An old split time between Qingdao and Korea ([~]3,500 generations ago) and multiple gene flows into Qingdao reject a simple scenario of a single recent northward migration. Selection signals in northern groups include genes associated with pigmentation, thermal sensing, lipid metabolism, and immunity. We observed a markedly reduced genetic diversity on X chromosome in northern populations, indicating ongoing strong sex-biased selection. Our findings portrait details of the northward range expansion in the species and highlight the role of adaptation for successful invasion at higher latitudes.

evolutionary biology↗

A connectomic resource for neural cataloguing and circuit dissection of the larval zebrafish brain

We present a correlated light and electron microscopy (CLEM) dataset from a 7-day-old larval zebrafish, integrating confocal imaging of genetically labeled excitatory (vglut2a) and inhibitory (gad1b) neurons with nanometer-resolution serial section EM. The dataset spans the brain and anterior spinal cord, capturing >180,000 segmented soma, >40,000 molecularly annotated neurons, and 30 million synapses, most of which were classified as excitatory, inhibitory, or modulatory. To characterize the directional flow of activity across the brain, we leverage the synaptic and cell body annotations to compute region-wise input and output drive indices at single cell resolution. We illustrate the datasets utility by dissecting and validating circuits in three distinct systems: water flow direction encoding in the lateral line, recurrent excitation and contralateral inhibition in a hindbrain motion integrator, and functionally relevant targeted long-range projections from a tegmental excitatory nucleus, demonstrating that this resource enables rigorous hypothesis testing as well as exploratory-driven circuit analysis. The dataset is integrated into an open-access platform optimized to facilitate community reconstruction and discovery efforts throughout the larval zebrafish brain.

neuroscience↗

FERONIA defines intact tissue boundaries through cuticle development

Plant cuticle is the first hydrophobic barrier between the epidermis and the environment. Upon wounding, damaged tissues undergo healing processes that involve cuticle or callus formation at the wound site. However, signaling pathways that initiate cuticle development and callus formation in the wound-proximal region are still poorly understood. Here, we reveal that the FERONIA receptor-like kinase facilitates cuticle development in the epidermis and FER-mediated cuticle formation limits the propagation of wound-induced reactive oxygen species (ROS), which trigger callus formation. Cuticle defects stimulate NADPH oxidase-dependent ROS production, which leads to unrestricted callus formation. However, the cuticle formed in mesophyll cells in the vicinity of the wound suppresses ROS propagation, thereby preventing unorganized callus formation beyond the wound-proximal site and activating programmed cell death adjacent to the wound. These findings provide valuable insights into cuticle development in aerial tissues and its defensive function for preserving the integrity of undamaged regions.

plant biology↗

The SAMM50 rs3761472 causes mitochondrial dysfunction and metabolic dysfunction-associated steatotic liver disease

Genome-wide association studies (GWAS) have identified the SAMM50 rs3761472 single nucleotide polymorphism (SNP) as a risk factor for metabolic dysfunction-associated steatotic liver disease (MASLD), although its in vivo functions remain unclear. SAMM50 encodes a mitochondrial outer membrane protein critical for maintaining mitochondrial structure. To investigate the biological effects of rs3761472, we generated Samm50-knock-in (KI) mice harboring a D110G substitution using CRISPR/Cas9. This variant impaired mitochondrial integrity by downregulating key regulators of mitochondrial architecture, dynamics, and quality control. This contributed to reduced ATP production and elevated oxidative stress, inflammation, and hepatocyte death. The mutation also induced insulin resistance and glucose intolerance. Samm50-KI mice fed a high-fat diet exhibited pronounced hepatic lipid accumulation and liver injury, highlighting its pathogenic role in MASLD progression. Our findings demonstrate that SAMM50 rs3761472 is a critical driver of mitochondrial dysfunction and MASLD susceptibility, supporting its potential as a therapeutic target and its relevance to precision medicine.

genetics↗

Implantable CMOS Deep-Brain Fluorescence Imager with Single-Neuron Resolution

Despite the advantages of optical imaging over electrophysiology, such as cell-type specificity, its application has been limited to the investigation of shallow brain regions (< 2 mm) because of the light scattering property of brain tissue. Passive optical conduits such as graded-index lenses and waveguides have permitted access to deeper locales but with restricted resolution and field of view, while creating massive lesions along the inserted path, with little pathway to improvement in the technology. As an alternative, we present the Acus device, an active implantable complementary metal-oxide-semiconductor (CMOS) neural imager with a 512-pixel silicon image sensor post- processed into a 4.1-mm-long, 120-m-wide shank with a collinear fiber for illumination, which is able to record transient fluorescent signals in deep brain regions at 400 frames/sec. Acus can achieve single-neuron resolution in functional imaging of GCaMP6s-expressing neurons at a frame rate of 400 frames/sec.

neuroscience↗

Lineage recording in monoclonal gastruloids reveals heritable modes of early development

Mammalian stem cells possess a remarkable capacity for self-organization, a property that underlies increasingly sophisticated in vitro models of early development. However, even under carefully controlled conditions, stem cell-derived models exhibit substantial "inter-individual" heterogeneity. Focusing on gastruloids, a powerful model of the early posterior embryo1, we sought to investigate the origins of this heterogeneity. To this end, we developed a scalable protocol for generating gastruloids that are monoclonal, i.e. derived from a single mouse embryonic stem cell (mESC). Single cell transcriptional profiling of monoclonal gastruloids revealed extensive inter-individual heterogeneity, with some hardly progressing, others resembling conventional gastruloids but biased towards mesodermal or neural lineages, and yet others bearing cell types rare or absent from conventional polyclonal gastruloids. To investigate this further, we leveraged DNA Typewriter2 to record the cell lineage relationships among the mESCs from which monoclonal gastruloids originate. Early in the expansion of "founder" mESCsprior to induction of the resulting aggregates to form gastruloidswe observe clear examples of fate bias or fate restriction, i.e. sister clades that exhibit markedly different cell type compositions. In a separate experiment with DNA Typewriter, we reconstructed a monophyletic "tree of trees", composed of [~]50,000 cells derived from [~]100 gastruloids, all descended from a single "founder of founders" stem cell. From these data, we find that founder mESCs that are more closely related are more likely to give rise to monoclonal gastruloids with similar cell type compositions. Our results suggest that fluctuations in the intrinsic states of mESCs are heritable, and shape their descendants fates across many cell divisions. Our study also showcases how DNA Typewriter can be used to reconstruct high-resolution, monophyletic cell lineage trees in stem cell models of early development.

developmental biology↗

Clonal Hematopoiesis Mutations Increase Risk of Alzheimer's Disease with APOE ϵ3/ϵ3 Genotype

Clonal hematopoiesis of indeterminate potential (CHIP) represents clonal expansion of blood cells, and increases the risk of hematological malignancies and cardiovascular disorders. Recent studies have studied CHIP mutations in individuals with Alzheimers disease (AD), but it is unclear whether their role in AD pathogenesis is protective, detrimental, or neutral. In this study, we used molecular-barcoded deep gene panel sequencing ([~]400X) to examine CHIP mutations in 298 blood samples from AD and neurotypical individuals 60 years and older. The AD patients exhibited a significantly higher burden of CHIP mutations compared to the age-matched controls (p < 2e-7, odds ratio (OR) = 2.89), particularly in low-frequency variants often not captured by standard whole exome or whole genome sequencing (WGS). This increase was driven by individuals with the APOE {varepsilon}3/{varepsilon}3 genotype and absent in {varepsilon}4 carriers. Analysis of an independent dataset from the Alzheimers Disease Sequencing Project (ADSP), comprised of WGS data from [~]30,000 individuals, confirmed increased CHIP mutations in AD versus control (p < 0.02, OR = 1.32), again driven by individuals with APOE {varepsilon}3/{varepsilon}3 genotype. CHIP mutations in AD patients also showed stronger positive selection than in controls. Our results indicate that AD patients show significantly more CHIP mutations in their blood than controls, involving more than one third of AD patients, and contributing to AD risk through a mechanism independent of APOE {varepsilon}4.

genetics↗

Longitudinal deep phenotyping in a mouse model of West syndrome reveals temporal dynamics of synapse remodeling, gliosis, and proteomic and lipidomic changes during seizure evolution

Neurodevelopmental disorders can have long-lasting effects, causing not only early pediatric symptoms but also a range of neurological issues throughout adulthood. West syndrome is a severe neurodevelopmental disorder marked by infantile spasms, an early symptom that typically subsides with age. However, many patients progress to other seizure forms, known as seizure evolution, which is closely linked to poor long-term outcomes. Despite its clinical significance, the neurobiological mechanisms behind seizure evolution in West syndrome remain poorly understood. Recent genetic studies have consistently identified the CYFIP2 p.Arg87Cys variant in West syndrome patients, and the Cyfip2+/R87C mouse model carrying this mutation has been shown to recapitulate key symptoms of the disorder, including infantile spasms. In this study, we aimed to gain deeper insight into seizure evolution by conducting longitudinal deep phenotyping of the Cyfip2+/R87C mouse model from the neonatal stage to seven months of age. We tracked seizure activity through behavioral and EEG recordings and employed multi-omic analyses, including tissue and single-cell level transcriptomics, ultrastructural analysis, proteomics, and lipidomics, to capture a comprehensive view of molecular and cellular changes. Our results showed that after an initial period of neonatal spasms, Cyfip2+/R87C mice entered a seizure-free phase, followed by spontaneous recurrent seizures in adulthood, ultimately leading to premature death. This progression was associated with synaptic remodeling, sequential activation of different glial cell types, lipid droplet accumulation in astrocytes, and significant proteomic and lipidomic changes in the brain. These findings suggest that seizure evolution in West syndrome involves complex, time-dependent interactions between neurons and glial cells, along with alterations in lipid metabolism. Our study highlights the potential of longitudinal multi-omic approaches to uncover underlying mechanisms of seizure evolution and suggests that targeting these changes could offer novel therapeutic strategies. Additionally, the dataset generated here may provide valuable insights for other epilepsy and neurodevelopmental disorder models.

neuroscience↗

High-throughput discovery of transmembrane helix dimers from human single-pass membrane proteins with TOXGREEN sort-seq

The oligomerization of the transmembrane helices of single-pass membrane proteins is crucial to biological function and its misregulation can lead to many diseases. The study of transmembrane helix oligomerization is facilitated by the availability of genetic reporter assays, which are essential tools for understanding the organization and biology of single-pass systems. In particular, reporter assays are crucial for mapping the oligomerization interfaces of transmembrane helices through scanning mutagenesis but their application is limited by the need to clone and measure each construct individually. Here, we present "TOXGREEN sort-seq", a high-throughput version of the TOXGREEN assay that enables the direct measurement of transmembrane helix oligomerization in large libraries using fluorescence-activated cell sorting and next-generation sequencing. We show that TOXGREEN sort-seq is robust and reproduce the direct measurements of individual constructs with good accuracy and sensitivity. The method produced high-quality mutational profiles from a library of 17,400 constructs designed to probe the interface of 100 potential GASright dimers predicted from sequences of human single-pass membrane proteins. We report the validated structural model of twelve dimers involved in a variety of biological functions, including immune response (interleukin-22 receptor subunit alpha-1, butyrophilin-like protein 3, hepatitis A virus cellular receptor 2), transport (transferrin receptor protein 1), and cell-surface signaling and proliferation (syndecan-3; semaphorins 5A, 6B and 6D). Remarkably, all three semaphorins in the dataset formed strong dimers and produced mutational profiles consistent with the computational structure. These findings open the possibility that dimerization may be relevant to these proteins activity and provide a validated interface for assessing their biological role.

biophysics↗

Characterization of Human Anterior Neural Organoids as a Model for Investigating Cohen Syndrome

Neural organoids display three-dimensional (3D) structures that resemble in vivo neural architectures. Previously, we developed a novel two-dimensional (2D) neural induction-based protocol for culturing spinal cord organoids, enabling size control and recapitulating neural tube morphogenesis. In this study, we evaluated the application of this concept to induce the anterior regions of the brain and generate human anterior neural organoids (hANOs). By inducing neuroepithelial (NE) cells in 2D and re-aggregating them led to tube-forming morphogenesis similar to that posterior spinal cord induction. The transcriptome profiles of these hANOs resembled the frontal cortex of 20 weeks post-conception (PCW) human embryos. Using this hANOs protocol, we investigated microcephaly phenotypes associated with Cohen syndrome (CS), caused by biallelic loss-of-function variants in VPS13B gene. Deleting VPS13B in human pluripotent stem cells resulted in Golgi dispersion and growth retardation onset in mutant hANOs, akin to CS patients with postnatal microcephaly. This delay is partly linked to reduced neuronal growth. Additionally, mature CS organoids showed enhanced hyper-excitability associated with an excitatory/inhibitory imbalance. In conclusion, this protocol is suitable for studying microcephaly phenotypes from human genetic mutations due to its simplicity and scalability.

neuroscience↗

Whole-Proteome Screening and Multi-Modal Profiling of Antigen-Specific CD4+ T Cells at Single-Cell Resolution

Systematic whole-proteome screening and comprehensive profiling of antigen-specific CD4+ T cells are crucial for advancing our understanding of CD4+ T cell immunity, yet such efforts remain technically challenging. Here, we present a high-throughput platform that employs large-scale class II single-chain trimer libraries to detect antigen-specific CD4+ T cells, while simultaneously profiling their antigen specificity, TCR/{beta} sequences, MHC restriction, whole transcriptomes, and patient/timepoint origins at single-cell resolution. We benchmarked SCTs against conventional pMHCs and validated the SCT library-based approach in direct ex vivo identification of antigen-specific CD4+ T cells in healthy donors. We then applied the platform to screen the entire SARS-CoV-2 receptor-binding domain in a longitudinal patient cohort, identifying 2,188 antigen-specific CD4+ T cells and revealing key features that define antigen immunogenicity. Extending to cancer, we performed whole-proteome screening of HPV-16 E6/E7 for TCR repertoire profiling in a precancerous cohort, uncovering functional heterogeneity of HPV-specific TCRs. By integrating high-throughput antigen screening with high-dimensional, multi-modal cellular characterization, our approach offers an unprecedented window into CD4+ T cell immunity across diverse disease contexts and empowers the development of new therapies.

bioengineering↗

Recognition-dependent activation of the RRS1-R/RPS4 immune receptor complex

The Arabidopsis TIR-NLR immune receptors RPS4 and RRS1 function together to enable recognition of multiple effector proteins including AvrRps4 and PopP2. We show here that both in the presence and absence of effector, RPS4 and RRS1 form an oligomer that does not change in size upon effector provision. Oligomer formation involves interactions between the RPS4 and RRS1 TIR domains and requires nucleotide binding capacity in RPS4. RPS4 mutants that lose TIR domain NADase activity abrogate immune activation but retain oligomerization. A cysteine residue in the RPS4 LRR domain contributes to oligomer stabilization. We propose that upon effector recognition, conformational changes in the complex relieve inhibition of RPS4 TIR domains by RRS1 TIR domains, enabling proximity between RPS4 TIR domains to create NADase activity.

plant biology↗

NeighbourNet: Scalable cell-specific co-expression networks for granular regulatory pattern discovery

Gene regulatory networks (GRNs) provide a fundamental framework for understanding the molecular mechanisms that govern gene expression. Advances in single-cell RNA sequencing (scRNA-seq) have enabled GRN inference at cellular resolution; however, most existing approaches rely on predefined clusters or cell states, implicitly assuming static regulatory programs and potentially missing subtle, dynamic variation in regulation across individual cells. To address these limitations, we introduce NeighbourNet (NNet), a method that constructs cell-specific co-expression networks. NNet first applies principal component analysis to embed gene expression into a low-dimensional space, followed by local regression within each cells k-nearest neighbourhood (KNN) to quantify co-expression. This approach improves computational efficiency and stabilises co-expression estimates, mitigating challenges posed by small sample sizes in KNN regression and the inherent noise and sparsity of scRNA-seq data. Beyond co-expression, NNet supports scalable downstream analyses, including (i) clustering and aggregating cell-specific networks into meta-networks that capture primary co-expression patterns, and (ii) integrating prior knowledge to annotate co-expression and infer active signalling interactions at the individual cell level. All functional modules of NNet are implemented with an efficient algorithm that enables application to large-scale single-cell datasets. We demonstrate NNets effectiveness through three case studies on transcription factor activity prediction, early haematopoiesis, and tumour microenvironments. Provided as an R package, NNet offers a novel framework for exploring cellular variation in co-expression and integrates seamlessly with existing single-cell analysis workflows.

bioinformatics↗

iPSC-Derived Cerebral Organoids Reveal Mitochondrial, Inflammatory and Neuronal Vulnerabilities in Bipolar Disorder

Bipolar disorder (BD) is increasingly recognized as a disorder with both mitochondrial dysfunction and heightened inflammatory reactivity, yet their contribution to neuronal activity remains unclear. To address these gaps, this study utilizes iPSC-derived cerebral organoids (COs) from BD patients and healthy controls to model disease-specific metabolic and inflammatory dysfunction in a physiologically relevant system. BD COs exhibited mitochondrial impairment, dysregulated metabolic function, and increased nod-leucine rich repeat and pyrin domain containing protein 3 (NLRP3) inflammasome activation sensitivity. Treatment with MCC950, a selective NLRP3 inhibitor, effectively rescued mitochondrial function and reduced inflammatory activation in both BD and control COs. Additionally, a Bioactive Flavonoid Extract (BFE) was explored as a potential therapeutic, demonstrating partial rescue of inflammasome activation. These findings highlight a mitochondria-inflammasome axis in BD pathophysiology and establish a novel platform for studying BD-associated cellular mechanisms, ultimately bridging the gap between molecular dysfunction and therapeutic development.

neuroscience↗