Biology subjects

Tan, Y.

Publications and source records attributed to Tan, Y..

At least 109 records · Page 6Linked to original sources

bioRxiv2023

Autophagy contributes to homeostasis in esophageal epithelium where high autophagic vesicle content marks basal cells with limited proliferation and enhanced self-renewal potential

Background & AimsAutophagy has been demonstrated to play roles in esophageal pathologies both benign and malignant. Here, we aim to define the role of autophagy in esophageal epithelium under homeostatic conditions. MethodsWe generated tamoxifen-inducible, squamous epithelial-specific Atg7 (autophagy related 7) conditional knockout mice to evaluate effects on esophageal homeostasis and response to the carcinogen 4-nitroquinoline 1-oxide (4NQO) using histological and biochemical analyses. We FACS sorted esophageal basal cells based upon fluorescence of the autophagic vesicle (AV)-identifying dye Cyto-ID, then subjected these cells to transmission electron microscopy, image flow cytometry, 3D organoid assays, RNA-Sequencing (RNA-Seq), and cell cycle analysis. 3D organoids were subjected to passaging, single cell (sc) RNA-Seq, cell cycle analysis, and immunostaining. ResultsGenetic autophagy inhibition in squamous epithelium resulted in increased proliferation of esophageal basal cells. Esophageal basal cells with high AV level (Cyto-IDHigh) displayed limited organoid formation capability upon initial plating but passaged more efficiently than their counterparts with low AV level (Cyto-IDLow). RNA-Seq suggested increased autophagy in Cyto- IDHigh esophageal basal cells along with decreased cell cycle progression, the latter of which was confirmed by cell cycle analysis. scRNA-Seq of 3D organoids generated by Cyto-IDLow and Cyto- IDHigh cells identified expansion of 3 cell populations, enrichment of G2/M-associated genes, and aberrant localization of cell cycle-associated genes beyond basal cell populations in the Cyto- IDHigh group. Ki67 expression was also increased in organoids generated by Cyto-IDHigh cells, including in cells beyond the basal cell layer. Squamous epithelial-specific autophagy inhibition induced significant weight loss in mice treated with 4NQO that further displayed perturbed epithelial tissue architecture. ConclusionsHigh AV level identifies esophageal epithelium with limited proliferation and enhanced self-renewal capacity that contributes to maintenance of the esophageal proliferation- differentiation gradient in vivo.

physiology↗

bioRxiv2023

Nuclear Lipid Droplets Exit to the Cytoplasm: A Novel Mechanism of non-nuclear pore-dependent material exchange

In cellular biology, the extrusion of large molecular complexes from the nucleus has consistently represented a considerable challenge. In this investigation, we reveal a hitherto unexplored mechanism facilitating the efflux of nuclear lipid droplets (nLDs) from the nucleus directly into the cytoplasm, a process integral to comprehending cellular processes and nuclear dynamics. Through high-throughput sequencing, immunoprecipitation, and immunofluorescence experimentation, we demonstrated that the type I nucleoplasmic reticulum engages with nLDs, enabling the dynamic protein Rab8as transfer to the nLDs and fostering their translocation to the nuclear membrane. Phosphorylation of LMNA/C at the S392 site, adjacent to the nLD-nuclear membrane contact site, induces local depolymerization of lamins, creating an aperture that enables gradual nuclear exit of nLDs. Following this, nLDs, carrying DNA fragments, are released into the cytoplasm through budding and subsequently undergo autophagy-mediated degradation. Furthermore, we demonstrate that RhoA-PKC signaling enhances nLD movement and LMNA/C phosphorylation, while its inhibition impedes nuclear nLD efflux. Our groundbreaking investigation illuminates non-nuclear pore-dependent mechanisms of material exchange and offers fresh perspectives on nuclear metabolic pathways. In Brief O_FIG O_LINKSMALLFIG WIDTH=197 HEIGHT=200 SRC="FIGDIR/small/556761v1_ufig1.gif" ALT="Figure 1"> View larger version (107K): org.highwire.dtl.DTLVardef@38a213org.highwire.dtl.DTLVardef@1898caorg.highwire.dtl.DTLVardef@d7270forg.highwire.dtl.DTLVardef@14582a2_HPS_FORMAT_FIGEXP M_FIG C_FIG In this study, Jin et al. elucidate a novel mechanism for the expulsion of nuclear lipid droplets (nLDs) from the nucleus. They demonstrate that the activation of RhoA within the nucleus recruits Rab8a to the surface of nLDs. Concurrently, PKC phosphorylation triggers the phosphorylation of LMNA/C at the S392 site, leading to a localized depolymerization of lamins. This creates an aperture that allows for the gradual exit of nLDs from the nucleus. The efflux process of nLDs involves three sequential steps: rupture of the nuclear fibril layer, fusion of nLDs with the inner nuclear membrane (INM), and subsequent fusion with the outer nuclear membrane (ONM). This enables nLDs to enter the cytoplasm, shedding light on a previously unknown process of large molecular entity expulsion from the nucleus.

molecular biology↗

bioRxiv2023

Long noncoding RNAs and mRNAs profiling in ovary during laying and broodiness in Taihe Black-Bone Silky Fowls (Gallus gallus domesticus Brisson)

Broodiness is one of the important factors affecting poultry egg production, with the black-bone Silky (Gallus gallus domesticus Brisson) exhibiting strong broodiness behavior. Changes in ovarian signaling can offer insights into the mechanisms influencing broodiness. However, research comparing the characteristics of long non- coding RNAs (lncRNAs) in the ovaries during the broody chickens (BC) and high egg- laying chickens (GC) groups of poultry is still limited. In this study, we employed RNA-seq to analyze the ovarian transcriptomes (lncRNAs and mRNAs) of eight brooding and high egg-laying Taihe Black-Bone Silky Fowls (TBsf). We identified a total of 16,444 mRNAs and 18,756 lncRNAs, among which 349 mRNAs and 651 lncRNAs (P < 0.05) showed significantly different expression (DE) between the BC and GC groups. Additionally, we identified the cis-regulated and trans-regulated target genes of differentially abundant lncRNA transcripts and constructed an lncRNA- mRNA trans-regulated interaction network associated with ovarian follicle development. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation analyses revealed that DE mRNAs and target genes of DE lncRNAs were associated with neuroactive ligand-receptor interaction, CCR6 chemokine receptor binding, G-protein coupled receptor binding, Cytokine-cytokine receptor interaction, and ECM-receptor interaction pathways. Our study provides a catalogue of lncRNAs and mRNAs related to ovarian development and constructs a predicted interaction network of differentially abundant lncRNAs and Differentially Expressed Genes (DEGs) in TBsf, thus enhancing our understanding of the interactions between lncRNAs and genes regulating brooding behavior. Author summaryIn this study, we performed transcriptome sequencing analysis of the ovaries from BC and GC groups in TBsf. A total of 349 significantly differentially expressed mRNAs and 651 significantly differentially expressed lncRNAs were detected. Furthermore, we identified 10 key genes that may affect reproductive performance in chickens: STC1, MMP13, IL8, AT2, FSHB, RARB, THOC7, FGF12, EPHA1, and NPY5R. Based on GO and KEGG enrichment analyses, we preliminarily explored five pathways that may influence egg production performance: neuroactive ligand-receptor interaction, CCR6 chemokine receptor binding, G-protein coupled receptor binding, cytokine-cytokine receptor interaction and ECM-receptor interaction. These genes and pathways may play crucial roles in improving broodiness behavior. This study establishes a foundation for subsequent screening of candidate functional genes and functional validation of important production traits in TBsf, providing a theoretical basis for further molecular breeding and enhancing egg-laying performance in TBsf.

bioinformatics↗

bioRxiv2023

Mechanosensation of the heart and gut elicits hypometabolism and vigilance in mice.

Interoception broadly refers to awareness of ones internal milieu. Vagal sensory afferents monitor the internal milieu and maintain homeostasis by engaging brain circuits that alter physiology and behavior. While the importance of the body-to-brain communication that underlies interoception is implicit, the vagal afferents and corresponding brain circuits that shape perception of the viscera are largely unknown. Here, we use mice to parse neural circuits subserving interoception of the heart and gut. We determine vagal sensory afferents expressing the oxytocin receptor, hereafter referred to as NDGOxtr, send projections to the aortic arch or stomach and duodenum with molecular and structural features indicative of mechanosensation. Chemogenetic excitation of NDGOxtr significantly decreases food and water consumption, and remarkably, produces a torpor-like phenotype characterized by reductions in cardiac output, body temperature, and energy expenditure. Chemogenetic excitation of NDGOxtr also creates patterns of brain activity associated with augmented hypothalamic-pituitary-adrenal axis activity and behavioral indices of vigilance. Recurrent excitation of NDGOxtr suppresses food intake and lowers body mass, indicating that mechanosensation of the heart and gut can exert enduring effects on energy balance. These findings suggest that the sensation of vascular stretch and gastrointestinal distention may have profound effects on whole body metabolism and mental health.

neuroscience↗

bioRxiv2023

Haplotype-phased genome revealed the butylphthalide biosynthesis and hybrid origin of Ligusticum chuanxiong

Butylphthalide, one type of phthalides, is one of the first-line drugs for ischemic stroke therapy, while no enzyme involved in its biosynthesis pathway has been reported. Here, we present the first haplotype-resolved genome of Ligusticum chuanxiong Hort., a long-cultivated and phthalide-rich medicinal plant in Apiaceae. Based on comprehensive candidate gene screening, four Fe (II)- and 2-oxoglutarate-dependent dioxygenases (2OGDs) and two CYPs were mined and further biochemically verified as phthalide C-4/C-5 desaturase (P4,5Ds) that converts senkyunolide A to l-n-butylphthalide (l-NBP) and ligustilide to butylidenephthalide. The substrate promiscuity and functional redundancy featured for P4,5Ds may contribute to the high phthalide diversity in L. chuanxiong. Notably, comparative genomic evidence supported L. chuanxiong as a diploid hybrid with L. sinense as a potential parent. The two haplotypes demonstrated exceptional structure variance and diverged around 3.42 million years ago (Ma). Our study is an icebreaker for the dissection of phthalide biosynthesis pathway and reveals the hybrid origin of L. chuanxiong. These findings will facilitate the future metabolic engineering for l-NBP production and breeding efforts for L. chuanxiong.

synthetic biology↗

bioRxiv2023

Concerted epithelial and stromal changes during progression of Barrett's Esophagus to invasive adenocarcinoma exposed by multi-scale, multi-omics analysis

Esophageal adenocarcinoma arises from Barretts esophagus, a precancerous metaplastic replacement of squamous by columnar epithelium in response to chronic inflammation. Multi-omics profiling, integrating single-cell transcriptomics, extracellular matrix proteomics, tissue-mechanics and spatial proteomics of 64 samples from 12 patients paths of progression from squamous epithelium through metaplasia, dysplasia to adenocarcinoma, revealed shared and patient-specific progression characteristics. The classic metaplastic replacement of epithelial cells was paralleled by metaplastic changes in stromal cells, ECM and tissue stiffness. Strikingly, this change in tissue state at metaplasia was already accompanied by appearance of fibroblasts with characteristics of carcinoma-associated fibroblasts and of an NK cell-associated immunosuppressive microenvironment. Thus, Barretts esophagus progresses as a coordinated multi-component system, supporting treatment paradigms that go beyond targeting cancerous cells to incorporating stromal reprogramming. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=187 SRC="FIGDIR/small/544265v1_ufig1.gif" ALT="Figure 1"> View larger version (62K): org.highwire.dtl.DTLVardef@64c375org.highwire.dtl.DTLVardef@15c6ef2org.highwire.dtl.DTLVardef@177dee0org.highwire.dtl.DTLVardef@c945e7_HPS_FORMAT_FIGEXP M_FIG Graphical AbstractTo obtain a comprehensive picture of the coordinated changes in epithelial, stromal and immune compartments during development of Barretts-associated esophageal adenocarcinoma, patient-matched samples corresponding to various phases of disease progression were collected from 12 patients, each of which had at a given time point lesions at multiple stages progression (matched-normal, metaplasia, dysplasia, and carcinoma). Matched "normal" gastric tissues were also collected. These sample were analyzed by single cell RNA-sequencing (scRNAseq) for single-cell resolution transcriptomics and Copy Number Variant (CNV), by proteomics for extracellular matrix (ECM) proteins, by Atomic Force Microscopy (AFM for tissue stiffness and by CODEX spatial proteomics imaging The integrative multi-omics analysis exposed drastic alterations in cell type composition and shifts in cell states in all three compartments. A large subpopulation of fibroblasts absent in the normal esophagus and characteristic of dysplasia and adenocarcinoma sample, that based on markers would indeed be considered cancer associated fibroblasts (CAF), appeared already in the metaplastic phase. This fibroblast subpopulation had transcriptomes virtually indistinguishable with fibroblasts of the cancer free gastric epithelium in these patients C_FIG

cancer biology↗

bioRxiv2023

Angiogenic Steroids Induce Pathologic Scarring in a Preclinical Swine Model Via Dysfunctional Extracellular Matrix Deposition.

BackgroundHypertrophic scarring is a major source of morbidity for surgery patients. Sex hormones are not classically considered to be modulators of scarring. However, based on clinical observations of increased frequency of hypertrophic scarring in patients on testosterone, we hypothesized that androgenic steroids induce abnormal scarring and developed a preclinical swine model to explore these effects. MethodsA total of six male (XY) and female (XX) mini-swine underwent castration and were randomly assigned to no testosterone (noT) or biweekly testosterone therapy (+T). Ten dorsal excisional wounds were created on each pig. To mimic a chronic wound, a subset of wounds were re-excised at two weeks. Scars (POD42) and chronic wounds (POD28) were harvested six weeks after initial wounding for analysis via histology, RNA-seq, and mechanical testing. ResultsHistologic analysis of POD42 scars from +T swine showed increased mean fibrosis area (16mm2 noT, 28mm2 +T; p=0.007) and thickness (0.246mm2 noT, 0.406mm2 +T; p<0.001) compared to noT swine. Scars in XX+T and XY+T pigs had greater tensile burst strength (p=0.024 and p=0.013 respectively) compared to scars in noT swine. Color deconvolution analysis showed greater deposition of type I and type III collagen as well as increased type I to type III collagen ratio in +T scars. Dermatopathologist scores of POD42 scars show +T exposure was associated with worse overall scarring scores compared to controls (p<0.05). On RNAseq, gene ontology analysis showed testosterone exposure was associated with significant upregulation of cellular metabolism and immune response gene sets. Pathway analysis showed testosterone upregulated Reactome pathways related to keratinization and formation of collagen and laminin. ConclusionWe developed a novel preclinical porcine model to study the effects of the sex hormone testosterone on scarring. Testosterone induces early proliferation of excessive granulation tissue, which eventually leads to increased scar tissue. T also appears to increase the physical strength of scars via supraphysiologic deposition of collagen and other ECM factors. The increase in burst strength observed for both XX and XY suggests that hormonal administration has a stronger influence on mechanical properties than chromosomal sex. Antiandrogen topical therapies may be a promising future area of research.

systems biology↗

bioRxiv2023

Extreme genome scrambling in cryptic Oikopleura dioica species

Genes are not randomly distributed throughout chromosomes. How gene order evolves and how selective constraints act to preserve or vary gene order, both at the macrosyntenic level of whole chromosomes or microsyntenic level of gene blocks, are central questions of evolutionary biology and genomics that remain largely unsolved. Here, after sequencing several genomes of the appendicularian tunicate Oikopleura dioica from different locations around the globe, we show an unprecedented amount of genome scrambling in animals with no obvious morphological differences, consistent with cryptic speciation. Our assemblies suggest that all members of this clade possess a common 3-chromosome karyotype, and that different species largely preserve gene content, despite the presence of thousands of rearrangements in gene order. The movements of genes are largely restricted to chromosome arms and sex-specific regions, which appear to be the primary unit of macrosynteny conservation, and examples of these within-arm movements can be seen in the Hox and Fgf gene families. Our approach employing whole-genome alignments demonstrates that segments containing protein-coding elements tend to be preserved at the microsyntenic scale, consistent with strong purifying selection, with appreciably less preservation of non-coding elements. Unexpectedly, scrambling did not preserve operon structure across species, suggesting an absence of selective pressure to maintain operon structure. As well, genome scrambling does not occur uniformly across all chromosomes, as short chromosome arms possess shorter genes, smaller operons, more breakpoints, and elevated dN/dS values compared to long chromosome arms. Estimation of divergence times among the cryptic O. dioica lineages yielded an estimated breakpoint accumulation rate of 6 to 25 breakpoints per megabase per million years, which is an order of magnitude higher than the rates for other ascidian tunicates or Drosophila species. Therefore, O. dioica appears to be an attractive animal system to unravel the mechanisms that underlie gene order and synteny conservation, as well as exploring the limits of genome scrambling without an apparent impact on phenotypic evolution.

genomics↗

bioRxiv2023

Rit2 loss in dopaminergic neurons drives a progressive Parkinsonian phenotype

Parkinsons disease (PD) is the second most prevalent neurodegenerative disease and arises from dopamine (DA) neuron death selectively in the substantia nigra pars compacta (SNc). Rit2 is a reported PD risk allele, and recent single cell transcriptomic studies identified a major RIT2 cluster in PD DA neurons, potentially linking Rit2 expression loss to a PD patient cohort. However, it is still unknown whether Rit2 loss itself is causative for PD or PD-like symptoms. Here we report that conditional Rit2 silencing in mouse DA neurons drove motor dysfunction that occurred earlier in males than females and was rescued at early stages by either inhibiting the DA transporter (DAT) or with L-DOPA treatment. Motor dysfunction was accompanied by decreased DA release, striatal DA content, phenotypic DAergic markers, DA neurons, and DAergic terminals, with increased pSer129-alpha synuclein and pSer935-LRRK2 expression. These results provide the first evidence that Rit2 loss is causal for SNc cell death and a PD-like phenotype, and reveal key sex-specific differences in the response to Rit2 loss.

neuroscience↗

bioRxiv2023

Regulating microbiome metabolic stability for stable indigenous liquor fermentation

BackgroundRegulating microbial metabolic stability is an ever-challenging goal in the food industry to ensure the productivity and quality of fermented foods. The microbiome underlying traditional Chinese liquor fermentation is such a representative microbiome metabolism that is affected by many dynamic abiotic/biotic factors. The complex microbial activities bring beneficial qualities (complex and rich aroma profiles, etc.) to the fermented product, but can also cause unstable fermentation outcomes. Here, we designed a three-step experiment (abiotic regulation; biotic regulation; lab-scale validation) to explore which factors cause unstable fermentation outcomes and how to regulate microbiome metabolic functional stability accordingly. ResultsWe found that 30.5% industrial fermentation of traditional Chinese liquor outcomes could be precisely predicted by initial abiotic factors. We could ensure the stability of partial fermentation batches by regulating the initial ratio of acidity to reducing sugar, moisture, and starch. Furthermore, in two representative unpredictable fermentation batches (named batch A and batch B), we found that unstable fermentation outcomes occurred even with similar initial abiotic factors after a dynamic three-phase fermentation. Unstable fermentation batches showed fluctuations in microbial community assembly that affected fermentation stability by altering the beneficial distribution (metabolic flux) of redundant metabolic pathways between yeasts and Lactobacilli. The metabolism of batch B was more stable than that of batch A due to the consistent overexpression of a specific set of bacterial metabolic genes. In repeated feed-batch fermentation processes, the difference in metabolic functional stability between the two batches was amplified 9.02 times. Batch B had significantly lower microbiome metabolic fluctuations than batch A, with higher robustness and lower complexity of the metabolic functional network. Moreover, we found that adjusting the initial microbial inoculation ratio could regulate both the metabolic beneficial distribution and temporal metabolic fluctuations of the microbiome to appropriately reduce the instability caused by biotic factors. ConclusionsThis study demonstrates that rationally regulating initial parameters and microbial inoculation ratio is a practical strategy to optimize indigenous liquor fermentation. The stable microbial beneficial distribution and high metabolic robustness are essential to obtain the ideal microbiome metabolic stability. Our study provides insights and shows the feasibility of enhancing metabolic functional stability through initial conditions in dynamic microbial ecosystems.

systems biology↗

bioRxiv2023

Multi-omics of the gut microbial ecosystem in the immunotherapy resistance in microsatellite instability-high gastrointestinal cancer patients

Despite the encouraging efficacy of anti-PD-1/PD-L1 immunotherapy in microsatellite instability-high/deficient mismatch repair (MSI-H/dMMR) advanced gastrointestinal cancer, many patients exhibit primary or acquired resistance. Using multi-omics approaches, we interrogated gut microbiome, blood metabolome and cytokines/chemokines of MSI-H/dMMR advanced gastrointestinal cancer patients (N=77) and identified a number of microbes (e.g. Alistipes putredinis) and metabolites (e.g. arginine and SCFA) highly associated with primary resistance. Fecal microbiota transplantation of patients stool replicated the clinical responsiveness as well as certain molecular signatures. Based on the clinical microbiome data, we developed a predictive machine learning model for primary resistance and achieved accuracy at 0.83 on an external validation set. Furthermore, several microbes were pinpointed which gradually changed during the process of acquired resistance. In summary, our study demonstrated the essential role of gut microbiome in drug resistance, and this could be utilized as a preventative diagnosis tool as well as therapeutic targets in the future.

cancer biology↗

bioRxiv2023

Video-rate Mid-infrared Photothermal Imaging by Single Pulse Photothermal Detection per Pixel

By optically sensing the mid-infrared absorption induced photothermal effect, midinfrared photothermal (MIP) microscope enables super-resolution IR imaging and scrutinizing of biological systems in an aqueous environment. However, the speed of current lock-in based sample-scanning MIP system is limited to 1.0 millisecond or longer per pixel, which is insufficient for capturing dynamics inside living systems. Here, we report a single pulse laserscanning MIP microscope that dramatically increases the imaging speed by three orders of magnitude. We harness a lock-in free demodulation scheme which uses high-speed digitization to resolve single IR pulse induced contrast at nanosecond time scale. To realize single pulse photothermal detection at each pixel, we employ two sets of galvo mirrors for synchronized scanning of mid-infrared and probe beams to achieve an imaging line rate over 2 kHz. With video-rate imaging capability, we observed two types of distinct dynamics of lipids in living cells. Furthermore, by hyperspectral imaging, we chemically dissected a single cell wall at nanometer scale. Finally, with a uniform field of view over 200 by 200 m2 and 2 Hz frame rate, we mapped fat storage in free-moving C. elegans and live embryos.

bioengineering↗

bioRxiv2023

Excessive apoptosis of naïve T cells resulting hyperactivation as a cause of mammalian aging

In mammals, the most remarkable T cell variations with aging are the shrinking of naive T cell pool and enlargement of memory T cell pool, which are partially caused by thymic involution. However, it remains an enigma whether these T-cell-related changes are consequences or causes of mammalian aging. In this study, we find that the T-cell specific Rip1 KO mice present similar age-related T cell changes and exhibit signs of accelerated aging, including inflammation, multiple age-related diseases and a shorter lifespan. Mechanistically, T cells lacking RIP1 displayed excessive apoptosis, leading to T cell compensatory proliferation, hyperactivation, increased inflammation, and ultimately premature death. Consistent with this, blocking apoptosis by co-deletion of Fadd in Rip1 deficient T cells significantly recovered the lymphopenia and imbalance between naive and memory T cell, substantially restored ageing-related phenotypes, and prolonged life span in T-cell specific Rip1 KO mice. These results suggest that changes in T cells play a causal role in mammalian aging. Therefore, replenishing or blocking apoptosis of naive T cells could offer new therapeutic approaches for aging and age-related diseases.

immunology↗

bioRxiv2023

Vampyroteuthis southchinaseais sp. nov.,a second Recent widely distributed species of Vampyromorpha (Cephalopoda, Coleoidea)

The vampire squid, Vampyroteuthis infernalis Chun, 1903, is currently the only extant species in the family Vampyroteuthidae Chun, 1903. However, specimens from the Gulf of Guinea, Africa, and California suggested the possibility of additional taxa. Here, we report the second species of Vampyroteuthis, collected from the South China Sea, China, which differs from V. infernalis by the tail shape, the lower beak, and the phylogenetic analysis of mitochondrial COI and nuclear large subunit ribosomal DNA (LSU) sequences: V. infernalis present by the lacking of the tail, photophores located approximately one-third of the points between the fins and end, and the lower beak with a broad, short wing; V. pseudoinfernalis Qiu, Liu & Huang, sp. nov. present by an acuate tail, a pair of photophores located at the midpoints between the fins and tail, and a lower beak with a broad, elongate wing.

zoology↗

bioRxiv2022

novoRNABreak: local assembly for novel splice junction and fusion transcript detection from RNA-seq data

We present novoRNABreak, a unified framework for cancer specific novel splice junction and fusion transcript detection in RNA-seq data obtained from human cancer samples. novoRNABreak is based on a local assembly model, which offers a tradeoff between the alignment-based and de novo whole transcriptome assembly (WTA) approaches, namely, being more sensitive in assembling novel junctions that cannot be directly aligned, and more efficient due to the strategy that focuses on junctions rather than full-length transcripts. The performance of novoRNABreak is demonstrated by a comprehensive set of experiments using synthetic data generated based on genome reference, as well as real RNA-seq data from breast cancer and prostate cancer samples. The results show that novoRNABreak can detect novel splice junctions and fusion transcripts efficiently with high sensitivity and reasonable specificity.

bioinformatics↗

bioRxiv2022

A Host-Harbored Metabolic Susceptibility of Coronavirus Enables Broad-Spectrum Targeting

Host-based antivirals could offer broad-spectrum therapeutics and prophylactics against the constantly-mutating viruses including the currently-ravaging coronavirus, yet must target cellular vulnerabilities of viruses without grossly endangering the host. Here we show that the master lipid regulator SREBP1 couples the phospholipid scramblase TMEM41B to constitute a host "metabolism-to-manufacture" cascade that maximizes membrane supplies to support coronaviral genome replication, harboring biosynthetic enzymes including Lipin1 as druggable viral-specific-essential (VSE) host genes. Moreover, pharmacological inhibition of Lipin1, by a moonlight function of the widely-prescribed beta-blocker Propranolol, metabolically uncouples the SREBP1-TMEM41B cascade and consequently exhibits broad-spectrum antiviral effects against coronaviruses, Zika virus, and Dengue virus. The data implicate a metabolism-based antiviral strategy that is well tolerated by the host, and a potential broad-spectrum medication against current and future coronavirus diseases.

cell biology↗

bioRxiv2022

Monopogen: single nucleotide variant calling from single cell sequencing

Distinguishing how genetics impact cellular processes can improve our understanding of variable risk for diseases. Although single-cell omics have provided molecular characterization of cell types and states on diverse tissue samples, their genetic ancestry and effects on cellular molecular traits are largely understudied. Here, we developed Monopogen, a computational tool enabling researchers to detect single nucleotide variants (SNVs) from a variety of single cell transcriptomic and epigenomic sequencing data. It leverages linkage disequilibrium from external reference panels to identify germline SNVs from sparse sequencing data and uses Monovar to identify novel SNVs at cluster (or cell type) levels. Monopogen can identify 100K~3M germline SNVs from various single cell sequencing platforms (scRNA-seq, snRNA-seq, snATAC-seq etc), with genotyping accuracy higher than 95%, when compared against matched whole genome sequencing data. We applied Monopogen on human retina, normal breast and Asian immune diversity atlases, showing that that derived genotypes enable accurate global and local ancestry inference and identification of admixed samples from ancestrally diverse donors. In addition, we applied Monopogen on ~4M cells from 65 human heart left ventricle single cell samples and identified novel variants associated with cardiomyocyte metabolic levels and epigenomic programs. In summary, Monopogen provides a novel computational framework that brings together population genetics and single cell omics to uncover genetic determinants of cellular quantitative traits.

bioinformatics↗

bioRxiv2022

Eosinophilic esophagitis-associated epithelial remodeling may limit esophageal carcinogenesis

Under homeostatic conditions, esophageal epithelium displays a proliferation/differentiation gradient that is generated as proliferative basal cells give rise to suprabasal cells then terminally differentiated superficial cells. This proliferation/differentiation gradient is perturbed in esophageal pathologies both benign and malignant. Esophageal cancer is among the deadliest forms of human malignancy with 5-year survival rates of <20%. Esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC) are the two most common subtypes of esophageal cancer. Gastroesophageal reflux disease (GERD) is a primary risk factor for EAC. Although GERD and the food allergy-mediated condition eosinophilic esophagitis (EoE) are both associated with chronic esophageal inflammation and epithelial remodeling, including basal cell hyperplasia, epidemiological evidence suggests that EoE patients do not develop esophageal malignancy. Here, we perform single cell RNA-sequencing in murine models of EoE and ESCC to delineate the effects that these two conditions have specifically upon the cellular landscape of esophageal epithelium. In mice with EoE or ESCC, we find expansion of cell populations as compared to normal esophageal epithelium. In mice with EoE, we detect expansion of 4 suprabasal populations coupled with depletion of 4 basal cell populations. By contrast, mice with ESCC display expansion of 4 basal populations as well as depletion of 3 superficial populations. We further evaluated modules of co-expressed genes in EoE- and ESCC-enriched epithelial cell clusters. Senescence, glucocorticoid receptor signaling, and granulocyte-macrophage colony-stimulating factor pathways were associated with EoE-enriched clusters while pathways associated with cell proliferation and metabolism were identified in ESCC-enriched clusters. Finally, by pairing murine models of EoE and ESCC, we demonstrate that exposure to EoE inflammation limits esophageal carcinogenesis. Our findings provide the first functional investigation of the relationship between EoE and esophageal cancer and suggest that esophageal epithelial remodeling events occurring in response to EoE inflammation may limit act to esophageal carcinogenesis which may have future implications for leveraging allergic inflammation-associated alterations in epithelial biology to prevent and/or treat esophageal cancer.

cell biology↗