Biology subjects

Hong, S.

Publications and source records attributed to Hong, S..

At least 55 records · Page 3Linked to original sources

bioRxiv2024

Dynamic Kidney Organoid Microphysiological Analysis Platform

Kidney organoids, replicating human development, pathology, and drug responses, are a promising model for advancing bioscience and pharmaceutical innovation. However, reproducibility, accuracy, and quantification challenges hinder their broader utility for advanced biological and pharmaceutical applications. Herein, we present a dynamic kidney organoid microphysiological analysis platform (MAP), designed to enhance organoid modeling and assays within physiologically relevant environments, thereby expanding their utility in advancing kidney physiology and pathology research. First, precise control of the dynamic microenvironment in MAP enhances the ability to fine-tune nephrogenic intricacies, facilitating high-throughput and reproducible human kidney organoid development. Also, MAPs miniaturization of kidney organoids significantly advances pharmaceutical research by allowing for detailed analysis of entire nephron segments, which is crucial for assessing the nephrotoxicity and safety of drugs. Furthermore, the MAPs application in disease modeling faithfully recapitulates pathological development and functions as a valuable testbed for therapeutic exploration in polycystic kidney diseases. We envision the kidney organoid MAP enhancing pharmaceutical research, standardizing processes, and improving analytics, thereby elevating the quality and utility of organoids in biology, pharmacology, precision medicine, and education.

bioengineering↗

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

Brainwaves Monitoring via Human Midbrain Organoids Microphysiological Analysis Platform: MAP

Understanding the development and pathogenesis of the human midbrain is critical for developing diagnostics and therapeutics for incurable neurological disorders including Parkinsons disease (PD)1-3. While organoid models are introduced to delineate midbrain-related pathogenesis based on experimental flexibility4-6, there is currently a lack of tools with high fidelity for tracing the long-term dynamics of intact brain networks-- an essential portrait of physiological states7,8. Here, we report a brain organoid microphysiological analysis platform (MAP) designed for long-term physiological development and in-situ real-time monitoring, akin to electroencephalogram (EEG), of midbrain organoids. We successfully achieved the on-chip homogeneous organogenesis of midbrain organoids and in-situ, non-disturbing electrophysiological tracking of the midbrain network activities. Throughout our long-term EEG monitoring via MAP, we captured the early-stage electrophysiological evolution of midbrain development, transitioning from discontinuous brief brainwave bursts to complex broadband activities. Furthermore, our midbrain organoid MAP facilitated the modeling and monitoring of neurotoxin-induced Parkinsonism, replicating the pathological dynamics of midbrain circuitry and exhibiting PD-like alterations in beta oscillation. We envision that the modeling and monitoring of brain organoid MAP will significantly enhance our understanding of human neurophysiology, neuropathogenesis, and drug discovery of neurodegenerative diseases.

bioengineering↗

bioRxiv2024

Tau condensation on DNA and localization on centromeres: A potential link to cell division

Tau protein, traditionally recognized for stabilizing microtubules and forming pathological aggregates, has recently been observed to form condensates in various contexts. While its condensation with RNA has been well studied, the interaction between tau and DNA, along with its biological significance, remains less explored. Here, using single-molecule experiments, we found that tau binds stably to naked DNA at nanomolar concentrations, leading to the local co- condensation of tau and DNA. These tau condensates on DNA can also interface with microtubules, leveraging taus known role in promoting microtubule growth and organization. The dynamic nature of these condensates facilitates the remodeling of the DNA-microtubule assembly. Interestingly, two phosphomimetic tau mutants, T231D/S235D and S262D, retained their affinity for DNA but differed in their ability to link microtubules to DNA. Furthermore, imaging of HEK-293 and SH-SY5Y cells in early mitosis revealed that tau localizes on centromeres, poised to capture nascent mitotic spindles. Building on these observations, we speculate that tau may play a novel role in mitosis, where tau clusters facilitate the early registration of mitotic spindles to chromosomes before kinetochore-mediated attachment. We also discuss the potential implications of this model in conditions where abnormal cell cycle re-entry and tau activity may disrupt cell division.

biophysics↗

bioRxiv2024

Astrocyte-derived MFG-E8 facilitates microglial synapse elimination in Alzheimer's disease mouse models

Region-specific synapse loss is an early pathological hallmark in Alzheimers disease (AD). Emerging data in mice and humans highlight microglia, the brain-resident macrophages, as cellular mediators of synapse loss; however, the upstream modulators of microglia-synapse engulfment remain elusive. Here, we report a distinct subset of astrocytes, which are glial cells essential for maintaining synapse homeostasis, appearing in a region-specific manner with age and amyloidosis at onset of synapse loss. These astrocytes are distinguished by their peri-synaptic processes which are bulbous in morphology, contain accumulated p62-immunoreactive bodies, and have reduced territorial domains, resulting in a decrease of astrocyte-synapse coverage. Using integrated in vitro and in vivo approaches, we show that astrocytes upregulate and secrete phagocytic modulator, milk fat globule-EGF factor 8 (MFG-E8), which is sufficient and necessary for promoting microglia-synapse engulfment in their local milieu. Finally, we show that knocking down Mfge8 specifically from astrocytes using a viral CRISPR-saCas9 system prevents microglia-synapse engulfment and ameliorates synapse loss in two independent amyloidosis mouse models of AD. Altogether, our findings highlight astrocyte-microglia crosstalk in determining synapse fate in amyloid models and nominate astrocytic MFGE8 as a potential target to ameliorate synapse loss during the earliest stages of AD.

neuroscience↗

bioRxiv2024

Cluster Buster: A Machine Learning Algorithm for Genotyping SNPs from Raw Data

Genotyping single nucleotide polymorphisms (SNPs) is fundamental to disease research, as researchers seek to establish links between genetic variation and disease. Although significant advances in genome technology have been made with the development of bead-based SNP genotyping and Genome Studio software, some SNPs still fail to be genotyped, resulting in "no-calls" that impede downstream analyses. To recover these genotypes, we introduce Cluster Buster, a genotyping neural network and visual inspection system designed to improve the quality of neurodegenerative disease (NDD) research. Concordance analysis with whole genome sequencing (WGS) and imputed genotypes validated the reliability of predicted genotypes, with dozens of high-performing SNPs across LRRK2, APOE, and GBA loci achieving at least 90% concordance per SNP location. Further analysis of concordance between Genome Studio genotypes and imputed and WGS genotypes revealed discrepancies between the genotyping technologies, highlighting the need for selective application of Cluster Buster on SNP locations based on concordance rates. Cluster Busters implementation significantly reduces manual labor for recovering no-call SNPs, refining genotype quality for the Global Parkinsons Genetics Program (GP2). This system facilitates better imputation and GWAS outcomes, ultimately contributing to a deeper understanding of genetic factors in NDDs.

bioinformatics↗

bioRxiv2024

PNPLA3(148M) Promotes Hepatic Steatosis by Interfering with Triglyceride Hydrolysis Through a Gain-of-Function Mechanism

Background & AimsPNPLA3(148M) (patatin-like phospholipase domain-containing protein 3) is the most impactful genetic risk factor for steatotic liver disease (SLD), thus motivating a search for therapeutic modulators of its expression. A key unresolved issue is whether PNPLA3(148M) confers a loss- or gain-of-function. Here we used multiple approaches to further test the hypothesis that PNPLA3 causes steatosis by sequestering ABHD5 (/{beta} hydrolase domain containing protein 5), the cofactor of ATGL (adipose TG lipase), thus limiting mobilization of hepatic triglyceride (TG). MethodsWe quantified the physical interactions between ABHD5 and PNPLA3/ATGL in cultured hepatocytes using NanoBiT complementation assays. Immunocytochemistry was used to compare the relative binding of PNPLA3 and ATGL to ABHD5 and to determine if PNPLA3 must associate with lipid droplets (LDs) to inhibit ATGL. Adenoviruses and adeno-associated viruses were used to express PNPLA3 in liver-specific Atgl-/- mice and ABHD5 in livers of Pnpla3148M/M mice, respectively. We used purified recombinant proteins to compare the TG hydrolytic activities of PNPLA3 and ATGL in the presence and absence of ABHD5. ResultsABHD5 interacted preferentially with PNPLA3 relative to ATGL in cultured hepatocytes and in vitro, with no differences observed between PNPLA3(WT) or PNPLA3(148M). PNPLA3(148M)-associated inhibition of TG hydrolysis required localization of PNPLA3 to LDs and the presence of ATGL. Finally, overexpression of ABHD5 reversed the hepatic steatosis in Pnpla3M/M mice. ConclusionsThese findings support the premise that PNPLA3(148M) promotes hepatic steatosis by accumulating on LDs and inhibiting ATGL-mediated lipolysis in an ABHD5-dependent manner. Our results predict that reducing, rather that increasing PNPLA3 expression will be the best strategy to treat PNPLA3(148M)-associated SLD. Impact and implicationsSteatotic liver disease (SLD) is a common complex disorder associated with both environmental and genetic risk factors. PNPLA3(148M) is the most impactful genetic risk factor for SLD and yet its pathogenic mechanism remains controversial. Here we provide evidence that PNPLA3(148M) promotes triglyceride (TG) accumulation by sequestering ABHD5, thus limiting its availability to activate ATGL. Although the substitution of methionine for isoleucine reduces the TG hydrolytic activity of PNPLA3, the loss-of-function is only indirectly related to the steatotic effect of the variant. Here we provide evidence that PNPLA3(148M) confers a gain-of-function by interfering with ATGL-mediated TG hydrolysis. These findings have implications for the design of potential PNPLA3-based therapies. Reducing, rather than increasing, PNPLA3 levels is predicted to reverse steatosis in susceptible individuals. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/606015v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@1dd7acaorg.highwire.dtl.DTLVardef@1a869dborg.highwire.dtl.DTLVardef@1bde743org.highwire.dtl.DTLVardef@99effc_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIABHD5 binds preferentially to PNPLA3 relative to ATGL. C_LIO_LIPNPLA3(WT) and PNPLA3(148M) compete similarly for binding and inhibition of ATGL. C_LIO_LIABHD5 activates the triglyceride lipase activity of PNPLA3, as well as ATGL. C_LIO_LIThe steatotic effect of PNPLA3(148M) requires expression of ATGL. C_LIO_LIOverexpression of ABHD5 can rescue the steatosis associated with PNPLA3(148M). C_LI

cell biology↗

bioRxiv2024

Fluorogenic Aptamer Optimizations on a Massively Parallel Sequencing Platform

Fluorogenic aptamers (FAPs) have become an increasingly important tool in cellular sensing and pathogen diagnostics. However, fine-tuning FAPs for enhanced performance remains challenging even with the structural details provided by X-ray crystallography. Here we present a novel approach to optimize a DNA-based FAP (D-FAP), Lettuce, on repurposed Illumina next-generation sequencing (NGS) chips. When substituting its cognate chromophore, DFHBI-1T, with TO1-biotin, Lettuce not only shows a red-shifted emission peak by 53 nm (from 505 to 558 nm), but also a 4-fold bulk fluorescence enhancement. After screening 8,821 Lettuce variants complexed with TO1-biotin, the C14T mutation is found to exhibit an improved apparent dissociated constant ([Formula] vs. 0.82 {micro}M), an increased quantum yield (QY: 0.62 vs. 0.59) and an elongated fluorescence lifetime ({tau}: 6.00 vs. 5.77 ns), giving 45% more ensemble fluorescence than the canonical Lettuce/TO1-biotin complex. Molecular dynamic simulations further indicate that the {pi}-{pi} stacking interaction is key to determining the coordination structure of TO1-biotin in Lettuce. Our screening-and-simulation pipeline can effectively optimize FAPs without any prior structural knowledge of the canonical FAP/chromophore complexes, providing not only improved molecular probes for fluorescence sensing but also insights into aptamer-chromophore interactions.

biophysics↗

bioRxiv2024

Cerebellar tonic inhibition orchestrates the maturation of information processing and motor coordination

Tonic inhibition in cerebellar granule cells (GC) is crucial in information coding fidelity for motor coordination. It emerges in activity-dependent and-independent manners, and their interplay evolves with age. However, specific molecular and cellular mechanisms and how their change affects network-level computation and motor behavior remain unclear. Here we show that, while net tonic inhibitory current remains unchanged, the main source of tonic GABA switches from synaptic spillover (neuronal activity-dependent) to astrocytic Best1 (activity-independent) throughout adolescence (4-8 weeks) in mice. Computational modeling based on experimental data demonstrated that this switch down-regulates the internally generated network activity mediating mutual inhibition between GC clusters receiving different inputs, thereby enhancing their independence. Consistent with simulations, 3D-posture analysis revealed an age-dependent increase in independent limb movements during spontaneous motion, which was impaired in Best1 knockout mice. Our findings highlight the late-stage development of complex motor coordination driven by the emergence of astrocyte-mediated tonic inhibition. O_LI6 main figures, 58 references, 5,924 words in the manuscript (excluding the abstract, tables, figure legends and references). C_LIO_LISupplementary information: 1 text (supplementary methods), 9 figures, 4 movies, and 1 table. C_LI

neuroscience↗

bioRxiv2024

In vivo tracking of ex vivo generated 89Zr-oxine labeled plasma cells by PET in a non-human primate model

B cells are an attractive platform for engineering to produce protein-based biologics absent in genetic disorders, and potentially for the treatment of metabolic diseases and cancer. As part of pre-clinical development of B cell medicines, we demonstrate a method to collect, ex vivo expand, differentiate, radioactively label, and track adoptively transferred non-human primate (NHP) B cells. These cells underwent 10- to 15-fold expansion, initiated IgG class switching, and differentiated into antibody secreting cells. Zirconium-89-oxine labeled cells were infused into autologous donors without any preconditioning and tracked by PET/CT imaging. Within 24 hours of infusion, 20% of the initial dose homed to the bone marrow and spleen and distributed stably and equally between the two. Interestingly, approximately half of the dose homed to the liver. Image analysis of the bone marrow demonstrated inhomogeneous distribution of the cells. The subjects experienced no clinically significant side effects or laboratory abnormalities. A second infusion of B cells into one of the subjects resulted in an almost identical distribution of cells, suggesting a non-limiting engraftment niche and feasibility of repeated infusions. This work supports the NHP as a valuable model to assess the potential of B cell medicines as potential treatment for human diseases.

bioengineering↗

bioRxiv2024

Hypothalamus-specific NSCs derived from hPSCs ameliorate age-associated dysfunction upon transplantation into aged mouse hypothalamus

The hypothalamus is the brain region that regulates systemic body metabolism and multiple brain functions. The adult hypothalamus harbors neural stem/precursor cell (NSC)-like cells. Along with age-related body changes, the hypothalamic NSC (htNSC) population declines, indicating the potential of htNSC replacement as an anti-aging strategy. Here, we developed protocol to generate htNSCs from human pluripotent stem cells (hPSCs). Implanting the hPSC-derived htNSCs into the hypothalamus of aged mice ameliorated age-related declines in metabolic fitness, physical capacity, and cognitive function. Mechanistically, these anti-aging effects were mediated by inter-tissue communication: enhanced neuronal activity in the htNSC-transplanted hypothalamus stimulated adipose tissues to produce and release the anti-aging molecule eNAMPT into systemic circulation via the sympathetic nervous system. Concurrently, the aged inflammatory environment in the hypothalamus was alleviated by peripheral anti-aging signals. Collectively, our findings support the potential of anti- or healthy aging therapies by targeting hypothalamus.

cell biology↗

bioRxiv2024

Ultra-secure storage and analysis of genetic data for the advancement of precision medicine

1Cloud computing provides the opportunity to store the ever-growing genotype-phenotype data sets needed to achieve the full potential of precision medicine. However, due to the sensitive nature of this data and the patchwork of data privacy laws across states and countries, additional security protections are proving necessary to ensure data privacy and security. Here we present SQUiD, a secure queryable database for storing and analyzing genotype-phenotype data. With SQUiD, genotype-phenotype data can be stored in a low-security, low-cost public cloud in the encrypted form, which researchers can securely query without the public cloud ever being able to decrypt the data. We demonstrate the usability of SQUiD by replicating various commonly used calculations such as polygenic risk scores, cohort creation for GWAS, MAF filtering, and patient similarity analysis both on synthetic and UK Biobank data. Our work represents a new and scalable platform enabling the realization of precision medicine without security and privacy concerns.

bioinformatics↗

bioRxiv2024

Meiotic DNA break resection and recombination rely on chromatin remodeler Fun30

DNA double-strand breaks (DSBs) are nucleolytically processed to generate single-stranded DNA tails for homologous recombination. In Saccharomyces cerevisiae meiosis, this 5-to-3 resection involves initial nicking by the Mre11-Rad50-Xrs2 complex (MRX) plus Sae2, then exonucleolytic digestion by Exo1. Chromatin remodeling adjacent to meiotic DSBs is thought to be necessary for resection, but the relevant remodeling activity was unknown. Here we show that the SWI/SNF-like ATPase Fun30 plays a major, non-redundant role in resecting meiotic DSBs. A fun30 null mutation shortened resection tract lengths almost as severely as an exo1-nd (nuclease-dead) mutation, and resection was further shortened in the fun30 exo1-nd double mutant. Fun30 associates with chromatin in response to meiotic DSBs, and the constitutive positioning of nucleosomes governs resection endpoint locations in the absence of Fun30. We infer that Fun30 directly promotes both the MRX- and Exo1-dependent steps in resection, possibly by removing nucleosomes from broken chromatids. Moreover, we found that the extremely short resection in the fun30 exo1-nd double mutant is accompanied by compromised interhomolog recombination bias, leading to defects in recombination and chromosome segregation. Thus, this study also provides insight about the minimal resection lengths needed for robust recombination.

molecular biology↗

bioRxiv2024

GenoTools: An Open-Source Python Package for Efficient Genotype Data Quality Control and Analysis

GenoTools, a Python package, streamlines population genetics research by integrating ancestry estimation, quality control (QC), and genome-wide association studies (GWAS) capabilities into efficient pipelines. By tracking samples, variants, and quality-specific measures throughout fully customizable pipelines, users can easily manage genetics data for large and small studies. GenoTools "Ancestry" module renders highly accurate predictions, allowing for high-quality ancestry-specific studies, and enables custom ancestry model training and serialization, specified to the users genotyping or sequencing platform. As the genotype processing engine that powers several large initiatives, including the NIHs Center for Alzheimers and Related Dementias (CARD) and the Global Parkinsons Genetics Program (GP2). GenoTools was used to process and analyze the UK Biobank and major Alzheimers Disease (AD) and Parkinsons Disease (PD) datasets with over 400,000 genotypes from arrays and 5000 sequences and has led to novel discoveries in diverse populations. It has provided replicable ancestry predictions, implemented rigorous QC, and conducted genetic ancestry-specific GWAS to identify systematic errors or biases through a single command. GenoTools is a customizable tool that enables users to efficiently analyze and scale genotype data with reproducible and scalable ancestry, QC, and GWAS pipelines.

genomics↗

bioRxiv2024

cMPL-Based Purification and Depletion of Human Hematopoietic Stem Cells: Implications for Pre-Transplant Conditioning

The transplantation of gene-modified autologous hematopoietic stem and progenitor cells (HSPCs) offers a promising therapeutic approach for hematological and immunological disorders. However, this strategy is often limited by the toxicities associated with traditional conditioning regimens. Antibody-based conditioning strategies targeting cKIT and CD45 antigens have shown potential in mitigating these toxicities, but their long-term safety and efficacy in clinical settings require further validation. In this study, we investigate the thrombopoietin (TPO) receptor, cMPL, as a novel target for conditioning protocols. We demonstrate that high surface expression of cMPL is a hallmark feature of long-term repopulating hematopoietic stem cells (LT-HSCs) within the adult human CD34+ HSPC subset. Targeting the cMPL receptor facilitates the separation of human LT-HSCs from mature progenitors, a delineation not achievable with cKIT. Leveraging this finding, we developed a cMPL-targeting immunotoxin, demonstrating its ability to selectively deplete host cMPLhigh LT-HSCs with a favorable safety profile and rapid clearance within 24 hours post-infusion in rhesus macaques. These findings present significant potential to advance our understanding of human hematopoiesis and enhance the therapeutic outcomes of ex vivo autologous HSPC gene therapies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=154 SRC="FIGDIR/small/581887v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@10b265aorg.highwire.dtl.DTLVardef@102ec94org.highwire.dtl.DTLVardef@fa269dorg.highwire.dtl.DTLVardef@fd2583_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO C_FIG

cell biology↗

bioRxiv2024

Glyoxalase 1: emerging biomarker and therapeutic target in cervical cancer progression

IntroductionCervical cancer presents a significant global health challenge, disproportionately impacting underserved populations with limited access to healthcare. Early detection and effective management are vital in addressing this public health concern. This study focuses on Glyoxalase-1 (GLO1), an enzyme crucial for methylglyoxal detoxification, in the context of cervical cancer. MethodsWe assessed GLO1 expression in cervical cancer patient samples using immunohistochemistry. In vitro experiments using HeLa cell lines were conducted to evaluate the impact of GLO1 inhibition on cell viability and migration. Single-cell RNA sequencing (scRNA-seq) and gene set variation analysis were utilized to investigate GLO1s role in the metabolism of cervical cancer. Additionally, public microarray data were analyzed to determine GLO1 expression across various stages of cervical cancer. ResultsOur analysis included 58 cervical cancer patients, and showed that GLO1 is significantly upregulated in cervical cancer tissues compared to normal cervical tissues, independent of pathological findings and disease stage. In vitro experiments indicated that GLO1 downregulation decreased cell viability and migration in cervical cancer cell lines. Analyses of scRNA-seq data and public gene expression datasets corroborated the overexpression of GLO1 and its involvement in cancer metabolism, particularly glycolysis. An examination of expression data from precancerous lesions revealed a progressive increase in GLO1 expression from normal tissue to invasive cervical cancer. ConclusionsThis study highlights the critical role of GLO1 in the progression of cervical cancer, presenting it as a potential biomarker and therapeutic target. These findings contribute valuable insights towards personalized treatment approaches and augment the ongoing efforts to combat cervical cancer. Further research is necessary to comprehensively explore GLO1s potential in clinical applications. SynopsisThis study examines Glyoxalase-1 (GLO1) in cervical cancer and reveals its significant upregulation in cancerous tissues compared to normal counterparts. In vitro experiments show that downregulating GLO1 decreases cell viability and migration. Single-cell RNA sequencing and gene expression analysis substantiate GLO1s involvement in cancer metabolism, notably in glycolysis. These findings identify GLO1 as a potential biomarker and therapeutic target, offering insights for personalized treatment approaches in cervical cancer management.

cancer biology↗

bioRxiv2024

Inositol polyphosphate multikinase regulates Th1 and Th17 cell differentiation by controlling Akt-mTOR signaling

Activated proinflammatory T helper (Th) cells, such as Th1 and Th17 cells, mediate immune responses against intra- and extra-cellular pathogens as well as cause the development of various autoimmune diseases. Inositol polyphosphate multikinase (IPMK) is a key enzyme essential for inositol phosphate and phosphoinositide metabolism, which is known to control major biological events such as growth; however, its role in the function of Th cells remains unclear. Here we show that the expression of IPMK is highly induced in distinct Th1 and Th17 subsets. Further, while conditional deletion of IPMK in CD4+ T cells is dispensable for Th2-dependent immune responses, both Th1- and Th17-mediated immune responses are markedly diminished when this enzyme is absent resulting in reduced resistance to Leishmania major infection and attenuation of experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis. In addition, IPMK-deficient naive CD4+ T cells display aberrant T cell activation and impaired differentiation into Th17 cells, which is associated with reduced activation of Akt, mechanistic target of rapamycin (mTOR), and STAT3. Mechanistically, IPMK as a phosphatidylinositol 3-kinase (PI3-kinase) controls the production of phosphatidylinositol (3,4,5)-trisphosphate, thereby promoting T cell activation, differentiation, and effector functions. Our findings suggest that IPMK acts as a critical regulator of Th1 and Th17 differentiation, highlighting the physiological importance of IPMK in Th1- and Th17-mediated immune homeostasis.

immunology↗

bioRxiv2023

Impact of CRISPR/HDR-editing versus lentiviral transduction on long-term engraftment and clonal dynamics of HSPCs in rhesus macaques

For precise genome editing via CRISPR/homology-directed repair (HDR), effective and safe editing of long-term engrafting hematopoietic stem cells (LT-HSCs) requires both sufficient HDR efficiency and protection of LT-HSC function and number. The impact of HDR on true LT-HSCs clonal dynamics in a relevant large animal model has not previously been studied. To track the HDR-edited cells, autologous rhesus macaque (RM) CD34+ cells were electroporated with the gRNA/Cas9 ribonucleoprotein (RNP) and HDR cassette barcode library structure and reinfused into RMs following myeloablation. For competitive model animals, fractionated CD34+ cells were transduced with a barcoded GFP-expressing lentiviral vector (LV) and electroporated via HDR machinery, respectively. CD33 knockout (KO) neutrophils were prevalent early following engraftment and then rapidly decreased, resulting in less than 1% total editing efficiency. Interestingly, in competitive animals, a higher concentration of i53 mRNA result in a less steep reduction in CD33 KO cells, presented a modest decrease in HDR rate (0.1-0.2%) and total indels (1.5-6.5%). In contrast, the drop off of LV-transduced GFP+ cells stabilized at 20% after 2 months. We next retrieved embedded barcodes and revealed that various clones contributed to early hematopoietic reconstitution, then after dominant clones appeared at steady state throughout the animals. In conclusion, CRISPR/HDR edited cells disappeared rapidly after the autologous transplantation in RM despite substantial gene editing outcome, whereas LV-transduced cells were relatively well maintained. Clonality of HDR-edited cells drastically shrank at early stage and then relied on several dominant clones, which can be mildly mitigated by the introduction of i53 mRNA.

cell biology↗