Biology subjects

Hou, Y.

Publications and source records attributed to Hou, Y..

At least 109 records · Page 6Linked to original sources

bioRxiv2023

Targeting CD45 by gene-edited CAR-T cells for leukemia eradication and hematopoietic stem cell transplantation preconditioning

Hematopoietic stem cell transplantation (HSCT) is widely used to treat patients with life-threatening hematologic and immune system disorders. The currently used nontargeted chemo-/radiotherapy conditioning regimens cause tissue injury and induce an array of immediate and delayed adverse effects, which limits the use of this potentially curative treatment. The growing demand to replace canonical conditioning regimens has led to the development of alternative approaches based on antibody-drug conjugates, naked antibodies and CAR T cells. Here, we propose a preconditioning strategy based on targeting CD45 on hematopoietic cells with CAR45 T cells. To avoid fratricide of CD45 CAR T cells, targeted genomic disruption of the CD45 gene was performed in human CD45 CAR T cells in combination with dasatinib treatment. CD45{Delta}CAR45 T cells showed impressive activity in terms of target cell elimination in vitro and depletion of tumor cells in vivo or human hematopoietic cells in humanized immunodeficient mice engrafted with human blood-derived HSCs. CD45{Delta}CAR45 NK cells also exhibited potent killing activity against tumor cell lines and human hematopoietic cells. Therefore, fratricide-resistant CAR45 T and NK cells have the potential to provide the benefits of full myeloablative conditioning and therapy for hematologic malignancies. Thus, we provide the proof of concept for the generation and preclinical efficacy of CAR T cells directed against CD45-expressing cells.

molecular biology↗

bioRxiv2023

Cell type-focused compound screen in human organoids reveals molecules and pathways controlling cone photoreceptor death

Human organoids that mirror their corresponding organs in cell-type diversity present an opportunity to perform large-scale screens for compounds that protect disease-affected or damage healthy cell types. However, such screens have not yet been performed. Here, we generated 20,000 human retinal organoids with GFP-labeled cone photoreceptors. Since degeneration of cones is a leading cause of blindness, we induced cone death and screened 2,707 compounds with known targets, for those that saved cones or those that further damaged cones. We identified inhibitors of CK1 or MAPK11 that protected cones, HSP90 inhibitors that saved cones in the short term but damaged them in the longer term, and broad HDAC inhibition by many compounds that significantly damaged cones. This work provides a database for cone-damaging compounds and describes compounds that can be starting points to develop neuroprotection for cones in diseases such as macular degeneration.

neuroscience↗

bioRxiv2023

A reference genome and its epigenetic landscape of potential Orychophragmus violaceus, an industrial crop species

Orychophragmus violaceus, also called er-yue-lan in China, is an annual plant of the family of Brassicaceae. The seed oil of O. violaceus contained two specific di-hydroxy fatty acids which were produced by functional divergence between two FAD2 WGD copies determine its industrial property. Here, we assembled a high-quality chromosome-level genome of O. violaceus via based on PacBio CLR technology and its cis-regulatory landscape of five mature tissues, including root, leaf, flower, seed and stem, based on ATAC-seq technology. 1.2 Gb draft genomic sequences were anchored to 12 pseudo-chromosomes and 49904 protein-coding genes were annotated on these chromosomes. To fully understand the epigenetic landscape of O. violaceus, we further performed WGBS-seq for leaf, flower and silique tissues. In total, our multi-omics data provide opportunity to find out the differences between two WGD copies and also a valuable resource for downstream breeding effort of this potential industrial species.

genomics↗

bioRxiv2023

Cep290 is cooperatively maintained at basal body by Cep131-Cep162 and Cby-Fam92 modules

Cilia play critical roles in cell signal transduction and organ development. Defects in cilia function result in a variety of genetic disorders. Cep290 is an evolutionarily conserved ciliopathy protein that bridges the ciliary membrane and axoneme at the basal body and plays critical roles in the initiation of ciliogenesis and TZ assembly. How Cep290 is maintained at basal body and whether axonemal and ciliary membrane localized cues converge to determine the localization of Cep290 remain unknown. Here, we report that the Cep131-Cep162 module near the axoneme and the Cby-Fam92 module close to the membrane synergistically control the basal body localization of Cep290 and the subsequent initiation of ciliogenesis. Concurrent deletion of any protein of the Cep131-Cep162 module and of the Cby-Fam92 module leads to a complete loss of Cep290 from basal body and blocks ciliogenesis at its initiation stage. Our results reveal that the first step of ciliogenesis strictly depend on cooperative and retroactive interactions between Cep131-Cep162, Cby-Fam92 and Cep290, which may contribute to the complex pathogenesis of Cep290-related ciliopathies.

cell biology↗

bioRxiv2023

Alstrom Syndrome protein Alms1 is required for maintaining meiotic centriole engagement in spermatocytes of Drosophila

Maintaining proper mother-daughter centriole engagement is crucial for controlling centrosome numbers and ensuring accurate cell division in both mitosis and meiosis. However, the mechanism responsible for this maintenance remains unclear. Here, we report that the Drosophila homolog of human ciliopathy gene Alstrom Syndrome 1 (Alms1) is required for maintaining centriole engagement during spermatocyte meiosis. We demonstrated that deletion of Alms1 results in premature centriole disengagement in prophase of meiosis I, leading to the formation of multipolar spindles and abnormal cell division in Drosophila spermatocytes. Further studies reveal that Alms1 localizes to the proximal centrioles, and functions downstream of cartwheel protein Sas-6 to regulate centriole engagement, and its highly conserved ALMS motif is required for Alms1s function in centriole engagement. Moreover, we show that the centriole size and pericentriolar materials (PCM) have antagonistic roles on maintaining centriole engagement in alms1 mutant flies. Our findings highlight the critical role of Alms1 as a "glue protein" in maintaining mother-daughter centriole pair cohesion, potentially advancing our comprehension of the pathogenesis of Alstrom Syndrome. Significance statementAlstrom syndrome (AS) is a human ciliopathy that results from mutations in the ALMS1 gene inherited in an autosomal recessive manner. Elucidating the roles of ALMS1 and the underlying molecular mechanisms of AS is of paramount importance. In this study, using Drosophila model, we discovered that ALMS1 is localized at the proximal centrioles, and is crucial for the proper centriole engagement, spindle polarity, cell division in spermatocytes. Our findings reveal the new role of ALSM1 in maintaining centriole engagement, and suggest that non-ciliary function of ALMS1 may contribute to the pathogenesis of Alstrom Syndrome, warranting further investigation.

cell biology↗

bioRxiv2023

Ser149 is another potential 14-3-3 epsilon binding site of Cdc25B in the G2/M transition of mouse fertilized eggs

Cell cycle division 25B (CDC25B) belongs to the family of cell cycle regulatory proteins. It drives G2/M transition by activating cyclin-dependent protein kinases (CDK1), also known as CDC2, whose activity is directly related to its subcellular localization and phosphorylation state.14-3-3 (YHWA) regulates cell division cycle by binding to Cdc25B as a chaperone protein in mammals. Previously, we found that Cdc25B-Ser149 plays an important role in G2/M transition of mouse fertilized eggs, but the molecular mechanism of this transition remains unclear. In this study, we assessed the role of 14-3-3{varepsilon} (YHWAE) interaction with phosphorylated Cdc25B-Ser149 in G2/M transition of mouse fertilized eggs. Co-expression of Cdc25B-Ser149A and 14-3-3{varepsilon} could effectively activate maturation promoting factor (MPF) through direct dephosphorylation of Cdc2-Tyr15, and induce G2 fertilized eggs to enter mitosis rapidly. However, co-expression of the phosphomimic Cdc25B-Ser149D or Cdc25B-WT and 14-3-3{varepsilon} showed no significant difference in comparison with control groups. 14-3-3{varepsilon} binds to Cdc25B-WT, which is abolished when Ser149 is mutated to Ala. In addition, we found that 14-3-3{varepsilon} and Cdc25B were co-localized in the cytoplasm at the G1, S and early G2 phases. Cdc25B was translocated from the cytoplasm to the nucleus at the late G2 phase. However, when Ser149 is mutated to Ala, the cytoplasmic localization of Cdc25B is completely abolished. Our findings suggest that Cdc25B-Ser149 is another specific binding site for 14-3-3{varepsilon} in G2/M transition of one-cell fertilized mouse eggs, which plays essential roles in the regulation of early development of fertilized mouse eggs.

cell biology↗

bioRxiv2023

Large-scale population genomics of Malayan pangolins reveals deep diversification and a new species

BackgroundArchipelagos and oceanic islands often present high percentage of endemism due to rapid speciation. The Malayan pangolin is a species distributing at both mainland (southern Yunnan, China) and oceanic islands via Malayan peninsula, which may result in deep differentiation among populations. In-depth investigation of population structure and genetic consequences for such species is of vital importance for their protection and conservation, practically for the critically endangered Malayan pangolin that is suffering from poaching, illegal trade, and habitat loss. ResultsHere we carried out a large-scale population genomic analysis for Malayan pangolins, and revealed three highly distinct genetic populations in this species, two of which are now being reported for the first time. Based on multiple lines of genomic and morphological evidence, we postulate the existence of a new pangolin species (Manis_1). Genetic diversity and recent inbreeding were both at a moderate level for both Malayan pangolins and Manis_1, but mainland Malayan pangolins presented relatively lower genetic diversity, higher inbreeding and fitness cost than island populations. ConclusionsWe found extremely deep and graded differentiation in Malayan pangolins, with two newly discovered genetic populations and a new pangolin species that is closely related to the Philippine pangolin than the typical Malayan pangolin, but a distant relative of the Indian pangolin. Anthropogenic factors did not significantly weaken the basis of genetic sustainability for Malayan pangolins, but mainland Malayan pangolins should be paid more attention for conservation due to higher genetic risks than island populations.

genomics↗

bioRxiv2023

The super-pangenome of Populus unveil genomic facets for adaptation and diversification in widespread forest trees

Understanding the underlying mechanisms between genome evolution and phenotypic and adaptive innovations is a key goal of evolutionary studies. Poplars are the worlds most widely distributed and cultivated trees, with extensive phenotypic diversity and environmental adaptability. Here we report a genus-level super-pangenome of 19 Populus genomes. After integrating pan-genomes with transcriptomes, methylomes and chromatin accessibility mapping, we reveal that the evolutionary fate of pan-genes and duplicated genes are largely associated with local genomic landscapes of regulatory and epigenetic architectures. Further comparative genomic analyses enabled to identify 142,202 structural variations (SVs) across species, which overlap with substantial genes and play key roles in both phenotypic and adaptive divergence. We experimentally validated a [~]180 bp presence/absence variant located in the promoter of the CUC2 gene, which contributed critically to leaf serration divergence between species. Together, this first super-pangenome resource in forest trees will not only accelerate molecular functional studies and genetic breeding of this globally important tree genus, but also lays a foundation for our understanding of tree biology.

evolutionary biology↗

bioRxiv2023

The ChickenGTEx pilot analysis: a reference of regulatory variants across 28 chicken tissues

Chicken is a valuable model for understanding fundamental biology, vertebrate evolution and diseases, as well as a major source of nutrient-dense and lean-protein-enriched food globally. Although it is the first non-mammalian amniote genome to be sequenced, the chicken genome still lacks a systematic characterization of functional impacts of genetic variants. Here, through integrating 7,015 RNA-Seq and 2,869 whole-genome sequence data, the Chicken Genotype- Tissue Expression (ChickenGTEx) project presents the pilot reference of regulatory variants in 28 chicken tissue transcriptomes, including millions of regulatory effects on primary expression (including protein-coding genes, lncRNA and exon) and post-transcriptional modifications (alternative splicing and 3 untranslated region alternative polyadenylation). We explored the tissue-sharing and context-specificity of these regulatory variants, their underlying molecular mechanisms of action, and their utility in interpreting adaptation and genome-wide associations of 108 chicken complex traits. Finally, we illustrated shared and lineage-specific features of gene regulation between chickens and mammals, and demonstrated how the ChickenGTEx resource can further assist with translating genetic findings across species. One-Sentence SummaryThe ChickenGTEx provides a multi-tissue reference of regulatory variants for chicken genetics and genomics, functional genomics, precision breeding, veterinary medicine, vertebrate evolution and even human biomedicine.

genetics↗

bioRxiv2023

A Gpr35 tuned gut-brain metabolic axis regulates depressive-like behavior

Gene-environment interactions shape animal behavior and the susceptibility to neurobehavioral symptoms such as depression. However, little is known about the signaling pathway that integrates genetic and environmental inputs with neurobehavioral outcomes, preventing the development of targeted therapies. Here we report that Gpr35 engages a gut microbe-to-brain metabolic pathway to modulate neuronal plasticity and depressive behavior in mice. Chronic stress decreases gut epithelial Gpr35, the genetic deletion of which induces despair and social impairment in a microbiome-dependent manner. We identify a dominant role for the imbalance of microbe-derived indole-3-carboxaldehyde (IAld) and indole-3-lactate (ILA) in the behavioral symptoms with Gpr35 deficiency. Mechanistically, these bacterial metabolites counteractively modulate dendritic spine density and synaptic transmission in the nucleus accumbens. Supplementation of IAld, which is similarly decreased in depressive patients, produce anti-depressant effects in mice with stress or gut epithelial Gpr35 deficiency. Together, these findings identify a genetics-shaped gut-brain connection underlying the susceptibility to depression and suggest a microbial metabolite-based therapeutic strategy to genetic predisposition.

animal behavior and cognition↗

bioRxiv2023

Multimodal Deep Learning Model Unveils Behavioral Dynamics of V1 Activity in Freely Moving Mice

Despite their immense success as a model of macaque visual cortex, deep convolutional neural networks (CNNs) have struggled to predict activity in visual cortex of the mouse, which is thought to be strongly dependent on the animals behavioral state. Furthermore, most computational models focus on predicting neural responses to static images presented under head fixation, which are dramatically different from the dynamic, continuous visual stimuli that arise during movement in the real world. Consequently, it is still unknown how natural visual input and different behavioral variables may integrate over time to generate responses in primary visual cortex (V1). To address this, we introduce a multimodal recurrent neural network that integrates gaze-contingent visual input with behavioral and temporal dynamics to explain V1 activity in freely moving mice. We show that the model achieves state-of-the-art predictions of V1 activity during free exploration and demonstrate the importance of each component in an extensive ablation study. Analyzing our model using maximally activating stimuli and saliency maps, we reveal new insights into cortical function, including the prevalence of mixed selectivity for behavioral variables in mouse V1. In summary, our model offers a comprehensive deep-learning framework for exploring the computational principles underlying V1 neurons in freely-moving animals engaged in natural behavior.

neuroscience↗

bioRxiv2023

Pathogen protein modularity enables elaborate mimicry of a host phosphatase

Pathogens produce diverse effector proteins to manipulate host cellular processes. However, how functional diversity is generated in an effector repertoire is poorly understood. Many effectors in the devastating plant pathogen Phytophthora contain tandem repeats of the "(L)WY" motif, which are structurally conserved but variable in sequences. Here, we discovered a functional module formed by a specific (L)WY-LWY combination in multiple Phytophthora effectors, which efficiently recruit the Serine/Threonine protein phosphatase 2A (PP2A) core enzyme in plant hosts. Crystal structure of an effector-PP2A complex shows that the (L)WY-LWY module enables hijacking of the host PP2A core enzyme to form functional holoenzymes. While sharing the PP2A-interacting module at the amino terminus, these effectors possess divergent C-terminal LWY units and regulate distinct sets of phosphoproteins in the host. Our results highlight the appropriation of an essential host phosphatase through molecular mimicry by pathogens and diversification promoted by protein modularity in an effector repertoire.

plant biology↗

bioRxiv2023

High-efficiency base editing for Stargardt disease in mice, non-human primates, and human retina tissue

Stargardt disease is a currently untreatable, inherited neurodegenerative disease that leads to macular degeneration and blindness due to loss-of-function mutations in the ABCA4 gene. We have designed a dual adeno-associated viral vector split-intein adenine base-editing strategy to correct the most common mutation in ABCA4 (c.5882G>A, p.G1961E). We optimized ABCA4 base editing in human models, including retinal organoids, iPSC-derived retinal pigment epithelial (RPE) cells, as well as adult human retinal- and RPE/choroid explants in vitro. The resulting gene therapy vectors achieved high levels of gene correction in mutation-carrying mice and in non-human primates, with an average editing of 37% of photoreceptors and 73% of RPE cells in vivo. The high editing rates in primates make way for precise and efficient gene editing in other neurodegenerative ocular diseases.

neuroscience↗

bioRxiv2023

The RNA helicase DDX1 associates with the nuclear RNA exosome and modulates R-loops

The RNA exosome is a ribonuclease complex that mediates both RNA processing and degradation. This complex is evolutionarily conserved, ubiquitously expressed, and required for fundamental cellular functions, including rRNA processing. The RNA exosome plays roles in regulating gene expression and protecting the genome, including modulating the accumulation of RNA-DNA hybrids (R-loops). The function of the RNA exosome is facilitated by cofactors, such as the RNA helicase MTR4, which binds/remodels RNAs. Recently, missense mutations in RNA exosome subunit genes have been linked to neurological diseases. One possibility to explain why missense mutations in genes encoding RNA exosome subunits lead to neurological diseases is that the complex may interact with cell- or tissue-specific cofactors that are impacted by these changes. To begin addressing this question, we performed immunoprecipitation of the RNA exosome subunit, EXOSC3, in a neuronal cell line (N2A) followed by proteomic analyses to identify novel interactors. We identified the putative RNA helicase, DDX1, as an interactor. DDX1 plays roles in double-strand break repair, rRNA processing, and R-loop modulation. To explore the functional connections between EXOSC3 and DDX1, we examined the interaction following double-strand breaks, and analyzed changes in R-loops in N2A cells depleted for EXOSC3 or DDX1 by DNA/RNA immunoprecipitation followed by sequencing (DRIP-Seq). We find that EXOSC3 interaction with DDX1 is decreased in the presence of DNA damage and that loss of EXOSC3 or DDX1 alters R-loops. These results suggest EXOSC3 and DDX1 interact during events of cellular homeostasis and potentially suppress unscrupulous expression of genes promoting neuronal projection.

biochemistry↗

bioRxiv2023

Noise-robust, physical microscopic deconvolution algorithm enabled by multi-resolution analysis regularization

Despite the grand advances in fluorescence microscopy, the photon budget of fluorescent molecules remains the fundamental limiting factor for major imaging parameters, such as temporal resolution, duration, contrast, and even spatial resolution. Computational methods can strategically utilize the fluorescence photons against the imaging noise, to break the abovementioned limits. Here, we propose a multi-resolution analysis (MRA) approach to recharacterize and extract the two main characteristics of fluorescence images: (1) high contrast across the edge, and (2) high continuity along the edge. By regularizing the solution using framelet and curvelet domain sparsity, we develop MRA deconvolution algorithm for fluorescence image, which allows fine detail recovery even with negative signal-to-noise-ratio (SNR), and can provide more than 2-fold physical resolution enhancement with conspicuously fewer artifacts than maximum likelihood estimation (MLE) methods. Furthermore, we develop DeepMRA deconvolution algorithm that can provide computational background inhibition through a bias thresholding mechanism while deconvolving a fluorescence image. Compared with conventional background mitigation schemes, this novel deconvolution canonical form can deal with severer background and better preserve the high-frequency and low-intensity details, which are commonly disrupted by other algorithms. We demonstrate that the MRA and DeepMRA deconvolution algorithms can improve the SNR and resolution of biological images in various microscopies, such as wide-field, confocal, spinning-disk confocal (SD-confocal), light-sheet, structured illumination microscopy (SIM), and stimulated excitation depletion (STED) microscopy.

bioengineering↗

bioRxiv2023

An Unexpected Role of Neutrophils in Clearing Apoptotic Hepatocytes In Vivo

Billions of apoptotic cells are removed daily in a human adult by professional phagocytes (e.g. macrophages) and neighboring nonprofessional phagocytes (e.g. stromal cells). Despite being a type of professional phagocyte, neutrophils are thought to be excluded from apoptotic sites to avoid tissue inflammation. Here we report a fundamental and unexpected role of neutrophils as the predominant phagocyte responsible for the clearance of apoptotic hepatic cells in the steady state. In contrast to the engulfment of dead cells by macrophages, neutrophils burrowed directly into apoptotic hepatocytes, a process we term perforocytosis, and ingested the effete cells from the inside. The depletion of neutrophils caused defective removal of apoptotic bodies, induced tissue injury in the mouse liver and led to the generation of autoantibodies. Human autoimmune liver disease showed similar defects in the neutrophil-mediated clearance of apoptotic hepatic cells. Hence, neutrophils possess a specialized immunologically silent mechanism for the clearance of apoptotic hepatocytes through perforocytosis, and defects in this key housekeeping function of neutrophils contribute to the genesis of autoimmune liver disease.

physiology↗

bioRxiv2023

Transient EZH2 suppression by Tazemetostat during in vitro expansion maintains T cell stemness and improves adoptive T cell therapy

The histone methyltransferase enhancer of zeste homolog 2 (EZH2)-mediated epigenetic regulation of T cell differentiation in acute infection has been extensively investigated. However, the role of EZH2 in T cell exhaustion remains under-explored. Here, using in vitro exhaustion models, we demonstrated that transient inhibition of EZH2 in T cells before the phenotypic onset of exhaustion with a clinically approved inhibitor, Tazemetastat, delayed their dysfunctional progression and maintained T cell stemness and polyfunctionality while having no negative impact on cell proliferation. Tazemetestat induced T cell epigenetic reprogramming and increased the expression of the self-renewing T cell transcription factor TCF1 by reducing its promoter H3K27 methylation preferentially in rapidly dividing T cells. In a murine melanoma model, T cells pre-treated with tazemetastat exhibited a superior response to anti-PD-1 blockade therapy after adoptive transfer. Collectively, these data unveil the potential of transient epigenetic reprogramming as a potential intervention to be combined with checkpoint blockade for immune therapy.

immunology↗

bioRxiv2023

Loss of the endocytic tumor suppressor HD-PTP phenocopies LKB1 and promotes RAS-driven oncogenesis.

Abstract/SummaryOncogenic RAS mutations drive aggressive cancers that are difficult to treat in the clinic, and while direct inhibition of the most common KRAS variant in lung adenocarcinoma (G12C) is undergoing clinical evaluation, a wide spectrum of oncogenic RAS variants together make up a large percentage of untargetable lung and GI cancers. Here we report that loss-of-function alterations (mutations and deep deletions) in the gene that encodes HD-PTP (PTPN23) occur in up to 14% of lung cancers in the ORIEN Avatar lung cancer cohort, associate with adenosquamous histology, and occur alongside an altered spectrum of KRAS alleles. Furthermore, we show that in publicly available early-stage NSCLC studies loss of HD-PTP is mutually exclusive with loss of LKB1, which suggests they restrict a common oncogenic pathway in early lung tumorigenesis. In support of this, knockdown of HD-PTP in RAS-transformed lung cancer cells is sufficient to promote FAK-dependent invasion. Lastly, knockdown of the Drosophila homolog of HD-PTP (dHD-PTP/Myopic) synergizes to promote RAS-dependent neoplastic progression. Our findings highlight a novel tumor suppressor that can restrict RAS-driven lung cancer oncogenesis and identify a targetable pathway for personalized therapeutic approaches for adenosquamous lung cancer.

cancer biology↗