Biology subjects

Kim, Y.

Publications and source records attributed to Kim, Y..

At least 163 records · Page 9Linked to original sources

bioRxiv2024

Structural Analysis of a Metamorphic Protein using AlphaFold2

Metamorphic proteins, which can adopt multiple stable conformations, challenge the traditional understanding of protein structure and function. KaiB is a metamorphic protein that regulates the circadian clock, a central regulator governing gene expression in most light-perceiving organisms on Earth. An interesting aspect is that the circadian clock can be reconstituted in vitro by mixing Kai proteins (KaiA, KaiB, and KaiC) with ATP and Mg2+. The phosphorylation state of KaiC oscillates with a 24-hour period. The fold-switched form of KaiB binds to KaiC to activate the dephosphorylation of KaiC, while the other fold of KaiB dissociates from KaiC, allowing phosphorylation to be activated by the binding of KaiA to KaiC. To understand the metamorphic process of KaiB, we utilized AlphaFold2, a protein structure prediction program, and sequence alignments. We found that a proline residue determines the fold of KaiB. We also confirmed that mutating this proline to lysine changes KaiB to a fold-switched conformation. This validates that AlphaFold2 can be used for the study of metamorphic proteins.

biochemistry↗

bioRxiv2024

A fast, muscle-actuated biohybrid swimming robot

The integration of biological actuators with soft scaffolds has led to biohybrid robots including microscale flagellate-like swimmers which generate thrust by waving their flagella-like tails. However, they achieve swimming speeds of only 0.014 body lengths per minute, Reynolds number (Re) [~] 10-3, which is much slower than natural flagellates (O(102 - 103) body lengths per minute). To investigate this, we applied theoretical and experimental methods, including fabrication of a swimmer that converts muscle contractions into large angular tail displacements, reaching swimming speeds of 86.8 m/s (0.58 body lengths per minute), surpassing low-Re predictions. Swimming dynamics sharply transition from a low-Re ([~] 10-3) to an intermediate-Re ([~] 0.1) regime when the actuation angle exceeded 4{degrees}. We used the swimmer to study the ability of muscle to adapt to mechanical stiffness and the beneficial effects of neuromuscular coculture on muscle development. These insights into mechanical and chemical cues will help optimize future biobots. TeaserHow are biological flagellate swimmers like E. coli and sperm cells so fast? We have built a new biohybrid robot to explore the theory.

bioengineering↗

bioRxiv2024

Deep Gaussian Process with Uncertainty Estimation for Microsatellite Instability and Immunotherapy Response Prediction Based on Histology

Determining tumor microsatellite status has significant clinical value because tumors that are microsatellite instability-high (MSI-H) or mismatch repair deficient (dMMR) respond well to immune check-point inhibitors (ICIs) and oftentimes not to chemotherapeutics. We propose MSI-SEER, a deep Gaussian process-based Bayesian model that analyzes H&E whole-slide images in weakly-supervised-learning to predict microsatellite status in gastric and colorectal cancers. We performed extensive validation using multiple large datasets comprised of patients from diverse racial backgrounds. MSI-SEER achieved state-of-the-art performance with MSI prediction, which was by integrating uncertainty prediction. We achieved high accuracy for predicting ICI responsiveness by combining tumor MSI status with stroma-to-tumor ratio. Finally, MSI-SEERs tile-level predictions revealed novel insights into the role of spatial distribution of MSI-H regions in the tumor microenvironment and ICI response.

bioinformatics↗

bioRxiv2024

Dendritome Mapping Unveils Spatial Organization of Striatal D1/D2-Neuron Morphology

Morphology is a cardinal feature of a neuron and mediates its functions, but profiling neuronal morphologies at scale remains a formidable challenge. Here we describe a generalizable pipeline for large-scale brainwide profiling of dendritic morphology of genetically-defined single neurons in the mouse brain. We generated a dataset of 3,762 3D-reconstructed and reference-atlas mapped striatal D1- and D2-medium spiny neurons (MSNs). Integrative morphometric analyses reveal distinct impacts of D1/D2 and anatomical locations on MSN morphology. To analyze striatal regional features of MSN dendrites without prior anatomical constraints, we assigned MSNs to a lattice of cubic boxes in the reference brain atlas, and summarized morphometric representation ("eigen-morph") for each box and clustered boxes with shared morphometry. This analysis reveals 6 modules with characteristic dendritic features and spanning contiguous striatal territories, each receiving distinct corticostriatal inputs. Finally, we found aging confers robust and concordant dendritic length and branching defects in D1/D2-MSNs, while Huntingtons disease (HD) mice exhibit MSN-subtype and striatal regional specific pathology. Together, our study demonstrates a systems-biology approach to profile dendritic morphology of genetically-defined single-neurons; and defines novel striatal D1/D2-MSN morphological territories and aging- or HD-associated pathologies.

neuroscience↗

bioRxiv2024

Noncovarying storage effect: positive selection on mutant alleles that amplify random fitness and demographic fluctuations

Temporally variable environments in natural populations generate fluctuations in not only the population size but also the fitness effects of mutant alleles. The theory of storage effect, a species/allelic diversity-promoting mechanism discovered in ecology, predicts that rare mutants with fluctuating fitness can be positively selected and then maintained in balanced polymorphism if the population is subdivided into two parts that are respectively exposed to and protected from fluctuating environment. Recent study found that, under pre-exisiting oscillation in population size, the mutant is positively selected to fixation if its fitness change correlates with the rate of population growth, which further amplifies population size oscillation. To further understand these eco-evolutionary dynamics and elucidate their generality in natural populations, this study built more realistic models that assume randomly, not cyclically, fluctuating selection and common demographic features, including heterogeneous ecological patches or an age-structured population. Mathematical analysis revealed that this novel evolutionary force is generated when the size of the subpopulation subject to weak selection does not covary with that of the other subpopulation. Simulations showed that this noncovarying storage effect is robust to various perturbations in the model. Multi-locus simulations revealed that oscillatory polymorphism at many loci can be simultaneously maintained and that positive feedback between demography and selection can accelerate the sequential fixations of fluctuation-amplifying mutations and thus lead to a drastic amplification of population size fluctuation. These results suggest that the noncovarying storage effect is a potentially prevalent evolutionary force in nature for maintaining genetic variation and causing large demographic fluctuations. ARTICLE SUMMARYNatural populations experience rapid environmental changes that cause fluctuations in the fitness of genetic variants and population size. This study investigates how evolutionary changes due to fitness differences interact with concurrent demographic changes. The theory of the storage effect, which is a mechanism for promoting genetic diversity, was extended to add random population size fluctuation with heterogeneous environmental patches or in a population divided into different age classes. A novel evolutionary force that either increases genetic variation or drives evolution toward further amplification of population size fluctuation, an unconventional contributor to large demographic fluctuations in nature, was identified and analyzed.

evolutionary biology↗

bioRxiv2024

Brain-wide connectivity and novelty response of the dorsal endopiriform nucleus in mice

The dorsal endopiriform nucleus (EPd) is an enigmatic cortical subplate structure located inside the piriform cortex that shares a similar developmental origin with the claustrum. Although the EPd has been previously implicated in epilepsy and olfactory processing, its anatomical organization, connectivity patterns, and function remain largely unclear due to a lack of specific molecular markers. Our previous mapping study serendipitously identified that the Oxt receptor (Oxtr) is densely expressed in the EPd. Subsequent immunohistochemical and spatial transcriptomic analyses confirmed that Oxtr expression is enriched in the EPd, revealing distinct molecular organization compared to the neighboring claustrum. Whole brain input-output mapping of EPd Oxtr-positive neurons unveils extensive bidirectional connections to the ventral half of the brain, orchestrating functional circuits regulating olfaction, internal state, and emotion. Furthermore, our in-vivo miniscope recordings show that EPd Oxtr neurons exhibit high baseline activity during exploratory behavior, with a sharp decrease in activity in response to novel stimuli. This suggests that the EPd regulates interoceptive states and likely plays a role in adapting to novel exteroceptive cues.

neuroscience↗

bioRxiv2024

A stepwise, modular design of building uniform brain assembloids representing the dynamic cellular interplay between neurons and glial cells

Current brain organoid technology fails to provide adequate patterning cues to induce a mature structure that represent the complexity of the human brain. Here, we developed a module-based cellular reconstitution technology to sequentially build uniform forebrain assembloids with mature cortical structures and functional connectivity. The uniformity and maturity of the newly-conceived forebrain assembloids were achieved by creating single-rosette-based organoids at the early stage, whose sizes were big and consistent with the treatment of Wnt and Hedgehog agonists, followed by spatial reconstitution with the Reelin-expressing neuronal layer and non-neuronal glial cells. The resulting single-rosette-based forebrain assembloids were highly uniform and reproducible without significant batch effects, solving major heterogeneity issues caused by difficulties in controlling the number and size of rosettes in conventional multi-rosette organoids. Furthermore, these forebrain assembloids structurally and functionally recapitulated the physiology of the human brain, including the six-layered cortical structure, functional connectivity, and dynamic cellular interplay between neurons and glial cells. Our study thus provided an innovative preclinical model to study a range of neurological disorders, understanding the pathogenesis of which requires an organoid system capable of representing the dynamic cellular interactions and the maturity of the human brain.

developmental biology↗

bioRxiv2024

Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair for somatic benchmarks

The Genome in a Bottle Consortium (GIAB), hosted by the National Institute of Standards and Technology (NIST), is developing new matched tumor-normal samples, the first to be explicitly consented for public dissemination of genomic data and cell lines. Here, we describe a comprehensive genomic dataset from the first individual, HG008, including DNA from an adherent, epithelial-like pancreatic ductal adenocarcinoma (PDAC) tumor cell line and matched normal cells from duodenal and pancreatic tissues. Data for the tumor-normal matched samples comes from seventeen distinct state-of-the-art whole genome measurement technologies, including high depth short and long-read bulk whole genome sequencing (WGS), single cell WGS, and Hi-C, and karyotyping. In future publications, these data will be used by the GIAB Consortium to develop matched tumor-normal benchmarks for somatic variant detection. We expect these data to facilitate innovation for whole genome measurement technologies, de novo assembly of tumor and normal genomes, and bioinformatic tools to identify small and structural somatic mutations. This first-of-its-kind broadly consented open-access resource will facilitate further understanding of sequencing methods used for cancer biology.

genomics↗

bioRxiv2024

Progressive overfilling of readily releasable pool underlies short-term facilitation at recurrent excitatory synapses in layer 2/3 of the rat prefrontal cortex

Short-term facilitation of recurrent excitatory synapses within the cortical network has been proposed to support persistent activity during working memory tasks, yet the underlying mechanisms remain poorly understood. We characterized short-term plasticity at the local excitatory synapses in layer 2/3 of the rat medial prefrontal cortex and studied its presynaptic mechanisms. Low-frequency stimulation induced slowly developing facilitation, whereas high-frequency stimulation initially induced strong depression followed by rapid facilitation. This non-monotonic delayed facilitation after a brief depression resulted from a high vesicular fusion probability and slow activation of Ca2+-dependent vesicle replenishment, which led to the overfilling of release sites beyond their basal occupancy. Pharmacological and gene knockdown (KD) experiments revealed that the facilitation was mediated by phospholipase C/diacylglycerol signaling and synaptotagmin 7 (Syt7). Notably, Syt7 KD abolished facilitation and slowed the refilling rate of vesicles with high fusion probability. Furthermore, Syt7 deficiency in layer 2/3 pyramidal neurons impaired the acquisition of trace fear memory and reduced c-Fos activity. In conclusion, Ca2+- and Syt7-dependent overfilling of release sites mediates synaptic facilitation at layer 2/3 recurrent excitatory synapses and contributes to temporal associative learning.

neuroscience↗

bioRxiv2024

Smooth muscle Cxcl12 activation is associated with vascular remodeling in flow-induced pulmonary hypertension

Patients with congenital heart disease (CHD) resulting in significant left-to-right shunting of blood are at risk for the development of pulmonary arterial hypertension (PAH). The underlying mechanism by which pulmonary overcirculation and shear stress lead to vascular remodeling remains unclear. Our study established a new "two-hit" murine model of severe pulmonary hypertension (PH) by combining left pneumonectomy and exposure to hypoxia (LP/Hx). Utilizing transgenic reporter lines, immunofluorescence staining, and advanced microscopy, we conducted cell-lineage tracing experiments for endothelial cells (ECs), smooth muscle cells (SMCs), and pericytes. We identified that SMCs is a primary contributor to distal arteriolar remodeling after LP/Hx. Subsequent qPCR analysis on isolated cells demonstrated that Cxcl12 was upregulated in both ECs and SMCs from LP/Hx animals. Likewise, CXCL12 was overexpressed in the SMC layer of arterioles in patients with acyanotic PAH-CHD. These findings provide novel insights into the contribution of SMCs and Cxcl12 to pulmonary flow-induced vascular remodeling. This newly established murine model of PH will serve as a new tool for research and targeted therapeutics for patients with PAH.

molecular biology↗

bioRxiv2024

Mouse Brain Extractor: Brain segmentation of mouse MRI using global positional encoding and SwinUNETR

In spite of the great progress that has been made towards automating brain extraction in human magnetic resonance imaging (MRI), challenges remain in the automation of this task for mouse models of brain disorders. Researchers often resort to editing brain segmentation results manually when automated methods fail to produce accurate delineations. However, manual corrections can be labor-intensive and introduce interrater variability. This motivated our development of a new deep-learning-based method for brain segmentation of mouse MRI, which we call Mouse Brain Extractor. We adapted the existing SwinUNETR architecture (Hatamizadeh et al., 2021) with the goal of making it more robust to scale variance. Our approach is to supply the network model with supplementary spatial information in the form of absolute positional encoding. We use a new scheme for positional encoding, which we call Global Positional Encoding (GPE). GPE is based on a shared coordinate frame that is relative to the entire input image. This differs from the positional encoding used in SwinUNETR, which solely employs relative pairwise image patch positions. GPE also differs from the conventional absolute positional encoding approach, which encodes position relative to a subimage rather than the entire image. We trained and tested our method on a heterogeneous dataset of N=223 mouse MRI, for which we generated a corresponding set of manually-edited brain masks. These data were acquired previously in other studies using several different scanners and imaging protocols and included in vivo and ex vivo images of mice with heterogeneous brain structure due to different genotypes, strains, diseases, ages, and sexes. We evaluated our methods results against those of seven existing rodent brain extraction methods and two state-of-the art deep-learning approaches, nnU-Net (Isensee et al., 2018) and SwinUNETR. Overall, our proposed method achieved average Dice scores on the order of 0.98 and average HD95 measures on the order of 100 {micro}m when compared to the manually-labeled brain masks. In statistical analyses, our method significantly outperformed the conventional approaches and performed as well as or significantly better than the nnU-Net and SwinUNETR methods. These results suggest that Global Positional Encoding provides additional contextual information that enables our Mouse Brain Extractor to perform competitively on datasets containing multiple resolutions.

neuroscience↗

bioRxiv2024

The small MAF transcription factor MAFG co-opts MITF to promote melanoma progression

Transcription factor deregulation potently drives melanoma progression by dynamically and reversibly controlling gene expression programs. We previously identified the small MAF family transcription factor MAFG as a putative driver of melanoma progression, prompting an in-depth evaluation of its role in melanoma. MAFG expression increases with human melanoma stages and ectopic MAFG expression enhances the malignant behavior of human melanoma cells in vitro, xenograft models, and genetic mouse models of spontaneous melanoma. Moreover, MAFG induces a melanoma phenotype switch from a melanocytic state to a more dedifferentiated state. Mechanistically, MAFG interacts with the lineage transcription factor MITF which is required for the pro-tumorigenic effects of MAFG. MAFG and MITF co-occupy numerous genomic sites and MAFG overexpression influences the expression of genes harboring binding sites for the MAFG[~]MITF complex. These results establish MAFG as a potent driver of melanomagenesis through dimerization with MITF and uncover an unappreciated mechanism of MITF regulation. Significance statementMITF is critically involved in melanoma progression and phenotype switching. We discovered that MAFG interacts with MITF to influence expression of MITF target genes and facilitate a shift toward a dedifferentiated melanoma cell state. This study demonstrates that MAFG promotes melanomagenesis by influencing MITF activity, an unappreciated mechanism of MITF regulation.

cancer biology↗

bioRxiv2024

Sex-dependent metabolic remodeling of kidneys revealed by arteriovenous metabolomics

Sex is a fundamental biological variable important in biomedical research, drug development, clinical trials, and prevention approaches. Among many organs, kidneys are known to exhibit remarkable structural, histological, and pathological differences between sexes. However, whether and how kidneys display distinct metabolic activities between sexes is poorly understood. By developing kidney-specific arteriovenous (AV) metabolomics combined with transcriptomics, we report striking sex differences in both basal metabolic activities and adaptive metabolic remodeling of kidneys after a fat-enriched ketogenic diet (KD), a regimen known to mitigate kidney diseases and improve immunotherapy for renal cancer. At the basal state, female kidneys show highly accumulated aldosterone and various acylcarnitines. In response to the KD, aldosterone levels remain high selectively in females but the sex difference in acylcarnitines disappears. AV data revealed that, under KD, female kidneys avidly take up circulating fatty acids and release 3-hydroxybutyrate (3-HB) whereas male kidneys barely absorb fatty acids but consistently take up 3-HB. Although both male and female kidneys take up gluconeogenic substrates such as glycerol, glutamine and lactate, only female kidneys exhibit net glucose release. Kidney transcriptomics data incompletely predict these sex differences, suggesting post-transcriptional/translational regulation mechanisms. This study provides foundational insights into the sex-dependent and diet-elicited metabolic flexibility of the kidneys in vivo, serving as a unique resource for understanding variable disease prevalence and drug responses between male and female kidneys.

biochemistry↗

bioRxiv2024

Electrostatic changes enabled the diversification of an exocyst subunit via protein complex escape

The evolution of cellular complexity hinges on the capacity of multimeric protein complexes to diversify without compromising their ancestral functions. A central question is how individual subunits within these complexes can evolve novel functions while maintaining the integrity of the original assembly. Here, we explore this question by tracing the evolutionary trajectory of the plant exocyst, an octameric complex essential for exocytosis in eukaryotes. Remarkably, the Exo70 subunit underwent dramatic expansion and functional divergence in plants. We demonstrate that electrostatic alterations in the N-terminal region of the Exo70 subunit precipitated its dissociation from the exocyst complex. This release mitigated paralog interference, thereby facilitating the subunits extensive functional co-option. Our findings reveal a nuanced mechanism by which a protein subunit, ancestrally constrained within a multimeric complex, can escape those constraints and evolve novel functions, shedding light on the molecular underpinnings of cellular innovation. One-Sentence SummaryEvolutionary diversification of an exocyst subunit is driven by electrostatic shifts that dissociates it from the ancestral complex.

evolutionary biology↗

bioRxiv2024

Optimizing transcriptome-based synthetic lethality predictions to improve precision oncology in early-stage breast cancer: BC-SELECT

BackgroundPatients with non-metastatic triple-negative (TNBC) or HER2-positive (HER2+) breast cancer do not have tools to predict treatment response or prioritize options prior to starting therapy. Pathologic complete response (pCR) is a proxy that requires neoadjuvant treatment. BC-SELECT leverages genetic interactions (e.g. synthetic lethality (SL)/rescue (SR)) to predict treatment response via pCR from breast cancer gene expression data. BC-SELECT involves (1) "gene-pair identification" that identifies clinically relevant partner genes from large-scale datasets for a given targeted therapy or immunotherapy target, and (2) "training / parameter tuning" using clinical trials to predict treatment response. We evaluated BC-SELECTs ability to predict pCR for trastuzumab, poly (ADP-ribose) polymerase (PARP) inhibitors, and immunotherapy, with tuning supported by three trials (n=86) and validation on nine unseen trials (n=722). ResultsBC-SELECT significantly predicted pCR in 6/9 trials, including all PARP inhibitors (ROC-AUCs 0.6-0.8; Odds Ratio (OR): 1.9-3.5) and immunotherapy (ROC-AUCs 0.7-0.8; OR: 3.2-7.1). BC-SELECT significantly distinguished between pCR and residual disease in 8/9 trials. ConclusionsNo current standard-of-care, pre-treatment approaches predict benefit in non-metastatic TNBC and HER2+ breast cancer. BC-SELECT leverages genetic interactions to predict treatment response from gene expression data. Our findings support development of BC-SELECT towards prioritizing PARP inhibitors and immunotherapy in non-metastatic breast cancer.

bioinformatics↗

bioRxiv2024

Prelimbic corticopontine neurons gate extinction learning

The prelimbic cortex is essential for association of temporally separated events, and impedes extinction of learned association. The network mechanism underlying reversal learning, however, remains elusive. Here, we found that mitochondria-dependent post-tetanic potentiation at synapses onto prelimbic corticopontine neurons impedes extinction learning without affecting initial associative learning. Rats underwent trace fear conditioning followed by extinction sessions. Pharmacological inhibition of post-tetanic potentiation using tetaraphenylphosphnium (TPP), a mitochondrial Ca2+ release blocker, accelerated extinction of trace fear memory, leaving trace fear memory formation intact. Optogenetic inhibition of corticopontine, but not commissural, neurons phenocopied these effects. Electrophysiological recordings and Ca2+ imaging revealed that TPP treatment reduced the persistent activity of corticopontine neurons encoding tone presentation. Mechanistically, associative learning triggers the bursting activity of prelimbic pyramidal neurons that induces post-tetanic potentiation of corticopontine neurons, an effect blocked by TPP treatment. Thus, we identified a prelimbic cell type- and local circuit-specific mechanism that selectively gates extinction learning.

neuroscience↗

bioRxiv2024

Gut microbiota dysbiosis induced by brain tumor modulates the efficacy of immunotherapy

BackgroundAlthough the influence of gut microbiota on various tumors has gained recognition, the intricate mechanisms underlying their effects on brain tumors remain largely unexplored. In this study, our objective was to unveil pivotal gut microbiota that contribute significantly to the anti-tumor immune response against brain tumors. ResultsDuring the progression of brain tumors, our research uncovered a notable shift in the gut microbiome, as revealed through comprehensive 16S rRNA sequencing analysis. This shift coincided with a substantial decrease in the concentration of tryptophan in fecal samples, indicating a potential link between tryptophan levels and microbiome composition. Intriguingly, dietary supplementation with tryptophan significantly mitigated these microbial alterations, suggesting a restorative effect on the gut microbiota composition. This intervention not only reversed the changes observed in the gut microbiome but also markedly improved survival rates, a phenomenon that was determined to be dependent on the gut microbiota. The mechanism underlying this improvement appears to involve an enhancement in T cell circulation, which in turn boosts the efficacy of immunotherapeutic approaches. Upon further investigation into the specific microbial species that were positively influenced by tryptophan supplementation, some candidates were screened. Among several gut microbiota strains restored by tryptophan supplementation, the most significant is Duncaniella dubosii. Through sole colonization into germ-free mice, we found that the presence of Duncaniella dubosii alone was able to replicate the beneficial effects observed with tryptophan supplementation. ConclusionsThis study highlights Duncaniella dubosiis crucial role in linking tryptophan supplementation to positive shifts in the gut microbiome, immune modulation, and enhanced survival during brain tumor progression. It underscores the complex interaction between diet, microbiota, and immune responses, offering novel insights for boosting cancer immunotherapys success.

microbiology↗

bioRxiv2024

Identification of the Polo-like kinase substrate required for homologous synapsis in C. elegans

The synaptonemal complex (SC) is a zipper-like protein structure that aligns homologous chromosome pairs and regulates recombination during meiosis. Despite its conserved appearance and function, how synapsis occurs between chromosome axes remains elusive. Here, we demonstrate that Polo-like kinases (PLKs) phosphorylate a single conserved residue in the disordered C-terminal tails of two paralogous SC subunits, SYP-5 and SYP-6, to establish an electrostatic interface between the SC central region and chromosome axes in C. elegans. While SYP-5/6 phosphorylation is dispensable for the ability of SC proteins to self-assemble, local phosphorylation by PLKs at the pairing center is crucial for SC elongation between homologous chromosome axes. Additionally, SYP-5/6 phosphorylation is essential for asymmetric SC disassembly and proper PLK-2 localization after crossover designation, which drives chromosome remodeling required for homolog separation during meiosis I. This work identifies a key regulatory mechanism by which localized PLK activity mediates the SC-axis interaction through phosphorylation of SYP-5/6, coupling synapsis initiation to homolog pairing.

cell biology↗