Biology subjects

Kim, C.

Publications and source records attributed to Kim, C..

At least 109 records · Page 6Linked to original sources

bioRxiv2022

PCLAF-DREAM Drives Alveolar Cell Plasticity for Lung Regeneration

Spatiotemporal control of stem and progenitor cells is essential for lung regeneration, the failure of which leads to lung disease. However, the mechanism of alveolar cell plasticity during regeneration remains elusive. We previously found that PCLAF remodels the DREAM complex for cell cycle re-entry. PCLAF expression is specifically enriched in proliferating lung progenitor cells, along with the DREAM target genes by lung damage. Genetic ablation of Pclaf inhibited alveolar type I (AT1) cell regeneration from alveolar type II (AT2) cells, inducing lung fibrosis. Mechanistically, the PCLAF-DREAM complex directly transactivates CLIC4, promoting TGF-{beta} signaling that regulates the balance between AT1 and AT2 cells. Furthermore, a drug candidate that mimics the PCLAF-DREAM transcriptional signatures for lung regeneration was identified and validated in organoids and mice. Our study unveils an unexpected role of the PCLAF-DREAM axis in controlling alveolar cell plasticity for lung regeneration and proposes a viable option for lung fibrosis prevention. One Sentence SummaryPCLAF-DREAM-driven alveolar cell plasticity is crucial for lung regeneration and can be pharmacologically targeted as a therapeutic strategy for lung fibrosis.

cell biology↗

bioRxiv2022

Nimbolide Targets RNF114 to Induce the Trapping of PARP1 and Poly-ADP-Ribosylation-Dependent DNA Repair Factors

PARP1 is an abundant nuclear enzyme that is critically involved in DNA damage response. Its main enzymatic function is to catalyze a protein post-translational modification known as poly-ADP-ribosylation (PARylation). Despite the tremendous progresses of PARP1 inhibitors (PARPi) in the clinic, the basic mechanism of action of PARPi is poorly understood. Recent studies point to PARP1 trapping as a key factor driving the cytotoxic and immunomodulatory functions of PARPi. However, the molecular underpinnings of PARP1 trapping remain elusive. Here, using an unbiased, quantitative proteomic screen, we identified RING finger protein 114 (RNF114), as a PARylation-dependent, ubiquitin E3 ligase involved in DNA damage response. Upon sensing DNA damage, RNF114 was recruited, in a PAR-dependent manner, to the DNA lesions, where it specifically targeted PARylated-PARP1 for ubiquitin-proteasomal degradation. The blockade of this pathway interfered with the removal of PARP1 from the DNA damage site, leading to profound PARP1 trapping. We show that a natural product, Nimbolide, targeted RNF114 to block the degradation and removal of PARylated-PARP1 from DNA lesions. Unlike conventional PARPi, nimbolide treatment induced the trapping of both PARP1 and PARylation-dependent DNA repair factors. This unique mechanism of action of nimbolide translated into its superior cytotoxic effects against BRCA-deficient cancers. Furthermore, we demonstrated that, as a super trapper of both PARylated-PARP1 and PARylation-dependent DNA repair factors, nimbolide was able to overcome the intrinsic and acquired resistance to PARPi. Finally, we showed that nimbolide treatment activated innate immune signaling and was able to synergize with various cytotoxic agents. These results point to the exciting possibility of targeting homologous recombination-deficient cancers using nimbolide and its analogs.

cancer biology↗

bioRxiv2022

A scalable implementation of the recursive least-squares algorithm for training spiking neural networks

Training spiking recurrent neural networks on neuronal recordings or behavioral tasks has become a popular way to study computations performed by the nervous system. As the size and complexity of neural recordings increase, there is a need for efficient algorithms that can train models in a short period of time using minimal resources. We present optimized CPU and GPU implementations of the recursive least-squares algorithm in spiking neural networks. The GPU implementation can train networks of one million neurons, with 100 million plastic synapses and a billion static synapses, about 1000 times faster than an unoptimized reference CPU implementation. We demonstrate the codes utility by training a network, in less than an hour, to reproduce the activity of > 66, 000 recorded neurons of a mouse performing a decision-making task. The fast implementation enables a more interactive in-silico study of the dynamics and connectivity underlying multi-area computations. It also admits the possibility to train models as in-vivo experiments are being conducted, thus closing the loop between modeling and experiments.

neuroscience↗

bioRxiv2022

Omicron sublineage BA.2.75.2 exhibits extensive escape from neutralising antibodies

Several sublineages of omicron have emerged with additional mutations that may afford further antibody evasion. Here, we characterise the sensitivity of emerging omicron sublineages BA.2.75.2, BA.4.6, and BA.2.10.4 to antibody-mediated neutralisation, and identify extensive escape by BA.2.75.2. BA.2.75.2 was resistant to neutralisation by Evusheld (tixagevimab + cilgavimab), but remained sensitive to bebtelovimab. In recent serum samples from blood donors in Stockholm, Sweden, BA.2.75.2 was neutralised, on average, at titers approximately 6.5-times lower than BA.5, making BA.2.75.2 the most neutralisation resistant variant evaluated to date. These data raise concerns that BA.2.75.2 may effectively evade humoral immunity in the population.

immunology↗

bioRxiv2022

ACCELERATING ANTIBODY DESIGN WITH ACTIVE LEARNING

Discovering therapeutic antibody starts by screening antibody library of phage-displayed, transgenic mouse or human B cells. The coverage of those kinds of libraries in the entire antibody sequence space is small; thus, the result highly depends on the quality of the library. Exploring sequence space by mutating a template antibody is also impossible to even with the state-of-the-art screening methods because of the cost. Deep learning helped with its pattern recognition nature to predict target binding, which is only applied to HCDR3 because the number of data deep learning needs increases exponentially. We construct a sequence generation model with transfer learning and active learning to leverage deep learning even in data deficiency. With only six thousands data, the generative model finds nine binding antibody sequences at least per antigen with novel HCDR3.

bioengineering↗

bioRxiv2022

Reduced oocyte quality and exacerbation of the maternal age effect are enduring consequences of low-level atrazine exposure in mouse

BACKGROUNDEgg development has unique features that render it vulnerable to environmental perturbation. The herbicide atrazine is an endocrine disruptor shown to have detrimental effects on reproduction across a number of vertebrate species. OBJECTIVESTo determine whether exposure to low levels of atrazine impairs meiosis in female mammals using a mouse model; in particular, whether and how the fidelity of oocyte chromosome segregation is affected, and whether the aging-related aneuploidy is exacerbated. METHODSFemale C57BL/6J mice were exposed to two levels of atrazine in drinking water, with the lower level corresponding to detected environmental contamination. To model exposure during development, atrazine was ingested by pregnant females at 0.5 days post coitum and continued until pups were weaned at 21 days post-partum. For adult exposure, 2-month-old females ingested atrazine for 3 months. For each exposure group, various indicators of oocyte quality were determined, including developmental capacity and chromosomal abnormalities during the two meiotic divisions. RESULTSDevelopmental exposure caused only minor effects on the fetal events of meiotic prophase-I and establishment of initial follicle pools. However, ovulation was enhanced while oocyte quality was significantly reduced. At the chromosome level, misalignment and numerical and structural abnormalities were increased at both meiotic divisions. Furthermore, fertilization efficiency was impaired in vitro, and apoptosis was elevated in blastocysts derived from the eggs of atrazine-exposed females. Similar levels of chromosomal defects were seen in oocytes following both developmental and adult exposure regimens suggesting that quiescent primordial follicles may be the consequential targets of atrazine. Importantly, defects were observed long after exposure was terminated. Moreover, dramatic increases in chromosomally abnormal oocytes were seen in older mice indicating that atrazine exposure during development exacerbates the effects of maternal aging on oocyte quality. Indeed, analogous to the effects of maternal age, atrazine exposure resulted in weakened cohesion between sister chromatids. CONCLUSIONLow-level atrazine exposure causes persistent changes to the female mammalian germline with potential consequences for reproductive lifespan and congenital disease.

pharmacology and toxicology↗

bioRxiv2022

Natriuretic peptides protect against apoptosis and increase cGMP around cardiomyocyte mitochondria

Natriuretic peptides (NPs) increase cGMP, show beneficial cardiovascular effects and regulate energy metabolism in other tissues. However, little is known about their direct effect on cardiac mitochondria and cardiomyocyte apoptosis. Here, we examined whether NPs increase cGMP around mitochondria and alter apoptosis in cardiomyocytes. We constructed a novel FRET-based biosensor with high selectivity towards cGMP and found that ANP and CNP increase cGMP at the outer mitochondrial membrane. Moreover, ANP and CNP increased phosphorylation of the pro-apoptotic protein Drp1 and CNP prevented fragmentation of mitochondria. Stimulating cardiomyocytes with ANP or CNP reduced apoptosis, caspase 9 activation and cytochrome c release, suggesting that NPs decrease apoptosis through the intrinsic pathway that involves mitochondria. We suggest that cGMP increase in the outer mitochondrial membrane microdomain that inhibits the pro-apoptotic protein Drp1, leading to reduced mitochondrial fragmentation and thereby reduced apoptosis.

pharmacology and toxicology↗

bioRxiv2022

Evasion of neutralizing antibodies by Omicron sublineage BA.2.75

An emerging SARS-CoV-2 Omicron sublineage, BA.2.75, is increasing in frequency in India and has been detected in at least 15 countries as of 19 July 2022. Relative to BA.2, BA.2.75 carries nine additional mutations in spike. Here we report the sensitivity of the BA.2.75 spike to neutralization by a panel of clinically-relevant and pre-clinical monoclonal antibodies, as well as by serum from blood donated in Stockholm, Sweden, before and after the BA.1/BA.2 infection wave. BA.2.75 largely maintains sensitivity to bebtelovimab, despite a slight reduction in potency, and exhibits moderate susceptibility to tixagevimab and cilgavimab. For sera sampled both before and after the BA.1/BA.2 infection wave, BA.2.75 does not show significantly greater antibody evasion than the currently-dominating BA.5.

immunology↗

bioRxiv2022

Pollen accumulation on hawkmoths varies substantially among moth-pollinated flowers

Using the pollen loads carried by floral visitors to infer their floral visitation behavior is a powerful technique to explore the foraging of wild pollinators. Interpreting these pollen records, however, requires assumptions about the underlying pollen dynamics. To compare visitor foraging across flower species, the most important assumption is that pollen is picked up and retained on the visitor at similar rates. Given differences in pollen presentation traits such as grain number or stickiness even among flowers with similar morphologies, however, the generality of this assumption is unclear. We investigated pollen accumulation on the hawkmoth Manduca sexta, testing the degree to which accumulation differed among flower species and how pollen stickiness affected this accumulation. In no-choice floral visitation assays to six plant species visited by long-tongued hawkmoths in the wild, M. sexta individuals were allowed to visit flowers 1, 2, or 5 times, after which the pollen on their proboscises was removed and counted. We found that the six plant species varied orders of magnitude in the number of pollen grains deposited on the moths, with some placing thousands of grains after a single visit and other placing none after five. Plant species with sticky pollen adhesion mechanisms placed more pollen on the moths and had relatively less pollen accumulation over successive visits than non-sticky plants. Intriguingly, moths carried fewer pollen grains after 5 visits than after 2 visits, suggesting that both sticky and non-sticky pollen was lost during foraging. Together, our results suggest that interpretation of pollen load data should be made cautiously, especially when comparing across plant species.

ecology↗

bioRxiv2022

Remdesivir does not affect mitochondrial DNA copy number or deletion mutation frequency in aged male rats

Remdesivir is a leading therapy in patients with moderate to severe coronavirus 2 (SARS-CoV-2) infection; the majority of whom are older individuals. Remdesivir is a nucleoside analog that incorporates into nascent viral RNA, inhibiting RNA-directed RNA polymerases, including that of SARS-CoV-2. Less is known about remdesivirs effects on mitochondria, particularly in older adults where mitochondria are known to be dysfunctional. Furthermore, its effect on age-induced mitochondrial mutations and copy number has not been previously studied. We hypothesized that remdesivir adversely affects mtDNA copy number and deletion mutation frequency in aged rodents. To test this hypothesis, 30-month-old male F333BNF1 rats were treated with remdesivir for three months. To determine if remdesivir adversely affects mtDNA, we measured copy number and mtDNA deletion frequency in rat hearts, kidneys, and skeletal muscles using digital PCR. We found no effects from three months of remdesivir treatment on mtDNA copy number or deletion mutation frequency in 33-month-old rats. For the 33-month-old control rats, the average mtDNA copy number per nucleus was 2567, 1100, and 1869 for heart, kidney, and quadriceps, respectively. MtDNA deletion mutation frequency was 2.6x10-4, 1.6x10-4 and 4.7x10-3for heart, kidney, and quadriceps, respectively. These data support the notion that remdesivir does not compromise mtDNA quality or quantity at old age in mammals. Future work should focus on examining additional tissues such as brain and liver, and extend testing to human clinical samples.

molecular biology↗

bioRxiv2022

Distributing task-related neural activity across a cortical networkthrough task-independent connections

Task-related neural activity is widespread across populations of neurons during goal-directed behaviors. However, little is known about the synaptic reorganization and circuit mechanisms that lead to broad activity changes. Here we trained a limited subset of neurons in a spiking network with strong synaptic interactions to reproduce the activity of neurons in the motor cortex during a decision-making task. We found that task-related activity, resembling the neural data, emerged across the network, even in the untrained neurons. Analysis of trained networks showed that strong untrained synapses, which were independent of the task and determined the dynamical state of the network, mediated the spread of task-related activity. Optogenetic perturbations suggest that the motor cortex is strongly-coupled, supporting the applicability of the mechanism to cortical networks. Our results reveal a cortical mechanism that facilitates distributed representations of task-variables by spreading the activity from a subset of plastic neurons to the entire network through task-independent strong synapses.

neuroscience↗

bioRxiv2022

Topology of gene regulatory compartments relative to the nuclear matrix

Summary ParagraphInside the nucleus, there are special compartments with characterized functions, some of which are involved in gene expression1. These compartments include transcriptional condensates and nuclear speckles, which contain factors required for transcription and splicing, respectively. While the characteristics of these intranuclear compartments were extensively investigated, spatial relationship between them is yet unclear. Meanwhile, RNA-protein structural network named the nuclear matrix has been observed inside the nucleus and suggested as a framework for the spatial segregation of the intranuclear space2-6. However, concept of the nuclear matrix was not widely accepted due to its lack of in vivo evidence7. Here, we report visualization of the nuclear matrix and intranuclear compartments using super-resolution fluorescence microscopy. We found the nuclear matrix is dynamic in live cells and easily disrupted upon transcription inhibition. Remarkably, we observed an orderly layered distribution of transcriptional condensates and nuclear speckles relative to the nuclear matrix. We also observed a separation of chromosome territories from transcriptional condensates and nuclear speckles by the nuclear matrix. Based on our findings, we propose a topological model for the regulation of transcription across the nuclear matrix.

cell biology↗

bioRxiv2022

SARM1 activation and its downstream pathways are distinct in neuronal compartments

Sterile alpha and TIR motif containing 1 (SARM1) is a critical regulator of axon degeneration that acts through hydrolysis of NAD+ following injury. Recent work has defined the mechanisms underlying SARM1s catalytic activity and advanced our understanding of SARM1 function in axons, yet the role of SARM1 signaling in other compartments of neurons is still not well understood. Here we show in cultured hippocampal neurons that endogenous SARM1 is present in axons, dendrites and cell bodies and that direct activation of SARM1 by the neurotoxin Vacor causes not just axon degeneration, but degeneration of all neuronal compartments. In contrast to the axon degeneration pathway defined in dorsal root ganglia (DRGs), SARM1-dependent hippocampal axon degeneration in vitro is not sensitive to calpain inhibition whereas dendrite degeneration downstream of SARM1 is calpain-dependent in this cell type. This data indicates SARM1 plays a critical role in neurodegeneration outside of axons and elucidates divergent pathways leading to degeneration in hippocampal axons and dendrites.

neuroscience↗

bioRxiv2022

Sus1 maintains a normal lifespan through regulation of TREX-2 complex-mediated mRNA export

Eukaryotic gene expression requires multiple cellular events, including transcription and RNA processing and transport. Sus1, a common subunit in both the Spt-Ada-Gcn5 acetyltransferase (SAGA) and transcription and export complex-2 (TREX-2) complexes, is a key factor in coupling transcription activation to mRNA nuclear export. Here we present that the SAGA DUB module and TREX-2 regulates distinctly yeast replicative lifespan in a Sir2-dependent and - independent manner, respectively. The growth and lifespan impaired by SUS1 loss depend on TREX-2 but not on the SAGA DUB module. Notably, an increased dosage of the mRNA export factors Mex67 and Dbp5 rescues the growth defect, shortened lifespan, and nuclear accumulation of poly(A)+ RNA in sus1{Delta} cells, suggesting that boosting the mRNA export process restores the mRNA transport defect and damage in the growth and lifespan of sus1{Delta} cells. Moreover, Sus1 is required for the proper association of Mex67 and Dbp5 with the nuclear rim. Together, these data suggest that Sus1 links transcription and mRNA nuclear export to the lifespan control pathway, indicating that prevention of an abnormal accumulation of nuclear RNA is necessary for maintaining a normal lifespan.

cell biology↗

bioRxiv2022

NVX-CoV2373 vaccination induces functional SARS-CoV-2-specific CD4+ and CD8+ T cell responses

NVX-CoV2373 is an adjuvanted recombinant full-length SARS-CoV-2 spike trimer protein vaccine demonstrated to be protective against COVID-19 in efficacy trials. Here we demonstrate that vaccinated subjects made CD4+ T cell responses after one and two doses of NVX-CoV2373, and a subset of individuals made CD8+ T cell responses. Characterization of the vaccine-elicited CD8+T cells demonstrated IFN{gamma} production. Characterization of the vaccine-elicited CD4+ T cells revealed both circulating T follicular helper cells (cTFH) and TH1 cells (IFN{gamma}, TNF, and IL-2) were detectable within 7 days of the primary immunization. Spike-specific CD4+ T cells were correlated with the magnitude of the later SARS-CoV-2 neutralizing antibody titers, indicating that robust generation of CD4+ T cells, capable of supporting humoral immune responses, may be a key characteristic of NVX-CoV2373 which utilizes Matrix-M adjuvant.

immunology↗

bioRxiv2022

Humoral and cellular immune memory to four COVID-19 vaccines

Multiple COVID-19 vaccines, representing diverse vaccine platforms, successfully protect against symptomatic COVID-19 cases and deaths. Head-to-head comparisons of T cell, B cell, and antibody responses to diverse vaccines in humans are likely to be informative for understanding protective immunity against COVID-19, with particular interest in immune memory. Here, SARS-CoV-2-spike--specific immune responses to Moderna mRNA-1273, Pfizer/BioNTech BNT162b2, Janssen Ad26.COV2.S and Novavax NVX-CoV2373 were examined longitudinally for 6 months. 100% of individuals made memory CD4+ T cells, with cTfh and CD4-CTL highly represented after mRNA or NVX-CoV2373 vaccination. mRNA vaccines and Ad26.COV2.S induced comparable CD8+ T cell frequencies, though memory CD8+ T cells were only detectable in 60-67% of subjects at 6 months. Ad26.COV2.S was not the strongest immunogen by any measurement, though the Ad26.COV2.S T cell, B cell, and antibody responses were relatively stable over 6 months. A differentiating feature of Ad26.COV2.S immunization was a high frequency of CXCR3+ memory B cells. mRNA vaccinees had substantial declines in neutralizing antibodies, while memory T cells and B cells were comparatively stable over 6 months. These results of these detailed immunological evaluations may also be relevant for vaccine design insights against other pathogens.

immunology↗

bioRxiv2022

The cGAS-STING pathway affects vertebral bone but does not promote intervertebral disc cell senescence or degeneration

The DNA-sensing cGAS-STING pathway promotes the senescence-associated secretory phenotype (SASP) and mediates type-I interferon inflammatory responses to foreign viral and bacterial DNA as well as self-DNA. Studies of the intervertebral disc in humans and mice demonstrate associations between aging, increased cell senescence, and disc degeneration. Herein we assessed the role of STING in SASP promotion in STING gain- (N153S) and loss-of-function mouse models. N153S mice evidenced elevated circulating levels of proinflammatory markers including IL-1{beta}, IL-6, and TNF- and exhibited a mild trabecular and cortical bone phenotype in caudal vertebrae. Interestingly, despite systemic inflammation, the structural integrity of the disc and knee articular joint remained intact, and cells did not show a loss of their phenotype or elevated SASP. Transcriptomic analysis of N153S tissues demonstrated an upregulated immune response by disc cells, which did not closely resemble inflammatory changes in human tissues. Interestingly, STING-/- mice also showed a mild vertebral bone phenotype, but the absence of STING did not improve the age-associated disc phenotype or reduce the abundance of SASP markers. Overall, the analyses of N153S and STING-/- mice that the cGAS-STING pathway is not a major contributor to SASP induction and consequent disc aging and degeneration but may play a minor role in the maintenance of trabecular bone in the vertebrae. This work contributes to a growing body of work demonstrating that systemic inflammation is not a key driver of disc degeneration.

cell biology↗

bioRxiv2022

Plastid-specific RsmD methyltransferase and ribosome maturation factor RimM are crucial for 16S rRNA maturation and proteostasis

Chloroplast pre-ribosomal RNA (rRNA) undergoes maturation, which is critical for ribosome assembly. While the central and auxiliary factors in rRNA maturation have been elucidated in bacteria, their mode of action remains largely unexplored in chloroplasts. We now reveal chloroplast-specific factors involved in 16S rRNA maturation, RsmD methyltransferase (AtRsmD) and ribosome maturation factor RimM-like protein (AtRimM) in Arabidopsis thaliana. A forward genetic screen aimed to find suppressors of the Arabidopsis yellow variegated 2 (var2) mutant defective in photosystem II (PSII) quality control found a causal nonsense mutation in AtRsmD. The substantially impaired 16S rRNA maturation and translation due to the mutation rescued the leaf variegation phenotype by lowering the levels of PSII core proteins in var2. The subsequent co-immunoprecipitation coupled with mass spectrometry analyses and bimolecular fluorescence complementation assay found that AtRsmD interacts with AtRimM. Consistent with their interaction, loss of AtRimM also considerably impairs 16S rRNA maturation, with less methylation in m2G915 in 16S rRNA catalyzed by AtRsmD. The atrimM mutation also rescued var2 mutant phenotypes, corroborating the functional interplay between AtRsmD and AtRimM towards 16S rRNA maturation and chloroplast proteostasis.

plant biology↗