title: Small proline-rich proteins 1 and 2 function as antimicrobial proteins in the skin

first: Tamia

middle: Alisha

last: Harris-Tryon

state: TX

address: 5323 Harry Hines Blvd., UT Southwester Medical Center- Department of Dermatology

institute: UT Southwestern Medical Center

summary: Using RNA-sequencing we tested  how human sebaceous glands cells respond to bacterial stimuli by comparing the mRNA profiles of sebaceous gland cells treated with lipopolysaccharide to vehicle treated sebaceous gland cells.

overall_design: Whole transcriptome sequecning of human immortalized sebaceous gland cells (SZ95 cells) treated with lipopolysaccharide compared to control (vehicle treated) cells.

first: Chenlu

last: Zhang


title: A primate-specific alternative splicing of CCNE1 (pCCNE1) is an activator for evolutionally-gained enhancers [RNA-seq]

status: Public on Mar 16 2022

city: Montréal

first: Yoshiaki

last: Tanaka

state: Québec

address: 5415 boul. l'Assomption

department: Medicine

country: Canada

institute: Centre de Recherche l'Hôpital Maisonneuve-Rosemont, Université de Montréal

type: Expression profiling by high throughput sequencing

summary: Divergence of protein and genetic function drives acquisition of novel phenotypes into organisms. Alternative splicing (AS) generates multiple proteins from a single gene and promotes the diversity of protein functions. The AS frequency has been increased throughout evolution and contributes to the complexity and the species specificity of cell and organ developmental programs. Retrotransposons (RTs) are major sources to configure the innovation and plasticity of the host genome and actively transcribed during human early development. However, it is not yet clear how the host genome responds to RTs in a reciprocal co-evolution. Here, we discovered that a primate-specific splicing variant of CCNE1 (pCCNE1) regulates primate-specific RTs to control human naïve pluripotency. Independent of the cell cycle regulatory function of ubiquitously-expressed CCNE1 (uCCNE1) with CDK2, we found that pCCNE1 competes with uCCNE1 in binding to the primate-specific RTs on a previously-uncharacterized DNA motif sequence. Especially, pCCNE1 preferentially activates hominid-specific SVA (SINE-VNTR-Alu) elements and synchronously upregulates their downstream host genes, which are uniquely expressed in human preimplantation embryos and naïve pluripotent stem cells (PSCs). Furthermore, pCCNE1 can activate dormant SVA (SINE-VNTR-Alu) enhancers and cooperatively activate their transcriptional regulatory activity with OCT4. Taken together, our results demonstrate that the evolutionary adaptation of human pluripotency via AS of CCNE1 contributes to the gain of novel molecular mechanisms for human-specific regulatory network, and how distinct phenotypes among species are created

overall_design: mRNA profiles of naïve and primed hESCs with knockdown of CCNE1 variant

first: Kun-Yong

last: Kim

first: In-Hyun

last: Park


title: The ability of resveratrol to attenuate ovalbumin-mediated allergic asthma is associated with changes in microbiota involving the gut-lung axis

status: Public on Mar 15 2022

city: Aldiwaneyah

first: Esraah

middle: Sattar Mahmood

last: Alharris

state: Alqadiseyah

address: 2465 Altahadee postal office

department: Pathology and Forensic Medicine

country: Iraq

institute: university of Alqadiseyah

summary: We evaluated the alteration in gut-lung microbiome axis in ovaalbumin-induced asthma mouse model treated by resveratrol

overall_design: We induced asthma in Balb/c mice by challenging them with ovalbumin intraperitoneally and intranasally then treated them by resveratrol. The pulmonary function test was done, the bronchoalveolar lavage done and the level of cytokines was measured, the level of mucin protein in the lung epithelial cells was shown . The gut and lung microbiome were analyzed along with the measuremnet of short chain fatty acids.Then the tight junction integrity was assessed by evaluation of tight junction protein gene expression and transepithelial electrical resistance.

first: Amira

last: Mohammed

first: Hasan

last: Alghetaa

first: Juhua

last: Zhou

first: Mitzi

last: Nagarkatti

first: Prakash

middle: S


title: RNA-seq to determine the impact of miR-34 loss in the Drosophila brain with age

city: Philadelphia

first: Ananth

last: Srinivasan

address: 433 S University Avenue

country: USA

institute: University of Pennsylvania

summary: Aging is a risk factor for neurodegenerative disease, but precise mechanisms that influence this relationship are still under investigation. Work in Drosophila melanogaster identified the microRNA miR-34 as a modifier of aging and neurodegeneration in the brain. MiR-34 mutants present aspects of early aging, including reduced lifespan, neurodegeneration, and a buildup of the repressive histone mark H3K27me3. To better understand how miR-34 regulated pathways contribute to age-associated phenotypes in the brain, here we transcriptionally profiled the miR-34 mutant brain. This identified that genes associated with translation are dysregulated in the miR-34 mutant. The brains of these animals show increased translation activity, accumulation of protein aggregation markers, and altered autophagy activity. To determine if altered H3K27me3 was responsible for this proteostasis dysregulation, we studied the effects of increased H3K27me3 by mutating the histone demethylase Utx. Reduced Utx activity enhanced neurodegeneration and mimicked the protein accumulation seen in miR-34 mutant brains. However, unlike the miR-34 mutant, Utx mutant brains did not show similar altered autophagy or translation activity, suggesting that additional miR-34-targeted pathways are involved. Transcriptional analysis of predicted miR-34 targets identified Lst8, a subunit of Tor Complex 1 (TORC1), as a potential target. We confirmed that miR-34 regulates the 3’ UTR of Lst8. Biological analysis of miR-34 mutant brains demonstrate that 4E-BP is hyperphosphorylated, consistent with increased Lst8 activity and changes in translation. Together, these results present novel understanding of brain aging and the role of the conserved miRNA miR-34 in impacting proteostasis in the brain with age.

overall_design: Two independently run RNA-sequencing experiments are presented here. Set 1 compares the transcriptional profiles of Drosophila melanogaster brains with and without miR-34 at two timepoints (3d, 20d). Set 2 compares the transcriptional profile of the Drosophila melanogaster brain with age (3d, 20d, 50d). All conditions have 3 biological replicates.

middle: R

first: Nancy

middle: M

last: Bonini


title: Variability of bovine milk EV measurements in health and subclinical mastitis

city: Zurich

first: Maria

middle: Desemparats

last: Saenz-de-Juano

address: Universitatstrasse 2

country: Switzerland

institute: ETH Zurich

type: Non-coding RNA profiling by high throughput sequencing

summary: Mastitis, the inflammation of the mammary gland, is one of the most prevalent diseases in dairy farming worldwide. Unfortunately, the disease is most often present in a subclinical type with no clear symptoms. The sooner the infection is detected, the less opportunities for the disease to progress and the more treatment options remain available. Milk microRNA (miRNA) encapsulated in extracellular vesicles (EV) have been proposed as potential biomarkers of different mammary gland conditions, including subclinical mastitis. However, little is known about the robustness of EV analysis regarding sampling time-point or natural infections. In order to estimate the reliability of EV measurements in raw bovine milk, we first evaluated the changes in EV size, concentration and miRNA cargo during three consecutive days. Then, we compared milk EV differences from natural infected quarters with high somatic cell count (SCC) with their healthy adjacent quarters with low SCC and quarters from uninfected udders. We found that milk EV miRNA cargo is very stable along three days and that infected quarters do not induce relevant changes in milk EV of adjacent healthy quarters, making them suitable controls. We observed cow-individual changes in immunoregulatory miRNA in quarters with chronic subclinical mastitis, pointing towards infection-specific alterations. Finally, we proposed bta-miR-223 as a potential indicator of subclinical mastitis prognosis in raw milk.

overall_design: 27 samples: 9 High Somatic Cell Count (High_SCC), 9 Low Somatic Cell Count (Low_SCC), 9 Healthy

middle: D

first: Giulia

last: Silvestrelli

first: Stefan

last: Bauersachs

first: Susanne

middle: E

last: Ulbrich


title: Large-scale H3.1/H3.2 - H3K9me3 deposition defines the epigenetic signature of extraembryonic lineage cells [ATAC-seq]

city: Tsukuba

first: Masashi

last: Hada

state: Ibaraki

address: Koyadai 3-1-1

department: Bioresource Research Center

country: Japan

institute: RIKEN

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The extraembryonic lineage in mammals is unique in its unipotent differentiation ability and gestation-limited development. Here we identified the epigenomic characters of mouse trophoblast stem cells (TSCs) focusing on the genome-wide enrichment of histone H3.1/H3.2 and H3K9me3. Comparative ChIP-sequencing (ChIP-seq) analysis of TSCs and embryonic stem cells (ESCs) revealed that the TSC genome uniquely contained large (over 1Mb) H3.1/H3.2-H3K9me3 domains in the intergenic regions. This feature was common to extraembryonic cells in mice and humans. Depletion of CAF1, a H3.1/H3.2 chaperone, led to downregulation of TSC marker genes such as Cdx2 and Elf5 and ectopic expression of Oct3/4, an ESC marker. Nuclear transfer cloning using TSCs resulted in extremely poor embryonic development, but removal of H3K9me3 from their genome resulted in birth of the first TSC-cloned mice. Thus, the signature of the extraembryonic epigenome is safeguarded by the H3.1/H3.2-H3K9me3 enrichment, which protects the genome from cell fate transition.

overall_design: ATAC-seq analysis of ESCs and TSCs.

first: Hisashi

last: Miura

first: Akie

last: Tanigawa

first: Shogo

last: Matoba

first: Kimiko

last: Inoue

first: Narumi

last: Ogonuki

first: Michiko

last: Hirose

first: Naomi

last: Watanabe

first: Ryuichiro

last: Nakato

first: Katsunori

last: Fujiki

first: Ayumi

last: Hasegawa

first: Akihiko

last: Sakashita

first: Hiroaki

last: Okae

first: Kento

first: Daiki

last: Shikata

first: Takahiro

last: Arima

first: Katsuhiko

last: Shirahige

first: Ichiro

last: Hiratani

first: Atsuo

last: Ogura


title: H3K27me3 occupancy in primary human peripheral blood derived- macrophages

city: Boston

first: Gracia

last: Bonilla

state: MA

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

summary: H3K27me3 in Primary Human Peripheral blood-derived macrophages

overall_design: Fresh human peripheral blood derived macrophages from healthy donors

first: Kate

middle: L

last: Jeffrey

first: Hajera

last: Amatullah

first: Ruslan

last: Sadreyev


title: Large-scale H3.1/H3.2 - H3K9me3 deposition defines the epigenetic signature of extraembryonic lineage cells [RNA-seq]

first: Masashi

last: Hada

overall_design: RNA-seq analysis of ESCs, TSCs, control TSCs, P150 knockdown TSCs, IVF 2-cell embryos, TSC-cloned 2-cell embryos, control TSC-cloned 2-cell embryos, and P150 knockdown TSC-cloned 2-cell embryos.

first: Hisashi

last: Miura

first: Akie

last: Tanigawa

first: Shogo

last: Matoba

first: Kimiko

last: Inoue

first: Narumi

last: Ogonuki

first: Michiko


title: The gene expression profile in human colorectal cancer cell (HT29) treated with linderapyrone derivative

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary: Linderapyrone derivative was deduced to inhibit Wnt signaling pathway via downregulation of related mRNA

overall_design: Comparing DMSO treated and linderapyrone derivative treated cells was performed to identify differentially expressed genes in HT29

first: Matsumoto

last: Takahiro

first: Kitagawa


title: Topoisomerase I and IIa occupancy in primary human peripheral blood derived- macrophages

address: 50 Blossom Street

summary: Primary Human Peripheral blood-derived macrophages

first: Lai

middle: P

last: Wong


title: Anti YTHDF2 RIP-seq to identify YTHDF2 target mRNAs in P0 mouse retinas

city: Shenzhen

first: Fugui

last: Niu

state: Guangdong

address: 1088 Xueyuan Avenue

department: Biology

country: China

institute: SUSTech

summary: To identify the target mRNAs of the m6A reader protein YTHDF2, we carired out anti YTHDF2 RNA Immunoprecipitation (RIP) followed by RNA-sequencencing. Using EZ-Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit (Millipore), RNA from P0 wild type mouse retinas was pulled down by rabbit polyclonal anti-YTHDF2 (proteintech) and then sequenced on Illumina HiSeq3000 platform. The filtered reads were mapped to the mouse reference genome (GRCm38) using STAR v2.5 with default parameters. The resulting bam files were fed to HTSeq tool to count the number of RNA-seq reads, which was further normalized to calculate FPKM. To determine which gene is enriched, we computed the FPKM from RIP elute to input and any fold change greater than 2 was considered enriched. Finally, Biological replicates of anti-YTHDF2 RIP-Seq identified 1639 transcripts. This study provides a gene list which shows mRNA binding with YTHDF2 in mouse retina.

overall_design: 2 replicates, each containing input and IP samples

first: Sheng-Jian

last: Ji

first: Lixin

last: Yang


title: Impact of mTOR inhibition on RNA expression in AT/RT

city: Baltimore

first: Jeffrey

last: Rubens

state: MD

address: 1800 Orleans St

department: Oncology

institute: Johns Hopkins University

summary: We report the impact of mTOR inhibition on RNA expression in AT/RT patient derived cell lines

overall_design: We treated the AT/RT cell lines BT37, CHLA02, CHLA06, and CHLA266 with TAK-228 20nM vs 0.1% DMSO control over 4 hours and performed RNASeq to identify changes in gene expression.


title: The GPR55 inhibitor (R,S’)-4’-methoxynaphthylfenoterol prevents pancreatic tumor growth via metabolic rewiring

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: (R,S′)-4'-Methoxy-1-naphthylfenoterol, (R,S′)-MNF, suppresses cellular growth of various cancer cell types. To assess the potency and mechanism of action of (R,S′)-MNF, we performed in vitro assays of cell proliferation, signal transduction via the G-protein-coupled atypical cannabinoid receptor GPR55, and expression of pro-oncogenic proteins in cultured human PANC-1 pancreatic cancer cells, followed by in vivo studies on the growth of PANC-1 cells in a nude mouse xenograft model. In addition to tumor growth, the tumor tissues were analyzed using multiplatform non-targeted and targeted metabolomics, global RNA microarray, and Western immunoblotting. (R,S′)-MNF significantly inhibited cell proliferation in these cells and blocked GPR55-mediated ERK activation without affecting mitochondrial bioenergetics. Moreover, (R,S′)-MNF was effective at reducing PANC-1 tumor growth in vivo, an outcome associated with altered lipid metabolism and metabolic reprogramming. Many of the metabolome changes in cysteine/methionine metabolism and associated oxidative stress, protein degradation, and pyrimidine nucleotide synthesis were validated using a targeted metabolomics approach. Transcriptomics analysis of PANC-1 xenograft tumors of (R,S′)-MNF-treated vs. vehicle-treated mice revealed striking downmodulation of genes involved in Hippo/YAP and Wnt/beta-catenin pathways, and coincided with reduced expression of YAP, beta-catenin, HIF-1alpha, and c-Myc proteins in response to (R,S′)-MNF administration. The contribution of Hippo and beta-catenin signaling pathways in GPR55 pro-oncogenic signaling provides insight into the mechanisms that drive tumorigenesis. The ability of (R,S′)-MNF to inhibit GPR55 may represent a novel anti-cancer treatment.

overall_design: Transcriptomic analysis of human PANC-1 xenograft tumors harvested from (R,S′)-MNF-treated vs. vehicle-treated mice (N=10 biological replicates per group)

first: Michel

last: Bernier

first: Danuta

last: Dudzik

first: Artur

last: Wnorowski

first: Guido

last: Keijzers

first: Alberto

last: Diaz-Ruiz

first: Nagendra

last: Singh

first: Yongqing

last: Zhang

first: Morten

last: Scheibye-Knudsen

first: Krzysztof

last: Jozwiak

first: Coral

last: Barbas

first: Irving

middle: W

last: Wainer


title: Nanostring nCounter Mouse Immune Exhausstion Panel (T-cells only)

status: Public on Mar 14 2022

city: Atlanta

first: Rae

last: Hunter

state: Georgia

address: 1760 Haygood Drive NE

department: Pediatrics

institute: Emory University

summary: Evaluation of the effects of IL-12 as an immuno-therapeutic in B cell acute lymphoblastic leukemia

overall_design: In this study, T-cells of the bone marrow of mice either untreated or treated with rIL-12 were isolated

first: Christopher

last: Porter


title: RNA Expression in the left lateral lobe of the liver in BALB/cJ and BALB/cByJ substrains of mice to identify candidate mechanisms for Oxycodone QTLs

first: Camron

last: Bryant

state: Massachusetts

address: 72 E Concord St

department: Pharmacology

institute: Boston University School of Medicine

summary: We found BALB/cByJ and BALB/cJ mice differ in their responses to oxycodone state dependent conditioned place preference, whole brain [oxycodone] and its metabolites [noroxycodone] and [oxymorphone] following oxycodone administration, the 53.5°C hot plate, mechanical stimulation in the von Frey test, and gross brain weight. We then identified a quantitative trait locus (QTL) on chromosome 15 for whole brain [Oxymorphone] (LOD = 7.07; p < 0.001), 13 for hot plate sensitivity (LOD = 10.7; p < 0.001; peak = 56 Mb) and a QTL for brain weight on chromosome 5 (LOD = 8.7; p < 0.001). These tissues were used to investigate the transcriptome of the liver in parental strain mice in order to generate hypothosis concerning the quantitative trait mechanism for our observed effects.

overall_design: 16 BALB/cJ (8 females, 8 males) and 16 BALB/cByJ mice (8 females, 8 males) were trained and tested for state-dependent OXY-CPP using 1.25 mg/kg OXY (i.p.) as described above and sacrificed immediately after day 9 testing (30 min post-OXY) by rapid decapitation. The lateral left lobe of the liver was collected and preserved in RNAlater. RNA was extracted in RNAlater-preserved tissue using Trizol (Qiagen), ethanol precipitation, filtering columns (Qiagen), DNAse digestion (Qiagen), and elution with RNAse and nucleotide free water (Yazdani et al., 2015) and diluted to 100 ng/ul. RNA library preparation (poly-A selection) and RNA-seq were conducted at the University of Chicago Genomics Facility on an Illumina NovaSEQ6000 using a NovaSEQ SP-100 bp flowcell/reagent cassette. We used the R/Bioconductor package “scruff” to conduct demultiplexing, read alignment, read counting, quality checking and data visualization (Wang et al., 2019). Reads were trimmed for quality using Trimmomatic (Bolger et al., 2014). Trimmed reads were then aligned to the mm10 mouse reference genome (Ensembl) to generate BAM files for alignment using STAR (Dobin et al., 2013). For differential gene analysis in the spinal cord, the featureCounts read summarization program was used to count reads mapping to the “exon” feature in a GTF file obtained from Ensembl (GRCm38). Genes without 10 reads per million in at least 3 samples were excluded from analysis using EdgeR, and differential gene expression analysis of normalized counts was conducted using an appropriate design matrix, and reported using the topTable function.

first: Jacob

middle: A

last: Beierle


title: Study on the Expression of miRNA in Exosome of EBV-positive Gastric Carcinoma Cells

city: Fuzhou

first: Sheng

state: Fujian

address: 20 Cha Zhong Lu

department: Department of Pathology

institute: The First Affiliated Hospital of Fujian Medical University

summary: We investigate the expression of miRNA in exosome of EBV-positive gastric carcinoma cells. The exosomes of EBV-positive and negative gastric carcinoma cells were separated by ultracentrifugation, the morphology of exosomes was identified by transmission electron microscopy, the exosome size was analyzed by Nanosight, and the expression of exosome membrane protein CD63 and CD81 was detected by western blot. High-throughput sequencing was used to detect miRNA expression profiles in gastric cancer cell lines and their exosomes. Under the ultra-microscopic electron microscope, the exosomes are seen as a typical translucent cup-like structure or a flat spherical structure. The nanoparticle tracking analyzer (Nanosight) showed that the exosomes were between 30 and 150 nm in diameter. Western blot(WB) assays showed that exosomes secreted by EBVaGC and EBVnGC cells expressed specific exosome membrane-associated proteins CD63 and CD81. High-throughput sequencing revealed that EBVaGC(SNU-719) and EBVnGC(AGS) and their secreted exosomes were highly expressed with certain human miRNAs, among which AGS-exo was highly expressed with hsa-miR-23b-3p, hsa-miR-320a-3p, and hsa-miR-4521. SNU-719-exo was highly expressed as hsa-miR-21-5p, hsa-miR-148a-3p and hsa-miR-7-5p. Nearly all EBV-related miRNAs (EBV-miRNA) were expressed in SNU-719 cells and their exosomes, among which EBV-miR-BART1-5p, EBV-miR-BART17-3p and EBV-miR-BART18-5p were the highest in SNU-719 cells, EBV-miR-BART1-5p, EBV-miR-BART18-5p and EBV-miR-BART17-3p were the highest in SNU-719-exo.

sample_organism:
Homo sapiens
human gammaherpesvirus 4

platform_organism:
Homo sapiens
human gammaherpesvirus 4

overall_design: Examination of the expression of miRNA in exosome of EBV-positive gastric carcinoma cells

first: Mengyao

last: Lin

first: Tianyi

first: Jiezhen

last: Li

first: Feng

last: Gao

first: Ke

last: Zheng

first: Shun

last: Hu

first: Guoping

first: Caihong

last: Ren

first: Xiangna

last: Chen

first: Fang

last: Guo


title: Large-scale H3.1/H3.2 - H3K9me3 deposition defines the epigenetic signature of extraembryonic lineage cells [ChIP-seq]

first: Masashi

last: Hada

overall_design: ChIP-seq analysis of H3K9me3, H3.1/H3.2, and H3.3 in ESCs, TSCs, control TSCs, and P150 knockdown TSCs.

first: Hisashi

last: Miura

first: Akie

last: Tanigawa

first: Shogo

last: Matoba

first: Kimiko

last: Inoue

first: Narumi

last: Ogonuki

first: Michiko

last: Hirose

first: Naomi

last: Watanabe

first: Ryuichiro

last: Nakato

first: Katsunori

last: Fujiki

first: Ayumi

last: Hasegawa

first: Akihiko

last: Sakashita

first: Hiroaki

last: Okae

first: Kento

first: Daiki

last: Shikata

first: Takahiro

last: Arima

first: Katsuhiko

last: Shirahige

first: Ichiro

last: Hiratani

first: Atsuo

last: Ogura


title: HDAC5 modulates PD-L1 expression and cancer immunity via p65 deacetylation in pancreatic cancer

city: Wuhan

first: Haixin

last: Yu

state: Hubei Province

address: 1277, Jiefang Avenue

institute: Wuhan union hospital

summary: We performed HDAC5 knockdown in pancreatic cancer cell line (PANC-1). The expression profiling showed NF-κB signaling as a potential HDAC5 targets and the conclusions were futher validated in vivo and in vitro.

overall_design: RNA sequencing in PANC-1 cell lines with shControl or shHDAC5

first: Y

last: Zhou

first: H

last: Wu


title: In vivo development and single-cell transcriptome profiling of human brain organoids in mouse corpus striatum

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

summary: Human brain organoids are three-dimensional cultures that recapitulate in vivo cell diversity and organization, which provide a novel source for transplantation therapies of neurological disorders. However, some remaining technical problems including surgical lesions which still limit the application of brain organoid transplantation. Here instead of transplanting mature organoids, we performed development of organoids in vivo (IVD-organoids) by injecting small early organoids into the adult mice corpus striatum. Single-cell transcriptome analysis suggested that IVD-organoids contain pericyte-like and hippocampal cells. Similar to previous studies in cerebral organoid transplantation, IVD-organoids also showed reduced cellular stress and death. We further demonstrated that more choroid plexus (ChP) cells were generated in IVD-organoids, which were important for maintaining brain homeostasis. Together, our study provides a novel method that allows in vivo generation of human brain organoids, which may serve as a potential cell therapy for neurological disease involving different brain regions.

overall_design: mRNA profiles of in vivo development brain organoids at single-cell level were generated by deep sequencing

first: Shichao

last: Huang

first: Fei

first: Gang

last: Pei


title: TGF-β signaling activated by cancer-associated fibroblasts determines the histological signature of lung adenocarcinoma

city: Bethesda

first: Ryo

last: Sato

address: 10 Center Dr

department: NHLBI

institute: National Institutes of Health

summary: Invasive lung adenocarcinoma (LADC) is classified histologically as lepidic, acinar, papillary, micropapillary, or solid. We found that A549 human LADC cells formed tumors with distinct histological features—solid-type or acinar-type tumors—depending on the site of development in immunodeficient mice and that a solid-to-acinar transition (SAT) could be induced by cancer-associated fibroblasts (CAFs) in 3D cocultures with A549. To clarify the molecular mechanisms contributing to SAT induction, we performed RNA-seq analysis of four A549 tumor cell samples derived from solid- or acinar-type tumor tissue formed in vivo or from 3D tumor colonies formed in the presence or absence of CAFs in vitro.

overall_design: RNA-seq analysis of A549 cells isolated from solid-type or acinar-type tumors in immunodeficient mice by laser microdissection and  A549 cells isolated from 3D cocultures in the presence or absence of CAFs by cell sorting.

first: Kosuke

last: Imamura

first: Takashi

last: Semba

first: Yusuke

last: Tomita

first: Sho

last: Saeki

first: Koei

last: Ikeda

first: Yoshihiro

last: Komohara

first: Makoto

last: Suzuki

first: Takuro

last: Sakagami

first: Hideyuki

last: Saya

first: Yoshimi


title: Agilent SBC-ceRNA microarray chips were employed to detect the 3 normal plasma cells (NPCs), 5 lgD MM samples and 5 lgG MM samples respectively.

city: Nanjing

first: Pinggang

last: Ding

address: 138 Xianlin Road

department: School of Medicine

institute: Nanjing University of Chinese Medicine

summary: We report the application of SBC-ceRNA microarray chips of diffenertially expressed circRNAs in IgD MM for high-throughput profiling of healthy controls, clinical IgG MM and IgD MM patients using SBC-ceRNA(homo 4*180K) chip.A total of 28,456 circRNAs were identified and 5939 were differentially expressed between IgD MM and IgG MM tissues

overall_design: 5 IgD samples,5 IgG MM samples and 3normal plasma cells (NPCs) from healthy controls to study the diffenertially expressed circRNAs in IgD MM.

first: Xiaozhu

last: Tang


title: Single embryo RNA-seq of control and hydroxyurea treated embryos produced by nuclear transfer of cumulus cells. Single cell RNAseq of cumulus cells was performed using the same protocol.

city: Munich

first: Maria

middle: Elena

last: Torres-Padilla

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

summary: Slow fork speed inducer, hydroxyurea, efficiently improved development of somatic cell nuclear transfered embryos to the blastocyst stage. Here, we performed single embryo RNA-seq approach to investigate whether nuclear transfer embryos exhibited a transcriptional programme similar to in vivo fertilised embryos.

overall_design: RNA-seq of control and hydroxyurea treated nuclear transfered embryos at the 2-cell stage (28 hours post activation) was performed using SMART-seq2. RNA from single cumulus cells was performed using the same protocol. RNA was sequenced with NetSeq.

first: T

last: Nakatani

first: K

last: Yamagata

first: L

last: Altamirano-Pacheco

first: M

last: Tokoro

first: Y

last: Hatano


title: Next Generation Sequencing Facilitates Quantitative Analysis of Germ Cell-specific Ythdf2 Mutants and Control Transcriptomes

city: Shanghai

first: xin

middle: xi

last: zhao

address: Yueyang Road, 320#, new building 615

institute: Shanghai Institute of Biochemistry and Cell Biology

summary: Given the reported molecular role of YTHDF2 in mRNA stability, we designed to investigate the biological mechanism underlying the defects of germ cell-specific ythdf2 mutants (Ythdf2-vKO) spermatogenesis using high-throughput RNA sequencing (RNA-seq). Testes were obtained from Ythdf2-vKO and control adult mice, then were used for RNA-seq. Our result showed that there were 266 genes (196 up and 70 down) deregulated in Ythdf2-vKO testes (P < 0.05, fold change ＞ 1.5) compared with control adult mice. Based on our previously reported m6A mRNA methylomes of mouse spermaogenic cells (PMID: 28914256), 66% of the upregulated genes (129 genes) in Ythdf2-vKO testes were modified with m6A. Further analysis based on our previously reported single-cell transcriptomics data of mouse spermatogenesis (PMID: 30061742), the 129 upregulated genes with m6A modification in Ythdf2-vKO testes mainly express at early stages of wild-type spermatogenesis. While the 70 down regulated genes in Ythdf2-vKO testes mainly exist at later stages of wild-type spermatogenesis. Our qPCR analysis confirmed the RNA-seq analysis. In summary, our results showed that YTHDF2 is essential for regulation of a wave of transcriptome dynamic transition during mice spermatogenesis.

overall_design: Transcriptome  of Ythdf2-vKO and control mice were generated by using Illumina Hiseq Xten, and were further analyzed according with our previoursly reported database.

first: Xin-Xi

last: Zhao

first: Zhen

last: Lin


title: Single cell changes in postnatal P7 and in adult cardiac endothelium upon VEGF-B overexpression

city: Helsinki

first: Markus

last: Räsänen

address: Haartmaninkatu 8

country: Finland

institute: Wihuri Research Insitute

summary: We have previously reported that mice expressing a cardiomyocyte-specific αMHC-VEGF-B transgene in the heart show a clear expansion of the coronary vasculature and cardiac hypertrophy, without significant changes in heart function. As a therapeutic way of administrating VEGF-B protective effects, we show that AAV-VEGF-B  induces the proliferation of endothelial cells (EC). All the samples were analyzed using the Chromium Single-cell 3'RNA-sequencing system.

overall_design: We analyzed in total 4 samples, aiming with all the samples at 3000 cells.

first: Kari

last: Alitalo


title: Exploring the underlying mechanism by which circHNRNPU_603aa exerted carcinogenesis and its potential targets in MM

city: nanjing

first: Wenren

last: Zuo

address: xianlin road

institute: nanjing university of chinese medicine

summary: A RIP experiment was performed in CAG WT and CAG circHNRNPU_603aa OE  cells using HA antibody as bait. The position of peak summit around transcript start sites of genes can predict the  interaction sites of protein and gene. We compared the peak summit of  CAG WT and CAG circHNRNPU_603aa OE cells to find the differences between CAG WT cells and CAG circHNRNPU_603aa cells.

overall_design: Examination of CAG EV and circHNRNPU_603aa OE cells.

first: Chunyang

last: Gu

first: Ye

last: Yang


title: Transcriptomes of maize seedlings under water and salinity treatment

city: Yangzhou

first: Yijun

last: Wang

state: Jiangsu

address: Wenhui

institute: Yangzhou University

summary:
Purpose: We aim to reveal maize transcriptomic changes with water and salinity treatment.
Methods: RNA-seq were used to reveal transcriptome of maize biological replicates with water and salinity treatment.
Results: Differentially expressed transcripts were identified by the comparison of biological replicates with water and salinity treatment.
Conclusions: We identified differentially expressed genes in respone to salinity treatment in maize.

overall_design: RNA-seq of biological replicates of roots and young shoots from genotypes SS and ST using HiSeq 2500 System with a 150 bp paired-end module.


title: Platelet mRNA in response to antiplatelet therapy exposure

city: Durham

first: Deepak

last: Voora

state: NC

address: 101 Science Dr

institute: Duke

summary: The purpose of this study was to identify changes in platelet mRNA that result from exposure to antiplatelet therapy.  A total of 84 healthy volunteers were recruited into a longitudinal study of various antiplatelet exposures with 58 completing all study visits.  This was a 5 visit study where each visit was separated by ~ 4 weeks.  At each Visit purified platelets using a CD45 negative selection protocol was performed in addition to platelet function testing using light transmittance aggregometry (ADP, EPI, and Collagen) and PFA100 (Col/EPI).  After the baseline visit (V1), participants were randomized to receive 81mg/day or 325mg/day aspirin x 4 weeks followed by Visit 2.  Participants then crossed over to the alternative dose of aspirin for 4 weeks followed by Visit 3.  Between Visits 3 and 4 participants washed out their aspirin for 4 weeks.  The final exposure was ticagrelor 90mg twice daily x 4 weeks until Visit 5.

overall_design: Randomized cross over clinical trial of daily 81 mg apsirin, 325 mg aspirin, aspirin washout, and 180 mg Ticagerlor.

first: Rachel

last: Myers


title: Optimizing Embryoid Bodies and Organoids by Chemical Cytoprotection [RASL-Seq]

city: Rockville

first: Ilyas

last: Singec

address: 9800 Medical Center Dr

department: NCATS

institute: NIH

summary: Embryoid bodies (EBs) and self-organizing organoids derived from human pluripotent stem cells (hPSC) recapitulate tissue development in a dish and hold great promise for disease modeling and drug development. However, current protocols are hampered by cellular stress and apoptosis during cell aggregation resulting in variability and impaired cell differentiation. Here, we demonstrate that EBs and cerebral organoid model can be optimized by using the CEPT small molecule cocktail, an integrated polypharmacology approach that ensures stress-free cell aggregation and survival. The use of CEPT for only 24 hours during cell aggregation has long-lasting consequences affecting morphogenesis, gene expression, and cellular differentiation. Various methods confirmed that CEPT treatment consistently resulted in higher experimental reproducibility compared to the widely used ROCK inhibitor Y-27632. Immunohistology data also showed that CEPT is universally applicable for successful generation of organoids of various developmental lineages, such as gut and kidney. Collectively, we discovered that viability and cell fitness during cell aggregation are critical quality control determinants that can be enhanced by CEPT, thereby establishing a robust foundation for bioengineering complex tissue models.

overall_design: This dataset contains RASL-Seq FASTQs and count files created by a custom aligner, since custom oligo-dt probes were used in library prep.

first: Claire

last: Weber

first: Seungmi

last: Ryu


title: Transcriptome analysis by RNA-seq of juvenile gastric cancer derived from the Cancer Institute Hospital of Japanese Foundation for Cancer Research.

city: Tokyo

first: Norio

last: Tanaka

address: Ariake 3-8-31, Koto

institute: Japanese Foundation Cancer Research

summary:
We performed the RNA-seq experiments for mRNA of juvenile gastric cancer tissue.
Raw data are not available for this Series due to patient privacy concerns.

overall_design: Messenger RNA were extracted from primary tumor of 5 juvenile cancer patients, prepared with Ilumina TruSeq Access mRNA  Library Prep Kit and sequenced  on the Illumina HiSeq


title: Transcriptome analysis of A549 cells upon LITATS1 knockdown

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

country: Netherlands

institute: Leiden University Medical Center

summary: We identified a tumor-supressing long non-coding RNA (lncRNA) named lncRNA induced by TGF-beta and antagonizes TGF-beta signaling 1 (LITATS1). It was found to mitigate epithelial-to-mesenchymal transition (EMT), cell migration and extravasation in a zebrafish exnograft model. To better dissect the downstream target genes and elucidate the signaling pathways altered by LITATS1, we depleted LITATS1 by specific shRNAs in A549 cells. Total RNA was collected and sent for RNA sequencing analysis. Afterwards, differentially expressd genes were used for the pathway enrichment analysis and gene set enrichment analysis (GSEA).

overall_design: LITATS1 is depleted by two independent shRNAs in A549 cells. RNA from cells transduced with the non-targeting shRNA (shNT) was set as a control. Three biological replicates were included in each group.

first: Chuannan

last: Fan

first: Tom

last: Kuipers

first: Peter

middle: t

last: Dijke


title: RNA-seq analysis of 2D- and 3D-cultured pancreatic cancer cells

city: Pohang

first: Yebin

last: Kim

state: Gyeongsangbukdo

address: Handongro 558

country: South Korea

institute: Handong Global University

summary: The aim of this study is to evaluate data by comparing transcriptome profiling (RNA-seq) and quantitative reverse transcription polymerase chain reaction (qRT-PCR) methods of pancreatic cancer cells grown in 2D and 3D- culture environments.

overall_design: Patient derived pancreatic cancer cells were cultured in 2D or 3D printing conditions for 6 days.

first: Jung

last: Han

first: TaeJin

last: Ahn

first: Seong

middle: J

last: Park

first: Yeabeen


title: Effects of of Nogo-B receptor deficiency on transcriptomic profilig in human brain microvascular endothelial cells

city: Mineola

first: Qing

middle: Robert

last: Miao

state: NY

address: 101 Mineola Blvd

department: Foundations of Medicine

institute: NYU Long Island School of Medicine

summary: We used RNA-seq analysis to determine the alteration of transcriptomic profiling in human brain microvascular endothelial cells

overall_design: We used the validated siRNA to knockdown Nogo-B receptor (NgBR) in human brain microvascular endothelial cells and isolated RNA to examoine the alteration of transcriptomic profiling using RNA-seq

first: Zhi

last: Fang

first: Wenquan

last: Hu


title: ADAR1 regulates growth & invasion in triple-negative breast cancer

city: Boston

first: Allison

middle: R.

last: Baker

address: 3 Blackfan Circle

institute: Harvard University

summary: ADAR1 catalyzes Adenosine-to-Inosine (A-to-I) editing of double-stranded RNA and regulates global expression output through its interactions with RNA and other proteins. ADARs play important roles in development and disease, and previous work has shown that ADAR1 is oncogenic in a growing list of cancer types. Here we show that ADAR1 is important for growth and invasion in triple negative breast cancer cells, as ADAR1 loss yields reduced growth, migration & invasion, and mammosphere formation. Global RNA-seq analyses demonstrate that ADAR1 regulates both coding and non-coding targets via expression level and/or A-to-I editing. We demonstrated that a recoding edit in FLNB (chr3:58156064) inhibits the tumor suppressive activities of the protein to promote growth & invasion. We show that several tumor suppressor microRNAs are also downregulated by ADAR1 to promote cell cycle progression and invasion. This work describes several novel mechanisms of ADAR1-mediated oncogenesis in triple negative breast cancer, providing support to strategies for targeting ADAR1 in this aggressive cancer type with few treatment options.

overall_design: poly(A+) and small RNAseq on BT20 cells transfected with siRNAs against ADAR1 (siControl, siADAR#1, siADAR#2)

first: Christos

last: Miliotis

first: Julia

last: Ramirez-Moya

first: Talia

last: Marc

first: Ioannis

last: Vlachos

first: Pilar

last: Santisteban

first: Frank

last: Slack


title: SWI/SNF antagonism of the PRC2 mediates estrogen-induced progesterone receptor expression

city: Grand Rapids

first: Ronald

last: Chandler

state: Michigan

address: 400 Monroe Ave NW

institute: Michigan State University

summary: Endometrial cancer (EC) is characterized by high estrogen levels unopposed by progesterone. Treatment with progestins is standard for early EC, but response to progestins is dependent on progesterone receptor (PGR) expression. Here, we show that the expression of PGR in endometrial epithelial cells is dependent on ARID1A, a DNA-binding subunit of the SWI/SNF chromatin remodeling complex that is commonly mutated in EC. In endometrial epithelial cells with estrogen receptor overexpression, we find that ARID1A promotes estrogen signaling and regulates common gene expression programs. Normally, endometrial epithelial cells expressing estrogen receptor respond to estrogen by upregulating the PGR. However, when ARID1A expression is lost, upregulation of PGR expression is significantly reduced. This phenomenon can also occur following loss of the SWI/SNF subunit BRG1, suggesting a role for ARID1A- and BRG1-containing complexes in PGR regulation. We find that PGR is regulated by a bivalent promoter, which harbors both H3K4me3 and H3K27me3 histone tail modifications. H3K27me3 is deposited by EZH2, and inhibition of EZH2 in the context of ARID1A loss results in restoration of estrogen-induced PGR expression. Our results suggest a role for ARID1A deficiency in the loss of PGR in late-stage EC, and a therapeutic utility for EZH2 inhibitors in EC.

overall_design: 12Z human endometriotic epithelial cells with stable expression of ESR1 were transfected with either siARID1A or non-targeting siRNA control. 48 hours later, cells were treated with 10 nM estradiol (E2) or vehicle (0.1% ethanol).  Cells were assayed 24 hours post-E2 treatment via RNA-seq.

first: Mike

last: Wilson

first: Jake

last: Reske


title: Large-scale H3.1/H3.2 - H3K9me3 deposition defines the epigenetic signature of extraembryonic lineage cells

city: Tsukuba

first: Masashi

last: Hada

address: Koyadai 3-1-1

institute: RIKEN

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

overall_design: Refer to individual Series


title: Intragenic Heterochromatin-dependent RNA Polyadenylation mediated by a Protein Complex in Arabidopsis

first: chunxiang

last: chen

state: Shanghai

address: 300 fenglin road, xuhui district, Shanghai

institute: Shanghai Center for Plant Stress Biology


title: Intragenic Heterochromatin-dependent RNA Polyadenylation mediated by a Protein Complex in Arabidopsis [RIP-seq]

summary: In eukaryotic cells, the constitutive heterochromatins, characterized by enrichments of DNA cytosine methylation and repressive histone modifications, are formed in both intergenic regions and gene body regions. The ASI1-AIPP1-EDM2 (AAE) complex has been shown to participates in the RNA polyadenylation (poly A) regulation of intronic heterochromatin-containing genes. While, how AAE complex components coordinately interacts with the chromatin and RNA remains largely unknown. Here, based on multi-omics analysis, we proved that ASI1 and EDM2 mostly target the common genomic regions and display high preference to intragenic heterochromatin within the transposable element (TE)-overlapping genes. Besides interplay with chromatin, ASI1 also displays high binding affinity to RNA transcripts from intragenic heterochromatin regions. Evidence from poly (A)-specific sequencing proved that AAE complex controls the choice of poly (A) sites not only in genes with intronic heterochromatin but also in heterochromatic TE-overlapping genes. Importantly, we revealed that AAE complex also participates in the alternative splicing of TE-overlapping gene RPP4. Moreover, evidences from gene expression and poly (A) sequencing revealed that RRM protein FPA functions antagonistically with AAE complex to control polyadenylation of histone demethylase gene IBM1 in locus-dependent manner. Taken together, our results provide fundamental evidences that AAE complex interacts with both the chromatin and RNA in the intragenic heterochromatin to regulate poly (A) site choice, and a bidirectional regulation mechanism of intragenic heterochromatin-dependent RNA processing exists in Arabidopsis. Our finding gained further insights into the molecular interaction pattern of AAE complex with targets and will help to better understand the complicated interplay between epigenetic modification-shaped chromatin and RNA processing.

overall_design: PAT-seq:2 samples examined and each sample has two replicates, Col-0, ASI1;ASI1 ChIP-seq:2 samples examined and each sample has two replicates and 1 input,Col-0,ASI1; EDM2 ChIP-seq:2 samples examined and each sample has two replicates and 1 input,Col-0,EDM2; ASI1 RIP-seq:2 samples examined, Col-0 and ASI1, each sample has two replicates and 1 input.

first: Yi-Zhe

last: Zhang

first: Juncheng

last: Lin

first: Chun-Xiang

last: Chen

first: Miki

last: Daisuke

first: Si-Si

last: Xie

first: Jian

first: Ya-Nan

last: Chang

first: Qingshun

middle: Q

last: Li

first: Jian-Kang

last: Zhu

first: Cheng-Guo

last: Duan


title: Intragenic Heterochromatin-dependent RNA Polyadenylation mediated by a Protein Complex in Arabidopsis [ChIP-seq]


title: Transcriptomic analysis from lateral ganglionic eminence (LGE) of control and Isl1 conditional knock-out (cKO) mice.

status: Public on Mar 13 2022

city: Cincinnati

first: Jacqueline

middle: Marie

last: Ehrman

state: Ohio

address: 3332 Burnet Avenue

department: Developmental Biology

institute: Cincinnati Children's Hopsital and Medical Center

summary: RNA-seq analysis was used to identify genes that are differentially expressed between control and Isl1 cKO LGEs.

overall_design: Bulk RNA-seq was performed on dissected E18.5 mouse LGE from littermate control and Isl1 cKO embryos in quadruplicate

first: Kenneth

last: Campbell

last: Waclaw

first: Hee-woong

last: Lim


title: MicroRNA and mRNA regulatory network in ALK-rearranged lung adenocarcinoma

first: Sophia

last: Subat

address: 3-8-31 Ariake, Koto-ward,

institute: Japanese Foundation for Cancer Research

type:
Expression profiling by array
Non-coding RNA profiling by array


title: MicroRNA and mRNA regulatory network in ALK-rearranged lung adenocarcinoma [miRNA]

summary:
We examined microarray data of miRNAs and mRNAs from 77 cases of lung adenocarcinoma, including 42 ALK-rearranged cases.
a multistep bioinformatics approach to build a miRNA–mRNA regulatory network in ALK-rearranged lung adenocarcinoma.

overall_design: 77 samples are analyzed included  42 cases with ALK-positive,  35 cases with ALK-negative . No replicates or control samples included.

first: Kentato

last: Inamura

first: Hironori

last: Ninomiya

first: Hiroko

last: Nagano

first: Mingyon

last: Mun

first: Sakae

last: Okumura

first: Kengo

last: Takeuchi

first: Yuichi

last: Ishikawa


title: MicroRNA and mRNA regulatory network in ALK-rearranged lung adenocarcinoma [mRNA]


title: Transcriptional adaptation and enhancer rewiring promote metabolic resistance in BRAFmutated multiple myeloma (scRNA-seq)

first: Birgit

last: Knoechel

state: MA

address: 450 Brookline Ave

department: pediatric oncology

institute: Dana Farber Cancer Institute

summary:
Purpose: We here applied single-cell RNA sequencing  of circulating MM cells from primary MM patients to perform transcriptional profiling of myeloma cells and study emerging resistance mechanisms in real-time.
Methods: A total of 1509 single CD138+/CD38+ myeloma and normal plasma cells from three patients and one normal donor were examined by full-length single-cell RNA sequencing.
Results: Quality filtering resulted in the retention of 1153 cells with an average of 4836 genes detected per cell. Rapid transcriptional adaptation was observed in the presence of BRAF/MEK inhibitor treatment.
Conclusions: Inhibition of the BRAF/MEK pathway in myeloma patients induces cellular adaptation accompanied by metabolic resistance and preferential transcriptional activation of OxPhos.

overall_design:
Single-cell RNA sequencing of 1509 CD138+/CD38+ myeloma and normal plasma cells from three patients and a normal donor before and while undergoing dabrafenib/ treatment
*** Raw data not submitted to GEO due to patient privacy concerns ***

first: Johannes

last: Waldschmidt

first: Jake

last: Kloeber

first: Praveen

last: Anand

first: Julia

last: Frede

first: Antonis

last: Kokkalis

first: Valeriya

last: Dimitrova

first: Sayalee

last: Potdar

first: Monica

middle: S

last: Nair

first: Tushara

last: Vijaykumar

first: Nam

middle: G

last: Im

first: Amy

last: Guillaumet-Adkins

first: Guangwu

last: Guo

first: Andrew

last: Yee

first: Jacob

last: Laubach

first: Paul

last: Richardson

middle: C

last: Anderson

first: Noopur

last: Raje

first: Jens

last: Lohr


title: Transcriptional adaptation and enhancer rewiring promote metabolic resistance in BRAFmutated multiple myeloma (bulkRNA-seq)

first: Birgit

last: Knoechel

summary:
Purpose: We examined how transcriptional state changes relate to clonal selection as BRAF inhibitor resistance develops in BRAF-mutated myeloma.
Methods: To this end we generated three single-cell clones from U266, a BRAFK601N -mutated myeloma cell line and DP6- a BRAFV600E myeloma cell line. All three U266 and DP6 clones were subjected to long-term dabrafenib treatment at their established IC50 doses (U266: 10uM, DP6 1nM). Bulk RNA-seq was performed before treatment, day 7, day 14, day 42 and at time of resistance.
Results: Transcriptional adaptation after seven days was homogeneous for all clones, but was different across both cell lines. Oxidative phosphorylation (OxPhos) emerged as the most consistently enriched signaling pathway in persistent cells from both cell lines as compared to baseline.
Conclusions: BRAF inhibition in BRAF-mutated myeloma cells leads to transcriptional reprogramming with induction of OxPhos-related genes within a brief period of time.

overall_design: Serial transcriptional profiling by bulk RNA-seq of three single cell-clones from two myeloma cell lines undergoing dabrafenib treatment.

first: Johannes

middle: M

last: Waldschmidt

last: Kloeber

first: Kenneth


title: Transcriptional adaptation and enhancer rewiring promote metabolic resistance in BRAFmutated multiple myeloma


title: RNA-Seq of BMDM from aged mice and the effect of trained immunity

status: Public on Mar 12 2022

city: Johnson City

first: David

last: Williams

state: TN

address: PO Box 70575

department: Surgery

institute: East Tennessee State University

summary: We generated BMDMs from aged C57BL/6J mice. BMDMs were treated with C.ablican derived β-glucan, which is known to induce trained immunity. mRNA was isolated form immune trained and control BMDMs using the Rneasy Kit from Qiagen. Library preparation and sequencing performed by Novogene. We found that trained immunity induced transcriptional changes in BMDMs from aged mice

overall_design: Examination of transcriptional changes as a result of trained immunity in BMDMs from aged mice.

first: P

last: Gill

first: Jenniver

middle: V

last: Hall

first: Tammy

middle: R

last: Ozment


title: TET2 and DNMT3A Mutations Exert Divergent Effects on DNA Repair and Sensitivity of Leukemia Cells to PARP Inhibitors

city: Camden

first: Jozef

last: Madzo

state: NJ

address: 403 Haddon Avenue

department: Bioinformatics

institute: Coriell Institute

summary: TET2 and DNMT3A regulate the sensitivity to PARP inhibitor

overall_design: To model the somatic loss-of-function mutations found in human blood diseases, mice with conditional inactivation of Dnmt3a and Tet2 in the hematopoietic system were generated and further crossed with mice harboring Flt3ITD mutation. Lin-cKit+ bone marrow cells (BMC) were extracted from bone marrow of mutant and control mice. Extracted BMC were treated with ruxolitinib.

first: Silvia

last: Maifrede

first: Tomasz

last: Skorski


title: Brain transcriptomes reveal the molecular mechanism of echolocation in bats

city: Kunming

first: yanni

last: zeng

state: China,Yunnan

address: No.32 Jiaochang Donglu Kunming, Yunnan,China

department: State Key Laboratory of Genetic Resources and Evolution

institute: Kunming Institute of Zoology Chinese Academy of Sciences

summary: we use RNA-seq to attain transcriotomes of 8 bat species

sample_organism:
Cynopterus sphinx
Rousettus leschenaultii
Eonycteris spelaea
Rhinolophus affinis
Hipposideros armiger
Taphozous melanopogon
Miniopterus fuliginosus
Myotis laniger

overall_design: sequencing for transcripotme from 5 echolocators and 3 non-echolocators, provides a transcriptome-wide survey of genetic basis of echolocation

first: Yong-Yi

last: Shen

first: Yan-Ni

last: Zeng

first: Ya-Ping

last: Zhang


title: Multi-modal analysis of Col1a1-GFP in vitro vs in vivo state

city: Iowa City

first: Dakota

middle: L

last: Jones

state: IA

address: 51 Newton Road

department: Department of Anatomy and Cell Biology

institute: University of Iowa

summary: We performed RNAseq and ATACseq on FACS isolated Col1a1-GFP lung mesenchyme in culture compared to directly sorted from lung tissue

first: Daniel

last: Tschumperlin


title: Transcriptional adaptation and enhancer rewiring promote metabolic resistance in BRAFmutated multiple myeloma (ChIP-seq)

summary:
Purpose:  We examined the mechanisms of transcriptional adaptation in persistent cells and asked if transcriptional state changes can be attributed to alterations in enhancer activity.
Methods: ChIPseq for the enhancer mark H3K27ac was performed in three single-cell clones derived from the multiple myeloma cell line U266 treted with dabrafenib vs. DMSO for 14
Results: We observed substantial epigenetic remodeling illustrated by a greater number of unique peaks in dabrafenib-persistent cells as compared to dabrafenib-naïve controls. Out of a total of 22756 merged peaks, which were called in at least three samples, 7645 (34%) were unique to persistent cells compared to 454 (2%) in untreated cells.
Conclusions: Altered transcriptional states are associated with enhancer rewiring in drug-resistant myeloma

overall_design: ChIPseq for the enhancer mark H3K27ac was performed in three single-cell clones derived from the multiple myeloma cell line U266 treted with dabrafenib vs. DMSO for 14 days.

first: Jake

first: Praveen

last: Anand

first: Julia

last: Frede

first: Antonis

last: Kokkalis

first: Valeriya

last: Dimitrova

first: Sayalee

last: Potdar

first: Monica

last: Nair

first: Tushara

last: Vijaykumar

first: Nam

last: Im

first: Amy

last: Guillaumet-Adkins

first: Guangwu

last: Guo

first: Andrew

last: Yee

first: Jacob

middle: P

last: Laubach

first: Paul

last: Richardson

last: Anderson

first: Noopur

last: Raje

first: Jens

last: Lohr


title: CircNCOR1 suppresses lymphatic metastasis in bladder cancer

city: Guangzhou

first: Changhao

last: Chen

state: Guangdong

address: 107 Yanjiangxi Road, Yuexiu District, Guangzhou, Guangdong Province, P. R. China

department: Urology

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

summary: Bladder cancer (BCa) is one of the most common genitourinary malignancies worldwide, with approximately 429,800 new cases and 165,100 deaths annually in the world. Recently, circular RNA (circRNA), a class of non-coding RNA generated from pre-mRNA back splicing, has emerged as crucial mediator in various tumor initiation and progression. To identify essential circRNA that involves in the progression of BCa, Next generation sequencing (NSG) was performed in four paired BCa tissues and normal adjacent tissues (NAT).

overall_design: To identify essential circRNA that contributes to the progression of BCa, NGS was performed in four paired BCa tissues and normal adjacent tissues (NAT). The RNA of tissue was extracted and hybridized on illumina Hiseq 2500.

first: Mingjie

last: An

first: Tianxin

last: Lin


title: Next Generation Sequencing Quantitative Analysis of altered expression of genes in LINC00665 overexpressing bladder cancer cells

summary: Bladder cancer (BCa) is one of the most commonly diagnosed urinary malignancies with an estimated yearly 550,000 new cases worldwide. Previous study revealed that LINC00665 was a crucial oncogene that widely involved in tumor initiation and progression. Yet the biological role and underlying regulatory mechanism of LINC00665 in lymph node (LN) metastasis of bladder cancer (BCa) remain unclear. Our study aims to explore the target genes of LINC00665 and the underlying mechanism in the LN metastasis of BCa.

overall_design: To detect the precise mechanism of LINC00665 in LN metastasis of BCa, the total RNA of T24 cells transfected with Vector plasmids or LINC00665-overexpressing plasmids was extracted and the next generation sequencing was conducted to explore the expressing profile difference between Vector and overexpression group. The result was obtained from three independent experiments.

first: Yuting

last: Li


title: Frugivorous bats drink but lost the key alcohol metabolism gene--Adh1

first: yanni

last: zeng

summary: RNA-seq was used to attain liver transcriptomes of 5 bat individuals

sample_organism:
Rousettus leschenaultii
Miniopterus schreibersii

overall_design: Sequencing for transcriptome from 3 Frugivorous bats and 2 insectivorous bats, provides a transcriptome-wide survey of genetic basis of the alcohol metabolism in Frugivorous bats

first: Lu

last: Liang

first: Yong-Yi

last: Shen

first: Yan-Ni

last: Zeng

first: Gui-Mei

first: Xing

first: Tai-Cheng

last: Zhou

first: He-Qun

last: Liu

first: Li

last: Zhong

first: David

last: Irwin

first: Xue-Juan

first: Shi-Fang

last: Wu

first: Ya-Ping

last: Zhang


title: Next Generation Sequencing Quantitative Analysis of altered expression of genes in circNCOR1 overexpressing bladder cancer cells

first: Changhao

summary: Bladder cancer (BCa) is one of the most common genitourinary malignancies worldwide, with approximately 429,800 new cases and 165,100 deaths annually in the world. Recently, circular RNA (circRNA), a class of non-coding RNA generated from pre-mRNA back splicing, has emerged as crucial mediator in various tumor initiation and progression. To identify molecular mechanism of circNCOR1 in the progression of BCa, Next generation sequencing (NSG) was performed to explore the target genes of circNCOR1 in BCa.

overall_design: To detect the precise mechanism of circNCOR1 in LN metastasis of BCa, the total RNA of UM-UC-3 cells transfected with Vector plasmids or circNCOR1-overexpressing plasmids was extracted and the next generation sequencing was conducted to explore the expressing profile difference between Vector and overexpression group. The result was obtained from three independent experiments.


title: MESH1 knockdown triggers proliferation arrest through TAZ repression

first: Jen-Tsan

last: Chi

address: 101 Science Drive, DUMC 3382

department: Molecular Genetics and Microbiology

institute: Duke University

summary: All organisms are constantly exposed to various stresses, necessitating adaptive strategies for survival. In bacteria, the main stress-coping mechanism is the stringent response triggered by the accumulation of “alarmone” (p)ppGpp to arrest proliferation and reprogram transcriptome. While mammalian genomes encode MESH1—the homolog of the (p)ppGpp hydrolase SpoT, current knowledge about its function remains limited. We found MESH1 expression tended to be higher in tumors and associated with poor patient outcomes. Consistently, MESH1 knockdown robustly inhibited proliferation, depleted dNTPs, reduced tumor sphere formation, and retarded xenograft growth. These antitumor phenotypes associated with MESH1 knockdown were accompanied by a significantly altered transcriptome, including the repressed expression of TAZ, a HIPPO coactivator, and proliferative gene. Importantly, TAZ restoration mitigated many anti-growth phenotypes of MESH1 knockdown, including proliferation arrest, reduced sphere formation, tumor growth inhibition, dNTP depletion, and transcriptional changes. Furthermore, TAZ repression was associated with the histone hypo-acetylation at TAZ regulatory loci due to the induction of epigenetic repressors HDAC5 and AHRR. Together, MESH1 knockdown in human cells altered the genome-wide transcriptional patterns and arrested proliferation that mimicked the bacterial stringent response through the epigenetic repression of TAZ expression.

overall_design: RNA was extracted by RNAeasy kits (Qiagen) from the RCC4 transfected with control siRNA or siRNA-targetting MESH1 (three replicates in each condition).

first: T

last: Sun

first: C

last: Ding


title: Gene expression of ErbB2-positive tumors harboring either wild type p110α or H1047R mutation

status: Public on Mar 11 2022

city: Montreal

first: Tung

last: Bui

state: Quebec

address: 1160 Pine Ave. W, R507

department: Biochemistry

institute: McGill University

summary:
A mouse model utilizing knock in strategy to coexpress both oncogenic ErbB2 (NeuNT) and a PI3KCA mutation H1047R
Microarray was used to determine gene expression change due to H1047R mutation by comparison between ErbB2 KI tumors expressing either wild type or mutant allele.

overall_design: Transgenic tumors were collected for total RNA for subsequent library prepration and Affymetrix microarray.

first: Alexandra

last: Simond


title: Transcriptome analysis by RNA-seq of patient or cell line derived xenograft of gastric cancer established in the Cancer Institute Hospital of Japanese Foundation for Cancer Research.

first: Norio

last: Tanaka

address: Ariake 3-8-31, Koto

institute: Japanese Foundation Cancer Research

summary:
We performed the RNA-seq experiments for mRNA of xenograft tumor tissue.
Raw data are not available for this Series due to patient privacy concerns.

overall_design: Messenger RNA were extracted from xenograft tumor tissue, prepared with Ilumina TruSeq Access mRNA  Library Prep Kit and sequenced  on the Illumina HiSeq


title: NanoSTRING nCounter Mouse Tumor Signaling 360 Panel for mouse ileum tissue

city: Seoul

first: Dong Young

last: Kim

address: 75 Nowon-ro

institute: KIRAMS

summary: Whether Wnt signaling-targeted genes and co-receptors were downregulated in STP1002 (TNKSi)-treated ileum tissues.

overall_design: Three mice were randomly selected from eight mice in each group. Control 3 mice, STP1002 5 mpk 3 mice, STP1002 10 mpk 3 mice, G007-LK 3 mice.

first: Jae-Sung

first: Dong

middle: Y


title: Integrated analysis of long non-coding RNAs expression profiles in THP-1 induced M0, M1 and M2 macrophage and GCC culture medium induced similar M2 (CM-sM2)

city: Shijiazhuang

first: Cong

address: Jian Kang Road 12th

institute: The fourth hospital of Hebei medical university

summary: We used microarray and bioinformatics analysis to find potential lncRNAs which may be useful in the polarization of  macrophages

overall_design: To screen for the functional lncRNAs involved in macrophages polarization, total RNA from THP-1 induced M0, M1, M2 and CM-sM2 cells were extracted and analyzed, we employed SBC-lncRNA (human 4*180K) microarray as a discovery platform to identify genes. [M0 were induced by PMA (50ng/ml) for 48h, M1 were induced by LPS (100ng/ml) and IFN-γ (20ng/ml) for 48h and M2 were induced by IL-4  (20ng/ml) for 48h both on the basis of M0. CM-sM2 were induced by 30% culture medium of  gastric cancer cells on the basis of M0.]

first: Lianmei

last: Zhao


title: Identification and Validation of Autophagy-Related Genes in Necrotizing Enterocolitis

city: Shanghai

first: Yuxin

last: Tian

address: 399 Wanyuan Road

institute: Children's Hospital of Fudan University

summary:
Background: Autophagy plays an essential role in the occurrence and progression of Necrotizing enterocolitis (NEC). We purposed to carry out the identification and validation of the probable autophagy-related genes of NEC via bioinformatics methods and experiment trials.
Methods: The autophagy-related differentially expressed genes (arDEGs) of NEC were identified by analyzing the RNA sequencing data of experiment neonatal mouse model and dataset GSE46619. Protein-protein interactions (PPI), gene-ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were used for the arDEGs. Then, co-expressed autophagy-related genes in two datasets were identified by Venn analysis and verified by qRT-PCR in experimental NEC.
Results: Autophagy increased in experimental NEC and 47 arDEGs were identified in experimental NEC by RNA-sequencing. The PPI results proclaimed those genes interplayed with each other. The GO and KEGG enrichment results of arDEGs reported some certain enriched pathways related to autophagy and macroautophagy. Furthermore, 22 arDEGs were identified in human NEC from dataset GSE46619. The GO and KEGG enrichment analysis of these genes showed similar enriched terms with the results in experimental NEC. Finally, HIF-1a, VEGFA, ITGA3, ITGA6, ITGB4 and NAMPT were identified as co-expressed autophagy-related genes by Venn analysis in human NEC from dataset GSE46619 and experimental NEC. The result of qRT-PCR revealed the expression levels of HIF-1a and ITGA3 upregulated, VEGFA and ITGB4 downregulated in experimental NEC.
Conclusion: We identified 47 arDEGs in experimental NEC and 22 arDEGs in human NEC via bioinformatics analysis. HIF-1a, ITGA3, VEGFA and ITGB4 may have effects on the progression of NEC through modulating autophagy.

overall_design: Intestinal mRNA profiles of 9-day old normal and NEC neonatal mice

first: Chun


title: MicroRNA Alterations Induced in Human Skin by Diesel Fumes, Ozone, and UV Radiation

city: Genova

first: Alessandra

last: Pulliero

state: Genova

address: Via A. Pastore 1

country: Italy

institute: Dipartimento di Scienze della Salute UNIGE

summary: Epigenetic alterations are a driving force of the carcinogenesis process. MicroRNAs play a role in silencing mutated oncogenes, thus defending the cell against the adverse consequences of genotoxic damages induced by environmental pollutants. These processes have been well investigated in lungs; however, although skin is directly exposed to a great variety of environmental pollutants, more research is needed to better understand the effect on cutaneous tissue. Therefore, we investigated microRNA alteration in human skin biopsies exposed to diesel fumes, ozone, and UV light for over 24 h of exposure. UV and ozone-induced microRNA alteration right after exposure, while the peak of their deregulations induced by diesel fumes was reached only at the end of the 24 h. Diesel fumes mainly altered microRNAs involved in the carcinogenesis process, ozone in apoptosis, and UV in DNA repair. Accordingly, each tested pollutant induced a specific pattern of microRNA alteration in skin related to the intrinsic mechanisms activated by the specific pollutant. These alterations, over a short time basis, reflect adaptive events aimed at defending the tissue against damages. Conversely, whenever environmental exposure lasts for a long time, the irreversible alteration of the microRNA machinery results in epigenetic damage contributing to the pathogenesis of inflammation, dysplasia, and cancer induced by environmental pollutants.

overall_design: We investigated microRNA alteration in human skin biopsies exposed to diesel fumes, ozone, and UV light for over 24 h of exposure

first: Giuseppe

last: Valacchi

first: Erika

last: Pambianchi

first: Simona

last: Coco

first: Alberto

last: Izzotti


title: Comparison between Periprostatic adipose tissue and abdominopelvic adipose tissue

city: Toulouse

first: David

last: Estève

address: 205 route de narbonne

country: France

institute: Institut de pharmacologie et de biologie structurale-IPBS

summary: White adipose tissue accumulates at various sites throughout the body and some adipose tissue depots exist in close proximity to organs, whose function they could influence in a paracrine manner. Prostate gland is surrounded by a poorly characterized adipose depot called periprostatic adipose tissue (PPAT) playing emerging roles in prostate-related disorders. Unlike all other adipose depots, PPAT secretes pro-inflammatory cytokines even in lean individuals and does not increase in volume during obesity. These unique features remain unexplained due to the poor structural and functional characterization of this tissue. We characterized the structural organization of PPAT in patients in comparison to abdominopelvic adipose tissue (APAT), an extraperitoneal adipose depot whose accumulation is correlated to BMI. Unbiased comparisons of PPAT and APAT transcriptomes found that most differentially expressed genes were related to the hypoxia response. This chronic hypoxic state was associated with inflammation and fibrosis, which explain the failure of PPAT to expand in obesity and open new mechanistic avenues to explain its role in prostate-related disorders including cancer.

overall_design: Paired periprostatic adipose tissue and abdominopelvic adipose tissue were compared from 3 different patients

first: Mathieu

last: Roumiguié

first: Delphine

last: Milhas

first: Catherine

last: Muller


title: Reprogramming of pro-inflammatory human macrophages to an anti-inflammatory phenotype by bile acids

city: Duesseldorf

first: Anna-Kathrin

last: Schupp

address: Moorenstr. 5

institute: Heinrich Heine University Duesseldorf

summary: Cholestasis is caused by autoimmune reactions, drug-induced hepatotoxicity, viral infections of the liver and the obstruction of bile ducts by tumours or gallstones. Cholestatic conditions are associated with impaired innate and adaptive immunity, including alterations of the cellular functions of monocytes, macrophages, NK cells and T-cells. Bile acids act as signalling molecules, affecting lipopolysaccharide (LPS)-induced cytokine expression in primary human macrophages. The present manuscript investigates the impact of bile acids, such as taurolithocholic acid (TLC), on the transcriptome of human macrophages in the presence or absence of LPS. While TLC itself has almost no effect on gene expression under control conditions, this compound modulates the expression of 202 out of 865 transcripts in the presence of LPS. Interestingly, pathway analysis revealed that TLC specifically supressed the expression of genes involved in mediating pro-inflammatory effects, phagocytosis, interactions with pathogens and autophagy as well as the recruitment of immune cells, such as NK cells, neutrophils and T cells. These data indicate a broad influence of bile acids on inflammatory responses and immune functions in macrophages. These findings may contribute to the clinical observation that patients with cholestasis present a lack of response to bacterial or viral infections.

overall_design: Gene expression profiling of macrophages treated with DMSO, LPS, TLC or LPS+TLC

first: Marianne

last: Wammers

first: Johannes

last: Bode

first: Christian

last: Ehlting

first: Stephanie

last: Wolf

first: René

last: Deenen

first: Karl

last: Köhrer

first: Dieter

last: Häussinger

first: Dirk

last: Graf


title: Tudor-domain containing protein 5-like promotes male sexual identity in the Drosophila germline and is repressed in females by Sex lethal

city: Balitmore

first: Mark

last: Van Doren

state: Maryland

address: 3400 N Charles street, Mudd Hall

department: Biology

institute: Johns Hopkins University

summary: Like humans, all sexually reproducing organisms require gametes to reproduce. Gametes are made by specialized cells called germ cells, which must have the correct sexual identity information to properly make sperm or eggs. In fruit flies, germ cell sexual identity is controlled by the RNA-binding protein Sxl, which is expressed only in females. To better understand how Sxl promotes female identity, we conducted an RNA expression profiling experiment to identify genes whose expression changes in response to the loss of Sxl from germ cells. Here, we identify Tudor domain containing protein 5-like (Tdrd5l), which is expressed 17-fold higher in ovaries lacking Sxl compared to control ovaries. Additionally, Tdrd5l plays an important role in males as male flies that are mutant for this gene cannot make sperm properly and thus are less fertile. Moreover, we find that Tdrd5l promotes male identity in the germline, as several experiments show that it can shift the germ cell developmental program from female to male. This study tells us that Sxl promotes female identity in germ cells by repressing genes, like Tdrd5l, that promote male identity. Future studies into the function of Tdrd5l will provide mechanistic insight into how this gene promotes male identity

overall_design: gene expression comparrison between bam male and female flies. Expression analysis was also conducted between Sxl RNAi females and mcherry RNAi females in a bam mutant backgrounds

first: Shekerah

last: Primus

first: Caitlin

last: Pozmanter

first: Kelly

last: Baxter


title: Distinct early-life stage gene expression effects of hybridization among European and North American farmed and wild Atlantic salmon populations

city: ST JOHN'S

first: Shahinur

middle: S.

last: Islam

state: Newfoundland and Labrador

address: 230 Elizabeth Avenue

institute: Memorial University of Newfoundland

summary: Due to multi-generation domestication selection, farmed and wild Atlantic salmon diverge genetically, which raises concerns about potential genetic interactions among escaped farmed and wild populations and disrupts local adaptation through introgression. When farmed strains of distant geographic origin are used,  it is unknown whether the genetic risks posed by escaped farmed fish will be greater than if more locally derived strains are used. Quantifying gene expression differences among divergent farmed, wild and F1 hybrids under controlled conditions is one of the ways to explore the consequences of hybridization. We compared the transcriptomes of late sac fry of a European (EO) farmed (“StofnFiskur”, Norwegian strain), a North American (NA) farmed  (Saint John River, NB strain), a Newfoundland (NF) wild population with EO ancestry, and related F1 hybrids using 44K microarrays. Our findings indicate that the wild population showed greater transcriptome differences from the EO farmed strain than that of the NA farmed strain.  We also found the largest differences in global gene expression between the two farmed strains. We detected fewer differentially expressed transcripts between F1 hybrids and domesticated/wild maternal strains. We also found that the differentially expressed genes between cross types over-represented GO terms associated with metabolism, development, growth, immune response, and redox homeostasis processes. These findings suggest that the interbreeding of escaped EO/NA farmed and NF wild population would alter gene transcription, and the consequences of hybridization would be greater from escaped EO farmed than NA farmed salmon, resulting in potential effects on the fitness of wild populations.

overall_design:
Salmon used in experimental crosses were derived from parental salmon of three main populations: Farm.NA, Farm.EO, and Wild. The origin of Farm.NA is the Saint John River, New Brunswick, Canada. Farm.NA gametes were collected from the aquaculture company Northern Harvest, based in Southern Newfoundland, Canada. Farm.EO, a Norwegian origin farm strain, is now produced at an Icelandic facility (StofnFiskur), from where the gametes were shipped by air for the experimental crosses. The wild population was derived from the Northeast Placentia River, Newfoundland, Canada. The microarray study was performed using a consortium for Genomic Research on All Salmonids Project (cGRASP)-designed Agilent (Mississauga, ON, CA) 44K salmonid oligonucleotide microarray (GEO accession number: GPL11299. The microarray experiment comprised 36 arrays: 6 cross types (Farm.NA, Hyb.NAff, Wild, Hyb.EOwf, Hyb.EOff, and Farm.EO) x 3 families per cross type x 2 biological replicates per family. F1 Farm.NA(f)-x-Wild(m) hybrid (referred to as “Hyb.NAff”); F1 Farm.EO(m)-x-Wild(f) hybrid (referred to as “HybEOwf”); and F1 Farm.EO(f)-x-Wild(m) hybrid (referred to as “Hyb.EOff”).
variable: Farm.NA: Farm.NA1, Farm.NA2, Farm.NA3, Farm.NA4, Farm.NA5, Farm.NA6
variable: Hyb.NAff: Hyb.NAff1, Hyb.NAff2, Hyb.NAff3, Hyb.NAff4, Hyb.NAff5, Hyb.NAff6
variable: Wild: Wild1, Wild2, Wild3, Wild4, Wild5, Wild6
variable: Hyb.EOwf: Hyb.EOwf1, Hyb.EOwf2, Hyb.EOwf3, Hyb.EOwf4, Hyb.EOwf5, Hyb.EOwf6
variable: Hyb.EOff: Hyb.EOff1, Hyb.EOff2, Hyb.EOff3, Hyb.EOff4, Hyb.EOff5, Hyb.EOff6
variable: Farm.EO: Farm.EO1, Farm.EO2, Farm.EO3, Farm.EO4, Farm.EO5, Farm.EO6

first: Xi

last: Xue

first: Albert

last: Caballero-Solares

first: Ian

last: Bradbury

first: Matthew

last: Rise

middle: A

last: Fleming


title: Transcriptome of bovine trophoblast stem cells (TSC) - in self-renewal and differentiation

city: Ithaca

first: Vimal

last: Selvaraj

address: 204 Morrison Hall

department: Animal Science

institute: Cornell University

summary: In this study, we examine the transcriptome of bovine TSCs under self-renewal that is sustained by inhibiting RhoA-Rock pathway. Using systems biology of spontaneous differentiation, we identify that TGFB1 induces differentiation of bovine TSCs. We analyse the transcriptome of TSCs under TGFB1 induced differentiation. We also analyze pathways of differentiation that are dependent and independent of RhoA-Rock signaling through analysis of the transcriptome of TSCs exposed to both TGFB1 and ROCK inhibition.

overall_design: Undifferentiated bovine blastocyst-derived trophectoderm cells from IVF embryos were cultured, and changes to the transcriptome were examined after exposure to RhoA-Rock inhibition and TGFB1 stimulation.

first: Viju

last: Pillai


title: C89 Induces the autophagy of Female Germline Stem cells Via inhibition of PI3K-AKT Signaling Pathway in vitro

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

summary: Purpose: To uncover the mechanism of C89-induced autophagy in FGSCs, we used RNA sequencing technology to compare the mRNA expression differences between the control groups and the C89 treated groups. FGSCs mRNA profiles of the control groups and the C89 treated groups were generated by deep sequencing, in triplicate. The library quality was determined using a Bioanalyzer 2100 (Agilent). The Illumina HiSeq 2500 platform was used for RNA sequencing. The quality of RNA-seq reads was examined using FastQC. Using an optimized data analysis workflow, we identified 15243 transcripts in the FGSCs of the control groups and the C89 treated groups. After applying a stringent filtering approach that compared control and C89-treated groups (adjusted p value, < 0.05; fold change, > 1.5 or < 0.5), we identified 937 upregulated and 1046 downregulated mRNAs. Approximately 13% of the transcripts showed differential expression between the control and C89-treated groups, with a fold change ≥1.5 and p value <0.05.And we found 4 differentially expressed mRNAs was related to autophagy and qRT-PCR was used to verify it. The GO and KEGG analyse reveal that the differential expression mRNAs were related to the process of cell proliferation, death and immunoreaction. Our study analyse of the control groups and the C89 treated groups transcriptomes, with biologic functions, generated by RNA-seq technology.The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that the PI3K-AKT pathway was related to the influence of C89 on FGSCs. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: C89-treated and control FGSCs mRNA profiles of 8h were generated by deep sequencing, in triplicate.

first: Xinyue

last: li


title: Ssb1/2-IntS complexes maintain splicing integrity and genomic stability through regulating RNA Polymerase II mediated snRNA levels

city: Brisbane

first: Jasmin

last: Straube

state: QLD

address: 300 Herston Rd

country: Australia

institute: QIMR Berghofer

summary: Ssb1(NABP2/OBFC2A) and Ssb2 (NABP1/OBFC2B) are two closely related proteins that show functional redundancies supported by their existence in two separate subcomplexes with identical proteins.  Ssb1 knockout causes perinatal lethality in mice, Ssb2 knockout does not associate with any observable phenotypes, however, double knockout of both Ssb1/2 causes embryonically lethality. Notably, conditional loss of both in adult mice leads to acute lethality due to bone marrow and gut failure. Here, we further demonstrate that the overlapping essential function of both Ssb1/2 is through their prime binding partner IntS3, a member of the multiprotein complex called the Integrator. The Integrator complex interacts with the largest subunit of RNA Polymerase II and is required for processing and termination of small nuclear RNAs (snRNAs). Here, we provide a firsthand evidence that the stability of the Integrator complex is compromised in mouse-embryonic fibroblasts (MEFs) with compound loss of both Ssbs. We further demonstrate that these MEFs show overexpression of unprocessed snRNAs which forces the cells to express alternative spliced variants of genes that are required for transcription and cell cycle regulation. This phenotype closely phenocopies loss of core integrator subunit, IntS11 as well as splicing components B and C. Interestingly, the phenotype gets partially restored by overexpression of wildtype Ssb1 but not by the Ssb-mutant defective in binding integrator subunit, IntS3, demonstrating the essential roles of Ssb1/2 in the maintenance of the Integrator complex and thereby, genomic stability.

overall_design: To understand the transcriptional changes caused by loss of Ssb1 and Ssb2 in Mouse embryonic fibroblasts, we performed RNA-sequencing on Vehicle and 4-OHT-treated control and Ssb1/Ssb2 conditional double-knockout mouse embryonic fibroblasts (MEFs)

first: Purba

last: Nag

first: Amanda

last: Bain

first: Kum

middle: K

last: Khanna


title: Intrinsic defects in lymph node stromal cells underpin poor germinal center responses during aging

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

country: United Kingdom

institute: Altos Labs

summary: The aim of this study was to understand how age impacts on the early response of follicular dendritic cells and marginal reticular cells to immunisation

overall_design: There are 39 samples in total, 19 samples of follicular dendritic cells, 20 samples of marginal reticular cells, all isolated from C57BL/6 mouse lymph nodes by cell sorting. Within each cell type, cells have been isolated from adult 8 week-old mice and aged 98 week old mice, from both unimmunsed mice and 2 days after immunisation with NP-KLH emulsified in Alum. Within each group there are five replicates, apart from the unimmunised Aged FDC group, where only four replicates have passed QC

first: Alice

last: Denton

first: Michelle

last: Linterman


title: RNA-Seq of HeLa cells

status: Public on Mar 10 2022

city: New Orleans

first: Tina

last: O'Grady

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

institute: Tulane Health Sciences Center

summary: HeLa cells were treated with ActD and RNA sequenced to examine RNA stability

overall_design: Three biological replicates of HeLa cells were treated with ActD and RNA sequenced at 0h, 1h, 2h and 4h post-treatment

first: Emeline

last: Mariavelle

first: Franck

last: Dequiedt


title: SARS-CoV-2 Nsp14 mediates the effects of viral infection on the host cell transcriptome

city: Waltham

first: Sebastian

last: Kadener

address: 415 South Street

institute: Brandeis University

summary: We performed a transcriptomic analysis of H293T cells expressing individual SARS-CoV2 proteins. Overexpression of Nsp14, a protein known to be involved in viral RNA replication, provoked a dramatic remodeling of the transcriptome, altering the expression of ≈4000 RNAs (3'RNAseq). These transcriptome changes strongly resemble the ones observed following SARS-CoV-2 infection. We performed a timecourse 3'RNA seq experiment and detected genes related to NFkB activation as deregulated soon after the transfection. We showed that the effect does not depend by the presence of the co-factor Nsp10 (total RNA seq) or by the exonuclease activity of Nsp14 (3' RNA seq of Nsp14 D90A/G92A and Nsp14D273 mutants). Finally we saw that the effect are mediated by the cellular enzyme IMPDH2, since treatment with MPA partially rescued the effect induced by Nsp14OE (3'RNA seq).

overall_design: control cells were transfected with eGFP (pLVX-EF1alpha-eGFP-2xStrep-IRES-Puro Addgene 141395). The other samples were transfected with Nsp14 (pLXV-EF1alpha-2xStrep-SARS-CoV-2-nsp14-IRES-Puro Addgene 141380) or the indicated plasmid (pLVX-EF1alpha-SARS-CoV-2-proteins-2xStrep-IRES-Puro Gordon et al., 2020)


title: Identification of MicroRNAs in Wound Healing Model Mice During Inflammation and Temporal Expression Analysis

city: Ningbo

first: cao

last: yuhao

state: Zhejiang Province

address: 818 Fenghua Road, Jiangbei District, Ningbo City, Zhejiang Province

institute: Medical School of Ningbo University

summary: The transcriptome sequencing of skin samples from wound tissues was utilized to discover miRNAs and their differential expression profiles between day 0 and day 7. On day 7, the criterion of log2 fold change >1 and P-value 0.01 was selected for data analysis, and 21 miRNAs were identified as being up-regulated and 1 as being down-regulated. The gene ontology analyses showed the target genes of miRNAs were related to biological processes, cellular components, and molecular function. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the target genes of miRNAs during skin wound healing showed the most enriched pathways were cancer, peroxisome, and lysosome. The study might provide an experimental foundation for further investigation on the mechanisms of wound healing, and some useful information for the miRNA-based treatments for wound healing.

overall_design: Nine mice were randomly divided into three groups. After anesthesia with 1% pentobarbital sodium, a hole punch with a diameter of 8 mm was used to model the skin wound on the mouse back.

first: Y

last: Cao

first: X

last: Song

first: P

last: Feng

first: F

last: Zhao


title: Midnolin Regulates Liver Cancer Cell Growth In Vitro and In Vivo

city: Duarte

first: wei

last: chen

state: CA

address: 1500 E Duarte Rd

department: Cancer Biology-BRI

institute: City of Hope National Medical Center

summary: Hepatocellular carcinoma (HCC) ranks worldwide as one of the most lethal cancers. In spite of the vast existing knowledge about HCC, the pathogenesis of HCC is not completely understood. Discovery of novel genes which contribute to HCC pathogenesis will provide new insights for better understanding and treating HCC. The relatively obscure gene midnolin has been studied for over two decades; however, its biological roles are largely unknown. Our study is the first to demonstrate the functional significance of midnolin in HCC/cancer: Midnolin expression correlates with poor prognosis in HCC patients, and suppression of midnolin severely inhibits tumorigenicity of HCC cells in vitro and in mice and disrupts retinoic acid/lipid metabolism in these cells.

overall_design: In order to investigate the role of midnolin in HCC, we generated midnolin knockdown (KD) Hepa1-6 stable cell line by transduction of lentivirus containing shRNA targeting midnolin, and then we evaluated the effect of midnolin KD on cell proliferation, colony formation, and tumor formation.

first: Soo-Mi

last: Kweon

first: Gayeoun

last: Kim

first: YunSung

last: Jeong

first: Wendong

last: Huang

first: Ju-Seog

last: Lee

first: Keane

last: Lai


title: Metabolomic and transcriptomic profiling of DRG in SNI rat reveal a common pattern of changes in metabolites and signaling pathways in Neuropathic Pain

city: Wuhan

first: Zhen

middle: Zhen

last: Xu

state: Hubei

address: 1277 Jiefang Avenue, Kong Hon District

department: Department of Anesthesiology

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: Neuropathic Pain (NP) is a clinically common chronic refractory pain syndrome which threat to approximately 7–10% of the global population physical and mental health. However, the mechanism of metabolism alteration in NP remains unclear. This study is intended to figure out the relationship between the alternation of metabolism and the progression of NP.

overall_design: In this study, transcriptomic data were obtained from Beijing Genomics institution (BGI) and Gene Expression Omnibus (GEO) database. Kyoto Encyclopedia of Genes and Genomes (KEGG) database was performed to enrich the pathways. Joint-pathway analysis performed on Metaboanalyst.ca

first: Xu

last: Zhen-Zhen

first: Wang

last: Yan-Ting

first: Feng

last: Yi-Qi

first: Wu

last: Qing-Ping


title: Sexual dimorphism in osteogenic differentiation

city: Bielefeld

first: Barbara

last: Kaltschmidt

address: Universitätsstr. 25

department: Molecular Neurobiology

institute: University of Bielefeld

summary: RNA-sequencing of adult human stem cells determining sexual dimorphisms in osteogenic differentiation.

overall_design: Male and female adult human stem cells underwent osteogenic differentiation for 14 and 30 days followed by RNA-sequencing.


title: The receptor-like cytosolic kinase RIPK activates NADP-malic enzyme 2 to generate NADPH for fueling the ROS production

city: Hangzhou

first: YAN

middle: BIN

last: WU

state: Zhejiang

address: 866 Yuhangtang Rd

department: College of Agriculture & Biotechnology

institute: Zhejiang University

summary: Reactive oxygen species (ROS) production is a conserved immune response, primarily mediated in Arabidopsis by the respiratory burst oxidase homolog D (RBOHD), a nicotinamide adenine dinucleotide phosphate (NADPH) oxidase associated with the plasma membrane. A rapid increase in NADPH is necessary to fuel RBOHD proteins and hence maintain ROS production. However, the molecular mechanism underlying the NADPH generation for fueling RBOHD remains unclear. In this study, we isolated a new mutant allele of flagellin-insensitive 4 (FIN4), encoding the first enzyme in de novo NAD biosynthesis. fin4 mutants show reduced NADPH levels and impaired ROS production. However, FIN4 and other genes involved in the NAD- and NADPH-generating pathways are not highly upregulated upon elicitor treatment. Therefore, we hypothesized that a cytosolic NADP-linked dehydrogenase might be post-transcriptionally activated to keep the NADPH supply close to RBOHD. RPM1-INDUCED PROTEIN KINASE (RIPK), a receptor-like cytoplasmic kinase, regulates broad-spectrum ROS signaling in plant immunity. We then isolated the proteins associated with RIPK and identified NADP-malic enzyme 2 (NADP-ME2), an NADPH-generating enzyme. Compared with wild-type plants, nadp-me2 mutants display decreased NADP-ME activity, lower NADPH levels, as well as reduced ROS production in response to immune elicitors. Furthermore, we found that RIPK can directly phosphorylate NADP-ME2 and enhance its activity in vitro. The phosphorylation of NADP-ME2 S371 residue contributes to ROS production upon immune elicitor treatment and the susceptibility to the necrotrophic bacterium, Pectobacterium carotovorum. Overall, our study suggests that RIPK activates NADP-ME2 to rapidly increase cytosolic NADPH, hence fueling RBOHD to sustain ROS production in plant immunity.

overall_design: Seedling mRNA profiles of ten-day old Arabidopsis thaliana Col-0 8 h after treatment with or without 3-OH-C10:0

first: Yan

last: Liang

first: Binyan

last: Wu

first: Ping

last: Li

first: Xiufang

last: Hong

first: Cuihong

first: Ran

last: Wang


title: Transcriptome analysis of B. pertussis-stimulated human airway epithelium

city: Bilthoven

first: Alberto

last: Miranda-Bedate

state: Utrecht

address: Antonie van Leeuwenhoeklaan 9

department: Department of Immune Mechanisms (IMM)

institute: RIVM

summary: We analysed the transcriptome, using an illumina RNAseq platform, of human airway epithelium cells after 6 hour stimulation with 3 different natural circulating B.pertussis strains

overall_design: human airway epithelium cells were stimulated for 6h with 3 different natural circulating B. pertussis strains after which the transcriptome was analysed by RNAseq

first: Michiel

last: Kroes

first: Elena

last: Pinelli

first: Ronald

last: Jacobi


title: H3K27me3 regulates macrophage cytokine transcription and impacts on Collagen Induced Arthritis [RNA-Seq]

city: Qingdao

first: zhao

last: zhan

state: Shandong

address: No.23 HongKong East Road,Laoshan District

department: School of Medicine and Pharmacy

institute: Ocean University of China

summary: The role of epigenetic regulation has been introduced in the process of macrophage polarization and the pathogenesis of inflammatory diseases. As a repressive epigenetic marker, tri-methylation of lysine 27 on histone H3 (H3K27me3) was shown to be important for transcriptional gene expression regulation. Here, we comprehensively analyzed H3K27me3 binding promoter sequences by ChIP-seq and corresponding genes function by RNA sequencing in two differentially polarized macrophage populations. The results revealed that H3K27me3 binds on the promoter regions of multiple critical cytokine genes and suppressed their transcription, especially in M-CSF derived macrophages but not GM-CSF derived counterparts. The in vivo study results suggested that symptoms of collagen induced arthritis (CIA) mice can be relieved by reversing the loss of H3K27me3 and reducing IL6 parasecretion of macrophages, suggesting that H3K27me3 might act as a switch in the pathological processes of rheumatoid arthritis (RA). Our results may provide a new approach for the treatment of inflammatory and autoimmune disorders.

overall_design: Examination of 4 different RNA transcription levels in GM-CSF induced BMDMs.

first: Zhao

last: Zhan


title: Zfp57 exerts maternal and sexually dimorphic effects on genomic imprinting

city: Shanghai

first: zhen

last: Xu

state: Shanghai

address: Mid Huaxia road 393

institute: ShanghaiTech university

summary: RNA-seq analysis was used to find the target genes of Zfp57 in mouse embryos.

overall_design: 23 samples

first: Z

first: Y

last: Zhang

first: X


title: Detection of genome-wide methylation changes in prion-infected central nervous system

city: Zaragoza

first: Inmaculada

last: Martín Burriel

state: Zaragoza

address: Miguel Servet, 177

department: Anatomy, Embriology and Animal Genetics

country: Spain

institute: University of Zaragoza

type: Methylation profiling by high throughput sequencing

summary: Scrapie is a Transmissible Spongiform Encephalopathy (TSE) that affects sheep and goats and it is considered a good natural animal model to study prion diseases. Although changes in DNA methylation occur in many neurodegenerative diseases including human prion diseases, potential DNA methylation alterations have not yet been investigated in the central nervous system (CNS) of any prion disease models or naturally infected cases. We present here a whole genome bisulfite sequencing analysis (WGBS) from thalamus of four naturally scrapie infected sheep and four controls. All animals were female, carried the ARQ/ARQ genotype for the PRNP allele and were sacrificed at similar age (4 to 6 years old). Even if genomes displayed similar average methylation levels, we identified 39 differentially methylated promoters (DMP) and a total of 8,907 differentially methylated regions (DMR). Gene Ontology enrichment revealed that hypomethylated DMRs were enriched in genes involved in transmembrane transport and cell adhesion whereas hypermethylated DMRs were related with intracellular signal transduction genes. Moreover, we compared the set of identified DMRs with genes previously described to be differentially expressed in scrapie and with a set of genes encoding proteins defined to be tenfold more abundant in specific types of CNS cells finding that some of these genes also harboured DMRs. Finally, a validation study using qPCR was conducted showing differences in the expression of five genes (PCDH19, SNCG, WDR45B, PEX1 and CABIN1) that matched the methylation changes observed in the genomic study. Altogether, these findings suggest a potential regulatory role of CNS DNA methylation in prion diseases.

overall_design: DNA methylation profiling using whole-genome bisulfite sequencing of 8 sheep thalamus samples, 4 samples from control sheep and 4 samples from sheep naturally infected with scrapie.

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last: Hernaiz

first: Arianne

last: Sanz

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last: Sentre

first: Beatriz

last: Ranera

first: Óscar

last: López-Pérez

first: Pilar

last: Zaragoza

first: Juan

middle: J

last: Badiola

first: Hicham

last: Filali

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last: Bolea

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last: Toivonen

last: Martín-Burriel


title: Long RNA in endothelial cells and EVs treated with VEGF or H2O

first: Tina

last: O'Grady

summary: RNA was harvested from endothelial cells treated with VEGF or H2O and their associated extracellular vesicles.

overall_design: 3 replicates each of: VEGF-treated HUVECs and their EVs, untreated HUVECs and their EVs

first: Makon-Sébastien

last: Njock

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last: Struman

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last: Dequiedt