RNA-seq Transcriptome Research Articles

Preventive effect and mechanism of Tibetan tea extract on thrombosis in arachidonic acid-induced zebrafish determined via RNA-seq transcriptome profiles.

Thrombosis is a key pathological event in cardiovascular diseases and is also the most important targeting process for their clinical management. In this study, arachidonic acid (AA) was used to induce thrombus formation in zebrafish larvae. Blood flow, red blood cell (RBCs) aggregation and cellular oxidative stress were measured to evaluate the antithrombotic effect of Tibetan tea (TT). Meanwhile, the potential molecular mechanism was further explored by transcriptome sequencing (RNA-seq). The results indicated that TT could significantly restore heart RBCs intensity of thrombotic zebrafish, whilst decreasing RBCs accumulation in the caudal vein. The transcriptome analysis revealed that the preventive effect of TT on thrombosis could be mostly attributed to changes in lipid metabolism related signaling pathways, such as fatty acid metabolism, glycerollipid metabolism, ECM-receptor interaction and steroid biosynthesis signaling pathway. This study demonstrated that Tibetan tea could alleviate thrombosis by reducing oxidative stress levels and regulating lipid metabolism.

A novel cuproptosis-related lncRNA signature predicts the prognosis and immunotherapy for hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is one of the most serious malignant tumors with a poor prognosis worldwide. Cuproptosis is a novel copper-dependent cell death form, involving mitochondrial respiration and lipoylated components of the tricarboxylic acid (TCA) cycle. Long non-coding RNAs (lncRNAs) have been demonstrated to affect the tumorigenesis, growth, and metastasis of HCC. We explored the potential roles of cuproptosis-related lncRNAs in predicting the prognosis for HCC. The RNA-seq transcriptome data, mutation data, and clinical information data of HCC patients were downloaded from The Cancer Genome Atlas (TCGA) database. The least absolute shrinkage and selection operator (LASSO) algorithm and Cox regression analyses were performed to identify a prognostic cuproptosis-related lncRNA signature. The receiver operating characteristic (ROC) analysis was used to evaluate the predictive value of the lncRNA signature for HCC. The enrichment pathways, immune functions, immune cell infiltration, tumor mutation burden, and drug sensitivity were also analyzed. We constructed a prognostic model consisting of 8 cuproptosis-related lncRNAs for HCC. The patients were divided into high-risk group and low-risk group according to the riskscore calculated using the model. Kaplan-Meier analysis revealed that the high-risk lncRNA signature was correlated with poor overall survival [hazard ratio (HR) =1.009, 95% confidence interval (CI) = 1.002-1.015; p= 0.010)] of HCC. A prognostic nomogram incorporated the lncRNA signature and clinicopathological features were constructed and showed favorable performance for predicting prognosis of HCC patients. In addition, the most immune-related functions were significantly different between the high-risk and low-risk groups. Tumor mutation burden (TMB) and immune checkpoints were also expressed differently between the two risk groups. Finally, HCC patients with low-risk score were more sensitive to several chemotherapy drugs. The novel cuproptosis-related lncRNA signature could be used to predict prognosis and evaluate the effect of chemotherapy for HCC.

The fusiform gyrus exhibits differential gene-gene co-expression in Alzheimer's disease.

Alzheimer's Disease (AD) is an irreversible neurodegenerative disease clinically characterized by the presence of β-amyloid plaques and tau deposits in various regions of the brain. However, the underlying factors that contribute to the development of AD remain unclear. Recently, the fusiform gyrus has been identified as a critical brain region associated with mild cognitive impairment, which may increase the risk of AD development. In our study, we performed gene co-expression and differential co-expression network analyses, as well as gene-expression-based prediction, using RNA-seq transcriptome data from post-mortem fusiform gyrus tissue samples collected from both cognitively healthy individuals and those with AD. We accessed differential co-expression networks in large cohorts such as ROSMAP, MSBB, and Mayo, and conducted over-representation analyses of gene pathways and gene ontology. Our results comprise four exclusive gene hubs in co-expression modules of Alzheimer's Disease, including FNDC3A, MED23, NRIP1, and PKN2. Further, we identified three genes with differential co-expressed links, namely FAM153B, CYP2C8, and CKMT1B. The differential co-expressed network showed moderate predictive performance for AD, with an area under the curve ranging from 0.71 to 0.76 (+/- 0.07). The over-representation analysis identified enrichment for Toll-Like Receptors Cascades and signaling pathways, such as G protein events, PIP2 hydrolysis and EPH-Epherin mechanism, in the fusiform gyrus. In conclusion, our findings shed new light on the molecular pathophysiology of AD by identifying new genes and biological pathways involved, emphasizing the crucial role of gene regulatory networks in the fusiform gyrus.

Development of a Novel Pyroptosis-Associated lncRNA Biomarker Signature in Lung Adenocarcinoma.

Pyroptosis is a novel type of cell death observed in various diseases. Our study aimed to investigate the relationship between pyroptosis-associated-long non-coding RNAs (lncRNAs), immune infiltration, and expression of immune checkpoints in the setting of lung adenocarcinoma and the prognostic value of pyroptosis-related lncRNAs. RNA-seq transcriptome data and clinical information from The Cancer Genome Atlas (TCGA) were downloaded, and consensus clustering analysis was used to separate the samples into two groups. Least absolute shrinkage and selection operator (LASSO) analyses were conducted to construct a risk signature. The association between pyroptosis-associated lncRNAs, immune infiltration, and expression of immune checkpoints were analysed. The cBioPortal tool was used to discover genomic alterations. Gene set enrichment analysis (GSEA) was utilized to investigate downstream pathways of the two clusters. Drug sensitivity was also examined. A total of 43 DEGs and 3643 differentially expressed lncRNAs were identified between 497 lung adenocarcinoma tissues and 54 normal samples. A signature consisting of 11 pyroptosis-related lncRNAs was established as prognostic for overall survival. Patients in the low-risk group have a significant overall survival advantage over those in the high-risk group in the training group. Immune checkpoints were expressed differently between the two risk groups. Risk scores were validated to develop an independent prognostic model based on multivariate Cox regression analysis. The area under time-dependent receiver operating characteristic curve (AUC of the ROC) at 1-, 3-, and 5-years measured0.778, 0.757, and 0.735, respectively. The high-risk group was more sensitive to chemotherapeutic drugs than the low-risk group. This study demonstrates the association between pyroptosis-associated lncRNAs and prognosis in lung adenocarcinoma and enables a robust predictive signature of 11 lncRNAs to inform overall survival.

IL-33 promotes inflammatory responses and exacerbates lung pathology in a mouse model of SARS-CoV-2 infection

Abstract The ongoing COVID-19 pandemic caused by SARS-CoV-2 has resulted in more than 6.6 million deaths worldwide as of the end of 2022. Clinical data revealed that dysregulated host immune responses may contribute to disease severity and poor recovery outcomes; however, the mechanisms that underlie immune dysregulation and disease severity are relatively unknown. Interleukin-33 (IL-33), a damage-associated molecular pattern (DAMP) molecule, is mainly expressed in nucleus of epithelial and endothelial cells. Elevated serum IL-33 levels have been recently reported in COVID-19 patients and might be associated with adverse outcomes. In this study, we infected B6 mice with a mouse-adapted SARS-CoV-2 MA10 and found that IL-33 was significantly increased in the lungs at day 2 post-infection, accompanied by highly upregulated inflammatory chemokines CXCL1, CXCL2 and CCL2. Next, we used IL-33 −/−mice and demonstrated that IL-33 deficiency resulted in less bodyweight loss at days 2 and 3 and decreased viral burden at day 4. Flow cytometry analyses showed that IL-33 −/−mice had reduced numbers of innate immune cells at day 2, including neutrophils, macrophages and NK cells. At day 4, IL-33 −/−mice displayed reduced activated T cells in the lungs as compared to WT mice. Lung tissue RNAseq transcriptomics revealed that IL-33 signals contributed to several inflammatory pathways, including type II interferon signaling, pathogen phagocytosis, macrophage activation, cytokine/chemokine and inflammatory responses and oxidative damage. Overall, these data uncover a detrimental role of the DAMP IL-33 in the lungs following SARS-CoV-2 infection and provide new insights to support the development of effective therapeutic strategies for COVID-19. Supported by grants from NIH (R21 AI153586)

Connexin-43: More than just a gap junction protein. Connexin-43 controls CD4+ T cell activation and clonal expansion

Abstract Activation and proliferation of antigen specific T cells depends on the interaction of multiple signaling molecules with the TCR/CD3 complex. We report that expression of connexin 43 (Cx43), a gap junction protein, is critical for the expansion of antigen-specific or self-reactive effector CD4 +T cells. While gap junction mediated intercellular communication has been the main focus of connexin research, the cytoplasmic C-terminus of Cx43 has multiple functions independent of membrane channel forming properties and may act as a docking molecule for assembling signaling complexes including the immunological synapse. We also report that antigen-specific Cx43-deficient CD4 +T cells transferred into recipient mice immunized with cognate antigenic peptide and adjuvant expanded poorly compared to wild type cells. This protected mice from experimental autoimmune encephalomyelitis (EAE). Decreased proliferation and expansion also protects lymphopenic mice repopulated with naive, Cx43 deficient CD4 +T cells, from inflammatory bowel disease. We have found that Cx43-deficient CD4 +T cells have a signaling defect affecting Erk, p38 and Akt signaling pathways. Transcriptome RNA-seq analysis comparing gene expression profiles of activated Cx43 sufficient and deficient CD4 +T cells shows that differentially expressed genes are enriched in genes involved in G protein and Ca 2+signaling, ATP metabolism, genes regulating cytoskeleton reorganization and T cell homing. In summary, our data demonstrate that Cx43 has a major impact on the generation of effector CD4 +T cells, their ability to respond to antigenic stimulation, or to precipitate autoimmune disease.

Resveratrol reliefs DEHP-induced defects during human decidualization

Di-(2-Ethylhexyl) phthalate (DEHP) is widely used as an additive in many plastic products. Studies have revealed that DEHP persistent exposure can affect embryonic development and lead to adverse female reproductive disorders. The establishment of pregnancy involves extensive changes in the endometrial tissue, including massive extracellular matrix (ECM) remodeling. Decidualization of the endometrium provides a suitable environment for subsequent growth by causing changes in the morphology of the uterine stromal cells, is a key process in human pregnancy. Resveratrol (RSV) is a natural polyphenolic plant antitoxin with a wide range of pharmacological effects. Growing evidence indicates that RSV has therapeutic effects on certain female reproductive disorders. In this study, the effect of DEHP on cell viability was investigated by cell proliferation assay. Cell decidualization was induced in vitro, and the downregulation of molecules associated with decidualization was confirmed through quantitative real-time PCR and western blot analysis. Immunofluorescence analysis revealed alteration in cell morphology, and found that administration of DEHP sufficiently induced ERα entry into the nucleus. The effect of DEHP on cells was fully verified by RNA-seq analysis. Interestingly, an upregulation of decidual molecules was observed after rescue with RSV, which was confirmed by RNA-seq transcriptome analysis and quantitative real-time PCR assay. Additionally, the expression of ECM remodeling-related genes was significantly restored by RSV administration. The study revealed the potential mechanisms of DEHP-induced decidualization defects and the functional relieving roles of RSV while providing a perspective therapeutic candidate for alleviating the DEHP-induced deficiencies in decidualization.

RNAseq transcriptome profiling reveals activation of immune responses and disrupted circadian patterns in the cerebral white matter of aged mice (P4-6.003)

<h3>Objective:</h3> We aim to map transcriptome profiles of mouse corpus callosum using young (5-month-old) and aged (24-month-old) mice. <h3>Background:</h3> Aging is a risk factor for several neurological diseases. Although the approach of transcriptome profiling by RNAseq has been used to examine age-related changes in RNA expression levels in the brain, how aging affects the transcriptome of cerebral white matter is still mostly unknown. <h3>Design/Methods:</h3> All experimental procedures followed NIH guidelines and were approved by the MGH Institutional Animal Care and Use Committee. Male C57BL6J mice (N=12 for the young; N=12 for the aged) were used. Mice were sacrificed at either ZT1, ZT7, ZT13, or ZT19 to obtain corpus callosum samples (N=3/group). Then, RNA samples were prepared and used for bulk RNAseq. <h3>Results:</h3> Regardless of the time zones for sample preparation, inflammatory responses were activated in aged mice. Especially, genes that are related to complement classical pathways were significantly upregulated in the aged corpus callosum compared to the young group. On the other hand, there were several upregulated genes in the young group. The most upregulated gene in the young corpus callosum was tenascin C, which is a major extracellular matrix glycoprotein, and the pathway analysis showed that the pathways of glial cell development (GO:0021782) and regulation of nervous system development (GO:0051960) were highly enriched in the list of differentially expressed genes (DEGs). Interestingly, the circadian patterns of some genes were disrupted in the aged corpus callosum. In addition, the number of DEGs between young and aged mice was more significant in ZT1 (inactive phase for mice) compared to ZT13 (active phase), suggesting that age-related differences in gene expression patterns may depend on circadian time points. <h3>Conclusions:</h3> Our current study provides a novel dataset for white-matter-specific transcriptome profiles in mice. Our data would help us understand the mechanism of age-related transcriptome changes in cerebral white matter. <b>Disclosure:</b> Dr. Ishikawa has nothing to disclose. Dr. Hamanaka has nothing to disclose. Dr. Mandeville has nothing to disclose. Mrs. Guo has nothing to disclose. Dr. Li has nothing to disclose. Akihiro Shindo has nothing to disclose. Eng Lo has nothing to disclose. Ken Arai has nothing to disclose.

Abstract LB272: Spatial cellular architecture predicts prognosis in glioblastoma

Abstract Intra-tumoral heterogeneity and cell-state plasticity are key drivers for the therapeutic resistance of glioblastoma (GBM). Studies based on single-cell RNA-seq and spatial transcriptomics have classified GBM cells into distinct transcriptional phenotypes. However, how the transcriptional diversity and spatial cellular organization are associated with patient prognosis remains incompletely resolved. Here, we developed a deep learning model to predict spatially resolved transcriptional programs from histology images. The model was trained on spatial transcriptomics data and validated in external testing cohorts. Applying the model to two separate patient cohorts led to the discovery of conserved relationships between tumor architecture and prognosis. Patient with poor prognosis had higher proportions of GBM cells expressing a hypoxia-induced transcriptional program. In addition, high clustering patterns of reactive astrocytes were associated with a poor prognosis. Conversely, when the reactive astrocytes were dispersed and connected to other cell types, the risk was decreased. To validate our results, we developed a separate deep learning model that used histology images to predict prognosis. Applying the model to spatial transcriptomics data discovered survival-associated regional gene expression programs. Genes related to glycoprotein metabolism and injury response were significantly upregulated in tumor cells with high aggressiveness. Our studies established a scalable approach to resolve the transcriptional heterogeneity of GBM and linked the spatial cellular architecture to clinical outcomes. Citation Format: Yuanning Zheng, Francisco Carrillo-Perez, Marija Pizurica, Olivier Gevaert. Spatial cellular architecture predicts prognosis in glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB272.

Therapeutic effects of polydeoxyribonucleotide in an in vitro neuronal model of ischemia/reperfusion injury

Polydeoxyribonucleotide (PDRN) is an agonist that selectively stimulates adenosine A2A receptor (ADORA2A), which suppresses inflammatory responses. Ischemia/reperfusion (I/R) injury plays a major role in the pathogenesis of ischemic stroke by inducing neuroinflammation. Therefore, this study aimed to investigate the therapeutic effects of PDRN in an in vitro I/R injury model. The in vitro model was established with differentiated Neuro-2a cells under oxygen and glucose deprivation condition. The cells were treated with PDRN for 24 h under reoxygenation condition. As the results of RNA-seq transcriptome analysis, CSF1, IL-6, PTPN6, RAC2, and STAT1 were identified of its relation to the effect of PDRN on inflammatory responses in the model. To further investigate therapeutic effects of PDRN, RT-qPCR, western blotting, LDH assay, and TUNEL assay were performed. PDRN significantly reversed the expression of genes and proteins related to inflammatory responses. The elevated ADORA2A expression by PDRN treatment downregulated JAK/STAT pathway in the model. Furthermore, PDRN inhibited neuronal cell death in the model. Consequently, our results suggested that PDRN alleviated inflammatory responses through inhibition of JAK/STAT pathway by mediating ADORA2A expression and inhibited neuronal cell death in the model. These results provide significant insights into potential therapeutic approaches involving PDRN treatment for I/R injury.

Integrating single-cell RNA-seq and spatial transcriptomics reveals MDK-NCL dependent immunosuppressive environment in endometrial carcinoma.

The tumor microenvironment (TME) play important roles in progression of endometrial carcinoma (EC). We aimed to assess the cell populations in TME of EC. We downloaded datasets of single-cell RNA-seq (scRNA-seq) and spatial transcriptome (ST) for EC from GEO, and downloaded RNA-Seq (FPKM) and clinical data of TCGA-UCEC project from TCGA. The datasets were analyzed using R software. We obtained 5 datasets of scRNA-seq, 1 of ST and 569 samples of RNA-seq. Totally, 0.2 billion transcripts and 33,408 genes were detected in 33,162 cells from scRNA-seq. The cells were classified into 9 clusters, and EC cells were originated from epithelial cells and ciliated cells. Gene set variation analysis (GSVA) indicated that the pathways enriched in the subclusters of epithelial cells and endothelial cells were significantly different, indicating great heterogeneity in EC. Cell-cell communication analyses showed that EC cells emitted the strongest signals, and endothelial cells received more signals than other cells. Further analysis found that subclusters of 1 and 2 of epithelial cells were showed a more malignant phenotype, which may confer malignant phenotype to subcluster of 0 of endothelial cells through MK pathway by MDL-NCL signal. We also analyzed communications between spatial neighbors with ST data and confirmed the findings on MDL-NCL in cell-cell communication. TCGA and GEO analyses indicated that the expression levels of NCL was inversely correlated with ImmuneScore. Our study revealed EC cells can confer malignant phenotype to endothelial cells by MDK-NCL signal, and NCL is associated with suppressed immune activity. EC cells may shape TME by inhibiting immune cells and "educating" stromal cells via MDK-NCL signal.

Abstract 4956: Discovering novel targetable pathways by combining functional and multi-omic data from primary ovarian cancer samples

Abstract Background: There is a critical necessity to reveal novel and tractable targets for anti-cancer treatments in indications with high unmet medical need, such as high grade serous ovarian cancer (HGSOC). However, standard process for target discovery using models such as outgrown cell lines and well-averaged readouts has yielded a less than 5% approval rate for drugs entering trials (Thomas et al. 2016 Bio.org). Here, we describe patient-centric target discovery through the use of disease relevant primary OC samples and single cell functional characterization using a platform with proven hemonc translatability (Kornauth et al. 2021, Snijder et al. 2017). We integrate data from our functional drug testing platform under multiple drug perturbations with matching genomic and transcriptomic data to reveal associations with novel downstream regulators of sensitivity. Methods: Sensitivity of the cancer cell compartment in primary malignant ascites samples (n = 20; 75% HGSOC) to 85 small molecule drugs, was evaluated using a proprietary and translatable deep learning-driven single cell imaging platform (Vladimer et al. 2017). Cancer cell sensitivity from the drugs was combined with WES, bulk-RNAseq and drug induced changes in phosphoproteome, and single cell RNAseq transcriptome to identify perturbed targets and pathways. Results: Here we describe a family of TKIs including ALKi that induce cytotoxicity of cancer cells in primary samples, not previously captured in publicly available cell line drug sensitivity screening data (Iorio et al. 2016). We report novel sensitivity of OC driven by non-canonical targets of ceritinib such as FAK1 or IGF1R, mediated by the downstream signaling hub YBX1 (Kuenzi et al. 2017), involved in NFB pathway regulation (Motolani et al. 2021). Indeed, transcriptomic scRNA analysis upon ceritinib treatment of primary OC cells revealed rapid perturbation of numerous NFB pathway members, alongside YBX1 inactivation. Conclusions: Combining functional endpoints and single cell-based differential expression analysis of primary OC samples, we have identified the NFB pathway and the regulator YBX1 as a promising novel sensitivity for HGSOC treatment development. These and several other important targetable nodes identified, sit outside the recently suggested JAK/STAT pathway (Izar et al. 2020), thereby demonstrating a pipeline towards novel drug target and pathway discovery driven by patient-centric, disease relevant models of high-need indications. Citation Format: Irene Gutierrez-Perez, Bekir Ergüner, Pisanu Buphamalai, Joost Van Ham, Paul Heinz, Valentin Aranha, Rin Okumura, Elisabeth Waltenberger, Isabella Alt, Claudia Baumgaertler, Maja Stulic, Edgar Petru, Christoph Minichsdorfer, Judith Lafleur, Lukas Hefler, Laudia Hadjari, Lucia Dzurillova, Jozef Sufliarsky, Nikolaus Krall, Thorsten Füreder, Gregory Ian Vladimer, Bojan Vilagos, Robert Sehlke. Discovering novel targetable pathways by combining functional and multi-omic data from primary ovarian cancer samples. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4956.

Abstract 5266: Metabolic rewiring and epigenetic reprogramming by the environmental carcinogen benzo[a]pyrene in a two-stage skin carcinogenesis mouse model and cancer interception by triterpenoid ursolic acid

Abstract Nonmelanoma skin cancer (NMSC) is the most common skin cancer burden on the U.S. population. Environmental exposure to chemical carcinogens is one of the major causes of NMSC initiation, promotion, and progression. Ursolic acid (UA) is a naturally abundant pentacyclic triterpenoid showing anticancer potentials against diverse cancers. In the current study, we developed a two-stage skin carcinogenesis model in SKH1 hairless mice by administering cancer-initiating agent benzo[a]pyrene (B[a]P) and promoting agent 12-O-tetra-decanoylphorbol-13-acetate to study the epigenetic, transcriptomic, and metabolic changes at different stages (5, 20, and 26 weeks) during the development of NMSC, and investigated how UA regulates B[a]P-mediated alterations for NMSC interception. We found that UA protects against B[a]P-induced tumorigenesis at different phases of NMSC. Epigenetic CpG methyl-seq showed UA abrogated B[a]P-mediated alterations in differentially methylated regions (DMRs) profiles. Transcriptomic RNA-seq data exhibited UA reversed the differentially expressed genes (DEGs) of several inflammatory genes, such as chemokine ligand 8 (Ccl8) and interleukin 17F (Il17f), and epigenetic genes, such as DNA-methyltransferase 3-like (Dnmt3l) and protein-l-isoaspartate O-methyltransferase domain-containing protein 1 (Pcmtd1) during different stages of NMSC. Association study between DEGs and DMRs showed that B[a]P promoted transcription of kallikrein-related peptidase 13 (Klk13) by promoter demethylation, while UA suppressed Klk13 expression through hypermethylation in the promoter during the initiation stage, indicating the early intervention of UA. Ingenuity pathway analysis further showed significant upregulation of macrophage-stimulating protein-recepteur d'origine nantais (MSP-RON) signaling pathway by B[a]P during the initiation stage while suppressed by UA treatment. The metabolomic study revealed UA modulated cancer-associated changes in metabolisms, including the TCA cycle and pyruvate metabolism/metabolites during the promotion phase, indicating UA plays a critical role in regulating B[a]P-regulated metabolic changes and intercepting NMSC progression. In summary, UA protects against the environmental carcinogen B[a]P-driven epigenetic, transcriptomic, and metabolic changes during the initiation, promotion, and progression of NMSC, potentially contributing to the anticancer effects of UA. (Supported by NIH R01 CA200129 to A.N.K) Citation Format: Md. Shahid Sarwar, Christina N. Ramirez, Hsiao-Chen Dina Kuo, Pochung Chou, Renyi Wu, Davit Sargsyan, Ahmad Shannar, Rebecca Mary Peter, Ran Yin, Yujue Wang, Xiaoyang Su, Ah-Ng Kong. Metabolic rewiring and epigenetic reprogramming by the environmental carcinogen benzo[a]pyrene in a two-stage skin carcinogenesis mouse model and cancer interception by triterpenoid ursolic acid. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5266.

Abstract 3728: A novel, simplified, streamlined workflow for high-throughput whole transcriptome RNA-seq library preparation for a variety of sample types

Abstract RNA sequencing (RNA-seq) has become an invaluable tool in the study of biology, but often requires multiple days to process samples from total RNA to final libraries that can be loaded on to a sequencer. Researchers use RNA-seq to gain insight into whole tumor gene expression, and in combination with other omics data make treatment decisions. In cancer research, time taken to yield sequencing results can be critical for clinical samples. Within oncology research, libraries are often prepared from RNA sourced from formalin-fixed, paraffin-embedded (FFPE) tissues which can be particularly challenging and is not compatible with all library preparation methods. Here, we present a new protocol that allows users to easily generate robust RNA-seq libraries from a variety of sample types in a single day from 25-250 ng of total RNA. Compatible with poly(A) enrichment or ribosomal RNA depletion, this new workflow has reduced preparation time by about 40% compared to current library prep kits without sacrificing quality of libraries or any sequencing metrics, including 5’-3’ coverage, GC bias. Our new method provides equivalent transcript expression in FFPE samples when compared with existing protocols. In addition to master mixed components and reduced incubation times, the reduction in bead cleanup steps significantly reduces hands-on time for library preparation, simplifying and streamlining the process. This new library preparation method is also ideal for processing samples of various inputs with a single condition at every step throughout the protocol, without modifying cycling conditions or dilutions based on input amount. This workflow provides a great advantage in efficiently generating RNA-seq libraries while simultaneously maintaining high quality sequencing results and compatibility with both high- and low-quality RNA such as FFPE. Citation Format: Chelsea Pinegar, Dora Posfai, Gautam Naishadham, Bradley W. Langhorst, Keerthana Krishnan. A novel, simplified, streamlined workflow for high-throughput whole transcriptome RNA-seq library preparation for a variety of sample types. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3728.

PD17-06 WILMS TUMOR: INSIGHTS INTO THE ROLE OF INTEGRINS DRIVING CANCER STEM CELLS SELF-RENEWAL VS. DIFFERENTIATION

You have accessJournal of UrologyCME1 Apr 2023PD17-06 WILMS TUMOR: INSIGHTS INTO THE ROLE OF INTEGRINS DRIVING CANCER STEM CELLS SELF-RENEWAL VS. DIFFERENTIATION Astgik Petrosyan, Valentina Villani, Paola Aguiari, Min Madhi, Roger De Filippo, Gregory Shackleford, Anat Erdreich-Epstein, Stefano Da Sacco, and Laura Perin Astgik PetrosyanAstgik Petrosyan More articles by this author , Valentina VillaniValentina Villani More articles by this author , Paola AguiariPaola Aguiari More articles by this author , Min MadhiMin Madhi More articles by this author , Roger De FilippoRoger De Filippo More articles by this author , Gregory ShacklefordGregory Shackleford More articles by this author , Anat Erdreich-EpsteinAnat Erdreich-Epstein More articles by this author , Stefano Da SaccoStefano Da Sacco More articles by this author , and Laura PerinLaura Perin More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000003272.06AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: Wilms Tumor (WT) is the most common pediatric renal cancer. Growing evidence links WT to aberrant nephrogenesis. While studies highlighted the genetic complexity of WT, little is known about the molecular mechanisms that regulate WT development. Here we report that uncommitted nephrogenic progenitors (NPs) expressing SIX2 and CITED1 (the master regulators of renal development) present characteristics of cancer stem cells (CSCs) and are the ones driving WT. We have also studied the role of integrins in these NPs in regulating WT development. METHODS: WT and human fetal kidney (hFK) samples were histologically analyzed, digested to single-cell suspension, incubated with Smartflare-probe to isolate SIX2+CITED1+ cells, and processed for RNA-seq, single-cell RNA-seq and spatial transcriptomics. Xenografts of WT-NPs and hFK-NPs were generated and tumor formation was assessed. Analyses of mechanisms that regulate self-renewal vs. differentiation were performed in vitro and in vivo. Knockdown with miREs against SIX2 and CITED1 was performed on WT-NPs and processed for RNA-seq. RESULTS: By comparing NPs from different WT subtypes and NPs from hFK we identified that cells expressing SIX2 and CITED1 fulfill CSC criteria, reliably recapitulating WT in transplantation studies. We showed that self-renewal vs. differentiation of SIX2+CITED1+ WT CSCs is regulated by the interplay between integrins ITGB1 and ITGB4. WT transplantation studies show that blocking ITGB1 or ITGB4 leads to higher number of SIX2+CITED1+ cells in the xenografts. Knockdown of SIX2 and CITED1 increased expression of kidney differentiation markers LHX1, WNT7B, PODXL, MECOM, reduced expression of nephrogenic markers MEOX1, TMEM100, EYA1, MAYFB, and increased expression of ITGB1, ITGB4, and LAMA5. CONCLUSIONS: These studies define SIX2+CITED1+ cells as the nephrogenic CSCs of WT, where ITGB1 and ITGB4 interplay may play a role in self-renewal vs. differentiation and serve as a potential target for new strategies to treat WT. Source of Funding: GOFARR Fund © 2023 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 209Issue Supplement 4April 2023Page: e497 Advertisement Copyright & Permissions© 2023 by American Urological Association Education and Research, Inc.MetricsAuthor Information Astgik Petrosyan More articles by this author Valentina Villani More articles by this author Paola Aguiari More articles by this author Min Madhi More articles by this author Roger De Filippo More articles by this author Gregory Shackleford More articles by this author Anat Erdreich-Epstein More articles by this author Stefano Da Sacco More articles by this author Laura Perin More articles by this author Expand All Advertisement PDF downloadLoading ...

Gender-specific dysregulations of nondifferentially expressed biomarkers of metastatic colon cancer

Colon cancer is a common cancer type in both sexes and its mortality rate increases at the metastatic stage. Most studies exclude nondifferentially expressed genes from biomarker analysis of metastatic colon cancers. The motivation of this study is to find the latent associations of the nondifferentially expressed genes with metastatic colon cancers and to evaluate the gender specificity of such associations. This study formulates the expression level prediction of a gene as a regression model trained for primary colon cancers. The difference between a gene’s predicted and original expression levels in a testing sample is defined as its mqTrans value (model-based quantitative measure of transcription regulation), which quantitatively measures the change of the gene’s transcription regulation in this testing sample. We use the mqTrans analysis to detect the messenger RNA (mRNA) genes with nondifferential expression on their original expression levels but differentially expressed mqTrans values between primary and metastatic colon cancers. These genes are referred to as dark biomarkers of metastatic colon cancer. All dark biomarker genes were verified by two transcriptome profiling technologies, RNA-seq and microarray. The mqTrans analysis of a mixed cohort of both sexes could not recover gender-specific dark biomarkers. Most dark biomarkers overlap with long non-coding RNAs (lncRNAs), and these lncRNAs might have contributed their transcripts to calculating the dark biomarkers’ expression levels. Therefore, mqTrans analysis serves as a complementary approach to identify dark biomarkers generally ignored by conventional studies, and it is essential to separate the female and male samples into two analysis experiments. The dataset and mqTrans analysis code are available at https://figshare.com/articles/dataset/22250536.

Inflorescence Trait Diversity and Genotypic Differentiation as Influenced by the Environment in Elymus nutans Griseb. from Qinghai–Tibet Plateau

The alpine forage grass species Elymus nutans Griseb. is widely distributed in the Qinghai–Tibet Plateau and the Himalayas due to its high adaptability. However, it has become threatened by climate warming and excessive grazing. Thus, understanding its genetic and phenotypic information is crucial to aid resource management and conservation efforts. In this study, microsatellite markers were developed based on RNA-seq transcriptome data from E. nutans Griseb. varieties ‘Aba’ and ‘Kangbei’, resulting in the identification of 48,457 SSRs from 304,554 de novo assembled unigenes. Seventeen polymorphic markers, 13 inflorescence phenotypic traits, and seed shattering values were determined for 31 E. nutans accessions collected from eastern Tibet. The molecular markers generated 134 well-amplified bands with a mean Nei’s genetic diversity of 0.31 and a Shannon information index of 0.46. Pairwise genetic similarity ranged from 0.554 to 0.895, with an average of 0.729. Based on the molecular marker data, all accessions were divided into two classes via the unweighted pair-group method with arithmetic mean (UPGMA), the Markov chain Monte Carlo method, and the principal coordinate analysis (PCA) method. We used Tassel analysis to determine 11 loci with a significant relationship to phenotypic traits, and Pearson’s correlation analysis showed that some inflorescence traits were significantly influenced by the environment. Furthermore, we detected strong patterns of isolation by both environment (IBE) and distance (IBD) via Mantel analysis. This study provides valuable insights into the genetic and phenotypic differentiation of E. nutans, informing germplasm resource evaluation and future breeding.

Transcriptional Control of hgcAB by an ArsR-Like Regulator in Pseudodesulfovibrio mercurii ND132.

The hgcAB gene pair encodes mercury (Hg) methylation capability in a diverse group of microorganisms, but its evolution and transcriptional regulation remain unknown. Working from the possibility that the evolutionary function of HgcAB may not be Hg methylation, we test a possible link to arsenic resistance. Using model Hg methylator Pseudodesulfovibrio mercurii ND132, we evaluated transcriptional control of hgcAB by a putative ArsR encoded upstream and cotranscribed with hgcAB. This regulator shares homology with ArsR repressors of arsenic resistance and S-adenosylhomocysteine (SAH)-responsive regulators of methionine biosynthesis but is distinct from other ArsR/SahR proteins in P. mercurii. Using quantitative PCR (qPCR) and RNA sequencing (RNA-seq) transcriptome analyses, we confirmed this ArsR regulates hgcAB transcription and is responsive to arsenic and SAH. Additionally, RNA-seq indicated a possible link between hgcAB activity and arsenic transformations, with significant upregulation of other ArsR-regulated arsenic resistance operons alongside hgcAB. Interestingly, wild-type ND132 was less sensitive to As(V) (but not As(III)) than an hgcAB knockout strain, supporting the idea that hgcAB may be linked to arsenic resistance. Arsenic significantly impacted rates of Hg methylation by ND132; however, responses varied with culture conditions. Differences in growth and metabolic activity did not account for arsenic impacts on methylation. While arsenic significantly increased hgcAB expression, hgcAB gene and transcript abundance was not a good predictor of Hg methylation rates. Taken together, these results support the idea that Hg and As cycling are linked in P. mercurii ND132. Our results may hold clues to the evolution of hgcAB and the controls on Hg methylation in nature. IMPORTANCE This work reveals a link between microbial mercury methylation and arsenic resistance and may hold clues to the evolution of mercury methylation genes (hgcAB). Microbes with hgcAB produce methylmercury, a strong neurotoxin that readily accumulates in the food web. This study addresses a critical gap in our understanding about the environmental factors that control hgcAB expression. We show that hgcAB expression is controlled by an ArsR-like regulator responsive to both arsenic and S-adenosylhomocysteine in our model organism, Pseudodesulfovibrio mercurii ND132. Exposure to arsenic also significantly impacted Pseudodesulfovibrio mercurii ND132 mercury methylation rates. However, expression of hgcAB was not always a good predictor of Hg methylation rates, highlighting the roles of Hg bioavailability and other biochemical mechanisms in methylmercury production. This study improves our understanding of the controls on hgcAB expression, which is needed to better predict environmental methylmercury production.

The translational landscape of human vascular smooth muscle cells identifies novel short open reading frame-encoded peptide regulators for phenotype alteration.

The plasticity of vascular smooth muscle cells (VSMCs) enables them to alter phenotypes under various physiological and pathological stimuli. The alteration of VSMC phenotype is a key step in vascular diseases, including atherosclerosis. Although the transcriptome shift during VSMC phenotype alteration has been intensively investigated, uncovering multiple key regulatory signalling pathways, the translatome dynamics in this cellular process, remain largely unknown. Here, we explored the genome-wide regulation at the translational level of human VSMCs during phenotype alteration. We generated nucleotide-resolution translatome and transcriptome data from human VSMCs undergoing phenotype alteration. Deep sequencing of ribosome-protected fragments (Ribo-seq) revealed alterations in protein synthesis independent of changes in messenger ribonucleicacid levels. Increased translational efficiency of many translational machinery components, including ribosomal proteins, eukaryotic translation elongation factors and initiation factors were observed during the phenotype alteration of VSMCs. In addition, hundreds of candidates for short open reading frame-encoded polypeptides (SEPs), a class of peptides containing 200 amino acids or less, were identified in a combined analysis of translatome and transcriptome data with a high positive rate in validating their coding capability. Three evolutionarily conserved SEPs were further detected endogenously by customized antibodies and suggested to participate in the pathogenesis of atherosclerosis by analysing the transcriptome and single cell RNA-seq data from patient atherosclerotic artery samples. Gain- and loss-of-function studies in human VSMCs and genetically engineered mice showed that these SEPs modulate the alteration of VSMC phenotype through different signalling pathways, including the mitogen-activated protein kinase pathway and p53 pathway. Our study indicates that an increase in the capacity of translation, which is attributable to an increased quantity of translational machinery components, mainly controls alterations of VSMC phenotype at the level of translational regulation. In addition, SEPs could function as important regulators in the phenotype alteration of human VSMCs.

Full-length transcriptome combined with RNA sequence analysis of Fraxinus chinensis.

The dry root or stem bark of Fraxinus chinensis is a famous herb Qin Pi which is known for its anti-inflammatory, analgesic, anti-tumor, liver protective and diuretic pharmacological effects, the fundamental chemical components are coumarin, phenylethanol glycosides and flavonoids. However, it is difficult to clarify the secondary metabolite synthesis pathway and key genes involved in the pathway because of lack genome information of Fraxinus chinensis. To generate a complete transcriptome of Fraxinus chinensis and to clarify the differentially expressed genes (DEGs) in leaves and stem barks. In this study, full-length transcriptome analysis and RNA-Seq were combined to characterize Fraxinus chinensis transcriptome. A total of 69,145 transcripts were acquired and regarded as reference transcriptome, 67,441 transcripts (97.47%) were annotated to NCBI non-redundant protein (Nr), SwissProt, the Kyoto Encyclopedia of Genes and Genomes (KEGG) and eukaryotic orthologous groups (KOG) databases. A total of 18,917 isoforms were annotated to KEGG database and classified to 138 biological pathways. In total, 10,822 simple sequence repeat (SSRs) and 11,319 resistance (R) gene were classified to 18 types, and 3947 transcription factors (TFs) were identified in full-length transcriptome analysis. Additionally, 15,095 DEGs were detected by RNA-seq in leaves and barks, including 4696 significantly up-regulated and 10,399 significantly down-regulated genes. And 254 transcripts were annotated into phenylpropane metabolism pathway containing 86 DEGs and ten of these enzyme genes were verified by qRT-PCR. It laid the foundation for further exploration of the biosynthetic pathway of phenylpropanoids and related key enzyme genes.