RESUMO
To reveal gene regulation mechanisms, it is essential to understand the role of regulatory elements, which are possibly distant from gene promoters. Integrative analysis of epigenetic and transcriptomic data can be used to gain insights into gene-expression regulation in specific phenotypes. Here, we discuss STITCHIT, an approach to dissect epigenetic variation in a gene-specific manner across many samples for the identification of regulatory elements without relying on peak calling algorithms. The obtained genomic regions are then further refined using a regularized linear model approach, which can also be used to predict gene expression. We illustrate the use of STITCHIT using H3k27ac ChIP-seq and RNA-seq data from the International Human Epigenome Consortium (IHEC).
Assuntos
Epigênese Genética , Epigenômica , Transcriptoma , Humanos , Epigenômica/métodos , Transcriptoma/genética , Elementos Facilitadores Genéticos , Software , Biologia Computacional/métodos , Sequenciamento de Cromatina por Imunoprecipitação/métodos , Regulação da Expressão Gênica , Algoritmos , Histonas/genética , Histonas/metabolismo , Perfilação da Expressão Gênica/métodosRESUMO
ETHNOPHARMACOLOGICAL RELEVANCE: Huachansu Capsule (HCSc) is a simple enteric-coated capsule refined from the skin of the dried toad, a traditional medicinal herb. It has been used clinically for many years to treat a variety of malignant tumors with remarkable efficacy. To date, a number of main components of HCSc have been reported to be cardiotoxic, but the specific mechanism of cardiotoxicity is still unknown. AIM OF THE STUDY: The aim of this study was to elucidate the possible cardiotoxic symptoms caused by high-doses of HCSc and to further reveal the complex mechanisms by which it causes cardiotoxicity. MATERIALS AND METHODS: UPLC-Q-Exactive Orbitrap MS and network toxicology were used to identify and predict the potential toxic components, related signaling pathways. Then, we used acute and sub-acute toxicity experiments to reveal the apparent phenomenon of HCSc-induced cardiotoxicity. Finally, we combined transcriptomics and metabolomics to elucidate the potential mechanism of action, and verified the putative mechanism by molecular docking, RT-qPCR, and Western blot. RESULTS: We found 8 toad bufadienolides components may be induced cardiac toxicity HCSc main toxic components. Through toxicity experiments, we found that high dose of HCSc could increase a variety of blood routine indexes, five cardiac enzymes, heart failure indexes (BNP), troponin (cTnI and cTnT), heart rate and the degree of heart tissue damage, while low-dose of HCSc had no such changes. In addition, by molecular docking, found that 8 kinds of main toxic components and cAMP, AMPK, IL1ß, mTOR all can be a very good combination, especially in the cAMP. Meanwhile, RT-qPCR and Western blot results showed that HCSc could induce cardiotoxicity by regulating a variety of heart-related differential genes and activating the cAMP signaling pathway. CONCLUSIONS: In this study, network toxicology, transcriptomics and metabolomics were used to elucidate the complex mechanism of possible cardiotoxicity induced by high-dose HCSc. Animal experiments, molecular docking, Western blot and RT-qPCR experiments were also used to verify the above mechanism. These findings will inform further mechanistic studies and provide theoretical support for its safe clinical application.
Assuntos
Cardiotoxicidade , Metabolômica , Transcriptoma , Animais , Metabolômica/métodos , Masculino , Transcriptoma/efeitos dos fármacos , Ratos , Bufanolídeos/toxicidade , Simulação de Acoplamento Molecular , Ratos Sprague-Dawley , Farmacologia em Rede , Cápsulas , Transdução de Sinais/efeitos dos fármacos , Perfilação da Expressão Gênica/métodos , AnurosRESUMO
Flowers of Crocus sativus L. are immensely important not only for arrangement of floral whorls but more because each floral organ is dominated by a different class of specialized compounds. Dried stigmas of C. sativus flowers form commercial saffron, and are known to accumulate unique apocarotenoids like crocin, picrocrocin and safranal. Inspite of being a high value crop, the molecular mechanism regulating flower development in Crocus remains largely unknown. Moreover, it would be very interesting to explore any co-regulatory mechanism which controls floral architecture and secondary metabolic pathways which exist in specific floral organs. Here we report transcriptome wide identification of MADS box genes in Crocus. A total of 39 full length MADS box genes were identified among which three belonged to type I and 36 to type II class. Phylogeny classified them into 11 sub-clusters. Expression pattern revealed some stigma up-regulated genes among which CstMADS19 encoding an AGAMOUS gene showed high expression. Transient over-expression of CstMADS19 in stigmas of Crocus resulted in increased crocin by enhancing expression of pathway genes. Yeast one hybrid assay demonstrated that CstMADS19 binds to promoters of phytoene synthase and carotenoid cleavage dioxygenase 2 genes. Yeast two hybrid and BiFC assays confirmed interaction of CstMADS19 with CstMADS26 which codes for a SEPALATA gene. Co-overexpression of CstMADS19 and CstMADS26 in Crocus stigmas enhanced crocin content more than was observed when genes were expressed individually. Collectively, these findings indicate that CstMADS19 functions as a positive regulator of stigma based apocarotenoid biosynthesis in Crocus.
Assuntos
Carotenoides , Crocus , Flores , Regulação da Expressão Gênica de Plantas , Proteínas de Domínio MADS , Proteínas de Plantas , Crocus/genética , Crocus/metabolismo , Carotenoides/metabolismo , Flores/genética , Flores/metabolismo , Flores/crescimento & desenvolvimento , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Proteínas de Domínio MADS/genética , Proteínas de Domínio MADS/metabolismo , Filogenia , Perfilação da Expressão Gênica/métodos , Cicloexenos/metabolismo , Transcriptoma , Terpenos/metabolismo , Glucosídeos/metabolismo , Glucosídeos/biossínteseRESUMO
Transcriptomics is an extremely important area of molecular biology and is a powerful tool for studying all RNA molecules in an organism. Conventional transcriptomic technologies include microarrays and RNA sequencing, and the rapid development of single-cell sequencing and spatial transcriptomics in recent years has provided an enormous scope for research in this field. This chapter describes the application, significance, and experimental procedures of a variety of transcriptomic technologies in antiviral natural immunity.
Assuntos
Perfilação da Expressão Gênica , Imunidade Inata , Transcriptoma , Imunidade Inata/genética , Humanos , Perfilação da Expressão Gênica/métodos , Animais , Viroses/imunologia , Viroses/genética , Análise de Sequência de RNA/métodos , Análise de Célula Única/métodos , Análise de Sequência com Séries de Oligonucleotídeos/métodosRESUMO
Traditional bioreactor systems involve the use of three-dimensional (3D) scaffolds or stem cell aggregates, limiting the accessibility to the production of cell-secreted biomolecules. Herein, we present the use a pulse electromagnetic fields (pEMFs)-assisted wave-motion bioreactor system for the dynamic and scalable culture of human bone marrow-derived mesenchymal stem cells (hBMSCs) with enhanced the secretion of various soluble factors with massive therapeutic potential. The present study investigated the influence of dynamic pEMF (D-pEMF) on the kinetic of hBMSCs. A 30-min exposure of pEMF (10V-1Hz, 5.82 G) with 35 oscillations per minute (OPM) rocking speed can induce the proliferation (1 × 105 â 4.5 × 105) of hBMSCs than static culture. Furthermore, the culture of hBMSCs in osteo-induction media revealed a greater enhancement of osteogenic transcription factors under the D-pEMF condition, suggesting that D-pEMF addition significantly boosted hBMSCs osteogenesis. Additionally, the RNA sequencing data revealed a significant shift in various osteogenic and signaling genes in the D-pEMF group, further suggesting their osteogenic capabilities. In this research, we demonstrated that the combined effect of wave and pEMF stimulation on hBMSCs allows rapid proliferation and induces osteogenic properties in the cells. Moreover, our study revealed that D-pEMF stimuli also induce ROS-scavenging properties in the cultured cells. This study also revealed a bioactive and cost-effective approach that enables the use of cells without using any expensive materials and avoids the possible risks associated with them post-implantation.
Assuntos
Reatores Biológicos , Campos Eletromagnéticos , Células-Tronco Mesenquimais , Osteogênese , Humanos , Células-Tronco Mesenquimais/citologia , Células-Tronco Mesenquimais/metabolismo , Perfilação da Expressão Gênica , Proliferação de Células , Diferenciação Celular , Células Cultivadas , TranscriptomaRESUMO
Several protocols have been established for the generation of lens organoids from embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs), and other cells with regenerative potential in humans or various animal models. It is important to examine how well the regenerated lens organoids reflect lens biology, in terms of its development, homeostasis, and aging. Toward this goal, the iSyTE database (integrated Systems Tool for Eye gene discovery; https://research.bioinformatics.udel.edu/iSyTE/ ), a bioinformatics resource tool that contains meta-analyzed gene expression data in wild-type lens across different embryonic, postnatal, and adult stages, can serve as a resource for comparative analysis. This article outlines the approaches toward effective use of iSyTE to gain insights into normal gene expression in the mouse lens, enriched expression in the lens, and differential gene expression in select mouse gene-perturbation cataract/lens defects models, which in turn can be used to evaluate expression of key lens-relevant genes in lens organoids by transcriptomics (e.g., RNA-sequencing (RNA-seq), microarrays, etc.) or other downstream methods (e.g., RT-qPCR, etc.).
Assuntos
Cristalino , Organoides , Regeneração , Cristalino/citologia , Cristalino/metabolismo , Organoides/metabolismo , Organoides/citologia , Animais , Camundongos , Regeneração/genética , Perfilação da Expressão Gênica/métodos , Biologia Computacional/métodos , Simulação por Computador , Humanos , Catarata/genética , Catarata/patologia , Catarata/metabolismo , Transcriptoma , Bases de Dados GenéticasRESUMO
Perchlorate (ClO4-) is a type of novel persistent inorganic pollutant that has gained increasing attention because of its high solubility, poor degradability, and widespread distribution. However, the impacts of perchlorate on aquatic autotrophs such cyanobacterium are still unclear. Herein, Synechocystis sp. PCC6803 (Synechocystis) was used to investigate the response mechanisms of perchlorate on cyanobacterium by integrating physiological and transcriptome analyses. Physiological results showed that perchlorate mainly damaged the photosystem of Synechocystis, and the inhibition degree of photosystem II (PSII) was severer than that of photosystem I (PSI). When the exposed cells were moved to a clean medium, the photosynthetic activities were slightly repaired but still lower than in the control group, indicating irreversible damage. Furthermore, perchlorate also destroyed the cellular ultrastructure and induced oxidative stress in Synechocystis. The antioxidant glutathione (GSH) content and the superoxide dismutase (SOD) enzyme activity were enhanced to scavenge harmful reactive oxygen (ROS) in Synechocystis. Transcriptome analysis revealed that the genes associated with "photosynthesis" and "electron transport" were significantly regulated. For instance, most genes related to PSI (e.g., psaf, psaJ) and the "electron transport chain" were upregulated, whereas most genes related to PSII (e.g., psbA3, psbD1, psbB, and psbC) were downregulated. Additionally, perchlorate also induced the expression of genes related to the antioxidant system (sod2, gpx, gst, katG, and gshB) to reduce oxidative damage. Overall, this study is the first to investigate the impacts and mechanisms of cyanobacterium under perchlorate stress, which is conducive to assessing the risk of perchlorate in aquatic environments.
Assuntos
Percloratos , Fotossíntese , Synechocystis , Synechocystis/efeitos dos fármacos , Synechocystis/fisiologia , Synechocystis/genética , Percloratos/toxicidade , Fotossíntese/efeitos dos fármacos , Perfilação da Expressão Gênica , Estresse Oxidativo/efeitos dos fármacos , Poluentes Químicos da Água/toxicidade , Complexo de Proteína do Fotossistema II/metabolismo , Transcriptoma/efeitos dos fármacosRESUMO
Background: Gliomas are aggressive brain tumors associated with a poor prognosis. Cancer stem cells (CSCs) play a significant role in tumor recurrence and resistance to therapy. This study aimed to identify and characterize glioma stem cells (GSCs), analyze their interactions with various cell types, and develop a prognostic signature. Methods: Single-cell RNA sequencing data from 44 primary glioma samples were analyzed to identify GSC populations. Spatial transcriptomics and gene regulatory network analyses were performed to investigate GSC localization and transcription factor activity. CellChat analysis was conducted to infer cell-cell communication patterns. A GSC signature (GSCS) was developed using machine learning algorithms applied to bulk RNA sequencing data from multiple cohorts. In vitro and in vivo experiments were conducted to validate the role of TUBA1C, a key gene within the signature. Results: A distinct GSC population was identified, characterized by high proliferative potential and an enrichment of E2F1, E2F2, E2F7, and BRCA1 regulons. GSCs exhibited spatial proximity to myeloid-derived suppressor cells (MDSCs). CellChat analysis revealed an active MIF signaling pathway between GSCs and MDSCs. A 26-gene GSCS demonstrated superior performance compared to existing prognostic models. Knockdown of TUBA1C significantly inhibited glioma cell migration, and invasion in vitro, and reduced tumor growth in vivo. Conclusion: This study offers a comprehensive characterization of GSCs and their interactions with MDSCs, while presenting a robust GSCS. The findings offer new insights into glioma biology and identify potential therapeutic targets, particularly TUBA1C, aimed at improving patient outcomes.
Assuntos
Neoplasias Encefálicas , Glioma , Células-Tronco Neoplásicas , Análise de Célula Única , Nicho de Células-Tronco , Transcriptoma , Glioma/genética , Glioma/patologia , Humanos , Células-Tronco Neoplásicas/metabolismo , Células-Tronco Neoplásicas/patologia , Neoplasias Encefálicas/genética , Neoplasias Encefálicas/patologia , Animais , Camundongos , Nicho de Células-Tronco/genética , Linhagem Celular Tumoral , Regulação Neoplásica da Expressão Gênica , Redes Reguladoras de Genes , Microambiente Tumoral/genética , Perfilação da Expressão Gênica , Prognóstico , Comunicação Celular/genéticaRESUMO
Background: Immunotherapy has revolutionized skin cutaneous melanoma treatment, but response variability due to tumor heterogeneity necessitates robust biomarkers for predicting immunotherapy response. Methods: We used weighted gene co-expression network analysis (WGCNA), consensus clustering, and 10 machine learning algorithms to develop the immunotherapy-related gene model (ITRGM) signature. Multi-omics analyses included bulk and single-cell RNA sequencing of melanoma patients, mouse bulk RNA sequencing, and pathology sections of melanoma patients. Results: We identified 66 consensus immunotherapy prognostic genes (CITPGs) using WGCNA and differentially expressed genes (DEGs) from two melanoma cohorts. The CITPG-high group showed better prognosis and enriched immune activities. DEGs between CITPG-high and CITPG-low groups in the TCGA-SKCM cohort were analyzed in three additional melanoma cohorts using univariate Cox regression, resulting in 44 consensus genes. Using 101 machine learning algorithm combinations, we constructed the ITRGM signature based on seven model genes. The ITRGM outperformed 37 published signatures in predicting immunotherapy prognosis across the training cohort, three testing cohorts, and a meta-cohort. It effectively stratified patients into high-risk or low-risk groups for immunotherapy response. The low-risk group, with high levels of model genes, correlated with increased immune characteristics such as tumor mutation burden and immune cell infiltration, indicating immune-hot tumors with a better prognosis. The ITRGM's relationship with the tumor immune microenvironment was further validated in our experiments using pathology sections with GBP5, an important model gene, and CD8 IHC analysis. The ITRGM also predicted better immunotherapy response in eight cohorts, including urothelial carcinoma and stomach adenocarcinoma, indicating broad applicability. Conclusions: The ITRGM signature is a stable and robust predictor for stratifying melanoma patients into 'immune-hot' and 'immune-cold' tumors, enhancing prognosis and response to immunotherapy.
Assuntos
Biomarcadores Tumorais , Imunoterapia , Aprendizado de Máquina , Melanoma , Humanos , Melanoma/terapia , Melanoma/imunologia , Melanoma/genética , Imunoterapia/métodos , Biomarcadores Tumorais/genética , Prognóstico , Neoplasias Cutâneas/imunologia , Neoplasias Cutâneas/terapia , Neoplasias Cutâneas/genética , Animais , Perfilação da Expressão Gênica , Transcriptoma , Regulação Neoplásica da Expressão Gênica , Camundongos , Microambiente Tumoral/imunologia , Microambiente Tumoral/genética , Resultado do Tratamento , Redes Reguladoras de GenesRESUMO
The molecular mechanisms that link stress and biological rhythms still remain unclear. The habenula (Hb) is a key brain region involved in regulating diverse types of emotion-related behaviours while the suprachiasmatic nucleus (SCN) is the body's central clock. To investigate the effects of chronic social stress on transcription patterns, we performed gene expression analysis in the Hb and SCN of stress-naïve and stress-exposed mice. Our analysis revealed a large number of differentially expressed genes and enrichment of synaptic and cell signalling pathways between resilient and stress-naïve mice at zeitgeber 16 (ZT16) in both the Hb and SCN. This transcriptomic signature was nighttime-specific and observed only in stress-resilient mice. In contrast, there were relatively few differences between the stress-susceptible and stress-naïve groups across time points. Our results reinforce the functional link between circadian gene expression patterns and differential responses to stress, thereby highlighting the importance of temporal expression patterns in homoeostatic stress responses.
Assuntos
Ritmo Circadiano , Habenula , Estresse Psicológico , Núcleo Supraquiasmático , Animais , Habenula/metabolismo , Núcleo Supraquiasmático/metabolismo , Estresse Psicológico/metabolismo , Estresse Psicológico/genética , Camundongos , Masculino , Ritmo Circadiano/genética , Camundongos Endogâmicos C57BL , Transcriptoma , Resiliência Psicológica , Expressão Gênica/genéticaRESUMO
Personalized treatment for patients with advanced solid tumors critically depends on the deep characterization of tumor cells from patient biopsies. Here, we comprehensively characterize a pan-cancer cohort of 150 malignant serous effusion (MSE) samples at the cellular, molecular, and functional level. We find that MSE-derived cancer cells retain the genomic and transcriptomic profiles of their corresponding primary tumors, validating their use as a patient-relevant model system for solid tumor biology. Integrative analyses reveal that baseline gene expression patterns relate to global ex vivo drug sensitivity, while high-throughput drug-induced transcriptional changes in MSE samples are indicative of drug mode of action and acquired treatment resistance. A case study exemplifies the added value of multi-modal MSE profiling for patients who lack genetically stratified treatment options. In summary, our study provides a functional multi-omics view on a pan-cancer solid tumor cohort and underlines the feasibility and utility of MSE-based precision oncology.
Assuntos
Neoplasias , Medicina de Precisão , Humanos , Medicina de Precisão/métodos , Neoplasias/genética , Neoplasias/tratamento farmacológico , Neoplasias/patologia , Feminino , Transcriptoma , Regulação Neoplásica da Expressão Gênica , Masculino , Perfilação da Expressão Gênica/métodos , Idoso , Pessoa de Meia-Idade , Derrame Pleural Maligno/genética , Derrame Pleural Maligno/patologia , Derrame Pleural Maligno/metabolismo , Estudos de Coortes , Biomarcadores Tumorais/genética , Biomarcadores Tumorais/metabolismo , Genômica/métodos , Antineoplásicos/uso terapêutico , Antineoplásicos/farmacologia , Resistencia a Medicamentos Antineoplásicos/genéticaRESUMO
Human induced pluripotent stem cells (iPSCs) have great potential in research, but pluripotency testing faces challenges due to non-standardized methods and ambiguous markers. Here, we use long-read nanopore transcriptome sequencing to discover 172 genes linked to cell states not covered by current guidelines. We validate 12 genes by qPCR as unique markers for specific cell fates: pluripotency (CNMD, NANOG, SPP1), endoderm (CER1, EOMES, GATA6), mesoderm (APLNR, HAND1, HOXB7), and ectoderm (HES5, PAMR1, PAX6). Using these genes, we develop a machine learning-based scoring system, "hiPSCore", trained on 15 iPSC lines and validated on 10 more. hiPSCore accurately classifies pluripotent and differentiated cells and predicts their potential to become specialized 2D cells and 3D organoids. Our re-evaluation of cell fate marker genes identifies key targets for future studies on cell fate assessment. hiPSCore improves iPSC testing by reducing time, subjectivity, and resource use, thus enhancing iPSC quality for scientific and medical applications.
Assuntos
Diferenciação Celular , Células-Tronco Pluripotentes Induzidas , Controle de Qualidade , Células-Tronco Pluripotentes Induzidas/metabolismo , Células-Tronco Pluripotentes Induzidas/citologia , Humanos , Diferenciação Celular/genética , Biomarcadores/metabolismo , Aprendizado de Máquina , Endoderma/citologia , Endoderma/metabolismo , Transcriptoma , Mesoderma/metabolismo , Mesoderma/citologia , Linhagem Celular , Ectoderma/metabolismo , Ectoderma/citologia , Organoides/metabolismo , Perfilação da Expressão Gênica/métodos , Proteína Homeobox Nanog/genética , Proteína Homeobox Nanog/metabolismo , Proteínas com Domínio TRESUMO
Akebia trifoliata is a medicinal plant with high oil content and broad pharmacological effects. To investigate the regulatory mechanisms of key metabolic pathways during seed development, we conducted an integrated multi-omics analysis, including transcriptomics, proteomics, and metabolomics, exploring the dynamic changes in carbon and lipid metabolism. Metabolomics analysis revealded that glucose and sucrose levels decreased, while glycolytic intermediate phosphoenolpyruvate and fatty acids increased with seed development, indicating a shift in carbon flux towards fatty acid synthesis. Integrated transcriptomic and proteomic analyses showed that 70 days after flowering, the expression levels of genes and proteins associated with carbon and fatty acid metabolism were upregulated, suggesting an increased energy demand. Additionally, LEC2, LEC1, WRI1, FUS3, and ABI3 were identified as vital regulators of lipid synthesis. By constructing a multi-omics co-expression network, we identified hub genes such as aroE, GAPDH, KCS, TPS, and hub proteins like PGM, PDH, ENO, PFK, PK, ACCase, SAD, PLC, and OGDH that play critical regulatory roles in seed lipid synthesis. This study provides new ideas for the molecular basis of lipid synthesis in Akebia trifoliata seeds and can facilitate future research on the genetic improvement through molecular-assisted breeding.
Assuntos
Carbono , Regulação da Expressão Gênica de Plantas , Metabolismo dos Lipídeos , Sementes , Sementes/metabolismo , Sementes/crescimento & desenvolvimento , Sementes/genética , Carbono/metabolismo , Proteômica/métodos , Redes Reguladoras de Genes , Metabolômica/métodos , Proteínas de Plantas/metabolismo , Proteínas de Plantas/genética , Transcriptoma , Perfilação da Expressão Gênica , Ácidos Graxos/metabolismo , Redes e Vias Metabólicas , MultiômicaRESUMO
Susceptibility to decompression sickness (DCS) is characterized by a wide inter-individual variability, the origins of which are still poorly understood. We selectively bred rats with at least a 3-fold greater resistance to DCS than standard rats after 6 generations. In order to better understand DCS mechanisms, we compared the static genome expression of these resistant rats from the 10th generation to their counterparts of the initial non-resistant Wistar strain, by a microarray transcriptomic approach coupled and crossed with a PCR plates miRnome study. Thus, we identified differentially expressed genes on selected males and females, as well as gender differences in those genes, and we crossed these transcripts with the respective targets of the differentially expressed microRNAs. Our results highlight pathways involved in inflammatory responses, circadian clock, cell signaling and motricity, phagocytosis or apoptosis, and they confirm the importance of inflammation in DCS pathophysiology.
Assuntos
Doença da Descompressão , MicroRNAs , Transcriptoma , Animais , Doença da Descompressão/genética , MicroRNAs/genética , MicroRNAs/metabolismo , Masculino , Feminino , Ratos , Perfilação da Expressão Gênica , Ratos Wistar , Regulação da Expressão GênicaRESUMO
BACKGROUND: Phlebotomus papatasi is considered the primary vector of Leishmania major parasites that cause zoonotic cutaneous leishmaniasis (ZCL) in the Middle East and North Africa. Phlebotomus papatasi populations have been studied extensively, revealing the existence of different genetic populations and subpopulations over its large distribution range. Genetic diversity and population structure analysis using transcriptome microsatellite markers is important to uncover the vector distribution dynamics, essential for controlling ZCL in endemic areas. METHODS: In this study, we investigated the level of genetic variation using expressed sequence tag-derived simple sequence repeats (EST-SSRs) among field and colony P. papatasi samples collected from 25 different locations in 11 countries. A total of 302 P. papatasi sand fly individuals were analyzed, including at least 10 flies from each region. RESULTS: The analysis revealed a high-level population structure expressed by five distinct populations A through E, with moderate genetic differentiation among all populations. These genetic differences in expressed genes may enable P. papatasi to adapt to different environmental conditions along its distribution range and likely affect dispersal. CONCLUSIONS: Elucidating the population structuring of P. papatasi is essential to L. major containment efforts in endemic countries. Moreover, the level of genetic variation among these populations may improve our understanding of Leishmania-sand fly interactions and contribute to the efforts of vaccine development based on P. papatasi salivary proteins.
Assuntos
Variação Genética , Insetos Vetores , Repetições de Microssatélites , Phlebotomus , Transcriptoma , Animais , Phlebotomus/genética , Phlebotomus/parasitologia , Insetos Vetores/parasitologia , Insetos Vetores/genética , Leishmania major/genética , Leishmaniose Cutânea/prevenção & controle , Leishmaniose Cutânea/parasitologia , Leishmaniose Cutânea/transmissão , Etiquetas de Sequências Expressas , Vacinas contra Leishmaniose/genética , Vacinas contra Leishmaniose/imunologia , FemininoRESUMO
MAIN CONCLUSION: Unlike Arabidopsis thaliana, defenses of Arabidopsis lyrata against Pieris brassicae larval feeding are not primable by P. brassicae eggs. Thus, egg primability of plant anti-herbivore defenses is not phylogenetically conserved in the genus Arabidopsis. While plant anti-herbivore defenses of the annual species Arabidopsis thaliana were shown to be primable by Pieris brassicae eggs, the primability of the phylogenetically closely related perennial Arabidopsis lyrata has not yet been investigated. Previous studies revealed that closely related wild Brassicaceae plant species, the annual Brassica nigra and the perennial B. oleracea, exhibit an egg-primable defense trait, even though they have different life spans. Here, we tested whether P. brassicae eggs prime anti-herbivore defenses of the perennial A. lyrata. We exposed A. lyrata to P. brassicae eggs and larval feeding and assessed their primability by (i) determining the biomass of P. brassicae larvae after feeding on plants with and without prior P. brassicae egg deposition and (ii) investigating the plant transcriptomic response after egg deposition and/or larval feeding. For comparison, these studies were also conducted with A. thaliana. Consistent with previous findings, A. thaliana's response to prior P. brassicae egg deposition negatively affected conspecific larvae feeding upon A. thaliana. However, this was not observed in A. lyrata. Arabidopsis thaliana responded to P. brassicae eggs with strong transcriptional reprogramming, whereas A. lyrata responses to eggs were negligible. In response to larval feeding, A. lyrata exhibited a greater transcriptome change compared to A. thaliana. Among the strongly feeding-induced A. lyrata genes were those that are egg-primed in feeding-induced A. thaliana, i.e., CAX3, PR1, PR5, and PDF1.4. These results suggest that A. lyrata has evolved a robust feeding response that is independent from prior egg exposure.
Assuntos
Arabidopsis , Borboletas , Herbivoria , Larva , Arabidopsis/genética , Arabidopsis/fisiologia , Borboletas/fisiologia , Animais , Larva/fisiologia , Óvulo/fisiologia , Regulação da Expressão Gênica de Plantas , Defesa das Plantas contra Herbivoria , TranscriptomaRESUMO
Age-related hearing loss (ARHL) or presbycusis is associated with irreversible progressive damage in the inner ear, where the sound is transduced into electrical signal; but the detailed mechanism remains unclear. Here, we sought to determine the potential molecular mechanism involved in the pathogeneses of ARHL with bioinformatics methods. A single-cell transcriptome sequencing study was performed on the cochlear samples from young and aged mice. Detection of identified cell type marker allowed us to screen 18 transcriptional clusters, including myeloid cells, epithelial cells, B cells, endothelial cells, fibroblasts, T cells, inner pillar cells, neurons, inner phalangeal cells, and red blood cells. Cell-cell communications were analyzed between young and aged cochlear tissue samples by using the latest integration algorithms Cellchat. A total of 56 differentially expressed genes were screened between the two groups. Functional enrichment analysis showed these genes were mainly involved in immune, oxidative stress, apoptosis, and metabolic processes. The expression levels of crucial genes in cochlear tissues were further verified by immunohistochemistry. Overall, this study provides new theoretical support for the development of clinical therapeutic drugs.
Assuntos
Presbiacusia , Análise de Célula Única , Animais , Presbiacusia/genética , Presbiacusia/patologia , Presbiacusia/metabolismo , Camundongos , Análise de Sequência de RNA , Transcriptoma , Perfilação da Expressão Gênica , Cóclea/metabolismo , Cóclea/patologiaRESUMO
BACKGROUND: Embryos are regeneration and wound healing masters. They rapidly close wounds and scarlessly remodel and regenerate injured tissue. Regeneration has been extensively studied in many animal models using new tools such as single-cell analysis. However, until now, they have been based primarily on experiments assessing from 1 day post injury. RESULTS: In this paper, we reveal that critical steps initiating regeneration occur within hours after injury. We discovered the regeneration initiating cells (RICs) using single-cell and spatial transcriptomics of the regenerating Xenopus laevis tail. RICs are formed transiently from the basal epidermal cells, and their expression signature suggests they are important for modifying the surrounding extracellular matrix thus regulating development. The absence or deregulation of RICs leads to excessive extracellular matrix deposition and defective regeneration. CONCLUSION: RICs represent a newly discovered transient cell state involved in the initiation of the regeneration process.
Assuntos
Regeneração , Cauda , Xenopus laevis , Animais , Transcriptoma , Análise de Célula Única , Matriz Extracelular/metabolismo , CicatrizaçãoRESUMO
Single-cell RNA sequencing (scRNA-seq) technologies can generate transcriptomic profiles at a single-cell resolution in large patient cohorts, facilitating discovery of gene and cellular biomarkers for disease. Yet, when the number of biomarker genes is large, the translation to clinical applications is challenging due to prohibitive sequencing costs. Here, we introduce scPanel, a computational framework designed to bridge the gap between biomarker discovery and clinical application by identifying a sparse gene panel for patient classification from the cell population(s) most responsive to perturbations (e.g. diseases/drugs). scPanel incorporates a data-driven way to automatically determine a minimal number of informative biomarker genes. Patient-level classification is achieved by aggregating the prediction probabilities of cells associated with a patient using the area under the curve score. Application of scPanel to scleroderma, colorectal cancer, and COVID-19 datasets resulted in high patient classification accuracy using only a small number of genes (<20), automatically selected from the entire transcriptome. In the COVID-19 case study, we demonstrated cross-dataset generalizability in predicting disease state in an external patient cohort. scPanel outperforms other state-of-the-art gene selection methods for patient classification and can be used to identify parsimonious sets of reliable biomarker candidates for clinical translation.
Assuntos
COVID-19 , Análise de Célula Única , Humanos , COVID-19/genética , COVID-19/virologia , Análise de Célula Única/métodos , Biologia Computacional/métodos , Transcriptoma , RNA-Seq/métodos , Neoplasias Colorretais/genética , Neoplasias Colorretais/classificação , Perfilação da Expressão Gênica/métodos , SARS-CoV-2/genética , Análise de Sequência de RNA/métodos , Software , Análise da Expressão Gênica de Célula ÚnicaRESUMO
The field of computational drug repurposing aims to uncover novel therapeutic applications for existing drugs through high-throughput data analysis. However, there is a scarcity of drug repurposing methods leveraging the cellular-level information provided by single-cell RNA sequencing data. To address this need, we propose DrugReSC, an innovative approach to drug repurposing utilizing single-cell RNA sequencing data, intending to target specific cell subpopulations critical to disease pathology. DrugReSC constructs a drug-by-cell matrix representing the transcriptional relationships between individual cells and drugs and utilizes permutation-based methods to assess drug contributions to cellular phenotypic changes. We demonstrate DrugReSC's superior performance compared to existing drug repurposing methods based on bulk or single-cell RNA sequencing data across multiple cancer case studies. In summary, DrugReSC offers a novel perspective on the utilization of single-cell sequencing data in drug repurposing methods, contributing to the advancement of precision medicine for cancer.