title: Differences in TCR repertoire and T cell activation underlie the divergent outcomes of anti-tumor immune responses in tumor-eradicating versus tumor-progressing hosts

city: Aurora

first: Jing

middle: Hong

last: Wang

state: Colorado

address: 12800 East 19th Ave, Mail stop 8333, RC1 North, Room 9400C

department: Immunology and Microbiology

institute: University of Colorado at Anschutz

summary:
Background: Anti-tumor immunity is highly heterogeneous between individuals; however, underlying mechanisms remain elusive, despite their potential to improve personalized cancer immunotherapy.  Head and neck squamous cell carcinomas (HNSCCs) vary significantly in immune infiltration and therapeutic responses between patients, demanding a mouse model with appropriate heterogeneity to investigate mechanistic differences.
Methods: We developed a unique HNSCC mouse model to investigate underlying mechanisms of heterogeneous anti-tumor immunity.  This model system may provide a better control for tumor-intrinsic and host-genetic variables, thereby uncovering the contribution of the adaptive immunity to tumor eradication.  We employed single-cell T-cell receptor (TCR) sequencing coupled with single-cell RNA sequencing to identify the difference in TCR repertoire of CD8 tumor infiltrating lymphocytes (TILs) and the unique activation states linked with different TCR clonotypes.
Results: We discovered that genetically identical wild-type recipient mice responded heterogeneously to the same SCC tumors orthotopically transplanted into the buccal mucosa.  While tumors initially grew in 100% of recipients and most developed aggressive tumors, ~25% of recipients reproducibly eradicated tumors without intervention.  Heterogeneous anti-tumor responses were dependent on CD8 T cells.  Consistently, CD8 TILs in regressing tumors were significantly increased and more activated.  Single-cell TCR-sequencing revealed that CD8 TILs from both growing and regressing tumors displayed evidence of clonal expansion compared with splenic controls.  However, top TCR clonotypes and TCR specificity groups appear to be mutually exclusive between regressing and growing TILs.  Furthermore, many TCRa/TCRb sequences only occur in one recipient. By coupling single-cell transcriptomic analysis with unique TCR clonotypes, we found that top TCR clonotypes clustered in distinct activation states in regressing vs. growing TILs.  Intriguingly, the few TCR clonotypes shared between regressors and progressors differed greatly in their activation states, suggesting a more dominant influence from tumor microenvironment than TCR itself on T cell activation status.
Conclusions: We reveal that intrinsic differences in the TCR repertoire of TILs and their different transcriptional trajectories may underlie the heterogeneous anti-tumor immune responses in different hosts. We suggest that anti-tumor immune responses are highly individualized and different hosts employ different TCR specificities against the same tumors, which may have important implications for developing personalized cancer immunotherapy.

overall_design:
(1) We present sequencing data of mouse tumor-infiltrating T cells (TIL) and splenic T cells sequenced by single-cell RNA sequencing in a mouse model of squamous cell carcinoma, A223. Cells from 17 samples (9 expression and 8 VDJ) were sequenced using the 10x genomics platform.
(2) We present sequencing data of the mouse tumor model of squamous cell carcinoma, A223. Samples include whole-exome sequencing and RNA-sequencing of A223 tumor cells grown in vitro.

first: Rachel

last: Woolaver


title: Serine biosynthesis is a metabolic vulnerability in FLT3-ITD-driven acute myeloid leukaemia

status: Public on Jan 13 2021

city: Boston

first: Stefan

last: Bjelosevic

state: MA

address: 450 Brookline Ave

department: Department of Pediatric Oncology

country: USA

institute: Dana-Farber Cancer Institute

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

summary: This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Stromal Dlk1 promotes epithelial proliferation and inhibits epithelial differentiation during the small intestine development

status: Public on Jan 14 2021

city: Adelaide

first: Susan

last: Woods

state: Select State

address: Level 5 South, SAHMRI building, North Terrace

department: School of Medicine

country: Australia

institute: The University of Adelaide

summary:
Background: Mesenchyme offers microenvironment for epithelial maturation during development of the small intestine. Molecular signature of immature mesenchyme has not yet been elucidated. DLK1 is known as a Notch ligand and has been reported to be highly expressed during embryogenesis. Although it has been investigated in other branching structure organs such as lung and salivary gland, DLK1’s role in intestinal development remains unknown.
Methods: Intestinal mesenchymal cells (IMCs) were collected from small intestines of embryonic day 14.5 (E14.5) and adult mice, respectively. Intestinal organoids collected from embryonic small intestines were co-cultured with IMCs. The effect of embryonic and adult IMCs on epithelial morphology and differentiation was compared using qPCR and immunocytochemistry. Organoid sustainability was compared to assess the mesenchymal effect on stemness. A global mRNA sequence analysis of differentially expressed transcripts in embryonic and adult IMCs was performed. Given DLK1 was among the morphogen genes that were differentially expressed, DLK1 expression was manipulated with recombinant protein or siRNA and its effect on organoids was investigated. The histology of DLK1 knock out mice and wild type littermates were compared with proliferation marker, Ki67 and secretory lineage staining.
Results: Embryonic IMCs induced cystic change of organoids and reduced budding structure when compared with adult IMCs. Secretory lineage differentiation of epithelium was found to be reduced and secondary organoids formation was increased when co-cultured with embryonic IMCs. 23 differentially expressed morphogen genes were identified with GSEA analysis. Genes expressed in cell membranes and extracellular space were filtered and DLK1 was identified as a key mesenchymal gene for morphogenesis. Immunohistochemistry showed that DLK1 was expressed exclusively in the stroma at the top of emerging villi and co-localized with PDGFRa in E14.5 small intestine. DLK1 expression in mesenchyme decreased after birth and shifted to epithelium in adulthood. Addition of recombinant DLK1 to adult IMCs inhibited organoid differentiation, whereas siDLK1 in embryonic IMCs increased epithelial differentiation to secretory lineage cells. DLK1 knock out mice showed restricted distribution of Ki67 positive cells in the base of villi compared with wild type littermate embryos. Secretory lineage cells were increased in DLK1 knock out mice at E19.5.
Conclusion: DLK1 is expressed in the mesenchyme of small intestines during embryogenesis and decreases with age. Our data suggest stromal DLK1 promotes epithelial proliferation and suppresses secretory lineage differentiation.

overall_design: Three of Intestinal mesenchymal cells (IMCs) were collected from small intestines of embryonic day 14.5 (E14.5) and adult mice, respectively. The primary culture were used for RNA extraction at passage number 2-3.

first: Mari

last: Ichinose

first: Nobumi

last: Suzuki

first: Tongtong

first: Yoku

last: Hayakawa

first: Patricia

last: García-Gallastegui

first: Eva

middle: M

last: Monsalve

first: Steve

last: Bauer

first: Jorge

last: Laborda

first: J

middle: J

last: García-Ramírez

first: Gaskon

last: Ibarretxe

middle: L

first: Daniel

last: Worthley


title: Identification of miRNAs during colorectal cancer progression and metastasis using a preclinical mouse model during LDM topotecan chemotherapy

city: Regensburg

first: Gerhard

last: Lehmann

address: Universitaetsstrasse 31

department: Biochemistry 1

country: Germany

institute: University of Regensburg

type: Non-coding RNA profiling by high throughput sequencing

summary: To find candidate circRNAs and to unravel their molecular functions during colorectal cancer progression and during LDM topotecan chemotherapy, we utilized a xenograft mouse model based on the HT29.hCG.Luc colorectal cancer cell line (referred to as HT29) implanted into SCID mice. HT29 cells were injected into the spleen and primary tumors developed. Three mice served as control group while two mice served as LDM topotecan treated group. After another 4-6 weeks, liver metastasis can be detected and resected for further investigation. For a global view on miRNA changes, we performed miRNA-Seq from HT29 cells, primary tumors and liver metastases from control mice (C-PT and C-LM) and liver metastases from treated mice (T-LM).

overall_design: 1000 ng of total RNA from HT29 cells, primary tumors (PT) and liver metastases (LM) was used for preparation of miRNA library. 3 mice were used for collecting RNA from C-PT and C-LM; 2 LDM topotecan treated mice were used for collecting RNA from T-LM; and 3 replicates were used for collecting RNA from HT29 cells.

first: Hung

last: Ho-Xuan

first: Norbert

last: Eichner

first: Christina

last: Hackl

first: Gunter

last: Meister


title: Identification of circular RNA and miRNAs during colorectal cancer progression and metastasis


title: STIM1 Mediates Calcium-dependent Epigenetic Reprogramming in Pancreatic Cancer

city: Rochester

first: Steven

middle: A

last: Johnsen

state: MN

address: 200 First Street SW

department: Gastroenterology Research

institute: Mayo Clinic


title: STIM1 Mediates Calcium-dependent Epigenetic Reprogramming in Pancreatic Cancer [ChIPseq_Par_GemR]

summary: We characterized Gemcitabine resistant pancreatic cancer tumors and show that the co-amplification of RRM1 and STIM1 confers novel and independent properties to gemcitabine resistant cells. The upregulation of RRM1 drives gemcitabine resistance, while the amplification of STIM1 leads to increased cytosolic calcium upon stress, eliciting ER stress resistance and NFAT activation.

overall_design: We performed H3K27ac ChIPseq in gemcitabine resistant L3.6pl (GemR) cells.

first: Feda

middle: H

last: Hamdan


title: Next Generation Sequencing Facilitates Quantitative Analysis of prostate cancer cell line LNCaP Transcriptomes

city: Taipei

first: Yen-Nien

last: Liu

state: Please Select

address: No. 250, Wu-Hsing Street

country: Taiwan

institute: Taipei Medical University

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived NGF-overexpressed LNCaP cells transcriptome profiling (RNA-seq) to microarray methods and to evaluate NGF signature for optimal high-throughput data analysis.
Method: LNCaP/EV and LNCaP/NGF cells were cultured in RPMI 1640 medium supplemented with 10% FBS. An RNeasy Midi Kit (Qiagen, Redwood City, CA, USA) was used for total RNA isolation. The cDNA library was prepared by KAPA mRNA HyperPrep Kits (Roche) and sequenced using the NovaSeqTM 6000 sequencing system (Illumina, San Diego, CA, USA) in 300~400-bp paired-end reads.
Results: Here we show that an androgen-deprivation therapy (ADT)-stimulated transcription factor, ZBTB46, upregulated NGF via ZBTB46 mediated-transcriptional activation of NGF. Our results reveal a role of the NGF in the development of NEPC that is linked to ZBTB46 upregulation.
Conclusion: Our study provides evidence that the ZBTB46-NGF axis has potential to be considered as a therapeutic target to impair NEPC progression.

overall_design: mRNA profile of prostate cancer cell line LNCaP cells with NGF cDNA expression compared to clls with NGF cDNA overexpression.


title: Microbiota alteration upon blueberry consumption

city: Little Rock

first: Umesh

middle: D

last: Wankhade

state: Arkansas

department: Pediatrics

institute: University of Arkansas Medical Sciences

summary: We demonstrate that blueberry supplementation led to global changes in the gut microbiome, which could possibly contribute to physiological changes in mice

overall_design: Blueberry supplemented diet fed to different groups of mice; WT and GPR109 Knockout; Male and female; blueberry-supplemented diet and control

first: Jin-Ran

last: Chen


title: Mutation of the cell cycle regulator p27Kip1 drives pseudohypoxic pheochromocytoma development

city: Neuherberg

first: Natalia

middle: S.

last: Pellegata

address: Ingolstädter Landstr.1

institute: HMGU

summary: Background: Pseudohypoxic tumors activate pro-oncogenic pathways typically associated with severe hypoxia even when sufficient oxygen is present, leading to highly aggressive tumors. Prime examples are pseudohypoxic pheochromocytomas and paragangliomas (p-PPGLs), neuroendendocrine tumors currently orphan of effective therapy. Previous attempts to generate mouse models for p-PPGLs all failed. Here, we describe that the rat MENX line, carrying a Cdkn1b (p27) frameshift-mutation, spontaneously develops pseudohypoxic pheochromocytoma (p-PCC). Methods: We compared rat p-PCCs with their cognate human tumors at different levels: histology, immunohistochemistry, catecholamine profiling, electron microscopy, transcriptome and metabolome. Vessels architecture and angiogenic potential of PCCs was analyzed by light-sheet fluorescence microscopy ex vivo and multi-spectral optoacoustic tomography (MSOT) in vivo. Results: Analysis of tissues at various stages, from hyperplasia to advanced grades, allowed us to correlate tumor characteristics with progression. Pathological changes affecting mitochrondrial ultrastructure where present already in hyperplasias. Rat PCCs secreted high levels of norepinephrine and dopamine. Transcriptomic and metabolomic analysis revealed changes in oxidative phosphorylation that aggravated over time, leading to an accumulation of the oncometabolite 2-hydroxyglutarate, and to hypermethylation, evident by loss of the epigenetic mark 5-hmC. While rat PCC xenografts showed high oxygenation, induced by massive neoangiogenesis, rat PCC transcriptomes possessed a pseudohypoxic signature of high Hif2a, Vegfa, and low Pnmt expression, thereby clustering with human p-PPGL. Conclusion: Endogenous rat PCCs recapitulate key phenotypic features of human p-PPGLs. Thus, MENX rats emerge as the best available animal model of these aggressive tumors. Our study provides evidence of a link between cell cycle dysregulation and pseudohypoxia.

overall_design: RNA-seq analysis of rat Pheochromocytoma (PCC), hyperplasia (HYP) and normal adrenal (NA),

middle: S

first: Hermine

last: Mohr


title: Whole transcriptome analysis of the antidepressant baicalin in chronic unpredictable mild stress mice

city: Zhengzhou

first: Shuaifei

last: Lu

state: Henan

address: Jinshui East Road 156

country: China

institute: Henan University of Chinese Medicine

summary: We identified 371 differentially genes including 216 up-regulated and 155 down-regulated genes by calculating the gene FPKM in each sample. The clustering analysis  showed that differentially genes were separated into two distinguishing branches.  Gene ontology analysis suggested that differentially genes mainly involved regulation of transcription (DNA-templated), transcription (DNA-templated), and protein phosphorylation in biological process, DNA binding, ATP binding and transferase activity in molecular function, and synapse, postsynaptic density, postsynaptic membrane in cellular component. Among these results indicated that the effect of baicalin may involve synapse function and ATP regulation.

overall_design: C57BL/6N mice was exposed to chronic unpredictable mild stress, and divided to CUMS group that was given saline, baicalin group that was treatment with  baicalin (20 mg/kg).

first: Lei-lei

last: Zhu

first: Yu-cheng

last: Li


title: Nrf2 overexpression increases risk of high tumor mutation burden in acute myeloid leukemia

city: Guiyang

first: Ping

address: 28 Guiyi Street, Yunyan District

institute: Affiliated Hospital of Guizhou Medical University

summary: We evaluated differentially expressed genes in Nrf2-High/Low group and found that high Nrf2 expression significantly inhibited the DNA MMR pathway in AML.

overall_design: AML patient specimens were divided into two groups either expressing high or low levels of Nrf2 based on qRT-PCR. In order to further understand the molecular mechanism of Nrf2 on the tumor mutation burden rate in AML, We examined transcriptome sequencing in the above patients, removed the unqualified samples, and analyzed the difference of gene expression.

first: Jishi

last: Wang

first: Dan

last: Ma


title: Genome-wide analysis of Chlamydia trachomatis-infected cells

city: Guangzhou

first: Emmanuel

middle: E

last: Dzakah

state: Guangdong

address: Lujing Lu, Yuexiu District

institute: Dermatology Hospital

summary: Chlamydia trachomatis is the most common sexually transmitted infection and the bacterial agent of trachoma globally. C. trachomatis undergoes a biphasic developmental cycle involving an infectious elementary body and a replicative reticulate body. Little is currently known about the expression of host cell mRNAs, lncRNAs, and miRNAs at different stages of C. trachomatis development.   Here, we performed RNA-seq and miR-seq on HeLa cells infected with C. trachomatis serovar E at 20 hpi and 44 hpi with or without IFN-γ treatment. Our study identified and validated differentially expressed host cell mRNAs, lncRNAs, and miRNAs during infection. Infection at 20 hpi showed the most differential upregulation of both coding and non-coding genes while infection at 44 hpi in the presence of IFN-γ resulted in a dramatic downregulation of a large proportion of genes. Using RT-qPCR, we validated the top 5 stage-specific upregulated mRNAs and miRNAs. One of the commonly expressed miRNAs at all three stages, miR-193b-5p, showed significant expression in clinical serum samples of C. trachomatis-infected patients as compared to sera from healthy controls and HIV-1-infected patients. Furthermore, at 20 hpi we observed significant upregulation of antigen processing and presentation, and T helper cell differentiation pathways whereas T cell receptor, mTOR, and Rap1 pathways were modulated at 44 hpi. Treatment with IFN-γ at 44 hpi showed the regulation of cytokine-cytokine receptor interaction, FoxO signaling, and Ras signaling pathways.   Our study documents a role for the stage-specific transcriptional manipulation of the host cell genome and important signaling pathways that are necessary for the survival of pathogen and could serve as potential biomarkers in the diagnosis and management of the disease.

overall_design: HeLa cells were infected with C. trachomatis and the cells were harvested at 20hr post-infection (hpi) and  44 hpi. Uninfected HeLa cells were used as negative controls (NC). To allow C. trachomatis transformation into the persistent aberrent reticulate body (ARB) stage, cells were treeted with 50 units of interferon-gamma for 44 hpi.  Cells were treated with 50 units of interferon-gamma for 44hr were used as negative control. Cells were harvested at the indicated time followed by RNA extraction. Total RNAs from all samples were used for RNA-seq and miR-sequencing at the Beijing Genome Institute (China).

first: Liping

last: Huang

first: Raohua

last: Xue

first: Shuai

last: Wei

first: Xiaolin

first: Hongliang

first: Jingwei

last: Shui

first: Foster

last: Kyei

first: Heping

last: Zheng

first: Bing

last: Yang

first: Shixing

last: Tang


title: Inorganic phosphate solubilization by rhizosphere bacterium Paenibacillus sonchi genomovar Riograndensis SBR5: gene expression and physiological functions

city: Trondheim

first: Luciana

last: Fernandes de Brito

address: Kjemi 3, 3.237, Gløshaugen, Sem Sælandsvei 6/8

department: Department of Biotechnology and food science

country: Norway

institute: Norwegian University of Science and Technology

summary: Due to the importance of phosphorus (P) in agriculture, crop inoculation with phosphate solubilizing bacteria (PSB) is a relevant subject of study. Paenibacillus sonchi genomovar Riograndensis SBR5 is a promising candidate for crop inoculation as it can fix nitrogen and excrete ammonium in a remarkably high rate. However, its trait of phosphate solubilization (PS) has not yet been studied in detail. Here, differential gene expression and functional analyses were performed in order to characterize PS in this bacterium. SBR5 was cultivated with two distinct P sources: NaH2PO4 as soluble phosphate source (SPi) and hydroxyapatite as insoluble phosphate source (IPi). Total RNA of SBR5 cultivated in those two conditions was isolated and sequenced and bacterial growth and product formation were monitored. In the IPi medium, the expression of 68 genes was upregulated, while 100 genes were downregulated. Among those, genes involved in carbon metabolism, including those coding for subunits of 2-oxoglutarate dehydrogenase were identified. Quantitation of organic acids showed that the production of tricarboxylic acid cycle-derived organic acids was reduced in IPi condition, while acetate and gluconate were overproduced. Increased concentrations of proline, trehalose, and glycine betaine revealed active osmoprotection during growth in IPi. The cultivation with hydroxyapatite also caused the reduction in the motility of SBR5 cells as a response to Pi depletion in the beginning of its growth. SBR5 was able to solubilize hydroxyapatite, which suggests that this organism is a promising PSB. Our findings are the initial step in the elucidation of the PS process in P. sonchi SBR5 and will be a valuable groundwork for further studies of this organism as a plant growth promoting rhizobacterium.

overall_design: Differential gene expression of SBR5 cultivated with two distinct phosphate sources: NaH2PO4 as soluble phosphate source (SPi) and hydroxyapatite as insoluble phosphate source (IPi)

first: Marina

last: Gil Lopez

first: Lucas

last: Straube

first: Luciane

last: Passaglia

first: Volker

middle: F

last: Wendisch


title: Transferrin improved the generation of cardiomyocyte from human pluripotent stem cells for myocardial infarction repair

city: Beijing

first: Jie

address: 30 Shuangqing Rd, Haidian District, Beijing, China

institute: Tsinghua University

summary: Human pluripotent stem cell (hPSC)-derived cardiomyocytes (CMs) hold great promise for the repair of the injured heart, but optimal cell production in a fully chemically defined and cost-effective system is essential for the efficacy and safety of cell transplantation therapies. In this study, we provided a simple and efficient strategy for cardiac differentiation from hPSCs and performed functional evaluation in a rat model of myocardial infarction. Using a chemically defined medium including four components, recombinant human albumin, ascorbic acid, human transferrin, and RPMI 1640, we developed a manageable and cost-effective protocol for robust generation of CMs from hPSCs. Interestingly, the addition of transferrin helped hPSCs to transit from TeSR-E8 medium to the simple cardiac differentiation medium and successfully initiated mesoderm differentiation without significant cell death. The CM generation efficiency was up to 85% based on cTnT expression. We performed transcriptome profiling from differentiation day 0 to 35, and characterized interesting dynamic change of cardiac genes. CMs derived from transferrin supplemented simple medium have similar transcriptome and the maturation level compared to cardiomyocytes generated in B27 minus insulin medium as well as their in vivo counterparts. Importantly, after transplantation, hPSC derived CMs survived in the infarcted rat heart, significantly improved the physiological function and reduced fibrosis. Our study offers an easy-to-use and cost-effective method for cardiac differentiation and facilitates the translational application of hPSC-derived CMs for heart repair.

overall_design: RNA-seq of 7 time points during in vitro cardiomyocyte differentiation using a transferrin-supported chemically defined medium

first: Fengzhi

last: Zhang

first: Hui

last: Qiu

first: Changyong


title: Next Generation Sequencing Profiles Transcriptomes of Control and shDANCR HCT116 Cell Lines

first: Xiaomin

last: Zhong

address: 74 Zhongshan Road 2nd

institute: Sun Yat-Sen University

summary:
Purpose: The goal  of this study is to compare Next Generation Sequencing-derived transcriptome profiling (RNA-seq) of a negative control cell line to two independent shDANCR cell lines.
Methods: mRNA profiles of HCT116 colorectal cancer cell lines transfected with lentiviruses containing a negative control vector and two independent shRNA vectors for DANCR knockdown were generated by deep sequencing using Illumina HiSeq2000. The sequence reads that passed quality filters were analyzed at the transcript level with the method of HISAT2, and StringTie followed by FPKM calculation.
Results: Using the described data analysis workflow, we mapped about 40 million sequence reads per sample to the human genome (GRCh38) and identified about 130,000 transcripts (transcribed from about 40,000 genes) per sample with StringTie. Approximately 2.5% of the genes showed differential expression between the Control and shDANCR cell lines, with a fold change ≥1.5 and p value <0.05.
Conclusions: Our study represents a detailed analysis of gene expression changes affected by DANCR knockdown in colorectal cancer cell line HCT116.

overall_design: mRNA profiles of  HCT116 Colorectal Cancer cell lines with a negative control vector and two independent shDANCR vectors were generated by deep sequencing using Illumina HiSeq2000.

first: Minmin

last: Xiong


title: RNA-seq analysis of HCT116, HCP-1 and DLD-1 cells after IOX1 treatment

city: Richmond

first: Jiong

last: Li

state: Virginia

address: 800 E Leigh Street, suite 212

institute: VCU

summary: In order to examine how IOX1 affects the global Wnt target gene transcriptome in colorectal cancer cells, we performed RNA-sequencing  in HCT116, DLD-1 and HCP-1 cells treated with IOX1. IOX1 led to global inhibition of Wnt target transcription in colorectal cancer cells.

overall_design: Examination of RNA-seq of colorectal cancer cells treated with IOX1.


title: TCTP participate in hepatic metabolism with regulate the gene expression involved in insulin resistance

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: The translationally controlled tumor protein (TCTP) has various cellular functions and molecular interactions, many related to its growth promoting and antiapoptotic properties. Recently, TCTP highly increased expression in high-fat diet-fed mice with insulin-resistant states. Despite TCTP is a multifunction protein, but its role in liver metabolism is still unknown. Here, we investigated the function and mechanism of TCTP in HepG2 cells. Knock-down the TCTP regulated 287 differentially expressed genes and these genes are highly associated with the cellular apoptosis and stress, NF-kB, Glycolysis/Gluconeogenesis, insulin resistance. TCTP deletion selectively downregulated the expression of PCK1 and G6PC in glucose metabolism. Furthermore, TCTP regulated the alternative splicing of genes enriched in phospholipid biosynthetic process, and glycerophospholipid metabolism. Our results implied that TCTP regulates liver cell transcriptome at both the transcriptional and alternative splicing levels. The TCTP regulatory network predicts the biological functions of TCTP in glycometabolism and lipid metabolism, which may be associated with liver metabolism and induces fatty liver disease through enhanced insulin resistant signaling.

overall_design: transcrptional analysis of TCTP knock-down and control in HepG2 cells

first: Kun

last: Dong


title: Intronic and intergenic inverted repeats form dsRNA that activate RNase L but escape detection from the IFN system

city: Princeton

first: Alexei

last: Korennykh

state: NJ

address: Washington Rd

department: Molecular Biology

institute: Princeton University

summary: Ribozero RNAseq of Control vs 23N Randomer treated A549 cells show intron and intergenic transcription from gene start/stop regions

overall_design: Ribozero RNAseq

first: Alisha

last: Chitrakar

first: Kristina

last: Solorio


title: A Betula luminifera transcriptome and analysis of shoot and root specific phosphate deficiency induced transcriptional and post transcriptional responses (RNA-Seq)

city: beijing

first: junhong

last: zhang

address: Xiangshan Road

institute: Chinese Academy of Forestry

summary: microRNAs (miRNAs) play important roles in responses to abiotic stresses, including nutrition stress, by regulating target gene expression. Phosphate (Pi) is often lacking in natural and agro-climatic environments, and plants have developed strategies to cope with low Pi (LP) availability. However, the miRNA-mediated regulation of these adaptive responses and their underlying coordinating signals are still poorly understood in forestry trees such as Betula luminifera. Four small RNA (sRNA) libraries, a mixed degradome cDNA library, and four transcriptomic libraries of B. luminifera roots and shoots treated under LP and normal conditions (CK) were constructed and sequenced using next-generation deep sequencing. sRNA sequencing analyses indicated that 66 and 60 miRNAs were differentially expressed in roots and shoots, respectively, under LP conditions. A total of 109 and 112 miRNA–target pairs were further validated in the roots and shoots, respectively, using degradome sequencing, including several novel target genes that were cleaved by isomiRNAs with lengths of 18 or 19 nucleotides, which were only differentially expressed in roots. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of differential miRNA targets indicated that the “ascorbate and aldarate metabolism” pathway responded to LP, and “circadian rhythm – plant” was specifically enriched in shoots. A comprehensive B. luminifera transcriptome derived from its roots and shoots was constructed, and a total of 76,899 unigenes were generated. A comparison of transcriptome identified 8,095 and 5,584 differentially expressed genes in roots and shoots, respectively, under LP conditions. Integrated analysis uncovered 14 and 16 miRNA–target pairs that showed negatively correlated expression profiles in roots and shoots, respectively. Moreover, a putative model of miRNA–target interaction involved in plant responses to LP stress is proposed. These results suggest that comprehensive analyses of sRNAs, degradome, and transcriptome provide a useful platform for investigating LP stress in B. luminifera, and may provide new insights into the genetic engineering of high use efficiency of Pi in forestry trees.

overall_design: Four transcriptomic libraries of B. luminifera roots and shoots treated under LP and normal conditions (CK) were constructed and sequenced using next-generation deep sequencing.

first: Junhong

first: Zaikang

last: Tong


title: A Betula luminifera transcriptome and analysis of shoot and root specific phosphate deficiency induced transcriptional and post transcriptional responses (miRNA)

overall_design: Four sRNA libraries of B. luminifera roots and shoots treated under LP and normal conditions (CK) were constructed and sequenced using next-generation deep sequencing.


title: Cell of Origin of Malignant Mesothelioma dictates the tumor subtype

city: Amsterdam

first: Oscar

last: Krijgsman

state: Outside the US or Canada

address: Plesmanlaan 121

department: Molecular Oncology and Immunology

country: Netherlands

institute: Netherlands Cancer Institute

summary: Malignant Mesothelioma (MM) is one of the most lethal human malignancies of the thoracic cavity. We have determined the cell of origin of these tumors by inactivating Nf2 and Trp53 in Cdkn2a-deficient mesothelial cells both in vitro and in vivo. Cloned, in vitro switched cell lines showed distinct protein marker profiles that upon grafting in recipient mice, gave rise to epithelial, sarcomatoid or biphasic MM. We show that corresponding cell types are present in the mesothelial lining, each capable to serve as a cell of origin of one of the distinct MM subtypes of which the RNA expression profile aligns with corresponding human samples. Therefore, the specific target cell is a critical factor in dictating the tumor subtype of MM.

overall_design: Human mesothelioma cells grown in immune deficiemt mouse

first: Hilda

middle: I

last: de Vries

first: Ji-Ying

last: Song

first: Rajith

last: Bhaskaran

first: Daniel

last: Peeper

first: Anton

last: Berns


title: DNA methylation profiling of SMARCB1 reconstitution in malignant rhabdoid tumor organoids

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

institute: DKFZ

type: Methylation profiling by genome tiling array

summary: We have generated DNA methylation profiles for patient-derived malignant rhabdoid tumor organoids and re-expressed SMARCB1 to assess SMARCB1-dependent changes in DNA methylation

overall_design: 6 samples were profiled on IlluminaHumanMethylation850k arrays: 3 patient-derived malignant rhabdoid tumor organoids with and without SMARCB1

first: Lars

last: Custers

first: Jarno

last: Drost

first: Marcel

last: Kool


title: High-throughput sequencing of extracellular vesicles from human dermal papilla cells

first: Yuxin

last: Chen

address: Nanfang Dadao Street, Baiyun district

institute: Nanfang Hospital of Southern Medical University

summary: The use of dermal papilla cells for hair follicle (HF) regeneration is long accepted much attention. However, cultured dermal papilla cells tend to lose the hair-inducible capability during passaging, which restricts its application. Increasing evidences indicate that dermal papilla cells exert their regulatory function of HF growth mainly through their unique paracrine properties, opening up a way to exosome therapies.This study aimed to explore the effects of exosomes from high and low-passaged human scalp follicle dermal papilla cells (DP-Exos) on hair follicle stem cells (HFSCs) activation and hair growth, and to investigate the underline mechanism. DP-Exos were isolated by ultracentrifugation and cultured with human scalp follicles and HFSCs. The hair elongation and cell proliferation was assessed. Quantitative real-time PCR (qRT-PCR) and Western-blot were performed to detect the expression levels of a class of miRNAs and proteins which have positive roles in regulating hair growth and HFSCs proliferation. High throughput miRNA sequencing of miRNAs in high (P8) and low-passaged (P3) DP-Exos was performed, and the utmost miRNA and its target gene was identified via bioinformatics analysis.

overall_design: DP-Exos were isolated by ultracentrifugation from dermal papilla cells. High throughput miRNA sequencing of miRNAs in high (P8) and low-passaged (P3) DP-Exos was performed.

first: Junfei

last: Huang


title: In vivo organization of bacterial transcription initiation complexes at a genome-scale [RNA-seq]

city: Daejeon

first: Byung-Kwan

last: Cho

address: 291 Daehak-ro

country: South Korea

institute: KAIST

summary: RNA polymerase (RNAP) is essential for the transcription of genetic information encoded in genomes in all three domains of life. To determine the precise organization of bacterial transcription initiation complexes (TIC) in vivo, we exploited high-throughput sequencing to the DNA obtained from exonuclease-treated immunoprecipitates of the TIC. It reveals that sigma (σ) factor is mostly engaged in RNAP holoenzyme up to 13-14 nucleotides from transcription start site during abortive initiation.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Directional RNA-seq was generated  in duplicates by using Illumina MiSeq

first: Suhyung

first: Yoo-Bok

first: Eun-Ju

last: Lee

first: Yeon

last: Woo

first: Jung-Hye

last: Roe

first: Sun

middle: C

last: Kim


title: In vivo organization of bacterial transcription initiation complexes at a genome-scale [TSS-seq]

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: TSS-seq (+TEX), and TSS-seq (-TEX) were generated  in duplicates by using Illumina MiSeq


title: In vivo organization of bacterial transcription initiation complexes at a genome-scale [ChIP-seq]

overall_design: ChIP-seq profiles of Sigma 70, RNAP (+Rifampicin), and RNAP (-Rifampicin) were generated by deep sequencing in duplicates using Illumina MiSeq.


title: Identification of circular RNAs during colorectal cancer progression and metastasis using a preclinical mouse model during LDM topotecan chemotherapy

city: Regensburg

first: Gerhard

last: Lehmann

address: Universitaetsstrasse 31

institute: University of Regensburg

summary: To find candidate circRNAs and to unravel their molecular functions during colorectal cancer progression and during LDM topotecan chemotherapy, we utilized a xenograft mouse model based on the HT29.hCG.Luc colorectal cancer cell line (referred to as HT29) implanted into SCID mice. HT29 cells were injected into the spleen and primary tumors developed. Three mice served as control group while two mice served as LDM topotecan treated group. After another 4-6 weeks, liver metastasis can be detected and resected for further investigation. For a global view on gene expression changes, we performed rRNA-depletion RNA-Seq from HT29 cells, primary tumors and liver metastases.

overall_design: 100 ng of total RNA from HT29 cells, primary tumors (PT) and liver metastases (LM) was used for preparation of rRNA-depleted RNA library using Ovation Human FFPE RNA-Seq Libray System according to manufacturer’s protocol. 3 mice were used for collecting RNA from C-PT and C-LM; 2 LDM topotecan treated mice were used for collecting RNA from T-LM; and 3 replicates were used for collecting RNA from HT29 cells.

first: Hung

last: Ho-Xuan

first: Petar

last: Glažar

first: Norbert

last: Eichner

first: Nikolaus

last: Rajewsky

first: Christina

last: Hackl

first: Gunter

last: Meister


title: In vivo organization of bacterial transcription initiation complexes at a genome-scale

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Mayaro Virus Infection Elicits an Innate Immune Response and Represses Autophagy in Anopheles stephensi

status: Public on Jan 26 2021

city: University Park

first: Cory

last: Henderson

state: PA

address: Room W127, Millennium Science Complex

department: molecular cellular and integrative biosciences

institute: Pennsylvania State University

summary: Mayaro virus (MAYV) is a mosquito-borne Alphavirus responsible for outbreaks in South  America and the Caribbean. In this study we infected Anopheles stephensi with MAYV and  sequenced mRNA and small RNA to understand how MAYV infection impacts gene transcription  and the expression of small RNAs in the mosquito vector. Genes involved with innate immunity  and autophagy are regulated in response to MAYV infection of An. stephensi, we also discover  novel miRNAs and describe their expression patterns following bloodmeal ingestion. These  results suggest that MAYV does induce a molecular response to infection in its mosquito vector  species and that MAYV may have mechanisms to evade the vector immune response.

overall_design: 18 total samples are sequenced from 3 different time points, (2, 7, and 14 days post infection). 3 replicates are sequenced from each time point and for each treatment, Mayaro virus infected and uninfected control samples.Each sample has mRNA and small RNA fractions sequenced separately.

first: Marco

last: Brustolin

first: Shivanand

last: Hegde

first: Grant

last: Hughes

last: Bergey

first: Jason

last: Rasgon


title: Motif-driven interactions between RNA and PRC2 regulate transcription elongation of target genes

status: Public on Jan 24 2021

city: Boston

first: Michael

last: Rosenberg

state: MA - Massachusetts

address: 185 Cambridge street

institute: Massachusetts General Hospital, Harvard Medical School

summary: the nature of the interaction between RNA and Polycomb repressive complex 2 (PRC2) has been an area of intensive investigation. Although PRC2 is now established as a bona fide RNA-binding protein, specific motifs have not been fully elucidated, nor has the association of PRC2-RNA complexes with active genes been reconciled. Here we employ denaturing CLIP to identify RNA motifs demonstrating high-affinity binding to PRC2 (Kd 11-80 nM). Mutating the motifs diminishes binding affinity in vitro and attenuates PRC2’s repressive function in vivo. A large fraction of interactions occurs at promoter-proximal regions and associates with POL-II pausing. Furthermore, although PRC2-associated nascent transcripts are highly expressed, ablating PRC2 further increases their expression. Thus, PRC2-RNA interactions are rheostats that operate at the level of transcription elongation to fine-tune gene activity, explaining why they frequently occur within active genes. PRC2-RNA interactions also impact expression of neighboring genes, supporting the classical model that RNA targets PRC2 to gene in cis. Our study supports a model in which RNA specifically targets PRC2 for two repressive functions — (i) control of POL-II pausing, and (ii) marking chromatin with H3K27me3.

overall_design: Here we employ denaturing CLIP to identify RNA motifs demonstrating high-affinity binding to PRC2 (Kd 11-80 nM). We also utilize PRO-seq assay to measure active elongation.

first: Roy

last: Blum

first: Barry

last: Kesner

first: Eric

last: Aeby

first: Jean-Michel

last: Garant

first: Attila

last: Szanto

first: Jeannie

middle: T

last: Lee


title: In vivo organization of bacterial transcription initiation complexes at a genome-scale [ChIP-exo]

first: Byung-Kwan

last: Cho

overall_design: ChIP-exo profiles of Sigma 70, RNAP (+Rifampicin), and RNAP (-Rifampicin) were generated by deep sequencing in duplicates using Illumina MiSeq.

first: Suhyung

first: Yoo-Bok

first: Eun-Ju

first: Yeon

last: Woo

first: Jung-Hye

last: Roe

first: Sun

last: Kim


title: LT-HSC from middle-age mice stimulated with IGF1 ATAC-seq

status: Public on Jan 12 2021

city: Bar Harbor

first: Jennifer

last: Trowbridge

state: Maine

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

summary: Long-term hematopoietic stem cells (LT-HSCs) are responsible for lifelong maintenance and regeneration of the blood system. Loss of LT-HSC function is a major contributor to decline in hematopoietic function with aging, leading to increased rate of infection, poor vaccination response, and increased risk of hematologic malignancies. While cellular and molecular hallmarks of LT-HSC aging have been defined, a barrier to achieving the goal of extending healthy hematopoietic function into older age is the lack of understanding of the nature and timing of the initiating events that cause LT-HSC aging. Here we show that hallmarks of LT-HSC aging and decline in hematopoietic function accumulate by middle age in mice, and that the hematopoietic cell-extrinsic bone marrow (BM) microenvironment at middle age is necessary and sufficient to cause LT-HSC aging. Using unbiased transcriptome-based approaches, we identify decreased production of IGF1 by mesenchymal stromal cells (MSC) in the local middle-aged BM microenvironment as a factor causing LT-HSC aging and show that direct stimulation of middle-aged LT-HSCs with IGF1 rescues hallmarks of aging. Together, our study demonstrates that the initiating events causing LT-HSC and hematopoietic aging emerge by middle age and are caused by hematopoietic cell-extrinsic changes in the BM microenvironment. Declining IGF1 in the BM microenvironment at middle age represents a compelling target for intervention using prophylactic therapies to effectively extend healthspan and prevent decline in hematopoietic function during aging.

overall_design: 2 replicates of each condition: middle-aged (control) and middle-aged stimulated with IGF1 (experimental) LT-HSCs. Young and young stimulated with IGF1 LT-HSCs are not included in this dataset.

first: Kira

last: Young


title: Identification of differentially expressed circRNAs in ossification of the posterior longitudinal ligament

city: Harbin

first: qichang

last: gao

state: Heilongjiang

address: youzheng street, Nangang district

department: orthopedics departmnet

institute: First Affiliated Hospital of Harbin Medical University

summary: Ossification of the posterior longitudinal ligament(OPLL) is a progressive abnormal calcification of the spinal ligament, which causes myelopathy and neurological symptoms. Both genetic and environmental factors play an important role in its occurrence and progress. In recent decades, many studies on OPLL have shown that it is a multifactorial disease. However, the role of circRNAs in the pathogenesis of OPLL is far from clear. In order to identify the transcriptional regulators of OPLL, we compared the expression of circRNAs in the posterior longitudinal ligament tissues from OPLL patients and healthy volunteers through microarray analysis. The analysis revealed a set of circRNAs specifically regulated in humans with heterotopic ossification of ligament tissue. These findings imply that circRNAs may play an important role in OPLL, which provides new ideas for the study of OPLL.

overall_design: The circRNA expression profiles of 3 OPLLs and 3 normal PLL tissues were analyzed by microarray analysis.

first: jiaao

last: gu


title: Elucidation of the open chromatin regions in the bronchial lymph nodes of dairy calves experimentally challenged with bovine respiratory syncytial virus, using ATAC-Seq

city: Dunsany

first: Dayle

last: Johnston

state: Ireland

address: AGRIC

department: Animal and Bioscience Research Department

country: Ireland

institute: Teagasc

summary: Bovine Respiratory Syncytial Virus (BRSV) is a cause of Bovine Respiratory Disease (BRD). The objective of this study was to elucidate the chromatin regions which were differentially open in the bronchial lymph nodes (BLN) of dairy calves experimentally challenged with BRSV, relative to unchallenged control calves. Holstein-Friesian calves were either challenged with BRSV inoculum (n=12) or mock challenged with PBS (n=6). Calves were euthanised on day 7 post-challenge. ATAC-Seq libraries were prepared from fresh BLN tissues and sequenced (75 bp paired-end). Sequence reads were aligned to the UMD3.1 reference genome and peak calling (q < 0.01) was performed with MACS2, employing the BAMPE model. Using Diffbind, 9,144 and 5,096 differentially accessible peaks were identified between BRSV challenged and control calves (P < 0.05, FDR < 0.05) using DeSeq2 and EdgeR, respectively. There were 169 and 110 genes previously found to be differentially expressed using RNA-Seq located within or up to 2kb upstream of the differentially accessible peaks identified by the DeSeq 2 and EdgeR analyses, respectively. There were 237 differentially accessible peaks positioned within 40 previously identified susceptibility loci for BRD. These open chromatin regions are likely involved in the gene transcriptional and regulatory response to infection by BRSV.

overall_design: Examination of a single tissue type (broncial lymph node) in two different treatment groups, BRSV challenged calves (n=12) and control calves (n=6)

first: JaeWoo

first: Jeremy

last: Taylor

first: Bernadette

last: Earley

first: Matthew

last: McCabe

first: Ken

last: Lemon

first: Catherine

last: Duffy

first: Michael

last: McMenamy

first: S

last: Cosby

first: Sinead

last: Waters


title: RNA seq data of Pseudomonas fragi 1793 biofilms formed on aerobically stored, chilled beef

city: Werribee

first: Nirmani

last: Wickramasinghe

state: VIC

address: 671, Sneydes Road

department: Public Health

institute: CSIRO

summary: Pseudomonas fragi is the predominant bacterial species associated with spoiled aerobically stored chilled meat worldwide. It readily forms biofilms on meat under refrigerated temperature conditions used in meat industry. Biofilm growth leads to slime development on meat which becomes a major quality defect. In this research, RNA sequencing was carried out for the main stages of P. fragi strain 1793 grown on aerobically stored meat, kept at 10 °C. RNA was extracted at different stages of the biofilm cycle namely initiation, maturation and dispersal. The key objectives of this study was to investigate which genes are expressed at each of these stages as well as to understand the causes of P. fragi biofilm dipersal.

overall_design: Study of transcriptomic profile of the RNA extracted during biofilm initiation, maturation and dispersal using pairwise comparisons between the three stages and COG function analysis of significantly differentially expressed genes


title: Fine particulate matter (PM2.5) promotes IgE-mediated mast cell activation through ROS/Gadd45b/JNK axis

city: Changsha

first: Ying

last: Wang

address: Xiangya Road

institute: Xiangya Hospital

summary:
Background: Mast cells play an important role in allergic responses and persistently exposure to environmental fine particulate matter (PM2.5) exacerbates allergic diseases,but the details remain elucidative.
Conclusions: PM2.5 regulates ROS production through Gadd45b/MEKK4/JNK pathway, facilitating IgE-mediated mast cell activation.

overall_design: RBL-2H3 cell with Normal saline and PM2.5 plus IgE+DNP-HSA

first: Ni

last: Tang


title: Intestinal deletion of 3-Hydroxy-3-Methylglutaryl-Coenzyme A Reductase promotes expansion of the resident stem cell compartment.

city: Houston

first: Alexandria

last: Doerfler

state: TX

address: 1 Baylor Plaza

department: Molecular Physiology and Biophysics

institute: Baylor College of Medicine

summary:
Objective: The intestine occupies the critical interface between cholesterol absorption and excretion. Despite this, surprisingly little is known about the role of de novo cholesterol synthesis in this organ, and its relationship to whole body cholesterol homeostasis. In addition to cholesterol, the mevalonate pathway is responsible for the synthesis of numerous non-sterol isoprenoids. Here we investigate the physiological importance of the mevalonate pathway within the intestine, through genetic deletion of the rate-limiting enzyme.
Approach and Results: Mice lacking 3-hydroxy-3-methylglutaryl-coenzyme A reductase (Hmgcr) in intestinal villus and crypt epithelial cells were generated using a Villin-Cre transgene. In contrast to intestine-specific Srebp-2 and Scap knockouts, mice with intestinal-specific loss of Hmgcr are viable through adulthood and fertile. Hmgcr was efficiently deleted based on mRNA levels, as well as quantitative analysis of Hmgcr alleles by droplet digital PCR. Lipidomics revealed substantial reductions in the abundance of numerous non-sterol isoprenoids and sterol intermediates within the epithelial layer, while cholesterol levels were preserved. Although the intestinal knockout mice are born smaller, there is no net defect in feed efficiency or triglyceride absorption due to compensatory changes in bile acid composition and intestinal growth. At the cellular level, loss of Hmgcr is compensated for quickly after weaning through a dramatic expansion of the stem cell compartment within the crypts.
Conclusions: Genetic loss of Hmgcr in the intestine is compatible with life, through mechanisms involving compensatory changes in bile acid composition, increased absorptive surface area, and expansion of the resident stem cell compartment.

overall_design: Intestinal epithelial scrapings and liver tissue mRNA profiles from Vil1Cre(+)Hmgcr(+/+) (WT) and Vil1Cre(+)Hmgcr(fl/fl) (i-KO)

first: Li

first: William

middle: R

last: Lagor


title: Reference of endogenous and pluripotent stem-cell derived cardiomyocyte maturation

city: Baltimore

first: Suraj

last: Kannan

state: MD

address: 720 Rutland Avenue Ross 954

department: Cardiology

institute: Johns Hopkins University

summary: The purpose of this study was to understand differences between maturation processes in endogenous and pluripotent stem cell-derived cardiomyocytes. To this end, we first expanded our previous reference of endogenous cardiomyocyte maturation, isolated by LP-FACS (see Kannan et al., bioRxiv 2020, and GSE147807). We subsequently generated PSCs from the same background strain and differentiated to CMs. CMs were isolated by conventional FACs.

overall_design: We isolated CMs from mice at the following timepoints (using LP-FACS for all timepoints from p8 onwards): e14, e18, p0, p1, p4, p8, p11, p14, p15, p18, p22, p28, p35, p56, and p84. We isolated PSC-CMs at D8, D10, D12, D15, D18, D25, D30, and D45.

first: M

last: Miyamoto

first: B

last: Lin

first: C

last: Kwon


title: Expression data from PC-3 cells transfected with siControl and siBTF3

city: Dalian

first: Hailing

last: Cheng

address: 467 Zhongshan Road

institute: The Second Hospital of Dalian Medical University

summary: BTF3 knockdown-induced transcriptional changes in PC-3 cells.

overall_design: PC-3 prostate cancer cells were transfected with siControl or siBTF3 for 48 hours, followed by RNA extraction and RNA sequencing analysis. Each has two biological repeats.

first: Yuan

last: Zhang

first: Pixu

last: Liu


title: Genome wide map of Runx3 bound regions in murine splenic CD8 T cells

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute

summary: Runx3 is an important transcription factor for the proper development of CD8+T cells.  The number and functionality of CD8+T cells is severely affected in the absence of Runx3.  To gain insight into the transcriptional program managed by Runx3 in CD8+T cells we conducted ChIP-seq on 50 million cells and CUT&RUN on 150,000 cells, using anti Runx3 antibodies.  Both assays revealed similar results.

overall_design: we isolated adult murine CD8 T cells from spleen and analyzed the genomic occupancy of Runx3 either by ChIP or CUT&RUN

first: Kira

last: Orlovsky

first: Elena

last: Appel

first: Ditsa

last: Levanon

first: Yoram

last: Groner


title: Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling [PBMC_10X]

status: Public on Jan 15 2021

city: SOUTH SAN FRANCISCO

first: Tracy

last: Yamawaki

state: California

address: 1120 VETERANS BLVD.

institute: AMGEN, INC.

summary: We systematically benchmarked seven high-throughput single-cell RNA-seq methods. We prepared 21 libraries under identical conditions of a defined mixture of two human and two murine lymphocyte cell lines, simulating heterogeneity across immune-cell types and cell sizes.  We evaluate methods by their cell recovery rate, library efficiency, sensitivity, and ability to recover expression signatures for each cell type.  We observed higher mRNA detection sensitivity with the 10x Genomics 5’ v1 and 3’ v3 methods.  We demonstrate that these methods have fewer drop-out events which facilitates the identification of differentially-expressed genes and improves the concordance of single-cell profiles to immune bulk RNA-seq signatures.

overall_design: single-cell RNAseq of human PBMCs

first: Daniel

last: Lu

last: Ellwanger

first: Dev

last: Bhatt

first: Paolo

last: Manzanillo

first: Vanessa

last: Arias

first: Hong

last: Zhou

first: Oh

middle: K

last: Yoon

first: Oliver

last: Homann

first: Songli

first: Chi-Ming

last: Li


title: Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density [Osteoclast_0_3days]

city: Strasbourg

first: maria

middle: del mar

last: muñiz moreno

state: Alsace

address: 1 Rue Laurent Fries

department: Translational medicine and neurogenetics

country: France

institute: IGBMC

type:
Expression profiling by array
Third-party reanalysis

summary: The genetic landscape of diseases associated with changes in bone mineral density (BMD), such as osteoporosis, is only partially understood. Here, we explored the International Mouse Phenotyping Consortium (IMPC) for the analysis of skeletal data from 3,974 mutant strains for bone mineral density (BMD), a measure that is frequently altered in a range of bone pathologies including osteoporosis. A total of 200 genes were found to significantly affect BMD. This gene pool comprised 141 genes that were previously not known to have a function in bone biology and was complementary to pools derived from recent human studies. Nineteen of the 141 BMD genes also caused skeletal abnormalities. Further, evidence suggested a direct role for several of the identified BMD genes in osteoclasts and osteoblasts, and candidate genes for further investigation were prioritized. Overall, the results add novel pathophysiological and molecular insight into bone health and disease

relation:
SubSeries of: GSE158151
Reanalysis of: GSM1383260
Reanalysis of: GSM1383261
Reanalysis of: GSM1383262
Reanalysis of: GSM1383263

overall_design: We downloaded and re-analysed the gene expression profile of the  datasets published by Kim et al., (2014) PMID: 25023277 with GEO  accession number GSE57468. We re-analysed only the Bone marrow-derived macrophage cells  (BMM) after 3days  of induction with RANKL compared to the BMMs  inducted at day 0, to identify osteoclast specific genes and their expression levels after 3 days of induction to apply GeneNet Schaefer and Strimmer algorythm for learning large-scale gene association networks  (http://www.strimmerlab.org/software/genenet/). This method allows to statistically assess the reliability of a given network (nodes and edges) using gene expression data to compute  q-values and posterior probabilities for each potential edge connecting in a pairwise manner the nodes of the network we built in silico using REACTOME ans STRING databases . Data pre-processing and annotation: The raw intensity measurements of the arrays downloaded from the GEO platform in .CEL where normalized using limma Quantile based  normalization algorithm producing the summaries at the probe/transcript level. The probes were gene and transcript annotated using the specific annotaton file MouseRef-8_V2_0_R3_11278551_A was downloaded from https://emea.support.illumina.com/downloads/mouseref-8_v2_product_files.html .  Differential expression analysis (DEA): We carried on the differential expression analysis in R environment using limma. We provide the limma quantile normalized expression data matrix to be used for GeneNet.

first: Maria

last: Muñiz Moreno

first: Yann

last: Herault

first: Philipp

last: Mayer-Kuckuk

first: Martin

last: Hrabe de Angelis


title: Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density [Unsorted_Osteoblast_7_17days]

relation:
SubSeries of: GSE158151
Reanalysis of: GSM43184
Reanalysis of: GSM43205
Reanalysis of: GSM43198
Reanalysis of: GSM43191
Reanalysis of: GSM43212
Reanalysis of: GSM43219

overall_design: We downloaded and re-analysed the gene expression profile of the  datasets published by Kalajzic et al., (2005) PMID: 15834136 with GEO  accession number GSE2332. We re-analysed only the Osteoblast precursors samples from 7 and 17 days of induction, to identify osteoblast specific genes and their expression levels to apply GeneNet Schaefer and Strimmer algorythm for learning large-scale gene association networks  (http://www.strimmerlab.org/software/genenet/). This method allows to statistically assess the reliability of a given network (nodes and edges) using gene expression data to compute  q-values and posterior probabilities for each potential edge connecting in a pairwise manner the nodes of the network we built in silico using REACTOME and STRING databases . Data pre-processing and annotation: The raw intensity measurements of the arrays downloaded from the GEO platform in .txt where normalized using limma Quantile based  normalization algorithm producing the summaries at the probe/transcript level. The probes were gene and transcript annotated using the specific R package mgu74av2.db . Differential expression analysis (DEA): We carried on the differential expression analysis in R environment using limma. We provide the limma normalized expression data matrix to be used for GeneNet.


title: Dissection of cMyc+ GC-B cells [WT]

city: London

first: Dinis

middle: Pedro

last: Calado

address: Midland Road

country: United Kingdom

institute: The Francis Crick Institute

summary: Transcriptomic profiling of plasma cells derived from wild type mice

overall_design: Splenic memory B cells and plasma cells from wild type mice (C57BL/6) 10 days after immunization with SRBC.

first: Amparo

last: Toboso-Navasa

first: Probir

last: Chakravarty


title: Microarray analysis of Brugia malayi microfilariae-derived extracellular vesicles (Evs) and supernatants

city: Bethesda

first: Sasisekhar

last: Bennuru

address: 10 Center Dr, Bldg 10, Rm 11N208

department: LPD

institute: NIH/NIAID

summary:
We report our microarray analysis of Brugia malayi microfilariae-derived miRNA comparing parasite-derived EVs and supernatants
Microarray analysis was performed using isolated RNA from three biological replicates of Brugia malayi microfilariae with a focus on the parasite-derived EVs and supernatant

overall_design: Alessandra ,Ricciardi

first: Roshanak

last: Semnani


title: Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density [Osteoblast_5days]

relation:
SubSeries of: GSE158151
Reanalysis of: GSM925429
Reanalysis of: GSM925430
Reanalysis of: GSM925431
Reanalysis of: GSM925432
Reanalysis of: GSM925433
Reanalysis of: GSM925434

overall_design: We downloaded and re-analysed the gene expression profile of the  datasets published by Nabavi et al., (2012) PMID: 23740245 with GEO  accession number GSE37676. We re-analysed the OB differentiation after Ascorbic Acid (AA) stimulation in Mc3T3-E1 cells, to identify osteoblast specific genes and their expression levels to apply GeneNet Schaefer and Strimmer algorythm for learning large-scale gene association networks  (http://www.strimmerlab.org/software/genenet/). This method allows to statistically assess the reliability of a given network (nodes and edges) using gene expression data to compute  q-values and posterior probabilities for each potential edge connecting in a pairwise manner the nodes of the network we built in silico using REACTOME and STRING databases . Data pre-processing and annotation: The raw intensity measurements of the arrays downloaded from the GEO platform in .CEL files where normalized using limma Quantile based  normalization algorithm producing the summaries at the probe/transcript level. The probes were gene and transcript annotated using the specific R package pd.mouse430.2 . Differential expression analysis (DEA): We carried on the differential expression analysis in R environment using limma. We provide the limma normalized expression data matrix to be used for GeneNet.

middle: M


title: Diagnosis of Alzheimer's disease specific phospholipase c gamma-1 SNV by deep-learning based approach for high throughput screening

city: Daegu

first: Jae-Yeol

last: Joo

address: 61, cheomdan-ro, Dong-gu,

institute: Korea Brain Research Institute

summary: Alzheimer’s disease (AD) is a multifactorial disease which is caused by inherited autosomal recessive as familial and late-onset as non-familial changes. However, the genetics of AD underlining variation or mutation are not well understood. Exon skipping through the occurrence of the unpredicted genetic events leads to variation of translation, but the event does not can be exploited for AD diagnosis. We identified a gene as phospholipase c gamma-1 (PLCγ1) with severe genetic modification in AD through deep-learning based high throughput screening which showed single nucleotide variants (SNVs). Genome-wide association study (GWAS) data from AD mouse model demonstrated that AD specific novel SNVs are preferentially occurred H3K27ac accumulated region at PLCγ1 gene body during the brain development. Moreover, exon skipping in mature mRNA was caused by single nucleotide insertion at 27th exon of PLCγ1 gene. In addition, we show mutation site was evolutionally conserved in various species included human which means important region for homeostasis. Collectively, our findings suggest the genetic variation and possibility of diagnosis potent of PLCγ1 for AD.

overall_design: Examination of PLCg1 and PLC beta submailies gene expression and SNVs profiling from 5xFAD mouse cortex

first: Key-Hwan

last: Lim

first: Sung-Hyun

last: Kim

first: Sumin

last: Yang


title: Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density [Sorted_Osteoblast_7_17days]

relation:
SubSeries of: GSE158151
Reanalysis of: GSM43225
Reanalysis of: GSM43216
Reanalysis of: GSM43195
Reanalysis of: GSM43188
Reanalysis of: GSM43202
Reanalysis of: GSM43209


title: Manifestations of gene expression profiles in human right atrial myocardium caused by mechanical stretch

city: Tokushima

first: Masaki

last: Morishima

state: Tokushima

address: 2-50-1, Kuramoto-cho

department: Tokushima University

country: Japan

institute: Clinical Research Center for Diabetes

summary: Analysis of gene expression patterns in enlarged left atrial appendage (LAA) in mitral/aortic valve replacement or coronary artery bypass graft surgery can help to identify a comprehensive panel of gene biomarkers for predicting clinical outcomes and to discover potential new therapeutic targets. However, the transcriptional profiles triggered by extended mechanical stretch in cardiac myocytes are not fully understood. Here we performed the first genome-wide study of gene expression changes in human enlarged left atium, resulting in 335 differentially expressed (> 2-fold, P < 0,05) genes in response to mechanical stretch.

overall_design: The study was approved by the ethics committees of Japanese Red Cross KUMAMOTO Hospital. Clinical data of the patients and those tissues were from 11 patients with enlarged left atrium (enlarged LA group) and 10 patients in normal size of atrium. (normal LA group)

first: Katsushige

last: Ono

first: Ryusuke

last: Suzuki


title: Co-transcriptional splicing regulates 3' end cleavage during mammalian erythropoiesis

city: New Haven

first: Karla

middle: M.

last: Neugebauer

state: CT

address: 333 Cedar Street

department: Molecular Biophysics & Biochemistry

institute: Yale University

summary: Pre-mRNA processing steps are tightly coordinated with transcription in many organisms. To determine how co-transcriptional splicing is integrated with transcription elongation and 3' end formation in mammalian cells, we performed long read sequencing of individual nascent RNAs and PRO-seq during mouse erythropoiesis. Splicing was not accompanied by transcriptional pausing and was detected when RNA polymerase II (Pol II) was within 75-300 nucleotides of 3' splice sites (3'SSs), often during transcription of the downstream exon. Interestingly, several hundred introns displayed abundant splicing intermediates, suggesting that splicing delays take place between the two catalytic steps. We also observed gene-specific differences in co-transcriptional splicing efficiency, and intron retention correlated with inefficient 3' end cleavage. Remarkably, a thalassemia patient-derived mutation introducing a cryptic 3'SS improves both splicing and 3' end cleavage of individual beta-globin transcripts, revealing that functional coupling between the two co-transcriptional processes is a determinant of productive gene output.

overall_design: Nascent RNA was purified from murine erythroleukemia (MEL) cells before and after erythroid differentiation and sequenced for long read sequencing (LRS) using PacBio RSII and Sequel I flowcells in two biological replicates. PRO-seq was performed on MEL cells before and after erythroid differentiation in three biological replicates.

first: Kirsten

last: Reimer

first: Claudia

last: Mimoso

first: Karen

last: Adelman


title: Next Generation Sequencing Facilitates Quantitative Analysis of Mycobacterium smegmatis C2 155 Transcriptomes treated with overexpression strains MS_Vec and MS_Rv2872

city: chongqing

first: yu

middle: xiao

last: wang

address: beibei tiansheng 2

institute: Southwest University

summary: To gain molecular insight into the role of Rv2872 in increased vancomycin resistance, change of the intracellular amino acids content and cell wall structure, the transcriptome of Rv2872 overexpression M. smegmatis was assessed through RNA-Seq analysis. The transcriptome data showed that the transcription of four genes involved in peptidoglycan synthesis was significantly lower in the MS_Rv2872 overexpression strain . The decreased vancomycin targets might underlie the observed vancomycin resistance. Consistent with altered intracellular amino acids levels in the recombinant M. smegmatis MS_Rv2872, the transcription level of relevant genes was also altered. This is also seen in the altered fatty acids levels. The data showed that 38  fatty acid metabolism genes were down regulated, and 15 were up regulated in the recombinant M.smegmatis MS_Rv2872.

overall_design: mRNA profiles of M.smegmatis overexpression strains MS_Vec and MS_Rv2872 by deep sequencing, using Illumina Hiseq Xten.

first: Jianping

last: Xie

first: Xiaoyu

last: Wang


title: Dissection of cMyc+ GC-B cells at single-cell level

first: Dinis

last: Calado

summary: Transcriptomic profiling and unsupervised clustering of cMyc+ GC-B cells identify the four subpopulations representing positive-selection stages.

overall_design: Splenic cMyc+ GC-B cells from cMyc-GFP reporter mice ten days after immunization with NP-CGG were isolated by flow cytometry and characterized by high-throughput sequencing at single-cell level.

first: Rinako

last: Nakagawa


title: Development and characterization of a novel endoxifen-resistant breast cancer cell line highlights numerous differences from tamoxifen-resistant models.

status: Public on Jan 11 2021

city: Rochester

first: xianfeng

last: chen

state: MN

address: 1216 2nd St SW

department: Biochem & Molecular Biology

institute: Mayo Clinic

summary: Despite the availability of effective drugs that target ERα-positive breast cancer, resistance commonly occurs, resulting in relapse, metastasis, and death. Tamoxifen remains the most commonly-prescribed endocrine therapy worldwide, and “tamoxifen resistance” has been extensively studied. However, little consideration has been given to the role of tamoxifen’s primary active metabolite, endoxifen, in driving resistance mechanisms. Endoxifen is the most abundant active tamoxifen metabolite detected in patients and functions differently from the parent drug and other primary metabolites, including 4-hydroxy-tamoxifen (4HT). Many studies have shown that patients who extensively metabolize tamoxifen into endoxifen have superior outcomes relative to patients who do not, further supporting a primary role for endoxifen in driving tamoxifen responses. Therefore, “tamoxifen resistance” may be actually better modeled by “endoxifen resistance” for such patients. Here, we report the development of a novel endoxifen-resistant breast cancer cell line and have extensively compared this model to tamoxifen (4HT) and fulvestrant (ICI) resistant models. Endoxifen-resistant cells were found to be phenotypically and molecularly distinct from 4HT-resistant cells and more closely resembled ICI-resistant cells overall. Specifically, endoxifen resistance was associated with ERα and PR loss, estrogen insensitivity, EMT-like features, a unique gene signature, and striking resistance to most FDA-approved second- and third-line therapies. Given these findings, and the importance of endoxifen in the efficacy of tamoxifen therapy, our data indicate that endoxifen-resistant models may be more clinically relevant than existing models and suggest that a better understanding of endoxifen resistance could substantially improve patient care.

overall_design: Examination of global gene expression changes in MCF7-derived endoxifen-resistant, 4HT-resistant, and ICI-resistant cell lines. Three replicates are provided for each of four samples: the three resistant lines as well as a long-term vehicle-treated control.

first: Calley

middle: J

last: Jones

first: Malayannan

last: Subramaniam

first: Michael

last: Emch

first: Elizabeth

last: Bruinsma

first: James

middle: N

last: Ingle

first: Matthew

middle: P

last: Goetz

first: John

last: Hawse


title: Interleukin-6 (IL-6) deficiency enhances intramembranous osteogenesis following stress fracture in mice

city: St. Louis

first: Jennifer

middle: Ann

last: McKenzie

state: MO

address: 425 S. Euclid

department: Orthopedics

institute: Washington University in St. Louis

summary: Interleukin-6 (IL-6) is highly upregulated in response to skeletal injury, suggesting it plays a role in the inflammatory phase of fracture repair. However, the impact of IL-6 on successful repair remains incompletely defined. Therefore, we investigated IL-6 in fracture repair using 12-week old IL-6 global knockout mice (IL-6 KO) and two models of fracture repair: full fracture and stress fracture. Callus formation 14 days after full fracture did not differ between IL-6 knockout mice and controls. However, IL-6 KO mice had an enhanced response 7 days after stress fracture compared to control, with increased callus (p=0.020) and bone formation (p=0.045). IL-6 KO did not alter the recruitment of neutrophils or macrophages to the stress fracture callus. IL-6 KO also did not alter the number of osteoclasts in the stress fracture callus. Based on RNA-seq, IL-6 KO resulted in only modest alterations to the gene expression at early time points after stress fracture. Wnt1 was more highly upregulated in IL-6 KO callus at both day 1 (fold change 12.5 vs. 5.7) and day 3 (fold change 4.7 vs. 1.9) compared to controls. Finally, using tibial compression to induce bone formation, we found that IL-6 KO directly impacted osteoblast function, increasing the propensity for woven bone formation. Herein, we report that IL-6 knockout enhanced formation of callus and bone following stress fracture injury, likely through direct action on the osteoblast’s ability to produce woven bone. This suggests a novel role of IL-6 as a suppressor of intramembranous bone formation.

overall_design: 36 samples, 12 non-loaded/intact control ulnae from IL6 WT (n=6) and IL6 KO (n=6). 12 samples from a stress fracture ulna at day 1 (24h) after injury from IL6 WT (n=6) and IL6 KO (n=6). 12 samples from stress fracture ulnae at day 3 (72h) after injury from IL6 WT (n=6 and IL6 KO (n=6) mice. All groups were a mix of male and female mice.

first: Brandon

middle: A

last: Coates

first: Susumu

last: Yoneda

last: Silva


title: Human Neurofibroma Matrisome Revealed by Single Cell RNA Sequencing

city: Dallas

first: Adwait Amod

last: Sathe

state: Texas

address: 5323 Harry Hines Blvd.

department: McDermott Center of Human Growth and Development

institute: UT Southwestern Medical Center

summary: This study revealed the type of ECM secreted by each cell type, provided a complete profiling of cNF collagen, and identified specific cNF fibroblast markers that will provide a molecular platform to further explore the biology of cutaneous neurofibroma

overall_design: Single cell RNA sequencing was conducted on samples of fresh human cutaneous neurofibroma cells isolated from skin in human

first: Jean-Philippe

last: Brosseau

first: Adwait

first: Yong

first: Toan

last: Nguyen

first: Donald

last: Glass II

first: Chao

last: Xing

first: Lu

middle: Q

last: Le


title: SELEX and RIP-Seq identification of nucleic acid sequences bound by CIRBP

city: Xi’an, Shaanxi

first: Chong

last: Xue

address: 169 Changlexi Road

department: Department of Occupational and Environmental Health

institute: Fourth Military Medical University

summary: SELEX (systematic evolution of ligands by exponential enrichment) and RNA Immunoprecipitation (RIP)-seq revealed that CIRBP directly binds the 3’UTR of Atp5g3.

overall_design: Using purified recombinant human Cirbp (His-tagged) protein to pull down single-strand oligonucleotides harboring 30-nt random sequences (randomly inserted bases  227 one after another), the affinity-selected RNAs was Illumina sequenced.

first: Ying

last: Liu

first: Huanyu

last: Lu

first: Yang

last: Zhou

first: Ruili

last: Guan

first: Jiye

last: Wang

first: Qian

last: Zhang

first: Tao

last: Ke

last: Aschner

first: Wenbin

first: Wenjing

last: Luo


title: RNA sequencing analysis of the genes regulated by TroR in Streptococcus suis

city: Yangzhou

first: Chengkun

last: Zheng

address: East wenhui road No.48

institute: Yangzhou University

summary: The transcriptome of the wild type strain and ΔtroR of Streptococcus suis was compared by RNA sequencing analysis. The data revealed that some genes, such as the troABCD operon, were significantly differentially expressed in the ΔtroR mutant.

overall_design: The transcription profiles of the ΔtroR mutant grown in Tryptic Soy Broth supplemented with 10% (vol/vol) newborn bovine serum (TSBS) were compared with that of the wild type strain. Each strain contains three biological replications.

first: Man

last: Wei

first: Jun

last: Qiu

first: Mengdie

last: Jia


title: Inhibition of cyclooxygenase activity by diclofenac inhibits varicose remodeling of mouse veins

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary:
BACKGROUND: As evidenced by epidemiological and etiological studies, the development of varicose veins is driven by risk-factors which support the development of venous hypertension and thus chronically augment circumferential stress of the venous wall (e.g. dysfunctional venous valves, pregnancy or obesity). We have previously verified the relevance of this biomechanical stimulus for the activation of venous endothelial as well as smooth muscle cells and the subsequent detrimental structural remodeling of the vein wall in experimental mouse models.
METHODS: Here, transcriptome analyses revealed an increase in the expression of cyclooxygenase 2 (COX-2) in human venous endothelial cells upon exposure to biomechanical stress. Subsequently, we investigated the impact of diclofenac – a cyclooxygenase inhibitor – on responses of isolated mouse veins to augmented wall stress in vitro and on varicose-like venous remodeling in vivo.
RESULTS: Diclofenac treatment decreased COX-2 protein abundance in mouse veins but had no significant impact on the expression of corresponding transcripts. Short-term exposure to elevated pressure levels stimulated the activity of matrix-metalloproteinase-2 (MMP-2) and mitogen activated protein kinases ERK1/2. Diclofenac decreased the level of activated MMP-2 and ERK1/2 in pressure-exposed mouse veins. Varikose-like remodeling of veins in the mouse auricle was significantly inhibited by transdermal application of diclofenac-containing phospholipid-micelles. This effect was associated with decreased COX-2 and MMP-2 abundance as well as cell proliferation.
CONCLUSION: The cyclooxygenase inhibitor diclofenac interferes with short term activation of MAP-kinases and matrix-metalloproteinases in cells of the wall stress-exposed venous wall while attenuating venous remodeling in vivo. Thus, nonsteroidal anti-inflammatory drugs may be suitable to interfere with processes promoting the progression of varicose vein development and biomechanical activation of venous cells.

overall_design: Comparison of HUVECs exposed to biomechanical stretch vs. static culture conditions

first: Thomas

last: Korff


title: Transcriptomic analysis of Streptococcus suis in response to excess manganese

summary: We explored the transcriptome change of Streptococcus suis in the presence of manganese by RNA sequencing. The data revealed that the genes in the troABCD operon were significantly downregulated in response to manganese.

overall_design: The transcription profiles of Streptococcus suis treated with manganese were compared with that treated with water. Each condition contains three biological replications. Please note that S. suis response to other metals were also conducted. RNA sequencing data for the control group (water treatment) have been submitted to the GEO database under accession number GSE153766 and are included here.


title: Barley seeds miRNome stability during long-term storage and aging

city: Błonie

first: Maja

last: Boczkowska

address: Instytut Hodowli i Aklimatyzacji Roślin - PIB Radzików, 1

country: Poland

summary: Seed aging is a complex biological process attracting the scientists’ attention for many years. High-throughput small RNA sequencing was applied to examine microRNAs contribution in barley seeds senescence. Unique samples of seeds that despite the same genetic makeup differed in viability after over 45 years of storage in a dry state were investigated. In total, 61 known and 81 novel miRNA were identified in dry seeds. The highest level of expression was found in four conserved miRNA families i.e. miR159, miR156, miR166 and miR168. However, the most astonishing result was the lack of significant differences in the level of almost all miRNAs in seed samples with significantly different viability. This result reveals that miRNAs in dry seeds are extremely stable. This is also the first identified RNA fraction that is not deteriorating along to the loss of seed viability. Moreover, the novel miRNA hvu-new41, with higher expression in seeds with the lowest viability was detected by RT-qPCR, has the potential to become an indicator of the decreasing viability of seeds during storage in a dry state. It might be responsible for the removal of (1-3.1-4)-beta-D-glucanase transcripts and lowering or completely blocking the synthesis of this key enzyme for seed germination.

overall_design: Examiantiopn of 3 barley seeds stocks: Rc - after seed regeneration i.e. non-stored control; Lv - seeds after storage 1972-2018 (germination 2%); Hv - seeds after storage 1972-2018 (germination 86,7%).

first: Marta

last: Puchta

first: Jolanta

last: Groszyk

first: Magdalena

last: Małecka

first: Marek

middle: D

last: Koter

first: Maciej

last: Niedzielski

first: Monika

last: Rakoczy-Trojanowska


title: A short ORF-encoded transcriptional regulator

city: San Diego

first: Lara

last: Ibrahim

address: 10550 N Torrey Pines Rd

institute: Scripps Research

summary: Recent technological advances have expanded the annotated protein coding content of mammalian genomes, as hundreds of previously unidentified, short open reading frame (ORF)-encoded peptides (SEPs) have now been found to be translated. Although several studies have identified important physiological roles for this emerging protein class, a general method to define their interactomes is lacking. Here, we demonstrate that genetic incorporation of the photo-crosslinking noncanonical amino acid AbK into SEP transgenes allows for the facile identification of SEP cellular interaction partners using affinity-based methods. From a survey of seven SEPs, we report the discovery of short ORF-encoded histone binding protein (SEHBP), a conserved microprotein that interacts with chromatin-associated proteins, localizes to discrete genomic loci, and induces a robust transcriptional program when overexpressed in human cells. This work affords a straightforward method to help define the physiological roles of SEPs and demonstrates its utility by identifying SEHBP as a short ORF-encoded transcription factor.

overall_design: Comparisons of the transcriptomes of HEK293T cells expressing empty vector and pCMV6-SEHBP-EGFP,

first: Minsoeb

last: Koh

first: Michael

last: Bollong

middle: H


title: Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density [Osteoclast_48H_samples]

first: maria

last: muñiz moreno

summary: The genetic landscape of diseases associated with changes in bone mineral density (BMD), such as osteoporosis, is only partially understood. Here, we explored the International Mouse Phenotyping Consortium (IMPC) for the analysis of skeletal data from 3,974 mutant strains for bone mineral density (BMD), a measure that is frequently altered in a range of bone pathologies including osteoporosis. A total of 200 genes were found to significantly affect BMD. This gene pool comprised 141 genes that were previously not known to have a function in bone biology and was complementary to pools derived from recent human studies. Nineteen of the 141 BMD genes also caused skeletal abnormalities. Further, evidence suggested a direct role for several of the identified BMD genes in osteoclasts and osteoblasts, and candidate genes for further investigation were prioritized. Overall, the results add novel pathophysiological and molecular insight into bone health and disease

relation:
SubSeries of: GSE158151
Reanalysis of: GSM1071626
Reanalysis of: GSM1071627
Reanalysis of: GSM1071628
Reanalysis of: GSM1071629
Reanalysis of: GSM1071630
Reanalysis of: GSM1071631

overall_design: We downloaded and re-analysed the gene expression profile of the  datasets published by Wang et al., (2013) PMID: 23593435 with GEO  accession number GSE43811. We re-analysed only the Osteoclastogenic cell line after 48h hours of induction compared to not inducted, to identify osteoclast specific genes and their expression levels after 48h of induction to apply GeneNet Schaefer and Strimmer algorythm for learning large-scale gene association networks  (http://www.strimmerlab.org/software/genenet/). This method allows to statistically assess the reliability of a given network (nodes and edges) using gene expression data to compute  q-values and posterior probabilities for each potential edge connecting in a pairwise manner the nodes of the network we built in silico using REACTOME ans STRING databases . Data pre-processing and annotation: The raw intensity measurements of the arrays downloaded from the GEO platform in .txt where normalized using limma Quantile based  normalization algorithm producing the summaries at the probe/transcript level. The probes were gene and transcript annotated using the specific annotaton file MoGene-1_0-st-v1.na36.mm10.transcript.csv  downloaded from https://www.thermofisher.com/es/es/home/life-science/microarray-analysis/microarray-data-analysis/genechip-array-annotation-files.html. Differential expression analysis (DEA): We carried on the differential expression analysis in R environment using limma. We provide the limma normalized expression data matrix to be used for GeneNet.

first: Maria

last: Muñiz Moreno

first: Yann

last: Herault

first: Philipp

last: Mayer-Kuckuk

first: Martin

last: Hrabe de Angelis


title: Single-Cell transcriptome analysis revealed the heterogeneity and microenvironment of gastrointestinal stromal tumors

city: Foshan

first: xiaofan

last: Mao

state: China

address: Lingnan Road North 81, Foshan, Guangdong, China

institute: The First People's Hospital of Foshan

summary: Gastrointestinal stromal tumor (GIST) is the most common mesenchymal tumor of human gastrointestinal (GI) tract. In this study, we performed single cell RNA sequencing on intra- and peri- tumor tissues from GIST patients in an aim to discover the heterogeneity of tumor cells in GIST and their interactions with other cells. We found 4 predominating cell types in GIST tumor tissue, including T cells, macrophages, tumor cells and NK cells. Tumor cells could be clustered into two groups: one was highly proliferating and associated with high risk of metastasis; the other seemed “resting” and associated with low risk. Their clinical relevance and prognostic values were confirmed by RNA-seq of 65 GIST samples. T cell was the largest cell type in our single cell data. Two groups of CD8+ effector memory (EM) cells were in the highest clonal expansion and performed the highest cytotoxicity but also the most exhausted among all T cells. A group of macrophages were found polarized to possess both M1 and M2 signatures, and increased along with tumor progression. Cell to cell interaction analysis revealed that adipose endothelial cells had high interactions with tumor cells to facilitate their progression. Macrophages were at the center of tumor microenvironment, recruiting immune cells to the tumor cite and having most interactions with both tumor and non-tumor cells. In conclusion, we obtained an overview of GIST microenvironment and revealed the heterogeneity of each cell type and their relevance to risk classifications, which provided novel theoretical basis for learning and curing GISTs.

first: Wei

last: Luo

first: Xiaofan


title: Nucleocytoplasmic Transport of RNA-Binding Proteins Regulates Neural Stem Cell Fates

city: Calgary

first: Guang

last: Yang

state: Alberta

address: 3330 Hospital Drive N.W.

department: Department of Medical Genetics

country: Canada

institute: University of Calgary

summary: The formation of the cerebral cortex requires balanced expansion and differentiation of neural progenitor cells, the fate choice of which requires regulation at many steps of gene expression. As progenitor cells often exhibit transcriptomic stochasticity, the ultimate output of cell fate-determining genes must be carefully controlled at the post-transcriptional level, but how this is orchestrated is poorly understood. Here, we report that de novo variants in an RNA-binding protein CELF2 cause human cortical malformations and perturb neural progenitor cell fate decisions in mice by disrupting the nucleocytoplasmic transport of CELF2. In self-renewing neural progenitors, CELF2 is localized in the cytoplasm where it binds and coordinates mRNAs that encode cell fate regulators and neurodevelopmental disorder-related factors. The translocation of CELF2 into the nucleus releases mRNAs for translation and thereby triggers neural progenitor differentiation. Our results reveal a mechanism by which transport of CELF2 between discrete subcellular compartments orchestrates an RNA regulon to instruct cell fates in cerebral cortical development.

overall_design: RNA immunopercipitation and sequencing (RIP-Seq) of the cytoplasmic fractionation on mouse corticies at E12.5. Three conditions were used: RIP for CELF2 specific proteins, RIP with non-specific binding antibody and total mRNA-Seq

first: Melissa

last: MacPherson

first: Sarah

middle: L

last: Erickson

first: Drayden

last: Kopp

first: Pengqiang

last: Wen

first: Mohammadreza

last: Aghanoori

first: Antonio

last: Vitobello

first: Quentin

last: Thomas

first: Nina

last: Gold

first: William

last: Brucker

first: Louise

last: Amlie-Wolf

first: Karen

last: Gripp

first: Olaf

last: Bodamer

first: Laurence

last: Faivre

first: Xing-Chan

last: Wei

first: Quan

last: Long

first: A

last: Innes


title: Multi-omics characterization of inflammatory bowel disease induced hyperplasia/dysplasia in the Rag2-/- / Il10-/- mouse model [RRBS]

city: Minneapolis

first: Qiyuan

last: Han

state: Minnesota

address: 2231 6th St. Se, Tretyakova lab 2-230

institute: University of Minnesota

type: Methylation profiling by high throughput sequencing

summary: Epigenetic dysregulation is likely to play a role in the observed association between inflammatory bowel disease (IBD) and colon tumor development. In the present work, DNA methylome, hydroxymethylome, and transcriptome analyses were conducted in proximal colon tissues harvested from the Helicobacter hepaticus-infected murine model of IBD. Reduced representation bisulfite sequencing (RRBS) and oxidative RRBS (oxRRBS) analyses identified 1606 differentially methylated regions (DMR) and 3011 differentially hydroxymethylated (DhMR) regions. These DMR/DhMR overlapped with genes that are associated with gastrointestinal disease, inflammatory disease, and cancer. RNA-seq revealed pronounced expression changes of a number of genes associated with inflammation and cancer. Several genes (e.g. Duox2, Tgm2, Cdhr5, Hk2) exhibited both changes in DNA methylation/ hydroxymethylation and altered gene expression levels. Overall, our results suggest that chronic inflammation triggers changes in methylation and hydroxymethylation patterns in the genome, altering the expression of key tumorigenesis genes and potentially contributing to the initiation of colorectal cancer.

overall_design: Proximal colon tissues from 3 Rag2-/- / Il10-/- mice and 3 H.hepaticus infected Rag2-/- / Il10-/- mice were used for RRBS/oxRRBS analysis.

first: Thomas

last: Kono

first: Charles

middle: G

last: Knutson

first: Natalia

middle: Y

last: Tretyakova


title: Multi-omics characterization of inflammatory bowel disease induced hyperplasia/dysplasia in the Rag2-/- / Il10-/- mouse model

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Multi-omics characterization of inflammatory bowel disease induced hyperplasia/dysplasia in the Rag2-/- / Il10-/- mouse model [RNA-Seq]

overall_design: Proximal colon tissues from 3 Rag2-/- / Il10-/- mice and 3 H.hepaticus infected Rag2-/- / Il10-/- mice were used for RNA-seq analysis.


title: Gene expression analysis of chicken p. major muscle using the NanoString nCounter technology

city: Newark

first: Behnam

last: Abasht

state: DE

address: 531 S. College Ave.

institute: University of Delaware

summary: Tissue samples were harvested with the Keyes biopsy punch (8 mm; manufactured by HNM) from the caudal edge of the right superficial pectoral muscle perpendicular to myofibers and to the keel bone. Total RNA was isolated from p. major samples using mirVana™ miRNA Isolation Kit. Quality checks were performed by measuring the concentration and “RNA Integrity Number” of individual RNA samples using NanoDrop 1000 and Agilent Bioanalyzer 2100. The RNA samples were normalized and sent to NanoString Inc. (Seattle, WA, USA) for the quantification of gene expression levels using NanoString nCounter® technology.  For this, 192 target genes, along with 12 housekeeping genes were selected based on multiple RNA-seq experiments conducted in our laboratories.

overall_design: This dataset include gene expression data from the p. major muscle tissue of 89 chickens,  consisted of 52 Wooden Breast-unaffected, 21 partially affected and 16 markedly affected birds. Most of the samples were from a commercial crossbred population (n=67), and the rest of the samples were from purebred line B (n=8) and purebred line C (n=14).


title: Comparative Analysis of the Tumor Immune-Microenvironment of Primary and Brain Metastases of Non-Small-Cell Lung Cancer

city: Seoul

first: Seung Geun

last: Song

address: 101 Daehak-ro, Jongno-gu

department: Department of Pathology

institute: Seoul National University College of Medicine

summary: To evaluate the characteristics of the tumor immune-microenvironment in brain metastases of non-small-cell lung cancer (NSCLC), we investigated the immunophenotype of primary NSCLC and its brain metastasis.

overall_design: Expression profiling of 770 immune-related genes in 28 tissues from primary and brain metastases of NSCLC was performed using the NanoString nCounter PanCancer Immune Profiling Panel.

first: Yoon Kyung

last: Jeon


title: Lamellar cells from Pacinian and Meissner corpuscles are touch sensors

first: Viktor

last: Feketa

address: 333 Cedar St SHM BE58

department: Cellular & Molecular Physiology

summary: In this experiment, genome-wide transcript expression was determined in duck bill skin by RNASeq.

overall_design: High-throughput deep sequencing of the mRNA isolated from duck bill skin. 3 biological replicates/sample.

first: Yury

last: Nikolaev

middle: V

first: Evan

middle: O

last: Anderson

first: Elena

last: Gracheva

first: Sviatoslav

last: Bagriantsev


title: Dysfunctions in nonsense-mediated decay, protein homeostasis, OXPHOS function, and brain connectivity in ALS-FUS mice with cognitive deficits

city: Singapore

first: Shuo-Chien

last: Ling

state: Singapore

address: 12 Science Drive 2, MD1, 16-03-H

department: Physiology

country: Singapore

institute: National University of Singapore

summary: Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) represent two ends of the same disease spectrum of adult-onset neurodegenerative diseases that affect the spinal cord and neocortex, respectively. Multiple common genetic loci such as FUS (fused-in-sarcoma) have been identified to have a role in ALS and FTD aetiology. Current work indicates that FUS mutations incur gain-of-toxic functions to drive ALS pathogenesis. However, how the disease-linked mutations of FUS may affect cognition remains elusive. Using a mouse model expressing an ALS-linked FUS mutation (R514G) that mimics mouse endogenous expression patterns, we found that FUS proteins showed an age-dependent accumulation despite the fact that the R514G protein was able to down-regulate mouse FUS mRNA during aging. Furthermore, these mice developed cognitive deficits accompanied by a reduction in spine density and long-term potentiation (LTP) within the hippocampus. At the physiological expression level, mutant FUS is distributed in the nucleus and cytosol without apparent FUS aggregates or nuclear envelope defects. Unbiased transcriptomic analysis reveals downregulated genes clustered in pathways involved in protein homeostasis, including components of ribosomal proteins and ubiquitin-proteasome pathway, and mitochondrial functions. Furthermore, using in vivo functional imaging, we uncovered that R514G mice exhibited widespread reduction in cortical volumes, yet enhanced functional connectivity between hippocampus, basal ganglia and neocortex. Taken together, our data suggest that disease-linked mutation in FUS may lead to change in proteostasis and dysfunctional mitochondria, which in turns affect brain structure and connectivity resulting in cognitive deficits.

overall_design: Bulk RNA-Seq of hippocampi of 12-month-old non-transgenic and hFUS-R514G mice

first: Wan

last: Ho

first: Ira

last: Agrawal

first: Sheue-Houy

last: Tyan

first: Emma

last: Sanford

first: Kenneth

last: Lim

first: Jolynn

last: Ong