Biology subjects

Kim, Y. B.

Publications and source records attributed to Kim, Y. B..

8 recordsLinked to original sources

bioRxiv2026

Targeted depletion of CD38+ autoreactive T cells prevents type 1 diabetes

Type 1 diabetes (T1D) is caused by T cell-mediated autoimmune destruction of insulin-producing islet {beta}-cells. Treatment with T-cell depleting therapies delays the progression of stage 2 and 3 T1D, but these agents exert broad immunosuppressive effects on T cell populations, including T regulatory cells (Tregs), which are key in promoting immune tolerance. We evaluated non-obese diabetic (NOD) mice and recently diagnosed T1D patients and identified CD38 as a marker for pathogenic T cell populations. Using adoptive T-cell transfer in Recombination Activating Gene 1 knockout NOD mice and in a humanized mouse model of autoimmune diabetes, we demonstrated that CD38-expressing autoreactive T cells drive diabetes pathogenesis. Furthermore, we found that selective depletion of CD38+ cells, using an anti-CD38 monoclonal antibody (mAb), prevents insulitis and diabetes onset without depleting CD4+CD25+ Tregs. Administration of anti-CD38 mAb did not adversely affect islet function and may selectively eliminate immunogenic senescent islet {beta}-cells. These results support the strategy of selectively depleting diabetogenic T cells using an anti-CD38 mAb to treat T1D and restore immune tolerance. Therefore, transient depletion of autoreactive T cells using anti-CD38 mAb may provide a novel strategy to prevent or abrogate {beta}-cell autoimmunity in T1D. One sentence summaryPathogenic autoreactive are characterized by CD38 overexpression, and their selective depletion with anti-CD38 monoclonal antibody prevents autoimmune diabetes.

immunology↗

bioRxiv2026

Microbiome-Targeted Reduction of Circulating Trimethylamine N-Oxide Mitigates Ischemic Stroke Risk

Elevated plasma trimethylamine N-oxide (TMAO) is an independent predictor of major adverse cardiovascular events and ischemic stroke. While inhibition of microbial TMA production has been explored, concerns regarding off-target effects and limited efficacy in complex microbial ecosystems have hindered clinical translation. Here, we report a microbiome-based therapeutic strategy based on the direct enzymatic degradation of intestinal TMA by Paracoccus aminovorans BM109. Through targeted screening, we identified BM109 as a commensal strain harboring a comprehensive set of enzymes capable of metabolizing TMA and TMAO into non-toxic end products under both aerobic and anaerobic conditions. In a chronic high-choline diet murine model, oral administration of BM109 resulted in a 38% reduction in systemic TMAO levels. In a rat model of transient middle cerebral artery occlusion (tMCAO), short-term pre-treatment reduced cerebral infarct size by 58% and significantly improved neurological outcomes. These effects were accompanied by favorable safety observations, including the absence of hemolytic activity and intestinal tissue damage. Collectively, our findings establish BM109 as a promising live biotherapeutic product that targets the gut microbiome-host metabolic axis. By reducing the systemic TMAO burden, BM109 represents a potential strategy for modulating cardiometabolic and cerebrovascular risk.

microbiology↗

bioRxiv2022

A novel mechanistic framework for precise sequence replacement using reverse transcriptase and diverse CRISPR-Cas systems

CRISPR/Cas systems coupled with reverse transcriptase (RT), such as the recently described Prime editing, allow for site-specific replacement of DNA sequences. Despite widespread testing of Prime editing, it is currently only compatible with type II CRISPR/Cas proteins such as Streptococcus pyogenes and Staphylococcus aureus Cas9. Enabling RT compatibility with other CRISPR/Cas domains, such as type V enzymes with orthogonal protospacer adjacent motif specificities and smaller protein size would expand the range of edits that can be made in therapeutic and industrial applications. We achieve this with a novel mode of DNA editing at CRISPR-targeted sites that reverse transcribes the edit into the target strand DNA (e.g., the complement of the PAM-containing strand), rather than the non-target strand DNA, as in Prime editing. We term this technology RNA encoded DNA replacement of alleles with CRISPR (hereafter, REDRAW). We show that REDRAW extends the utility of RT-mediated editing beyond type II to include multiple type V CRISPR domains. REDRAW features a broad (8-10 bases) targeting window, at which all types of substitutions, insertions and deletions are possible. REDRAW combines the advantages of type V CRISPR domains with the extensive range of genetic variation enabled by RT-mediated, templated sequence replacement strategies.

molecular biology↗

bioRxiv2022

Baculoviral COVID-19 Delta DNA vaccine cross-protects against SARS-CoV2 variants in K18-ACE2 transgenic mice

After severe acute respiratory syndrome coronavirus-2 (SARS-CoV2) made the world tremble with a global pandemic, SARS-CoV2 vaccines were developed. However, due to the coronaviruss intrinsic nature, new variants emerged, such as Delta and Omicron, refractory to the vaccines derived using the original Wuhan strain. We developed an HERV-enveloped recombinant baculoviral DNA vaccine against SARS-CoV2 (AcHERV-COVID19S). A non-replicating recombinant baculovirus that delivers the SARS-CoV2 spike gene showed a protective effect against the homologous challenge in a K18-hACE2 Tg mice model; however, it offered only a 50% survival rate against the SARS-CoV2 Delta variant. Therefore, we further developed the AcHERV-COVID19 Delta vaccine (AcHERV-COVID19D). Cross-protection experiments revealed that mice vaccinated with the AcHERV-COVID19D showed 100% survival upon challenge with Delta and Omicron variants and 71.4% survival against prototype SARS-CoV2. These results support the potential of the viral vector vaccine, AcHERV-COVID19D, in preventing the spread of coronavirus variants such as Omicron and SARS-CoV2 variants. Author SummaryAfter the SARS-CoV2 pandemic, it is known that the existing vaccine has diminished efficacy against the emerging variants. We developed a baculoviral COVID19 DNA vaccine for the Delta variant (AcHERV-COVIS19D). Compared to AcHERV-COVID19S, designed to protect from the prototype of SARS-CoV2, AcHERV-COVID19D elicited higher humoral and cellular immunity and showed perfect protection against SARS-CoV2 delta strain and Omicron challenge. The broad and robust cellular immunity of the AcHERV-COVID19D vaccine appears to have played a significant role in the cross-protection of the Omicron variant. Our AcHERV-COVID19D can be a potential vaccine against emerging SARS-CoV2 variants.

immunology↗

bioRxiv2021

A Standardized Protocol for Quantifying the Behavioral Dynamics of Food-seeking in Mice

Food is generally hidden in a natural environment and require free-living animals to search for it. Although such food-seeking behaviors involve motivation and exploration, previous studies examined food-seeking simply by measuring the time spent in the food zone or the frequency of pursuing food-cued context. Moreover, after discovering food, animals need to taste and smell it in order to evaluate their nutritional value or possible toxicity. However, researchers could not easily distinguish food-seeking from food-evaluating behaviors because food was visible or accessible throughout each test. Herein, we describe a behavioral protocol that triggers animals to show the behavioral dynamics of food-seeking (e.g., navigation, nose-digging, and paw-digging) and that exclusively elicits food-seeking without provoking any other food-evaluating behaviors. First, we prepared an open-field box with the floor covered with bedding. After we hid foods under the bedding of each corner, the test mice were habituated in this arena for four days (pre-test phase). On the next day (test phase), they were placed under the same conditions, but the foods previously hidden were removed. This process enabled the mice to perceive their surroundings as a food-hidden environment, which induced the animal to exhibit sustained food-seeking. In conclusion, the protocol presented here is a powerful method for provoking multiple forms of food-seeking and quantifies food-seeking independently from other food-related behavioral stages.

neuroscience↗

bioRxiv2020

LH LepR neurons directly drive sustained food seeking behavior after AgRP neuronal deactivation via neuromodulation of NPY

The physiological need for energy evokes motivated feeding behaviours that help to ensure survival. However, the neural mechanisms underlying the generation of food motivation remain poorly understood. We investigated these mechanisms by subdividing feeding-related motivated behaviours into food-seeking, evaluating, and swallowing. Micro-endoscopic results indicated that neurons containing leptin receptors (LepRs) in the lateral hypothalamus (LH) are the major food-specific subpopulation of LHGABA neurons. Optogenetic manipulation of LHLepR neurons bidirectionally regulated both food-seeking and evaluating. Furthermore, micro-endoscope data revealed that distinct LHLepR neurons encode seeking and evaluating. Computational modelling analysis demonstrated that LHLepR neurons encode motivation, whereas neurons containing agouti-related peptide and neuropeptide Y (AgRP/NPY) encode the need for food. Additionally, slice studies revealed that NPY decreases inhibitory input to LHLepR neurons via LHGABA interneurons. This mechanism explains the permissive gate role of hunger (food need) in seeking/evaluating motivation. Together, the present study provides a comprehensive neural mechanism of how physiological needs drive distinct motivated behaviours.

neuroscience↗

bioRxiv2019

Metastatic function of METTL18 in breast cancer via actin methylation and Src

Recently, a SET domain containing 3 (SETD3) was identified as an actin histidine methyltransferase, functioning to control replication and pathogenesis in multiple mouse models for enterovirus infection as well as the regulation of smooth muscle contractility linked to primary dystocia. Here, in this study, we report another type of actin histidine methyltransferase, METTL18, that regulates the metastatic potential of breast cancer in human. Among methyltransferases, METTL18 was highly amplified in human breast cancer. In particular, poor prognosis was associated with high expression of METTL18 in HER2-negative breast cancer patients. This gene product was also found to be a critical component of metastatic responses. Loss of METTL18 expression significantly reduced metastatic responses of breast tumor cells both in vitro and in vivo. Mechanistically, it was observed that METTL18 increased actin polymerization, upregulated complex formation with HSP90AA1 and Src, enhanced the activity of an intermediate form of Src with tyrosine phosphorylation at both Y416 and Y527, and induced cellular metastatic responses, including morphological change, migration, and invasion of MDA-MB-231 cells in vitro and in mice. Methylated actin at His73 served as a critical site for interaction with HSP90AA1 and Src to activate p85/PI3K and STAT3. Our findings suggest that METTL18 plays critical roles in metastatic responses of HER2-negative breast cancer cells via actin polymerization and the generation of an intermediate form of Src.

cancer biology↗

bioRxiv2018

PBHoover and CigarRoller: a method for confident haploid variant calling on Pacific Biosciences data and its application to heterogeneous population analysis

MotivationSingle Molecule Real-Time (SMRT) sequencing has important and underutilized advantages that amplification-based platforms lack. Lack of systematic error (e.g. GC-bias), complete de novo assembly (including large repetitive regions) without scaffolding, can be mentioned. SMRT sequencing, however suffers from high random error rate and low sequencing depth (older chemistries). Here, we introduce PBHoover, software that uses a heuristic calling algorithm in order to make base calls with high certainty in low coverage regions. This software is also capable of mixed population detection with high sensitivity. PBHoovers CigarRoller attachment improves sequencing depth in low-coverage regions through CIGAR-string correction.\n\nResultsWe tested both modules on 348 M.tuberculosis clinical isolates sequenced on C1 or C2 chemistries. On average, CigarRoller improved percentage of usable read count from 68.9% to 99.98% in C1 runs and from 50% to 99% in C2 runs. Using the greater depth provided by CigarRoller, PBHoover was able to make base and variant calls 99.95% concordant with Sanger calls (QV33). PBHoover also detected antibiotic-resistant subpopulations that went undetected by Sanger. Using C1 chemistry, subpopulations as small as 9% of the total colony can be detected by PBHoover. This provides the most sensitive amplification-free molecular method for heterogeneity analysis and is in line with phenotypic methods sensitivity. This sensitivity significantly improves with the greater depth and lower error rate of the newer chemistries.\n\nAvailability and ImplementationExecutables are freely available under GNU GPL v3+ at http://www.gitlab.com/LPCDRP/pbhoover and http://www.gitlab.com/LPCDRP/CigarRoller. PBHoover is also available on bioconda: https://anaconda.org/bioconda/pbhoover.\n\nContactfaramarz@sdsu.edu

bioinformatics↗