Biology subjects

Yao, M.

Publications and source records attributed to Yao, M..

At least 73 records · Page 4Linked to original sources

bioRxiv2021

Spatial transcriptome sequencing revealed spatial trajectory in the Non-Small Cell Lung Carcinoma

Deepening understanding in the heterogeneity of tumors is critical for clinical treatment. Here we investigate tissue-wide gene expression heterogeneity throughout a multifocal lung cancer using the spatial transcriptomics (ST) technology. We identified gene expression gradients in stroma adjacent to tumor regions that allow for re-understanding of the tumor micro-environment. The establishment of these profiles was the first step towards an unbiased view of lung cancer and can serve as a dictionary for future studies. Tumor subclones were detected by ST technology in our research, while we contrast the EMT ability among in subclones which inferred the possible trajectory of tumor metastasis and invasion, which was confirmed by constructing the pseudo-time model of spatial transition within subclones. Together, these results uncovered lung cancer spatial heterogeneity, highlight potential tumor micro-environment differences and spatial evolution trajectory, and served as a resource for further investigation of tumor microenvironment.

cancer biology↗

bioRxiv2021

Characterization of α2-Adrenergic Receptors Mediated Vasoconstriction in ex vivo model

Introductionrat tail serves as a thermoregulatory organ by dilating or constricting tail blood vessels and rat tail lateral veins play a role in cutaneous circulation. However, this cutaneous vessel has never been examined and evaluated as a potential candidate ex vivo model to study peripheral vascular diseases. This study aims to investigate vascular tone mediated through 2-adenergic receptor on rat tail vein under different temperatures. MethodsVasoconstriction stimulated by 2-adrenergic receptor selective agonists UK14304, guanabenz was thoroughly examined in isolated rat tail lateral vein. Susceptibility of cutaneous vessel to temperature changes was investigated under 37 {degrees}C and 28 {degrees}C. Differentiated vascular reactivity exhibited at different temperature was further explored with different 2-adrenergic receptor selective agonists and validated with antagonism by 1-adrenergic receptor and 2-adrenergic receptor selective antagonist prazosin and RX821002, respectively. ResultsVascular tone of freshly isolated vein remained same compared with that of stored in pre-gassed physiologic buffer at 4 {degrees}C overnight. Presence of endothelium and repeated administration of UK14304 did not alter contractile property. Vessels away from torso (distal) showed significantly different contractile character compared with portion close to torso (proximal) at 28 {degrees}C but kept uniform at 37 {degrees}C. Enhanced vasoconstriction along with increased potency of 2-adrenergic receptor agonists UK14304 and guanabenz was consistently present at 28 {degrees}C, independent of temperature change orders. Potentiated vasoconstriction present at 28 {degrees}C was later proved via 2-adrenergic receptor alone. DiscussionHarvest and preparation of rat tail lateral vein was described in details. Contractile property of venous preparations stimulated by 2-adrenergic receptor selective agonists was first time examined. Differentiated vasoconstriction at moderate cooling temperature was described and confirmed to through 2-adrenergic receptor activation. Rat tail lateral vein is found valuable for studies of cutaneous circulation altered by temperature changes.

pharmacology and toxicology↗

bioRxiv2021

Development of a mini-replicon-based reverse-genetics system for rice stripe tenuivirus

Negative-stranded RNA (NSR) viruses include both animal- and plant-infecting viruses that often cause serious diseases in human and livestock, and in agronomic crops. Rice stripe tenuivirus (RSV), a plant NSR virus with four negative-stranded/ambisense RNA segments, is one of the most destructive rice pathogens in many Asian countries. Due to the lack of a reliable reverse-genetics technology, molecular studies of RSV gene functions and its interaction with host plants are severely hampered. To overcome this obstacle, we developed a mini-replicon-based reverse-genetics system for RSV gene functional analysis in Nicotiana benthamiana. We first developed a mini-replicon system expressing RSV genomic RNA3 eGFP reporter (MR3(-)eGFP), a nucleocapsid (NP), and a codon usage optimized RNA-dependent RNA polymerase (RdRpopt), respectively. Using this mini-replicon system we determined that RSV NP and RdRpopt are indispensable for the eGFP expression from MR3(-)eGFP. The expression of eGFP from MR3(-)eGFP can be significantly enhanced in the presence of NSs and P19-HcPro-{gamma}b. In addition, NSvc4, the movement protein of RSV, facilitated eGFP trafficking between cells. We also developed an antigenomic RNA3-based replicon in N. benthamiana. However, we found that the RSV NS3 coding sequence acts as a cis-element to regulate viral RNA expression. Finally, we made mini-replicons representing all four RSV genomic RNAs. This is the first mini-replicon-based reverse-genetics system for monocot-infecting tenuivirus. We believe that this mini-replicon system described here will allow the studies of RSV replication, transcription, cell-to-cell movement and host machinery underpinning RSV infection in plants. IMPORTANCEPlant-infecting segmented negative-stranded RNA (NSR) viruses are grouped into 3 genera: Orthotospovirus, Tenuivirus and Emaravirus. The reverse-genetics systems have been established for members in the genera Orthotospovirus and Emaravirus, respectively. However, there is still no reverse-genetics system available for Tenuivirus. Rice stripe virus (RSV) is a monocot-infecting tenuivirus with four negative-stranded/ambisense RNA segments. It is one of the most destructive rice pathogens and causes significant damages to rice industry in Asian countries. Due to the lack of a reliable reverse-genetics system, molecular characterizations of RSV gene functions and the host machinery underpinning RSV infection in plants are extremely difficult. To overcome this obstacle, we developed a mini-replicon-based reverse-genetics system for RSV in Nicotiana benthamiana. This is the first mini-replicon-based reverse-genetics system for tenuivirus. We consider that this system will provide researchers a new working platform to elucidate the molecular mechanisms dictating segmented tenuivirus infections in plant.

pathology↗

bioRxiv2021

Acoustic Remote Control of Bacterial Immunotherapy

Rapid advances in synthetic biology are driving the development of genetically engineered microbes as therapeutic agents for a multitude of human diseases, including cancer. In particular, the immunosuppressive microenvironment of solid tumors creates a favorable niche for systemically administered bacteria to engraft in the tumor and release therapeutic payloads. However, such payloads can be harmful if released in healthy tissues where the bacteria also engraft in smaller numbers. To address this limitation, we engineer therapeutic bacteria to be controlled by focused ultrasound, a form of energy that can be applied noninvasively to specific anatomical sites such as solid tumors. This control is provided by a temperature-actuated genetic state switch that produces lasting therapeutic output in response to briefly applied focused ultrasound hyperthermia. Using a combination of rational design and high-throughput screening we optimized the switching circuits of engineered cells and connected their activity to the release of immune checkpoint inhibitors. In a clinically relevant cancer model, ultrasound-activated therapeutic microbes successfully turned on in situ and induced a marked suppression of tumor growth. This technology provides a critical tool for the spatiotemporal targeting of potent bacterial therapeutics in a variety of biological and clinical scenarios.

synthetic biology↗

bioRxiv2020

Modified N-linked glycosylation status predicts trafficking defective human Piezo1 channel mutations

Mechanosensitive channels are integral membrane proteins that sense mechanical stimuli. Like all membrane proteins, they pass through biosynthetic quality control in the endoplasmic reticulum and Golgi that results in them reaching their destination at the plasma membrane. Here we show that N-linked glycosylation of two highly conserved asparagine residues in the cap region of mechanosensitive Piezo1 channels are necessary for the mature protein to reach the plasma membrane. Both mutation of these asparagines (N2294Q/N2331Q) and treatment with an enzyme that hydrolyses N-linked oligosaccharides (PNGaseF) eliminates the fully glycosylated mature Piezo1 protein. The N-glycans in the cap are a pre-requisite for higher-order glycosylation in the propeller regions, which are present in loops that are essential for mechanotransduction. Importantly, trafficking-defective Piezo1 variants linked to generalized lymphatic dysplasia and bicuspid aortic valve display reduced fully N-glycosylated protein. The higher order glycosylation status in vitro correlates with efficient membrane trafficking and will aid in determining the functional impact of Piezo1 variants of unknown significance.

biophysics↗

bioRxiv2020

Mechanosensitive calcium signaling in filopodia

Filopodia are ubiquitous membrane projections that play crucial role in guiding cell migration on rigid substrates and through extracellular matrix by utilizing yet unknown mechanosensing molecular pathways. As recent studies show that Ca2+ channels localized to filopodia play an important role in regulation of their formation and since some Ca2+ channels are known to possess mechanosensing properties, activity of filopodial Ca2+ channels might be tightly interlinked with the filopodia mechanosensing function. We tested this hypothesis by monitoring changes in the intra-filopodial Ca2+ level in response to application of stretching force to individual filopodia of several cell types. It has been found that stretching forces of tens of pN strongly promote Ca2+ influx into filopodia, causing persistent Ca2+ oscillations that last for minutes even after the force is released. Most of the known mechanosensitive Ca2+ channels, such as Piezo 1, Piezo 2 and TRPV4, were found to be dispensable for the observed force-dependent Ca2+ influx. In contrast, L-type Ca2+ channels appear to be a key component in the discovered phenomenon. Since previous studies have shown that intra-filopodial transient Ca2+ signals play an important role in guidance of cell migration, our results suggest that the force-dependent activation of L-type Ca2+ channels may contribute to this process. Overall, our study reveals an intricate interplay between mechanical forces and Ca2+ signaling in filopodia, providing novel mechanistic insights for the force-dependent filopodia functions in guidance of cell migration. Significance statementWe found that tensile forces of tens of pN applied to individual filopodia trigger Ca2+ influx through L-type Ca2+ channels, producing persistent Ca2+ oscillations inside mechanically stretched filopodia. Resulting elevation of the intra-filopodial Ca2+ level in turn leads to downstream activation of calpain protease, which is known to play a crucial role in regulation of the cell adhesion dynamics. Thus, our work suggests that L-type channel-dependent Ca2+ signaling and the mechanosensing function of filopodia are coupled to each other, synergistically governing cell adhesion and motion in a force-dependent manner. Since L-type Ca2+ channels have been previously found in many different cell types, such as neural or cancer cells, the above mechanism is likely to be widespread among various cell lines.

cell biology↗

bioRxiv2020

Ultrasound-mediated mechanical forces selectively kill tumor cells

Ultrasound has been used to target tumors either through local heating or local nanobubbles but these methods damage surrounding normal cells in the target area. Recent studies show that tumor cells are susceptible to mechanical stresses and undergo calcium-dependent apoptosis under conditions that promote normal cell growth. Here we report that low-frequency ultrasound causes apoptosis of tumor cells by activating a calpain-dependent mitochondrial pathway that depends upon calcium entry through the mechanosensitive Piezo1 channels. This is a general property of all tumor cell lines tested so far irrespective of tissue origin. In animals, ultrasound irradiation causes tumor killing in the chick chorioallantoic membrane (CAM) model with relatively little damage to the chick embryos. Further, patient-derived pancreatic tumor organoids are killed by ultrasound treatment. Because low-level ultrasound causes apoptosis of tumor cells from many different tissues in different microenvironments, it may offer a safe non-invasive approach to augment tumor treatments.

cancer biology↗

bioRxiv2020

Integrative identification by Hi-C revealed distinct advanced structural variations in Lung Adenocarcinoma tissue

Advanced three-dimensional structure variations of chromatin in large genome fragments, such as conversion of A/B compartment, topologically associated domains (TADs) and chromatin loops are related closely to occurrence of malignant tumors. However, the structural characteristics of lung cancer still remain uncovered. In this study, we used high-throughput chromosome (HiC) confirmation capture to detect 2 non-smoking female lung adenocarcinoma (LUAD) tumor and paired normal tissues. The results indicated that significant chromatin variations were detected in tumor tissues compared with normal tissues. At compartment scale, the main conversion type of compartment is A[->]B in tumor tissues, which concentrated mainly on chromosome 3 (33.6%). Total of 216 tumor-specific TADs were identified in tumor tissues, which distributed mainly in chr1 (19), chr2 (15) and chr3(17). Finally we observed 41 distinct enhancer-promoter loops in tumor tissue, which associated closely to tumor-related pathways including MAPK, PI3K-AKT, Ras, Wnt and Ras1. The most important observation in this study was that we identified 5 important genes (SYT16, NCEH1, NXPE3, MB21D2, and DZIP1L), which were detected in both A[->]B compartment, TADs and chromatin loops. Four of these genes (NCEH1, NXPE3, MB21D2, and DZIP1L) located on q arm of chromosome 3, which also revealed the importance of chr3 in occurrence of structural variations in LUAD.

cancer biology↗

bioRxiv2020

Reappraisal of Spinach-based RNA Visualization in Plants

RNAs can be imaged in living cells using molecular beacons, RNA-binding labeled proteins and RNA aptamer-based approaches. However, Spinach RNA-mimicking GFP (RMG) has not been successfully used to monitor cellular RNAs in plants. In this study, we re-evaluated Spinach-based RNA visualization in different plants via transient, transgenic, and virus-based expression strategies. We found that like bacterial, yeast and human cellular tRNAs, plant tRNAs such as tRNALys (K) can protect and/or stabilize the spinach RNA aptamer interaction with the fluorophore DFHBI enabling detectable levels of green fluorescence to be emitted. The tRNALys-spinach-tRNALys (KSK), once delivered into "chloroplast-free" onion epidermal cells can emit strong green fluorescence in the presence of DFHBI. Transgenic or virus-based expression of monomer KSK, in either stably transformed or virus-infected Nicotinana benthamiana plants, failed to show RMG fluorescence. However, incorporating tandem repeats of KSK into recombinant viral RNAs, enabled qualitative and quantitative detection, both in vitro and ex vivo (ex planta), of KSK-specific green fluorescence, though RMG was less obvious in vivo (in planta). These findings demonstrate Spinach-based RNA visualization has the potential for ex vivo and in vivo monitoring RNAs in plant cells. One sentence summarySpinach-based RMG technology was reevaluated to have potential for ex vivo and in vivo monitoring RNAs in plant cells.

plant biology↗

bioRxiv2020

Transcriptome analysis of resistant and susceptible pepper (Capsicum annuum L.) in response to Xanthomonas campestris pv. Vesicatoria

Bacterial spot (BS) disease of pepper, incited by Xanthomonas campestris pv. Vesicatoria (Xcv), is one of the most serious diseases. For a comparative analysis of defense response to Xcv infection, we performed a transcriptome analysis of BS -susceptible cultivar ECW and -resistant cultivar VI037601 using the HiSeq 2500 sequencing platform. Approximately 140.15 G clean data were generated from eighteen libraries. From the libraries generated, we identified 52,041 genes including 35,336 reference genes, 16,705 novel transcripts, and 4,794 differentially expressed genes (DEGs). There were 1,291, 2,956, 1,795 and 2,448 DEGs in ECW-24h-vs-ECW-0h, ECW-48h-vs-ECW-0h, VI037601-24h-vs-VI037601-0h and VI037601-48h-vs-VI037601-0h groups, respectively. Interestingly, DEGs involved in disease response in the resistant variety were induced at an earlier stage and at higher levels compared with the susceptible variety. Key enriched categories included amino sugar and nucleotide sugar metabolism, sesquiterpenoid and triterpenoid biosynthesis and MAPK signaling pathway. Moreover, 273 DEGs only differentially expressed in VI037601 and 436 overlapping DEGs in ECW and VI037601 post Xcv inoculation, including NBS-LRR genes, oxidoreductase gene, WRKY and NAC transcription factors were identified, which were mainly involved in metabolic process, response to stimulus and biological regulation pathways. Quantitative RT-PCR of sixteen selected DEGs further validated the RNA-seq differential gene expression analysis. Our results will provide a valuable resource for understanding the molecular mechanisms of pepper resistance to Xcv infection and improving pepper resistance cultivars against Xcv.

bioinformatics↗

bioRxiv2020

Epigenetic clock and methylation studies in elephants

Age-associated DNA-methylation profiles have been used successfully to develop highly accurate biomarkers of age ("epigenetic clocks") in humans, mice, dogs, and other species. Here we present epigenetic clocks for African and Asian elephants. These clocks were developed using novel DNA methylation profiles of 140 elephant blood samples of known age, at loci that are highly conserved between mammalian species, using a custom Infinium array (HorvathMammalMethylChip40). We present epigenetic clocks for Asian elephants (Elephas maximus), African elephants (Loxodonta africana), and both elephant species combined. Two additional human-elephant clocks were constructed by combing human and elephant samples. Epigenome-wide association studies identified elephant age-related CpGs and their proximal genes. The products of these genes play important roles in cellular differentiation, organismal development, metabolism, and circadian rhythms. Intracellular events observed to change with age included the methylation of bivalent chromatin domains, targets of polycomb repressive complexes, and TFAP2C binding sites. These readily available epigenetic clocks can be used for elephant conservation efforts where accurate estimates of age are needed to predict demographic trends.

developmental biology↗

bioRxiv2020

Cascade Diversification Directs the Generation of Neuronal Diversity in Hypothalamus

The hypothalamus contains an astounding heterogeneity of neurons to achieve its role in regulating endocrine, autonomic and behavioral functions. Despite previous progress in deciphering the gene regulatory programs linked to hypothalamus development, its molecular developmental trajectory and origin of neuronal diversity remain largely unknown. Here we combine transcriptomic profiling of 43,261 cells derived from Rax+ hypothalamic neuroepithelium with lineage tracing to map a developmental landscape of mouse hypothalamus and delineate the developmental trajectory of radial glial cells (RGCs), intermediate progenitor cells (IPCs), nascent neurons and peptidergic neurons in the lineage hierarchy. We show that RGCs adopt a conserved strategy for multipotential differentiation but generate both Ascl1+ and Neurog2+ IPCs, which display regionally differential origins in telencephalon. As transit-amplifying cells, Ascl1+ IPCs differ from their telencephalic counterpart by displaying fate bifurcation to produce both glutamatergic and GABAergic neurons. After classifying the developing neurons into 29 subtypes coded by diverse transcription factors, neurotransmitters and neuropeptides, we identified their molecular determinants via regulon analysis and further found that postmitotic neurons at nascent state possess the potential to resolve into more diverse subtypes of peptidergic neurons. Together, our study offers a single-cell framework for hypothalamus development and reveals that multiple cell types along the order of lineage hierarchy contribute to the fate diversification of hypothalamic neurons in a stepwise fashion, suggesting that a cascade diversifying model can deconstruct the origin of neuronal diversity.

developmental biology↗

bioRxiv2020

Force-dependent Piezo1 recruitment to focal adhesions regulates adhesion maturation and turnover specifically in non-transformed cells

Mechanosensing is an integral part of many physiological processes including stem cell differentiation, fibrosis, and cancer progression. Two major mechanosensing systems - focal adhesions and mechanosensitive ion channels, can convert mechanical features of the microenvironment into biochemical signals. We report here surprisingly that the mechanosensitive Ca2+-channel Piezo1, previously perceived to be diffusive on plasma membranes, binds to matrix adhesions in a force-dependent manner, promoting adhesion maturation and cell spreading in normal but not in tumor cells. In the absence of Piezo1, matrix adhesions are smaller in normal cells mimicking transformed cells where adhesions do not change with or without Piezo1. A novel adhesion-targeted calcium sensor shows robust Piezo1-dependent, calcium influx at adhesions in normal cells; but not in transformed cells. A linker domain in Piezo1 is needed for binding to adhesions and overexpression of the domain blocks Piezo1 binding to adhesions decreasing adhesion size and cell spread area. Thus, we suggest that Piezo1 is a novel component of focal adhesions in non-transformed cells that catalyzes adhesion maturation and growth through force-dependent calcium signaling, but this function is absent in most cancer cells.

cell biology↗

bioRxiv2020

Fine Sieving of Collected Atmospheric Particles using Oil Electrophoresis (iSCAPE)

It is rather challenging to separate atmospheric particles from nano-to micro-metre mixed in a sample. Here, a system named iSCAPE was invented to efficiently sieve particles out from a mixture by employing an electrostatic field and a non-conductive mineral oil. Tests with atmospheric particles of different cities as well as soil and road dust samples demonstrated that the iSCAPEd particles under different operating conditions moved rapidly with different velocities and both directions. Particles of different sources such as ambient air, soil or road were shown to have different polarity-charged particle fractions, and exhibited clearly different particle electrical mobility graphs after the iSCAPE sieving from seconds to minutes. Data also revealed that after the sieving some particles were enriched at specific mobility ranges. Bacterial ATP measurements implied that the iSCAPE can be also used to efficiently separate bacteria of different sizes and charge polarity. Experimental data here suggest that the iSCAPE sieving strongly replies on the electrostatic field strength, mineral oil viscosity and the run time. In theory, the iSCAPE system can be used to extract any desired targets from a complex sample, thus opening up many outstanding opportunities for environmental, biomedical and life science fields. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=69 SRC="FIGDIR/small/894998v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@8d50f9org.highwire.dtl.DTLVardef@1bf1b1aorg.highwire.dtl.DTLVardef@18c70ddorg.highwire.dtl.DTLVardef@145c317_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2019

Predictive Coding Models for Pain Perception

Pain is a complex, multidimensional experience that involves dynamic interactions between sensory-discriminative and affective-emotional processes. Pain experiences have a high degree of variability depending on their context and prior anticipation. Viewing pain perception as a perceptual inference problem, we propose a predictive coding paradigm to characterize evoked and non-evoked pain. We record the local field potentials (LFPs) from the primary somatosensory cortex (S1) and the anterior cingulate cortex (ACC) of freely behaving rats--two regions known to encode the sensory-discriminative and affective-emotional aspects of pain, respectively. We further use predictive coding to investigate the temporal coordination of oscillatory activity between the S1 and ACC. Specifically, we develop a phenomenological predictive coding model to describe the macroscopic dynamics of bottom-up and top-down activity. Supported by recent experimental data, we also develop a biophysical neural mass model to describe the mesoscopic neural dynamics in the S1 and ACC populations, in both naive and chronic pain-treated animals. Our proposed predictive coding models not only replicate important experimental findings, but also provide new prediction about the impact of the model parameters on the physiological or behavioral read-out--thereby yielding mechanistic insight into the uncertainty of expectation, placebo or nocebo effect, and chronic pain.

neuroscience↗

bioRxiv2019

Pathway engineering in yeast for synthesizing the complex polyketide bikaverin

Fungal polyketides display remarkable structural diversity and bioactivity, and therefore the biosynthesis and engineering of this large class of molecules is therapeutically significant. Here, we successfully recoded, constructed and characterized the biosynthetic pathway of the formation of bikaverin, a tetracyclic polyketide with antibiotic, antifungal and anticancer properties, in S. cerevisiae. We used a green fluorescent protein (GFP) tagging strategy to identify the low expression of Bik1 (polyketide synthase) as the bottleneck step in the pathway, and a promoter exchange strategy to increase expression of Bik1 and bikaverin yield. To further increase product yield, we used an enzyme-fusion strategy to couple the monooxygenase (Bik2) and methyltransferase (Bik3) to efficiently channel intermediates between modifying enzymes, leading to a dramatic improvement of Bikaverin yield of nearly 60-fold. This study demonstrates that the biosynthesis of complex polyketides biosynthesis can be established and efficiently engineered in S. cerevisiae, highlighting the great potential for natural product synthesis and large-scale fermentation in yeast.

synthetic biology↗

bioRxiv2019

Rats Sniff Off Toxic Air

Breathing air is a fundamental human need, yet its safety, when challenged by various harmful or lethal substances, is often not properly guarded. For example, air toxicity is currently monitored only for single or limited number of known toxicants, thus failing to fully warn against possible hazardous air. Here, we discovered that within minutes living rats emitted distinctive profiles of volatile organic compounds (VOCs) via breath when exposed to various airborne toxicants such as endotoxin, O3, ricin, and CO2. Compared to background indoor air, when exposed to ricin or endotoxin aerosols breath-borne VOC levels, especially that of carbon disulfide, were shown to decrease; while their elevated levels were observed for O3 and CO2 exposures. A clear contrast in breath-borne VOCs profiles of rats between different toxicant exposures was observed with a statistical significance. Differences in MicroRNA regulations such as miR-33, miR-146a and miR-155 from rats blood samples revealed different mechanisms used by the rats in combating different air toxicant challenges. Similar to dogs, rats were found here to be able to sniff against toxic air by releasing a specific breath-borne VOC profile. The discovered science opens a new arena for online monitoring air toxicity and health effects of pollutants. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/739003v3_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@f419cdorg.highwire.dtl.DTLVardef@1ca1582org.highwire.dtl.DTLVardef@4a35ceorg.highwire.dtl.DTLVardef@128b6f_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2019

Identification of porcine RUNX1 as an LPS-dependent gene expression regulator in PBMCs by Super deepSAGE sequencing of multiple tissues

Genome-wide identification of gene expression regulators may facilitate our understanding of the transcriptome constructed by gene expression profiling experiment. These regulators may be selected as targets for genetic manipulations in farm animals. In this study, we developed a gene expression profile of 76,000+ unique transcripts for 224 porcine samples from 28 normal tissues collected from 32 animals using Super deepSAGE (serial analysis of gene expression by deep sequencing) technology. Excellent sequencing depth has been achieved for each multiplexed library, and principal component analysis showed that duplicated samples from the same tissues cluster together, demonstrating the high quality of the Super deepSAGE data. Comparison with previous research indicated that our results not only have excellent reproducibility but also have greatly extended the coverage of the sample types as well as the number of genes. Clustering analysis discovered ten groups of genes showing distinct expression patterns among those samples. Binding motif over representative analysis identified 41 regulators responsible for the regulation of these gene clusters. Finally, we demonstrate a potential application of this dataset to infectious and immune research by identifying an LPS-dependent transcription factor, runt-related transcription factor 1 (RUNX1), in peripheral blood mononuclear cells (PBMCs). The selected genes are specifically responsible for the transcription of toll-like receptor 2 (TLR2), lymphocyte-specific protein tyrosine kinase (LCK), vav1 oncogene (VAV1), and other 32 genes. These genes belong to the T and B cell signaling pathways, making them potential novel targets for the diagnostic and therapy of bacterial infections and other immune disorders.

genomics↗