title: Ogt Controls Adult Neurogenesis through Modulating Notch Signaling Activity in Mice

city: hangzhou

first: Junchen

last: Chen

state: zhejiang

address: zhejiang university, kaixuan road

institute: zhejiang university

summary: Ogt catalyzed O-linked N-acetylglucosamine (O-GlcNAcylation, O-GlcNAc) plays an important function in diverse biological processes and diseases. However, the roles of Ogt in regulating neurogenesis remain largely unknown. Here, we show that Ogt deficiency or depletion in adult neural stem cells (aNSCs) leads to the diminishment of aNSCs pool and the aberrant neurogenesis, and consequently impairs cognitive function of adult mice. RNA sequencing reveals that Ogt deficiency alters the transcription of genes relating to cell cycle, neurogenesis, and neuronal development. Mechanistic studies show that Ogt directly interacts with Notch1 and catalyzes the O-GlcNAc modification of Notch TM/ICD fragment. The decreased O-GlcNAc modification of TM/ICD increases the binding of E3 ubiquitin ligase Itch to TM/ICD and promotes its degradation. Itch knockdown rescues neurogenic defects in Ogt-deficient mice. OGT also regulates human cortical neurogenesis in forebrain organoids derived from induced pluripotent stem cells. Our findings reveal the essential roles and mechanisms of Ogt and O-GlcNAc modification in regulating mammalian neurogenesis and cognition.

overall_design: Transcriptome Sequencing of control and Ogt knockdown adult neural stem cells. Two replicates for each group.

first: Liqi

last: Shu

first: Ying

last: Zhou

first: Qiang

last: Zhu

first: Liping

last: Li

first: Min

last: Wang

first: Xuejun

last: Cheng

first: Qian

first: Xiaoxue

last: Dong

first: Weixiang

last: Guo

first: Binggui

last: Sun

first: Zhexing

last: Wen

first: Wen

last: Yi

first: Xuekun


title: An unbiased approach to defining bona fide tumor neoepitopes that mediate cancer immunity

status: Public on Dec 15 2020

city: Farmington

first: Marmar

last: Moussa

state: CT

address: Farmington

department: School of Medicine

country: USA

institute: University of Connecticut

type: Expression profiling by high throughput sequencing

summary: Identification of neoepitopes that are effective in cancer therapy is a major challenge in creating cancer vaccines. Here, using an entirely unbiased approach, we have queried all possible neoepitopes in a mouse cancer model and asked which of those are effective in mediating tumor rejection, and independently, in eliciting a measurable CD8 response. This analysis uncovers a new universe of effective anticancer neoepitopes which have strikingly different properties from conventional epitopes and suggests a novel algorithm to predict them. It also reveals that our current methods of prediction discard the majority of true anticancer neoepitopes. These results from a single mouse model have been validated in another, independent mouse cancer model, and are consistent with data with human studies. T cells elicited by the active neoepitopes identified here demonstrate a stem-like early dysfunctional phenotype associated with effective responses against viruses and tumors of transgenic mice. These abundant and novel anticancer neoepitopes can be exploited for generation of personalized human cancer vaccines.

overall_design: Single cell RNA-seq analysis of CD8+ PD-1+ TILs from mice immunized with a TRMN and a non-TRMN Mice (n=3 per group) were immunized with un-pulsed BMDCs or BMDCs pulsed with peptides Fam171bMUT (a TRMN) or Cd9MUT (a non-TRMN) and challenged with MC38-FABF. Tumors were harvested day 25 post tumor challenge and live CD8+PD-1+ TILs isolated by FACS and sequenced by scRNA-seq (10x genomics). Approximately 4400 CD8+ PD-1+ TILs were analyzed in each library.

first: Mariam

last: George

first: Cory

last: Brennick


title: Silencing of the Long Noncoding RNA MYCNOS1 Suppresses Activity of MYCN-Amplified Retinoblastoma Without RB1 Mutation

city: Bangkok

first: Rossukon

last: Kaewkhaw

address: 270 Rama VI Road Ratchathewi

country: Thailand

institute: Mahidol University

summary: MYCNOS (MYCN opposite strand) is co-amplified with MYCN in pediatric cancers including retinoblastoma. MYCNOS encodes several RNA variants whose functions have not been elucidated in retinoblastoma. Here, we attempted to decipher the role of MYCNOS variant 1 (MYCNOS1) on the activity of MYCN-amplified retinoblastoma. We observed that MYCNOS1 supports progression of retinoblastoma. Inhibition of MYCNOS1 expression may be needed to suppress MYCN activity when treating MYCN-amplified cancers without RB1 mutation.

overall_design: Tumor tissue was dissociated, and the resulting cells were cultured in the growth medium developed previously in Saengwimol et al. "A three-dimensional organoid model recapitulates tumorigenic aspects and drug responses of advanced human retinoblastoma". Functional study of MYCNOS1 expression was conducted in patient-derived tumor cells and in retinoblastoma cell line via short hairpin RNA-mediated gene silencing.

first: Vijender

last: Chaitankar


title: MicroRNA profiling in oesophageal adenocarcinoma cell lines and patient serum samples reveals a role for miR-451a in radiation resistance [baseline RT-PCR]

city: Bedford Park

first: George

last: Mayne

state: SA

address: Room 3D213, Dept of Surgery, Flinders Medical Center

department: Surgery

country: Australia

institute: Flinders University of South Australia

summary:
miRNA was extracted from a range of Oesophageal Adenocarcinoma cell lines using the miRNeasy Mini Kit (Qiagen, #217004, Chadstone, Australia) and RNase-free DNase Set (Qiagen, #79254, Chadstone, Australia). miRNA was reverse transcribed using a  Custom OpenArray® miRNA RT pool (Life Technologies cat # A25630) and the TaqMan® microRNA Reverse Transcription Kit (Life Technologies cat # 4366596). cDNA Pre-amplifications were carried out with a  Custom OpenArray® PreAmp pool (Life Technologies cat # 4485255) and TaqMan PreAmp Master Mix (Life Technologies cat # 4488593). PCR runs were performed using a QuantStudio™ 12K Flex Real-Time PCR System.
Baseline qPCR expression profiling of miRNAs from 8 oesophageal Adenocarcinoma cell lines, prior to treating the cell lines with either 2Gy ionising radiation, 20 µM Cisplatin, or 50 µM 5-fluorouracil (5-FU).

overall_design: OpenArray high throughput real time PCR of microRNAs --  duplicates for 8 oesophageal adenocarcinoma cell lines.

first: Frederike

last: Butz

first: Ann-Kathrin

last: Eichelmann

middle: C

first: Tingting

first: Isabell

last: Bastian

first: Karen

last: Chiam

first: Shashikanth

last: Marri

first: Pamela

middle: J

last: Sykes

first: Bas

middle: P

last: Wijnhoven

first: Eelke

last: Toxopeus

first: Michael

middle: Z

last: Michael

first: Christos

middle: S

last: Karapetis

first: Richard

last: Hummel

first: David

middle: I

last: Watson

first: Damian

last: Hussey


title: A transcriptome-based deep neural network classifier for identifying the site of origin in mucinous cancer

city: Pohang

first: Sang Ick

last: Park

address: 558, Handong-ro, Buk-gu

country: South Korea

institute: Handong University

summary:
Background
There is a lack of tools for identifying the site of origin in mucinous cancer. This study aimed to evaluate the performance of a transcriptome-based classifier for identifying the site of origin in mucinous cancer.
Methods
Transcriptomic data of 1,878 non-mucinous and 82 mucinous cancer specimens, with 7 sites of origin, namely, the uterine cervix (CESC), colon (COAD), pancreas (PAAD), stomach (STAD), uterine endometrium (UCEC), uterine carcinosarcoma (UCS), and ovary (OV), obtained from The Cancer Genome Atlas, were used as the training and validation sets, respectively. Transcriptomic data of 14 mucinous cancer specimens from a tissue archive were used as the test set. For identifying the site of origin, a set of 100 differentially expressed genes for each site of origin was selected. After removing multiple iterations of the same gene, 626 genes were chosen, and their RNA expression profiles, at each site of origin, were used to train the deep neural network classifier. The performance of the classifier was estimated using the training, validation, and test sets.
Results
The accuracy of the model in the training set was 0.977, while that in the validation set was 0.939 (77/82). In the test set, the model showed an accuracy of 0.857 (12/14). t-SNE analysis revealed that samples in the test set were part of the clusters obtained for the training set.
Conclusion
Although limited by small sample size, we showed that a transcriptome-based classifier could correctly identify the site of origin of mucinous cancer.

overall_design: Train-validate a classifier using publicly available database. Estimate the performance of the classifier in a test set of archival tissues. This submission is the test set of 14 samples, but raw data is not available for the 8 CAM samples because the files were deleted. FPKMs are available for all 14 samples.

first: Taejin

last: Ahn

first: Kidong

last: Kim

first: Sarah

first: Sangick


title: MicroRNA profiling in oesophageal adenocarcinoma cell lines and patient serum samples reveals a role for miR-451a in radiation resistance [control and miR-451a inhibitor treatments]

first: George

last: Mayne

summary: Many patients with Oesophageal Adenocarcinoma (OAC) that undergo chemoradiotherapy do not benefit from treatment due to therapy resistance. We therefore investigated the association of microRNAs, which regulate gene expression, with the response to individual treatments, focusing on radiation, to both better understand the mechanisms involved in resistance and to find potential biomarkers. Intrinsic radiation resistance and chemotherapy drug resistance were assessed in 8 OAC cell lines, and miRNA expression profiling was performed via high throughput qPCR. miRNAs were discovered that were either uniquely associated with resistance to radiation, cisplatin, or 5-FU, or were common to 2 or all 3 of the treatments.  Target mRNA pathway analyses indicated several potential mechanisms of treatment resistance. miRNAs associated with the in-vitro treatment responses were then investigated for association with pathologic response to neoadjuvant chemoradiotherapy (nCRT) in pre-treatment serums of 39 patients with OAC. Hsa-miR-451a was associated uniquely with resistance to radiation treatment in the cell lines, and with the response to nCRT in patient serums. Inhibition of hsa-miR-451a in the radiation resistant OAC cell line OE19 increased radiosensitivity (Survival Fraction 73% vs. 87%, p=0.0003), and altered RNA expression.

overall_design: Three independent experiments  were performed for the control and miR-451a inhibitor treatments.

first: Frederike

first: Ann-Kathrin

first: Tingting

last: Wang


title: MicroRNA profiling in oesophageal adenocarcinoma cell lines and patient serum samples reveals a role for miR-451a in radiation resistance [miRNA-Seq]

type: Non-coding RNA profiling by high throughput sequencing

last: Butz

last: Eichelmann

first: Isabell

first: Karen

first: Shashikanth

first: Pamela


title: MicroRNA profiling in oesophageal adenocarcinoma cell lines and patient serum samples reveals a role for miR-451a in radiation resistance

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

overall_design: Refer to individual Series


title: Translational Regulation of Metabolic Dynamics during Effector-Triggered Immunity

status: Public on Dec 16 2020

city: Durham

first: Xinnian

last: Dong

state: NC

address: 124 Science Drive

department: Biology

institute: Duke University

summary: It is not fully known whether translational regulation also occurs in later stage immune responses, such as effector-triggered immunity (ETI), which often leads to strong metabolic dynamics. In this study, we performed a genome-wide ribosome profiling in Arabidopsis upon ETI activation and discovered that specific groups of genes were translationally regulated, especially metabolic genes in aromatic amino acid, phenylpropanoid, camalexin, and sphingolipid metabolism. The involvement of these components in the induction of ETI was confirmed by genetic analysis, amino acid profiling and exogeneous application of phenylalanine or an inhibitor of aromatic amino acid biosynthesis. Our findings provide new insight into the diverse translational regulation in the plant immune responses and demonstrate that translational coordination of metabolic gene expression is an important strategy for ETI activation.

overall_design: Arabidopsis transgenic lines carrying the 35S:uORFsTBF1-LUC construct in WT Col-0 (C) background or rps2 (R) background were grown on soil at 22 °C under a 12/12-h light/dark cycle with 55% humidity. Leaf tissue (0.3 g) of 4 week old transgenic plants was collected 8 hours post inoculation with either Psm ES4326/AvrRpt2 (OD600nm = 0.01) (A) or 10 mM MgCl2 as Mock (M). For WT plants, 3 replicates of Mock and AvrRpt2 were collected for RNA-seq (RS) and Ribo-seq (RF). For rps2, 2 replicates were collected for Mock and AvrRpt2 RS and RF.

first: Heejin

last: Yoo

middle: H

last: Greene

first: Mung

last: Yuan

first: Guoyong

last: Xu

first: Derek

last: Burton

first: Lijing

last: Liu

first: Jorge

last: Marques


title: BEX2 suppresses mitochondrial activity and is required for dormant cancer stem cell maintenance in intrahepatic cholangiocarcinoma

city: Natori, Miyagi

first: Keiichi

last: Tamai

address: 1-47, Nodayama, Shiote, Medeshima

country: Japan

institute: Miyagi Cancer Center

summary: To clarify the role of BEX2, we analyzed the differential gene expressions between BEX2 knock down cells and control.

overall_design: HuCCT1 cells were knock down with short-hairpin RNA.

first: Mao

last: Nakamura-Shima

first: Rie

last: Shibuya-Takahashi

first: Shinnichiro

last: Kanno

first: Akira

last: Yasui

first: Mai

last: Mochizuki

first: Wataru

last: Iwai

first: Yuta

last: Wakui

first: Makoto

last: Abue

first: Kuniharu

last: Yamamoto

first: Koh

last: Miura

first: Masamichi

last: Mizuma

first: Michiaki

last: Unno

first: Sadafumi

last: Kawamura

first: Ikuro

last: Sato

first: Jun

last: Yasuda

first: Kazunori

last: Yamaguchi

first: Kazuo

last: Sugamura

first: Kennichi

last: Satoh


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and NS-DADm mice myocardium Transcriptomes

city: Houston

first: Sichong

last: Qian

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived heart transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Methods: myocardium mRNA profiles of 6-week-old wild-type (WT) and whole-body knock-in mutations in DADs of both NCOR and SMRT (NS-DADm) mice were generated by Agilent 2100 Bio analyzer. we filter the low quality reads (More than 20% of the bases qualities are lower than 10),reads with adaptors and reads with unknown bases (N bases more than 5%)to get the clean reads. Then we map those clean reads onto reference genome, followed with novel gene prediction, SNP &INDEL calling and gene splicing detection. Finally, we identify DEGs (differentially expressed genes) between samples and do clustering analysis andfunctional annotations
Results: Using an optimized data analysis workflow, we find genes upregulated and enriched in NS-DADm myocardium that were consistent with HDAC3 inhibitor treated heart compared with WT
Conclusions: Our study represents the first detailed analysis of genes expression in myocardium of HDAC3 enzymatic activity-dead NS-DADm mice

overall_design: Myocardium mRNA profiles of 6-week old wild type (WT) and NS-DADm mice

first: Zheng

last: Sun


title: circRNA-sequencing

city: Shenyang

first: hua

last: Zhou

address: 155 North Najing St, Shenyang, Liaoning, China

country: China

institute: The First Hospital of China Medical University

summary: We aim to identify profiling of circRNAs in renal biopsies from lupus nephritis (LN) patients. In this study, seven frozen renal biopsies from  patients with LN class IV were used for circRNA profiling by second generation of RNA sequencing. Three kidney tissue 5 cm far from renal tumors were used as normal control .

overall_design: normal control group and  lupus nephritis group

first: Hua


title: Expression Profiles of HepG2 cells treated with 7 compounds

city: Maastricht

first: Danyel

last: Jennen

address: Universiteitssingel 40

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

summary: The transcriptomics-based in vitro assay for predicting chemical genotoxicity in vivo published by Magkoufopoulou et al (2012) was validated by the independent study performed in HepG2 cells for which the gene expression data are described here. The data were reanalyzed for the OpenRiskNet project (Horizon2020 EINFRA-22-2016 Programme; Grant Agreement 731075).

overall_design: The study investigated differential gene expression in HepG2 cell line mRNA following 24 and 48 hours of exposure to 2 genotoxic carcinogens, 2 non-genotoxic carcinogens, 3 non-genotoxic non-carcinogens and their solvents. Three biological replicates per compound/solvent. In total 54 arrays.

middle: G


title: Oxidative Stress Impact on the Transcriptome of Differentiating Neuroblastoma Cells

city: Newcastle

first: Behnaz

last: Khavari

state: NSW

address: 1 University Dr Callaghan

department: School of Biomedical Sciences and Pharmacy

institute: University of Newcastle

summary: Prenatal environmental exposures that have been shown to induce oxidative stress (OS) during pregnancy, such as smoking and alcohol consumption, are risk factors for the onset of schizophrenia and other neurodevelopmental disorders (NDDs). While the OS role in the etiology of neurodegenerative diseases is well known, its contribution to the genomic dysregulation associated with psychiatric disorders is less well defined. In this study we used SH-SY5Y cell line and applied RNA-sequencing to explore transcriptomic changes in response to OS before or during neural differentiation. We observed differential expression of many genes, most of which localised to the synapse and involved in neuronal differentiation. These genes were enriched in schizophrenia-associated signalling pathways, including PI3K/Akt, axon guidance, and signalling by retinoic acid. Interestingly, circulatory system development was affected by both treatments, which is concordant with observations of increased prevalence of cardiovascular disease in patients with NDDs. We also observed a very significant increase in the expression of immunity-related genes, supporting current hypotheses of immune system involvement in psychiatric disorders. These data suggest that early life exposure to OS has a disruptive influence on neuronal gene expression that may perturb normal differentiation and neurodevelopment, thereby contributing towards overall risk for developing psychiatric diseases.

overall_design: Oxidative stress was chemically induced in  SH-SY5Y cells by the addition of 10mM hydrogen peroxide (H2O2) using two treatment protocols. In the first approach, the cells were simultaneously exposed to H2O2 and ATRA during the entire 7 days of differentiation (co-treatment protocol). In the alternative pre-treatment approach, cells were treated with 10mM H2O2 72 hours before commencement of the ATRA differentiation protocol. For each approach, there existed 3 replicates for peroxide-treated and 3 replicates for untreated samples.

first: Ebrahim

last: Mahmoodi

first: Michael

last: Geaghan

first: Murray

last: Cairns


title: Androgen Regulates SARS-CoV-2 Receptor Levels and Is Associated with Severe COVID-19 Symptoms in Men [scRNA-Seq]

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Biochemistry and Biophysics

institute: UCSF

summary: Here, we established a high-throughput drug screening strategy to identify therapeutic candidates that reduce ACE2 levels in human embryonic stem cell (hESC) derived cardiac cells and lung organoids. Drug target analysis of validated hit compounds, including 5 alpha reductase inhibitors, revealed androgen signaling as a key modulator of ACE2 levels. Treatment with antiandrogenic drugs reduced ACE2 expression in both human cardiac and lung epithelial cells and protected hESC-derived lung organoids against SARS-CoV-2 infection. To build an in vitro model of viral infection in human lung tissue, we set out to generate lung organoids from hESC using a slightly modified combination of previously established differentiation methods (Carvalho et al., 2019; Jacob et al., 2017; Miller et al., 2019). We performed single cell RNA sequencing of fully differentiated organoids to unbiasedly characterize the cell types present and validate them as a model of SARS-CoV-2 infection and antiandrogenic drug treatment.

overall_design: In total, five organoids were sequenced from two independent differentiations. From one differentation, two replicate matrigel embedded organoids were collecetd and sequeced. From the second, independent differentation, two matrigel embeded organoids and one organoid kept in suspension were sequenced.

first: Albertas

last: Navickas

first: Ryan

middle: M

last: Samuel

first: Sohit

last: Miglani

first: Aidan

last: Winters

first: Faranak

last: Fattahi


title: Androgen Regulates SARS-CoV-2 Receptor Levels and Is Associated with Severe COVID-19 Symptoms in Men


title: Gene expression analysis comparing a selected strain of rainbow trout with superior growth and immune performance to a commercial reference strain during baterial infection with Flavobacterium psychrophilum

city: Hagerman

first: Jacob

middle: W.

last: Bledsoe

state: Idaho

address: 3059F National Fish Hatchery Road

department: Aquaculture Research Institute

institute: University of Idaho

summary: Through 8 generations of selection, our group has developed a strain of rainbow trout that exhibits high growth rates on an economically and environmentally sustainable all plant protein, high-soy diet. The selected strain also shows superior performance in bacterial and viral disease challenges compared to commercial trout strains, and even a strain specifically selected over many generations for viral and bacterial disease resistance. The selection criteria was strictly focused on performance on plant-based diets, and therefore the physiological mechanisms responsible for the strain’s superior disease resistance remain unresolved. To better characterize the physiological mechanism behind the superior performance of the selected strain we compared the intestinal gene expression of the select strain to that of a commercial control line of trout during an experimental bacterial infection with Flavobacterium psychrophilum (Fp) (CSF 259-93), the causative agent of bacterial cold water disease (BCWD) in salmonids. At 65 days post hatch, all female rainbow trout from the select and commercial strain were stocked separately into four 150L tanks each, at a density of 45 fish per tank. For both strains of trout, three tanks of fish were experimentally infected with Fp by intramuscular injection and one control tank was mock challenged by sham injection. Sampling was conducted at 5 days post challenge (dpc) (Early Infection) and 21 dpc (Late/Recovered Infection). Two intestinal samples from each tank were pooled and two pools from each tank were utilized for RNAseq library preparation. The select strain of trout showed significantly better survival rates (Log-Rank Test, p < 0.0001) over the 21 day infection period, with 70 and 95 % mortality among the select and commercial strain, respectively. Reads from the RNAseq samples were quantified at the transcript level prior to evaluating differential transcript usage and differential gene expression between the strains of trout, infection time points, and disease status.

overall_design: At 65 days post hatch, all female rainbow trout from the select and commercial strain were stocked separately into four 150L tanks each, at a density of 45 fish per tank. There were three infected tanks and one mock challenged tank per strain. Intestinal samples were collected from all tanks at 5 days post challenge (dpc) and 21 dpc. Two intestinal samples from each tank were pooled and two pools from each tank were utilized for RNAseq library preparation. At each time point, there are 6 pooled samples of infected fish and 2 pooled samples of mock challenged fish per strain. However, due to  high mortality in the commercial strain, only one tank of infected commercial trout was sampled at 21 dpc.

middle: W

first: Ken

last: Overturf

first: Brian

last: Small


title: MicroRNA profiling in oesophageal adenocarcinoma cell lines and patient serum samples reveals a role for miR-451a in radiation resistance [patients with Oesophageal Adenocarcinoma]

first: George

last: Mayne

summary: Many patients with Oesophageal Adenocarcinoma (OAC) that undergo chemoradiotherapy do not benefit from treatment due to therapy resistance. We therefore investigated the association of microRNAs, which regulate gene expression, with the response to individual treatments, focusing on radiation, to both better understand the mechanisms involved in resistance and to find potential biomarkers. Intrinsic radiation resistance and chemotherapy drug resistance were assessed in 8 OAC cell lines, and miRNA expression profiling was performed via high throughput qPCR. miRNAs were discovered that were either uniquely associated with resistance to radiation, cisplatin, or 5-FU, or were common to 2 or all 3 of the treatments.  Target mRNA pathway analyses indicated several potential mechanisms of treatment resistance. miRNAs associated with the in-vitro treatment responses were then investigated for association with pathologic response to neoadjuvant chemoradiotherapy (nCRT) in pre-treatment serums of 39 patients with OAC. Hsa-miR-451a was associated uniquely with resistance to radiation treatment in the cell lines, and with the response to nCRT in patient serums. Inhibition of hsa-miR-451a in the radiation resistant OAC cell line OE19 increased radiosensitivity (Survival Fraction 73% vs. 87%, p=0.0003), and altered RNA expression.  Pathway analysis of effected small non-coding RNAs and corresponding mRNA targets suggest potential mechanisms of radiation resistance in OAC.

overall_design: 39 patients with locally advanced (no distant metastases) Oesophageal Adenocarcinoma who received a nCRT protocol that included radiation (41.4 Gy), carboplatin and paclitaxel.

first: Frederike

last: Butz

first: Ann-Kathrin

last: Eichelmann

first: Tingting

last: Wang

first: Isabell

last: Bastian

first: Karen

last: Chiam

first: Shashikanth

last: Marri

first: Pamela

last: Sykes

first: Bas

last: Wijnhoven

first: Eelke

last: Toxopeus

last: Michael

first: Christos

last: Karapetis

first: Richard

last: Hummel

first: David

last: Watson

first: Damian

last: Hussey


title: Androgen Regulates SARS-CoV-2 Receptor Levels and Is Associated with Severe COVID-19 Symptoms in Men [bulk RNA-Seq]

first: Hani

last: Goodarzi

overall_design: Cells during HLO differentiation were harvested on Day 0 (hPSCs), 5, 9, 15, 25, 35, and 50, in duplicates, and used for RNAseq library preparation.

first: Albertas

last: Navickas

first: Ryan

last: Samuel

first: Abolfazl

last: Arab

first: Faranak

last: Fattahi


title: MSI1 promotes the expression of the GBM stem cell marker CD44 by impairing miRNA-dependent degradation. [RNA-Seq]

city: Halle

first: Markus

last: Glaß

address: Kurt-Mothes-Str. 3a

department: Institute of Molecular Medicine

country: Germany

institute: Martin Luther University Halle-Wittenberg

summary: The stem cell marker Musashi1 (MSI1) is highly expressed during neurogenesis and in Glioblastoma (GBM). In cancer and non-malignant progenitor cells, MSI1 promotes self-renewal and impairs differentiation, involving the regulation of mRNA translation. However, a comprehensive understanding of MSI1’s role in promoting GBM-driving networks remains to be deciphered.

overall_design: In this study we use GBM-derived in vitro models of pediatric and adult origin, including isolated primary tumorspheres, to characterize GBM-driving roles of MSI1. We demonstrate that MSI1 is highly expressed in GBM recurrences, a major defiance in terms of surgery and chemo-/radiotherapy. In adult as well as pediatric GBM cell models, MSI1 promotes stem cell-like characteristics, most prominently elevated self-renewal potential and de-differentiation. For the first time, we provide evidence that MSI1 promotes the expression of stem cell markers like CD44, co-expressed with MSI1 within the migrating cell front of primary GBM samples. In GBM cell models MSI1 impairs CD44 downregulation by miRNAs revealing a new function of MSI1 in promoting stem cell properties, the 3’UTR- and miRNA-dependent control of mRNA turnover. This regulation is impaired by the previously reported MSI1 inhibitor luteolin. In sum, our findings reveal a role of MSI1 in stabilizing stem cell marker-encoding mRNAs in GBM and provide further evidence for its therapeutic target potential in GBM treatment.

first: Rebecca

last: Pötschke

first: Jacob

last: Haase

first: Claudia

last: Misiak

first: Luiz

middle: O

last: Penalva

first: Caspar

middle: D

last: Kühnöl

first: Stefan

last: Hüttelmaier


title: MSI1 promotes the expression of the GBM stem cell marker CD44 by impairing miRNA-dependent degradation. [RNA-Seq II]

first: Pötschke

last: Rebecca

first: Haase

last: Jacob

first: Glaß

last: Markus

first: Misiak

last: Claudia

first: Penalva

last: Luiz O.

first: Kühnöl

last: Caspar D.

first: Hüttelmaier

last: Stefan


title: MSI1 promotes the expression of the GBM stem cell marker CD44 by impairing miRNA-dependent degradation.


title: Gene expression data in A172 cell line transfected with Anti-miR-196a-5p miRNA or its respective negative control under hypoxia (0.2% O2)

city: New Delhi

first: Dr. Ritu

last: Kulshreshtha

state: New Delhi

address: Room 134, Block I

department: Dept of Biochemical Engineering and Biotechnology

country: India

institute: Indian Institute of Technology

summary:
miR-196a-5p is robustly upregulated under hypoxia in GBM cell lines and is highly expressed in GBM tumour samples. This study identifies the genes differentially expressed upon miR-196a-5p inhibition in A172 glioblastoma cell line under hypoxia (0.2% O2).
GeneChip PrimeView Human Gene Expression Array was used to assess mRNA expression profile in response to miR-196a-5p inhibition in A172 cell line under hypoxia (0.2% O2).

overall_design: A172 cells were transfected with either Anti-miR-196a-5p miRNA or its respective negative control under hypoxia (0.2% O2). The cells were harvested in hypoxia workstation for RNA isolation 48 hours post-transfection. RNA was used for the gene expression analysis using Affymetrix GeneChip PrimeView system.

first: Sonam

last: Takkar

first: Ritu

first: Sourabh

last: Ghosh


title: Transcriptome profiles of sturgeon lateral line electroreceptor and mechanoreceptor during regeneration

city: Shanghai

first: Jian

last: Wang

address: 999 Huchenghuan road, Pudong New Area

institute: Shanghai Ocean University

summary: The larvae were treated with 200 μM neomycin to deplete the hair cells in neuromast and ampullary organ. Two kinds of sensory epithelia at the ventral side of head were separated at 12 hour-post treatment (hpt) and 24 hpt, respectively. Mechano- and electro- sensory epithelia before neomycin treating were collected respectively as control (untreated).The epithelia near but without two kinds of sensors (EPs) were also collected. Total RNAs were extracted by TRIzol (Invitrogen) using standard protocols. RNA libraries were prepared by TruSeq RNA Sample Prep Kit (Illumina), following the manufacturer's instructions.

overall_design: 14 samples

first: Chunxin

last: Fan


title: Genome-wide transcriptome changes under nitrogen (N), water (W) and N+W stress in root and shoot tissues of contrasting rice genotypes, IR 64 and Nagina 22 at seedling stage

first: Amitha Mithra

last: Sevanthi

address: LBS Centre, Pusa Campus

institute: ICAR - National Institute for Plant Biotechnology

summary: Here we report the genome-wide transcriptomic changes resulting from low N stress, low water (W) stress and both the stresses (N-W-) from root and shoot tissues in two rice genotypes,IR 64 (IR64) and Nagina 22 (N22).The former is a better N user but drought stress sensitive while the latter is the internationally known drought tolerant variety but with poor NUE. Though it is well known that adverse effect of the major abiotic stress, drought, on rice is exacerbated by low supply of N, there are no studies yet on the genome-wide effect of co-occurrence of these two major inputs, water and N. We identified a total of 8926 unique differentially expressed genes (DEGs) across all stress treatments compared to optimal input supply. Interestingly, we identified only 1174, 698 and 903 DEGs in root tissues of IR 64, and 1197, 187 and 781 DEGs in N22; while nearly double the number of DEGs were found in shoot tissues, i.e., 3357, 1006 and 4005 in IR 64 and 4004, 990 and 2143 DEGs (log 2 fold change and FDR p value <0.05) in N22 under N-W+, N+W- and N-W-stress treatments.Overall, more than 70% of the genes showed a similar response in both the genotypes. Of the 15 differentially expressed N transporter genes including the high affinity nitrate transporters, ammonium transporters and urea transporter, IR64 showed differential expression in all of them whereas N22 showed differential expression only in  11 under N-W-and/or  N-W- stress(es). Four of the N transporters (NRT2.1, NRT2.4, OsNAR2.2 and OsAMT2_1) were also differentially expressed under N+W-condition. A low affinity nitrate transporter, OsNPF7.2, was differentially expressed only in N22 shoots under all three stress conditions implicating its genotype specific role in nitrate transport in above ground part.  Genes involved in allantoin and melatonin metabolism were down regulated only under N stress in both the genotypes but not under drought. Three negative regulators of N stress, NIGT1, OsBT and OsACTPK1 were downregulated in IR64 while NIGT1 transcript  alone was downregulated in N22 under N stress. Of the 8926 DEGs, 26.15% were completely novel represented by 916 conserved hypothetical proteins and 1418 hypothetical conserved_gene/gene/proteins.

overall_design: A total of four treatments in three replications with Optimal input supply ( including water and Nitrogen), and three stress  treatments (N, W, and N+W) in rice seedlings of two genotypes, IR 64 and Nagina 22

first: Amitha

first: Subodh

middle: K

last: Sinha

first: Manju

last: Rani

first: Sureshkumar

last: Venkadesan

first: Pranab

last: Mandal


title: MSI1 promotes the expression of the GBM stem cell marker CD44 by impairing miRNA-dependent degradation. [miRNA-Seq]

first: Markus

last: Glaß

first: Rebecca

last: Pötschke

first: Jacob

last: Haase

first: Claudia

last: Misiak

first: Luiz

last: Penalva

first: Caspar

last: Kühnöl

first: Stefan

last: Hüttelmaier


title: Transcriptional analysis of MC38 colorectal tumor cells sorted from mice fed high-fat or control diet

city: Boston

first: Alison

last: Ringel

state: MA

address: 240 Longwood Ave

department: Cell Biology

institute: Harvard Medical School

summary: Examination of transcriptional changes associated with diet-induced obesity in syngeneic MC38 tumors.

overall_design: Transcriptional analysis of GFP+ MC38 colorectal cancer cells sorted 12 days post-implantation from subcutaneous MC38 tumors in C57BL6/J mice. Dataset includes 8 samples from mice fed control diet and 6 samples from mice fed high-fat diet.

middle: E

first: Marcia

last: Haigis

first: Arlene

last: Sharpe


title: Experimental study on gene expression profile of medial meniscus after resection of anterior cruciate ligament and lateral collateral ligament

city: Haikou

first: Fang

middle: Ye

last: Han

state: Hainan

address: No. 19 Xiuhua Road

department: Department of Orthopaedic Surgery

institute: Hainan Provincial People’s Hospital

summary: To explore the molecular mechanisms of meniscal degeneration after resection of anterior cruciate ligament and lateral collateral ligament, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential role in the development of meniscal degeneration. The anterior cruciate ligament (ACL) and lateral collateral ligament (LCL) of the right rear limbs of Wuzhishan minipig was resected at the same time, and the left rear limbs was sham operated. There were significant differences in gene expression between the two groups. A total of 893 differentially expressed genes were identified, of which 537 were upregulated and 356 were downregulated. This study indicated that several molecular mechanisms were implicated in the development of meniscal degeneration, thus improving our understanding of meniscal degeneration and offering molecular targets for future therapeutic advances.

overall_design: Gene expression of medial meniscus was measured 26w after resection of anterior cruciate ligament and lateral collateral ligament or sham operation. Seven experiments were performed at each group.

first: Ye

last: Fang

first: Yu

last: Liu

first: Jing

last: Lin


title: Transcriptional analysis of CD8+ T lymphocytes isolated from syngeneic MC38 tumors and tumor-draining lymph nodes from mice fed high-fat or control diet

summary: Examination of transcriptional changes associated with diet-induced obesity in CD8+ T lymphocytes that infiltrate syngeneic MC38 tumors.

overall_design: Transcriptional analysis of CD8+ T cells sorted 12 days post-implantation from subcutaneous MC38 tumors or tumor-draining lymph node in C57BL6/J mice. Dataset includes 8 samples sorted from tumor-draining lymph nodes in mice fed control diet, 5 samples sorted from tumor-draining lymph nodes in mice fed high-fat diet, 8 samples sorted from dissociated MC38 tumors in mice fed control diet, and 5 samples sorted from dissociated MC38 tumors in mice fed high-fat diet.


title: Transcriptional analysis of CD45+ leukocytes isolated from syngeneic MC38 tumors from mice fed high-fat or control diet

summary: Examination of transcriptional changes associated with diet-induced obesity in tumor-infiltrating CD45+ leukocytes from syngeneic MC38 colorectal tumors.

overall_design: Single-cell transcriptional analysis of CD45+ leukocytes isolated 12 days post-implantation from subcutaneous MC38 tumors in C57BL6/J mice fed control or high-fat diet. Each sample contains CD45+ cells combined from 3 mice.


title: Recapitulation of murine thymopoiesis in vitro from single hematopoietic stem cells

city: Los Angeles

first: Gay

middle: Miriam

last: Crooks

state: California

address: 610 Charles E. Young Drive, East

department: Pathology & Laboratory Med

institute: University of California Los Angeles

summary: We report a serum-free, 3-D murine artificial thymic organoid (ATO) system that mimics normal murine thymopoiesis from four different mouse strains with the production of all T cell populations, from early thymic progenitors to functional single positive (CD8SP and CD4SP) TCRaband TCRyd cells. RNA sequencing aligned ATO-derived populations with phenotypically identical primary thymocytes. ATOs initiated with Rag1-/- marrow produced the same differentiation block as seen in the endogenous thymus, and Notch signaling patterns in ATOs mirrored primary thymopoiesis.  ATOs initiated with defined hematopoietic stem cells (HSCs) and progenitors from marrow and thymus recapitulated subsequent stages and the normal kinetics of T cell differentiation. Remarkably, a single HSC deposited into ATOs generated a complete trajectory of T cell differentiation producing a similar diverse TCR repertoire across clones.  ATOs represent a technically simple, highly reproducible and powerful experimental platform for the study of clonal thymopoiesis from HSCs.

overall_design: Our goal was to analyze and compare the transcriptome of murine thymocyte populations generated in Artificial Thymic Organoids (ATOs) from murine bone marrow-derived hematopoietic stem cells with that of murine thymocyte populations isolated from primary thymus.

first: Amelie

last: Montel-Hagen

first: Victoria

last: Sun

first: David

last: Casero

first: Steven

last: Tsai

first: Alexandre

last: Zampieri

first: Nicholas

last: Jackson

first: Suwen

last: Li

first: Shawn

last: Lopez

first: Yuhua

last: Zhu

first: Brent

last: Chick

first: Chee

last: Chin

first: Christopher

last: Seet


title: Analysis of Differentially Regulated Genes in Lung Tissue

city: Kobe

first: Gusty

middle: Rizky Teguh

last: Ryanto

state: Hyogo

address: 7-5-1, Kusunoki, Chuo

department: Cardiovascular Medicine

institute: Kobe University

summary: Pulmonary arterial hypertension (PAH) is a progressive fatal disease that is characterized by pathological pulmonary artery remodeling, in which endothelial cell (EC) dysfunction is critically involved. We herein describe a previously unknown role of endothelial angiocrine in pulmonary hypertension. By searching for genes highly expressed in lung microvascular ECs, we identified inhibin--A (INHBA) as an angiocrine factor produced by pulmonary capillaries. We found that excess production of INHBA by ECs impairs the endothelial function in an autocrine manner by functioning as activin A (ActA). Mechanistically, ActA induces bone morphogenetic protein receptor type 2 (BMPRII) internalization and targeting to lysosomes for degradation, resulting in BMPRII signal deficiency in ECs. When endothelial ActA-BMPRII link is overdriven in mice, hypoxia-induced pulmonary hypertension was exacerbated, whereas conditional knockout of INHBA in ECs prevents the progression of pulmonary hypertension. These data collectively indicate a critical role for the dysregulated endothelial ActA-BMPRII link in the progression of pulmonary hypertension, and thus endothelial INHBA/ActA is an attractive pharmacotherapeutic target for the treatment of PAH.

overall_design: For cells, commercially available human microvascular ECs of the dermis and the lungs (MVECs-D and MVECs-L), human pulmonary artery ECs (PAECs) and human coronary artery ECs (CAEC) (n=1-2) were cultured until they reach subconfluency (~90%), at which the RNA was extracted using TRIzol. For human tissue samples, RNAs for 5-donor pooled human lungs, heart, kidneys, and liver of were commercially obtained. Labeled cRNA was prepared using 1 vial of the mixed RNAs for each sample according to the One-Color Microarray-Based Gene Expression Analysis ver. 6.5 protocol, and 600 ng of cRNAs was used for hybridization with microarray chips (SurePrint G3 Human GE; G4851B) for 17 h. After washing, signals were scanned using an Agilent DNA microarray scanner, and the data were analyzed using Feature Extraction ver. 10.7.1.1 (Agilent Technologies).

middle: R

first: Koji

last: Ikeda

first: Noriaki

last: Emoto


title: MC38 tumors from mice fed high-fat or control diet

first: Alison

last: Ringel

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

overall_design: Refer to individual Series


title: SP80-3280 drought and re-watering

city: Sao Paulo

first: Augusto

middle: Lima

last: Diniz

state: SP

address: Av Lineu Prestes

department: Biochemistry

country: Brazil

institute: University of Sao Paulo

summary: A greenhouse experiment was conducted at the Federal University of Alagoas in Maceio, Brazil. One-eye sett of sugarcane was planted in 20 liters plant pots, arranged in a completely randomized design and cultivated for 5 months before water privation.

overall_design: In this experiment, we aimed to analyze large scale gene expression changes in leaf +1 and roots of sugarcane (cultivar SP80-3280) under drought and re-watering conditions. Tissue samples were collected after 4 and 6 days of water privation and after 2 days of re-watering. Well-watered plants were used as a control. Total RNA was extracted and used for hybridization experiments on a customized 4x44K oligoarray (Agilent Technologies) for sugarcane (CaneRegNet). The oligoarrays were read using the GenePix 4000B scanner device (Molecular Devices) and the fluorescence data was processed by Feature Extraction software 9.5.3 (Agilent Technologies).

first: Danielle

last: Silva


title: Gene expression analysis comparing a selected strain of rainbow trout with superior growth and immune performance to a commercial reference strain during critical early life stages

first: Jacob

last: Bledsoe

summary: Through 8 generations of selection, our group has developed a strain of rainbow trout that exhibits high growth rates on an economically and environmentally sustainable all plant protein, high-soy diet. The selected strain is resistant to development of soy-induced enteritis, an inflammatory intestinal pathology that occurs often in high-value carnivorous aquaculture species. To better characterize the physiological mechanism behind the superior performance of the selected strain we compared the homeostatic intestinal gene expression of the select strain to that of a commercial control line of trout. Samples were collected at early life stages known to be critical in the development of host-microbe interactions in the gut of rainbow trout. All female cohorts of both strains were reared alongside starting from eggs. Intestinal samples from 5 fish per group (2 fish strains; 2 developmental stages; 20 samples total) were used to generate mRNA selected stranded RNA-seq libraries for high throughput sequencing. Reads were quantified at the transcript level prior to evaluating differential transcript usage and differential gene expression between the two strains of trout and the developmental stages.

overall_design: An all-female cohort of the select and commercial strains of rainbow trout were reared in flow-through spring water (15°C) starting from eggs. From first feeding to the conclusion of the experiment, both strains received a commercial trout starter diet. Intestinal samples were collected from both groups after ten days of feeding which occurred at 20 days post hatch (dph), and at 65 dph, which is just prior to the time when we traditionally switch the fish to an all plant protein diet. RNAseq libraries were prepared for five intestinal samples per experimental group for a total of 20 samples.

first: Ken

last: Overturf

first: Brian

middle: C

last: Small


title: Genome-wide DNA methylation analysis reveals dynamic changes in metabolic and immune-regulatory pathways during uncontrolled SIV infection

city: Evry

first: Jorg

last: Tost

address: 2 rue Gaston Cremieux

country: France

institute: CEA-Institut de Genomique, Centre National de Genotypage

type: Methylation profiling by genome tiling array

summary: The molecular mechanisms underlying HIV-induced inflammation remain incompletely defined although they associate with morbidity and progression to AIDS. Here we used non-human primate models of pathogenic and nonpathogenic simian immunodeficiency virus (SIV) infection in respectively macaques and African green monkeys. We longitudinally analyzed DNA methylation changes in CD4+ T cells from lymph node and blood using species-compatible probes on human 450K methylation BeadArrays. Selected identified sites were validated using bisulfite-pyrosequencing of an independent cohort of uninfected, viremic and SIV controller macaques. Tissue- and species-specific DNA methylation changes were observed after SIV infection. The most affected genes in pathogenic SIV infection were related to metabolic pathways and Th1 signaling. SIV-infected macaques displayed increased insulin sensitivity early in the chronic phase of infection, which correlated with T cell activation. Moreover, DNA methylation changes in the Th1 pathway were associated with altered gene expression. Out of the 11 selected genes for validation, six genes showed differential methylation in viremic and uninfected macaques. In contrast, no significant differences were found between uninfected and SIV-controller macaques. In summary, pathogenic SIV infection associates with DNA methylation changes in genes related to metabolism and immune-regulation.

sample_organism:
Macaca mulatta
Chlorocebus sabaeus

overall_design: Genome-wide changes in DNA methylation in CD4+ T cells isolated from lymphnodes and blood were analyzed longitudinally in the 5 AGM (O7199, O7249, SV081, SV082 and SV084) and 4 MAC (53482, 54189, 54410 and 85696). DNA methylation was measured at three timepoints for MAC: before infection, during acute (day 14 p.i.) and during early chronic infection (day 62-65 p.i.). For AGM, we measured changes in DNA methylation in CD4+ T cells at the same three time points in LN and at two time points in blood (before infection and early chronic infection, as not enough material was available during acute infection). In addition, pre-infection and chronic infection samples (up to day+1787 p.i. for AGM and +850 p.i. for MAC) from another fourteen AGM (06003-3, A7737, A8533, B2338, SV092, SV071, SV072, SV073, SV074, SV075, SV104, SV1101, SV1102, SV1103) and twelve MAC (9801046, 9808282, 9813552, VI219, 503052, 503068, 504034, 98R0016, 98R0078, O90528, 81998, 90874)  were also analyzed to increase sample size. The genome-wide analysis was performed using Infinium HumanMethylation450K BeadChip (Illumina) restricting the analysis to a subset of probes that target CpGs at a unique location on the MAC and AGM genomes composed of 171,912 probes for AGM and 168,466 probes for MAC.

first: Simon

middle: P

last: Jochems

first: Beatrice

last: Jacquelin

first: Florence

last: Busato

first: Fabien

last: Pichon

first: Michaela

last: Müller-Trutwin


title: Analysis of Differentially Regulated Genes in Lung Microvasculature

overall_design: For cells, commercially available human microvascular ECs of the dermis and the lungs (MVECs-D and MVECs-L), human pulmonary artery ECs (PAECs) and human coronary artery ECs (CAEC) (n=1-2, two repeated experiments) were cultured until they reach subconfluency (~90%), at which the RNA was extracted using TRIzol. For human tissue samples, RNAs for 5-donor pooled human lungs, heart, kidneys, and liver of were commercially obtained. Labeled cRNA was prepared using 1 vial of the mixed RNAs for each sample according to the One-Color Microarray-Based Gene Expression Analysis ver. 6.5 protocol, and 600 ng of cRNAs was used for hybridization with microarray chips (SurePrint G3 Human GE; G4851B) for 17 h. After washing, signals were scanned using an Agilent DNA microarray scanner, and the data were analyzed using Feature Extraction ver. 10.7.1.1 (Agilent Technologies).


title: Gene expression analysis comparing a selected strain of rainbow trout with superior growth and immune performance to a commercial reference strain during infection with infectious hematopoietic necrosis virus

summary: Through 8 generations of selection, our group has developed a strain of rainbow trout that exhibits high growth rates on an economically and environmentally sustainable all plant protein, high-soy diet. The selected strain also shows superior performance in bacterial and viral disease challenges compared to commercial trout strains, and even a strain specifically selected over many generations for viral and bacterial disease resistance. The selection criteria was strictly focused on performance on plant-based diets, and therefore the physiological mechanisms responsible for the strain’s superior disease resistance remain unresolved. To better characterize the physiological mechanism behind the superior performance of the selected strain we compared the intestinal gene expression of the select strain to that of a commercial control line of trout during an experimental viral infection using the CSF 220-90 isolate of Infectious Hematopoietic Necrosis virus (IHNv). At 65 days post hatch, all female rainbow trout from the select and commercial strain were stocked separately into four 150L tanks each, at a density of 45 fish per tank. For both strains of trout, three tanks of fish were experimentally infected with IHNv by static bath and one tank was mock challenged by static bath (Sham). Sampling was conducted at 4 days post challenge (dpc) (Early Infection) and 20 dpc (Late/Recovered Infection). Two intestinal samples from each tank were pooled and two pools from each tank were utilized for RNAseq library preparation. Infections were mild with mortality rates near 50% over the 21 day trial and no significant difference in mortality rates between the two strains of trout. Reads from the RNAseq samples were quantified at the transcript level prior to evaluating differential transcript usage and differential gene expression between the strains of trout, infection time points, and disease status.

overall_design: At 65 days post hatch, all female rainbow trout from the select and commercial strain were stocked separately into four 150L tanks each, at a density of 45 fish per tank. There were three infected tanks and one mock challenged tank per strain. Intestinal samples were collected from all groups at 4 days post challenge (dpc) and 20 dpc. Two intestinal samples from each tank were pooled and two pools from each tank were utilized for RNAseq library preparation. At each time point, there are 6 pooled samples of infected fish and 2 pooled samples of mock challenged fish per strain.


title: Senescence and TGF-β producing Tregs drive HIV persistence and impaired immune homeostasis

city: Cleveland

first: Rafick

last: Pierre-Sekaly

state: OH

address: 2103 Cornell Avenue

department: Pathology

institute: Case Western Reserve University

summary: The purpose of this study was to determine differences in gene expression profiles between Immune Responders (IR) and Immune non-Responders (INR) individuals. We have observed significant changes in the gene expression profiles between IRs and INRs and identified a subgroup of INR subjects that has a unique/distinct transcriptional profile and that clustered the furthest from IR subjects.

overall_design: Immune responder and non-responder individuals included in the study were HIV-infected and ART-treated for at least 3 years. Immune non-responder patients had CD4 T cells <350/µL and immune responder patients had CD4 T cells >500/µL. Whole blood was collected and lysed in RLT for RNA extraction.  Reverse transcription reactions were performed to obtain cDNAs which were hybridized to the Illumina Human HT-12 version 4 Expression BeadChip according to the manufacturer’s instruction, and quantified using an Illumina iScan System. The data were collected with Illumina GenomeStudio software.

first: Khader

last: Ghneim

first: Ashish

last: Arunkumar Sharma

first: Susan

last: Periera Ribeiro

first: Sahaana

last: Arumagam

first: Samuel

last: Darko

first: Slim

last: Fourati

first: Jeffrey

last: Ahlers

first: Deanna

last: Kulpa

first: Xuan

last: Xu

first: Filipa

last: Blasco  Lopes

first: Jessica

last: Brehm

first: Aarthi

last: Talla

first: Flavio

last: Matassoli

first: Benigno

last: Rodriguez

first: Carey

last: Shive

first: Razvan

last: Cristescu

first: Andrey

last: Loboda

first: Robert

last: Balderas

first: I-Ming

last: Wang

first: Peter

last: Hunt

first: Daniel

last: Lamarre

last: Douek

first: Daria

last: Hazuda

first: Michael

last: Lederman

first: Steven

last: Deeks

first: Rafick-Pierre

last: Sekaly


title: Expression data from mouse melanocytes and melanoma

status: Public on Dec 14 2020

first: Hensin

last: Tsao

address: 55 Fruit St

institute: Massachusetts General Hospital

summary:
Melan-a cells were transduced with control vector and c-kit(K641E) to generate mVec and mKitK641E(PT) cell lines. mKitK641E(T) cells were generated by extracting cells from in vivo tumor growth of mKitK641E(PT) cells.
We used microarrays to detail the global programme of gene expression of mVec, mKitK641E(PT) and mKitK641E(T) cell lines.

overall_design: Total RNAs were extracted from mVec, mKitK641E(PT) and mKitK641E(T) cell lines and hybridized on Affymetrix microarrays.


title: Brain gene expression in systemic hypothyroidism and in mouse models of MCT8 deficiency: The Mct8-Oatp1c1-Dio2 triad.

city: Madrid

first: Enrique

last: Vazquez de Luis

state: Madrid

address: Melchor Fernandez Almagro, 3

country: Spain

institute: CNIC

summary: The monocarboxylate transporter 8 (Mct8) protein is a primary T4 and T3 (TH) transporter. Mutations of the MCT8-encoding, SLC16A2 gene alters thyroid function and thyroid hormone metabolism, and severely impairs neurodevelopment (Allan-Herndon-Dudley syndrome, AHDS). Mct8-deficient mice manifest thyroid alterations but lack neurological signs. It is thought that Mct8 deficiency in mice is compensated by T4 transport through the Slco1c1-encoded organic anion transporter polypeptide 1c1 (Oatp1c1). This allows local brain generation of sufficient T3 by the Dio2-encoded type 2 deiodinase (D2). The Slc16a2/Slco1c1 (MO) and Slc16a2/Dio2 (MD) double knock out mice lacking T4 and T3 transport, or T3 transport and T4 deiodination, would be more approriate models of AHDS. The goal of this work was to compare the cerebral hypothyroidism of systemic hypothyroidism (SH) caused by thyroid gland blockade with that present in the double KOs.

overall_design: We performed RNA sequencing using RNA from the cerebral cortex and striatum from SH mice and the double KO on postnatal days 21-23. Systemic hypothyroidism was induced in WT male mice of the C57BL/6J strain by administration of 0.02% 1-methyl-2-mercapto-imidazol plus 1% KClO4 in the drinking water ad libitum to the pregnant and lactating dams. Antithyroid treatment started on E9 and continued until P21.

first: Beatriz

middle: B

last: Morte

first: Pilar

last: Gil-Ibañez

first: Heike

last: Heuer

first: Juan

middle: J

last: Bernal


title: Mitochondrial RNA in Alzheimer’s Disease Circulating Extracellular Vesicles

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Alzheimer's disease (AD) is the most common type of dementia.  Extracellular amyloid β (Aβ) plaques and intracellular Tau-containing neurofibrillary tangles are major AD lesions that identify Alzheimer’s pathology and to neuronal loss.  However, given that these structures are also seen in cognitively normal persons (healthy controls, HC) and in persons who have mild cognitive impairment (MCI), extensive efforts have been undertaken to identify other diagnostic or prognostic indicators.  Here, we characterized the RNA contents of extracellular vesicles (EVs) in the plasma of age-matched individuals who are healthy or have MCI or AD.  Using RNA sequencing analysis, we found that mitochondrial (mt)RNAs, including MT-ND1 through MT-ND6 and other protein-coding and noncoding mtRNAs, were strikingly elevated in MCI- and AD-associated plasma EVs compared with healthy control EVs.  In cultured cells derived from astrocytes, microglia, and neurons, exposure to the toxic conditions in the AD environment (Aβ fibers and H2O2), EVs contained mitochondrial structures (as detected by electron microscopy) as well as mitochondrial RNAs.  We propose that in the MCI and AD brain environment, toxicity causing mitochondrial damage results in the packaging of mitochondrial components for export in EVs, and further propose that mitochondrial RNAs in plasma EVs are robust diagnostic and prognostic markers in AD.

overall_design: We used 4ml of plasma from 5 Healthy donors, 5 patients with mild cognitive impairment, 5 patient with Alzheimer's disease.

first: Kyoung-Mi

last: Kim

first: Qiong

last: Meng

first: Olivia

last: de Acha López

first: Maja

last: Mustapic

first: Aiwu

last: Cheng

first: Erden

last: Eren

first: Gautam

last: Kundu

first: Yulan

last: Piao

first: Rachel

last: Munk

first: William

middle: H

last: Wood 3rd

first: Lesley

first: Ji-Heon

last: Noh

last: Delannoy

first: Kotb

last: Abdelmohsen

first: Dimitrios

last: Kapogiannis

first: Myriam

last: Gorospe


title: MDAMB231 transcriptome response to SKP2 knockdown

city: Durham

first: Wei

last: Chen

address: 101 Science Drive

department: Center for Genomic and Computational Biology

institute: Duke University

summary: The SKP2 was knockdown by siRNAs in MDA-MB231 cells and RNA-Seq was used to define the transcriptome response to SKP2

overall_design: Compare the transcriptome profile between NC (nontargeting control) and two individual ZIP7 siRNA in MDAMB231 cells


title: Mutations in Bcl9 and Pygo genes cause congenital heart defects by tissue-specific perturbation of Wnt/β-catenin signaling

city: Zürich

first: Christian

last: Mosimann

address: Winterthurerstrasse 190

department: Institute of Molecular Life Sciences

country: Switzerland

institute: University of Zürich

summary: A CRISPR-Cas9-based zebrafish screen for candidate genes causative of human heart disease uncovers cardiac defects when perturbing Bcl9.

first: Anastasia

last: Felker

first: Elena

last: Chiavacci

last: Cabello


title: The miRNA profile after knockdown of Bmi1 in QBC939 cells

city: Jinan

first: Xin

last: Zhang

state: Shandong

address: 107 Wenhua Xi Road

institute: Qilu Hospital, Shandong University

summary: We profile the expression of miRNAs upon Bmi1 Knockdown in QBC939 cells

overall_design: Comparison of Bmi1 knockdown in QBC939 cells against cells transfected with scrambled siRNA. 3 independend transfections per shRNA were used.


title: CRISPR screen identifies genes that sensitize AML cells to double negative T cell therapy

city: Toronto

first: Musaddeque

last: Ahmed

state: ON

address: 101 College St

country: Canada

institute: University health Network


title: CRISPR screen identifies genes that sensitize AML cells to double negative T cell therapy [guide RNA]

summary: Here, we used a targeted CRISPR/Cas9 screen to identify genes that confer susceptibility of AML cells to DNT cell therapy.

overall_design: The CRISPR screen employed in our pooled Epidrug library consisted of ~12,500 sgRNAs targeting 317 epigenetic regulators, 657 FDA-approved drug targets based on Drugbank v4.3, and control genes, with 10 sgRNAs per gene on average. The sgRNAs were designed using the CRISPR-DO tool. Stable Cas9-expressing cell lines (AML2 and AML3) were generated. Cas9-expressing AML cell lines were infected with the library at an MOI of ~ 0.3 and coverage of 300x. 24-48h post-infection, cells were selected with puromycin for 72h and then cultured for ~7 days, maintaining 300x coverage prior to our screening assay. To detect early apoptotic AML cells, we co-incubated the transduced AML3 cells with DNTs at a 1:1 E:T ratio for 2h to induce apoptosis in ~40-50% of the targets, depleted DNTs by magnetic separation, and performed FACS to separate Annexin V+ (live) and Annexin V- (dead or dying) target cells. Genomic DNA was extracted from replicate samples and sgRNA inserts were amplified by PCR. The input amount of genomic DNA was calculated to achieve 250x coverage of the library and resulting libraries were sequenced on an Illumina HiSeq2500.

first: Housheng

last: He


title: CRISPR screen identifies genes that sensitize AML cells to double negative T cell therapy [RNA-Seq]

overall_design: Total RNA was extracted from AML3 cells using the RNeasy Plus Mini Kit (Qiagen Cat. 74314) following manufacture’s guidelines. On column DNase I digestion was performed for 15 mins at room temperature and RNA purity was assessed by Nanodrop (260/280, > 2.0). RNA-seq libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (634418, Takara). Libraries were verified using TapeStation (Tape 2200, Agilent Technologies) and 150-bp paired-end sequencing was performed


title: CITE-Seq profiling of CLL under ibrutinib treatment  reveals transcriptional evolution of leukemic and immune cells.

city: TOULOUSE

first: Anne

last: QUILLET-MARY

state: Select

address: Av Hubert Curien, CS 53717, CS 53717

department: INSERM U1037/CNRS ERL5294

institute: CRCT

summary: Ibrutinib, an irreversible Bruton Tyrosine Kinase (BTK) inhibitor, has revolutionized Chronic Lymphocytic Leukemia (CLL) treatment, but resistances to ibrutinib have emerged in relation or not to BTK mutations. Evolution patterns of CLL before and after ibrutinib therapy are often focused only on leukemic cells but must be investigated in the context of the CLL microenvironment. Single cell RNA-seq and related technologies allow a deeper characterization of cancer and normal cells.  We therefore investigated whether ibrutinib treatment drives molecular changes in CLL. Here, we report the monitoring of a CLL patient under ibrutinib treatment using Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-Seq) technology. We report that the short clinical relapse of this patient, driven by BTK mutation, is associated with intra-clonal heterogeneity and transcriptional and phenotypical modifications in both B leukemic and immune cells. These results open new therapeutic strategies for ibrutinib-refractory CLL patients.

overall_design: CITESeq profiling

first: Sarah

last: CADOT

first: Carine

last: VALLE

first: Marie

last: TOSOLINI

first: Frédéric

last: PONT

first: Laetitia

last: LAGEAUD

first: Camille

last: LAURENT

first: Jean-Jacques

last: FOURNIE

first: Loïc

last: YSEBAERT


title: Expression data from  APC 50% or 80% -treated HFDPCs

city: Tsukuba,

first: Meriem

last: Bejaoui

state: Ibaraki

address: 1 Chome-1-1 Tennodai

institute: University of Tsukuba

summary:
Gene expression profiling reveals a potential role of APC 50% or APC 80% in stimulating hair growth in dermal papilla cells.

HFDPCs were human primary cells line, treated with 5 μg/ml APC 50% for 48 h. Microarray gene expression profiling was conducted for three biological replicates

HFDPCs were human primary cells line, treated with 5 μg/ml APC 80% for 48 h. Microarray gene expression profiling was conducted for three biological replicates

overall_design: RNA was extracted using Isogen (Nippon Gene Co. Ltd., Toyama, Japan). The integrity of RNA was quantified using NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA). RNA samples were prepared for gene expression profiling analysis with GeneChip® 3' Expression Arrays using 3' IVT PLUS Reagent Kit (Affymetrix Inc., Santa Clara, CA, USA). Two hundred and fifty ng of total RNA from each sample was used to generate amplified and biotinylated complementary RNA (cRNA) from poly (A) RNA in a total RNA sample according to the user manual. IVT Incubation time was 16 hour. GeneAtlas® Hybridization, Wash and Stain Kit was used for hybridizing 3' IVT Array Strips according to the user manual (P/N 08-0306). Human genome array strips (HG-U219) were hybridized for 16 hours in a 45oC incubator, washed and stained and finally imaging was done with the GeneAtlas Fluidics and Imaging Station.


title: Translation in amino acid-poor environments is limited by tRNAGln charging

city: New York

first: Bryan

last: King

state: NY

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

summary: An inadequate supply of amino acids leads to accumulation of uncharged tRNAs, which can bind and activate GCN2 kinase to reduce translation. Here, we show that glutamine-specific tRNAs selectively become uncharged when extracellular amino acid availability is compromised. In contrast, all other tRNAs retain charging of their cognate amino acids in a manner that is dependent upon intact lysosomal function. In addition to GCN2 activation and reduced total translation, the reduced charging of tRNAGln in amino acid-deprived cells also leads to specific depletion of proteins containing polyglutamine tracts including core binding factor α1, mediator subunit 12, transcriptional coactivator CBP and TATA-box binding protein. Treating amino acid-deprived cells with exogenous glutamine or glutaminase inhibitors restores tRNAGln charging and the levels of polyglutamine-containing proteins. Together, these results demonstrate that the activation of GCN2 and the translation of polyglutamine-encoding transcripts serve as the key sensors of glutamine availability in mammalian cells.

overall_design: Mouse embryonic fibroblasts were cultured for 6h with or without amino acids in the presence of glutaminase inhibitor (CB-839) or vehicle (DMSO). RNA was extracted from cells and treated with either 10mM sodium periodite ("oxidized") or sodium chloride ("non-oxidized) prior to sequencing library preparation to calculate tRNA charging ratios.

first: Natasha

middle: N

last: Pavlova

first: Craig

last: Thompson


title: Transcriptome analysis of pFD::amiR-PECT1 under non-inductive light conditions

status: Public on Dec 13 2020

city: Seoul

first: Zeeshan

last: Nasim

address: Anam-ro 145, Seongbuk-Gu

department: School of Life Sciences and Biotechnology

institute: Korea University

summary: We sequenced mRNA of WT and pFD::amiR-PECT1 from shoot apex, seedling grown at 23°C short days, 10 and 16 days after germination at ZT 8

overall_design: Examination of mRNA level in WT and pFD::amiR-PECT1 knockdown line grown at 23°C

first: Hendry

last: Susila

first: Ji

last: Ahn


title: Sarcomeric regulation of serum response factor signaling in cardiomyocyte maturation by actinin-2

city: boston

first: Yuxuan

last: Guo

address: 320 Longwood Ave, Enders 1250,

department: Department of Cardiology

institute: Boston childrens hospital

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

overall_design: Refer to individual Series


title: Id1 in mutant KRAS lung adenocarcinoma

city: Pamplona

first: Silvestre

last: Vicent

state: Outside the US or Canada

address: 55 PIO XII Ave

department: Oncology

institute: Center for Applied Medical Research (CIMA)

summary: Analysis of global gene expression changes in mutant KRAS lung adenocarcinoma cells upon Id1 inhibition

overall_design: H1792 cell were infected with an inducible GFP shRNA or a Id1 shRNA. Cell were grown with 1 ug/ml doxuxycline for 3 days. Then, cells were trypsinized and the same amount of cells was plated for 24 hours before RNA harvesting.

first: Ignacio

last: Gil-Bazo


title: LncRNA PVT1 and miR-214 in hepatocellular carcinoma

status: Public on Dec 12 2020

first: Jupeng

last: Yuan

address: Jiyan road 440#

department: Cancer Research Center

institute: Shandong Cancer Hospital Affiliated to Shandong University

summary: We aimed to detect the mRNA expression levels in HepG2 cells after trasfection with NC RNA, miR-214 mimics or PVT1 siRNAs.

overall_design: We detected the mRNA expression levels in HepG2 cells trasfected with NC RNA, miR-214 mimics or PVT1 siRNAs. Whole genome gene expression of these samples was measured using OneArray Plus chips.

first: Ming

last: Yang

first: Xiangyu

last: Xiong


title: Hepatocyte Host Factor IFI44L Regulates the Innate and Acquired Immune Responses to Hepatitis B Virus

city: Yoshida-gun

first: Takuto

last: Nosaka

state: Fukui

address: 23-3 Matsuoka, Eiheiji-cho

department: Second Department of Internal Medicine

institute: University of Fukui

summary: Objective: Curing hepatitis B requires the complete elimination of covalently closed circular DNA (cccDNA). Interferon (IFN)-γ is produced by cytotoxic T lymphocytes and has noncytolytic antiviral potential; however, elimination of cccDNA could not be achieved. To enhance the regulatory effect of IFN-γ, we comprehensively analyzed the host factors that associated with cccDNA amplification and IFN-γ effects using the in vitro HBV infection system that exhibits various transcription levels. Design: Primary human hepatocytes were infected with HBV using genomic plasmids carrying the basic core promoter 1762/1764 and/or the precore 1896 mutation and treated with IFN-γ, IFN-α, and entecavir. Comprehensive expression analysis and functional studies were performed to analyze the host factors related to the cccDNA regulation using RNA microarray and siRNA analysis. Results: HBV infection system accurately reproduced the HBV life cycle and exhibited various transcription levels. Microarray analysis revealed that 53 genes increased depending on the cccDNA levels. Of 53 genes, the expression of IFN-induced protein 44-like (IFI44L) was the most upregulated by IFN-γ and IFN-α but not entecavir, and associated with the anti-viral effects of IFN-γ. siRNA analysis revealed that IFI44L negatively regulates the innate immune response and IFN-γ function to suppress HBV transcription and propagation by inhibiting the activation of NF-κB and STAT1 pathways.

overall_design: To develop an in vitro HBV infection assay system that exhibits various transcription levels, HBV clones of genotype C2 with basal core promoter (BCP) 1762/1764 and/or precore 1896 mutations (wt/wt; Low transcription, wt/mu; Medium t., mu/mu; High t.) were applied. HBV plasmids were transiently transfected into HepG2 cells and the supernatant was added to the medium of PXB cells and treated with IFN-γ, IFN-α, and entecavir (ETV). Comprehensive expression analysis was performed to analyze the host factors related to the cccDNA regulation using RNA microarray.

first: Tatsushi

last: Naito

first: Hidetaka

last: Matsuda

first: Masahiro

last: Ohtani

first: Katsushi

last: Hiramatsu

first: Tsutomu

last: Nishizawa

first: Hiroaki

last: Okamoto

first: Yasunari

last: Nakamoto


title: Piwi suppresses transcription of Brahma-dependent transposons via Maelstrom in ovarian somatic cells

city: Tokyo

first: Kaoru

last: Sato

address: 35-2 Sakae-cho, Itabashi-ku

institute: Tokyo Metropolitan Institute of Gerontology

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Drosophila Piwi associates with PIWI-interacting RNAs (piRNAs) and represses transposons transcriptionally through heterochromatinization; however, this process is poorly understood. Here, we identify Brahma (Brm), the core adenosine triphosphatase of the SWI/SNF chromatin remodeling complex, as a new Piwi interactor, and show Brm involvement in activating transcription of Piwi-targeted transposons before silencing. Bioinformatic analyses indicated that Piwi, once bound to target RNAs, reduced the occupancies of SWI/SNF and RNA polymerase II (Pol II) on target loci, abrogating transcription. Artificial piRNA-driven targeting of Piwi to RNA transcripts enhanced repression of Brm-dependent reporters compared with Brm-independent reporters. This was dependent on Piwi cofactors, Gtsf1/Asterix (Gtsf1), Panoramix/Silencio (Panx), and Maelstrom (Mael), but not Eggless/dSetdb (Egg)–mediated H3K9me3 deposition. The lambdaN-box B–mediated tethering of Mael to reporters repressed Brm-dependent genes in the absence of Piwi, Panx, and Gtsf1. We propose that Piwi, via Mael, can rapidly suppress transcription of Brm-dependent genes to facilitate heterochromatin formation.

overall_design: Transcriptome-wide examination of gene expression changes  in Piwi-, Mael-, Brm-depleted OSCs. Genome-wide examination of changes in chromatin binding levels of Drosophila SWI/SNF complexes including Brm in Drosophila ovaries and OSCs.

first: Ryo

last: Onishi

first: Kensaku

last: Murano

first: Lumi

last: Negishi

first: Haruhiko

last: Siomi

first: Mikiko


title: XmaI-RRBS on Luminal B breast carcinoma samples taken prior to chemotherapy

city: Moscow

first: Alexey

middle: Igorevich

last: Kalinkin

state: Russia

address: Moskvorechie st., 1

department: Epigenetics

country: Russia

institute: RCMG

type: Methylation profiling by high throughput sequencing

summary: Luminal B breast carcinoma samples were taken prior to chemotherapy in order to identify epigenomic profiles predictive of neoadjuvant chemotherapy efficacy

overall_design: Reduced representation bisulfite sequencing by XmaI-RRBS (Tanas et al., 2017)

middle: I

first: Alexander

middle: S

last: Tanas


title: RNA-seq analysis of mouse cardiomyocytes treated with dnMKL1

first: Yuxuan

last: Guo

summary: The goal of this study is to analyze the impact of dnMKL1 on transcription during cardiomyocyte maturation in mouse

overall_design:
Wildtype mice were injected with AAV9-dnMKL1-GFP or AAV9-GFP specifically in cardiomyocytes at P1.  Five biological replicates were analyzed in each group.
In each experiment, cardiomyocytes were isolated by retrograde collagenase perfusion and purified by fluorescence activated cell sorting.
Total RNA was extracted from FACS sorted cells. RNA-seq libraries were generated using SMART-seq and Nextera kits and were sequenced on a NextSeq550 sequencer. FASTQ Data were aligned by STAR and count matrix generated by FeatureCounts.

first: William

last: Pu


title: XmaI-RRBS on triple negative breast carcinoma samples taken prior to chemotherapy

summary: Triple negative breast carcinoma samples were taken prior to chemotherapy in order to identify epigenomic profiles predictive of neoadjuvant chemotherapy efficacy


title: RNA-seq analysis of Actn2 knockout in mouse cardiomyocytes

summary: The goal of this study is to analyze the impact of Actn2 depletion on transcription during cardiomyocyte maturation in mouse

overall_design:
Actn2F/F and Actn2F/+ mice were injected with AAV9-cTNT-Cre specifically in cardiomyocytes at P1.  Five biological replicates were analyzed in each group.
In each experiment, cardiomyocytes were isolated by retrograde collagenase perfusion and purified by fluorescence activated cell sorting.
Total RNA was extracted from FACS sorted cells. RNA-seq libraries were generated using SMART-seq and Nextera kits and were sequenced on a NextSeq550 sequencer. FASTQ Data were aligned by STAR and count matrix generated by FeatureCounts.


title: Effect of Spag4 knockdown in 293T cells

city: Bonn

first: Moritz

last: Kebschull

address: Welschnonnenstr. 17

department: Department of Periodontology

institute: University of Bonn

summary: To test the effect of Spag4 knockdown, we compared knockdown and control cells subjected to 48h 2uM camptothecin treatment or vehicle.

overall_design: Total RNA from Spag4-knockdown 293T/17 cells compared to control cells both vehicle and camptothecin-stimulated

first: Justus

first: Panos

last: Papapanou


title: Functional dissection of MIEN1 trans-regulation provides new evidence for colorectal cancer genome editing-based therapeutics

city: Dunedin

first: Oscar

middle: Javier

last: Ortega-Recalde

state: Otago

address: 60 Hanover Street

department: Anatomy

country: New Zealand

institute: University of Otago

summary: MIEN1 has been described as a key actor in colorectal cancer (CRC) biogenesis. We have used CRISPR/Cas9 technique to delete the promoter region of MIEN1 in HT-29 CRC cells. RNA-seq experiments revealed that several biological processes related to migration/metastasis were enriched by differentially expressed genes. Genetically modified cells shown decreased migration capacity.

overall_design: RNA-seq experiments of WT and genetically modified HT-29 cells.

first: Diana

last: Sierra-Diaz

first: Adrien

last: Morel

first: Karen

middle: M

last: Jiménez

first: July

last: Buitrago

first: Danyela

last: Valero-Rubio

first: Nora

last: Contreras

first: David

last: Baquero

first: Andrés

last: Barco

first: Rafael

last: Parra-Medina

last: Monroy

first: Carlos

last: Figueroa

first: Paul

last: Laissue


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and poh1-/- splenic foxp3＋Treg cells

city: Shanghai

first: yun

last: liu

address: Xie tu road

department: Shanghai Cancer Institute

institute: Shanghai Jiaotong University School

summary:
Purpose: The goals of this study are to compare the transcriptome profiling of Wild Type and poh1-/- splenic foxp3＋Treg cells
Methods:Splenic CD4+Foxp3+ (YFP+) cells mRNA profiles of 2-week-old poh1+/+ Foxp3Cre+ wild type and poh1fl/fl Foxp3Cre+ mice were generated by deep sequencing, using Illumina HiSeq 2500. The sequence reads that passed quality filters were analyzed with edgeR. qRT–PCR validation was performed using SYBR Green assays
Results:Using an optimized data analysis workflow, we mapped about 50 million sequence reads per sample to the mouse genome (build mm10). Among all genes expressed, 1067 genes were upregulated and1391 genes were downregulated in poh1−/− Foxp3+ Treg cells relative to their expression in POH1 +/+ Treg cells. The gene-expression altered in POH1-ablated cells adversely correlated with those expressed in Treg cells in TCR-dependent manner. The gene sets were downreglated in POH1-deficiency Treg cells encoding various cell-surface receptors and intracellular molecules involved in migration, suppressive function and signature of Treg cells.
Conclusions:Gene expression in POH1-deficiency Treg cells was markedly diverse compared with that in POH1-sufficient Treg cells.

first: Yun

last: Liu

first: Yongzhong


title: Expression profiling analysis to identify POH1-regulated genes

first: Boshi

last: Wang

address: No.800 Dongchuan Road

institute: Shanghai Cancer Institute

summary: This work determined the POH1 regulated genes in the absence or presence of TGF-β in SMMC-7721 cells through genome-wide transcriptome sequencing.

overall_design: SMMC-7721 cells stably expressing vector control or exogenous POH1 were cultured in the absence or presence of TGF-β. 24 hours after TGF-β treatment, cells were subjected to RNA sequencing analysis.


title: Allele specific expression and gene regulation help explain transgressive thermal tolerance in non-native hybrids of the endangered California tiger salamander (Ambystoma californiense)

city: Los Angeles

first: Robert

middle: D.

last: Cooper

state: CA

address: 612 Charles E. Young Drive East

institute: UCLA

summary: Hybridization between native and non-native species is an ongoing global conservation threat. Hybrids that exhibit traits and tolerances that surpass parental values are of particular concern, given their potential to outperform native species. Effective management of hybrid populations requires an understanding of both physiological performance and the underlying mechanisms that drive transgressive hybrid traits. Here, we explore several aspects of the hybridization between the endangered California tiger salamander (Ambystoma californiense; CTS) and the introduced barred tiger salamander (Ambystoma mavortium; BTS). We assayed critical thermal maximum (CTMax) to compare the ability of CTS, BTS and F1 hybrids to tolerate acute thermal stress, and found that hybrids exhibit a wide range of CTMax values, with 33% (4/12) able to tolerate temperatures greater than either parent. We then quantified the genomic response, measured at the RNA transcript level, of each salamander, to explore the mechanisms underlying thermal tolerance strategies. We found that CTS and BTS have strikingly different values and tissue-specific patterns of overall gene expression, with hybrids expressing intermediate values. F1 hybrids display abundant and variable degrees of allele specific expression (ASE), likely arising from extensive compensatory evolution in gene regulatory mechanisms between CTS and BTS. We found evidence that the proportion of genes with allelic imbalance in individual hybrids correlates with their CTMax, suggesting a link between ASE and expanded thermal tolerance that may contribute to the success of hybrid salamanders in California. Future climate change may further complicate management of CTS if hybrid salamanders are better equipped to deal with rising temperatures.

overall_design: Examination of differential expression in response to acute thermal stress

middle: D

first: H

last: Shaffer


title: FAM83H-AS1 silencing in MCF7 breast cancer cells

city: CDMX

first: Alberto

last: Cedro-Tanda

state: CMDX

address: Periferico sur #4809

country: Mexico

institute: INMEGEN

summary:
We silenced FAM83H-AS1 shRNAs in cell line MCF7 carried a ~75% silencing compared to thenegative control (NC).
We evaluated the role of FAM83H-AS1 on oncogenic phenotypes in the MCF7 breast cancer cell line model. The knockdown of FAM83H-AS1 was achieved with ~75% of silencing efficiency. A complete transcriptomic analysis after silencing of FAM83H-AS1 revealed an impact on the global expression.

overall_design: We analyzed expression profile of knockdown of FAM83H-AS1 in MCF7 cell line using the Affymetrix Human Transcriptome Array 2.0 platform. Array data was processed by Affymetrix Exon Array Computational Tool.

first: Alfredo

last: Hidalgo-Miranda

first: Magdalena

last: Ríos-Romero


title: Clinical value of nine circulating miRNAs in prognosis and diagnosis of PDAC

city: Ciudad de México

first: Pedro

middle: Antonio

last: Avila

state: CDMX

address: Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco

department: Molecular Biomedicine

institute: CINVESTAV

summary: Pancreatic ductal adenocarcinoma (PDAC) is the most common malignancy of the pancreas. Since early disease symptoms are undefined and specific biomarkers are lacking, about 80% of patients present with advanced, inoperable tumors that represent a daunting challenge. Therefore, new sensitive and minimally invasive diagnostic tools are required to detect pancreatic cancer. The miRNA has been emerged as promising cancer biomarkers for PDAC. Nowadays, have been identified several miRNAs in serum or plasma of PDAC patients. However, there are not many of common miRNAs between them, and not all the studies have compared the serum/ plasma expression with the corresponding miRNAs present in the pancreatic tumor tissue. Due to this and considering that PDAC is the seventh leading cause of cancer death in Mexico, we initially identified the miRNAs that are differentially expressed in tissue from PDAC patients residing in the Mexican Republic, to later find out which of these miRNAs are overexpressed in the serum of patients with this type of cancer. In this way, nine common miRNAs were identified in tissue and serum of PDAC patients, of which four of them (miRNAs 223-3p, miR 210-3p, miR100-5p and miR-221 3p) could be proposed as a signature for the diagnosis of PDAC with a sensitivity and specificity of 0.74 and 0.82 respectively for patients residing in the Mexican Republic. The 56 target mRNA of these 9 miRNAs were found to be mainly enriched in fatty acid oxidation, glucose homeostasis, amino acid transport organonitrogen compound catabolism. Finally, four of the target mRNA may serve as a prognostic marker for PDAC in tissue samples.

overall_design: Formalin-fixed and paraffin-embedded tissue (FFPE) from 25 PDAC surgical specimens and 13 non cancerous pancreatic tissue samples (5 blocks from post-mortem studies and 4 blocks of pancreas adjacent to the tumor) were included in our study. In order to isolate the total areas of the tumor and excluding stromal cells, tissue macrodissection was performed. For the microRNA differential expression analysis, the GeneChip microRNA 4.0 array (Thermo Fisher Scientific, Waltham, MA, USA) was used.

first: Lissuly

last: Álvarez

first: Eric

middle: G

last: Salmerón Bárcenas

middle: A

last: Ávila-López

first: Georgina

last: Hernández

first: Roberto

last: Goepfer  Albores

first: Héctor

last: Saldivar-Cerón

first: Miguel

last: Vargas

first: Rosaura

last: Hernández-Rivas


title: Interdependence between histone marks and steps in Pol II transcription [Antczak.submission]

city: Ithaca

first: Charles

last: Danko

address: Hungerford Hill Rd

country: USA

institute: Baker Institute

summary: ChRO-seq provides quantative information about gene expression levels in liver tissue taken at necropsy from two healthy Quarter Horse mares.

overall_design: ChRO-seq data was generated from the liver of two horses that serve as the focus of the Functional Annotation of Animal Genomes (FAANG) project (Burns et al., 2018; Giuffra et al., 2019; Kingsley et al., 2019). We used this data to recover gene expression patterns that will later be used in efficient annotation of functional elements in diverse tissues from understudied species.

first: Edward

last: Rice

first: Donald

last: Miller

first: Carrie

last: Finno

first: Jessica

middle: L

last: Petersen

first: Rebecca

middle: R

last: Bellone

first: Douglas

middle: F

last: Antczak


title: RNA sequencing revealed abnormal gene expression and benefits of vitamin C treatment in cloned bovine embryos

city: Yangling

first: Lei

last: Zhang

state: Shaanxi

address: taicheng road

institute: NWAFU

summary: Somatic cell nuclear transfer (SCNT) in mammals has been mostly unsuccessful. In this study, we measured and compared transcription profiles of cloned and fertilized embryos using RNA sequencing. Before zygotic genome activation (ZGA), fewer genes were activated in the cloned embryos than in vitro fertilization (IVF), leading to insufficient activation of protein transport and degradation functions. In blastocysts, terms of “embryo development” and “adherens junction” represented major differences for repressed genes in SCNT compared to IVF. Vitamin C (Vc) was found to relax donor cell chromatin and promote cloned embryo development. RNA sequencing indicated that Vc treatment restored some abnormal genes and processes in the cloned embryos. Processes of autophagy, RNA-editing and cell junction were not fully established, but they were improved by Vc treatment. Overexpression of ZNF641, one of the completely restored genes by Vc treatment, improved the cloned embryos’ potential. Finally, Vc treatment rescued some long non-coding RNAs that were aberrantly expressed in the cloned embryos. Collectively, many important genes and biological processes were abnormal in the cloned embryos, some of which can be improved by Vc treatment. This investigation provides several practical aspects that could be useful for improving cloning efficiency and its future applications.

overall_design: Comparison of gene expression in preimplantation embryos derived from IVF, SCNT and Vc-treated SCNT,respectively.

first: Zekun

last: Guo


title: RNA-seq analysis of mouse cardiomyocytes at postnatal day 6 (P6) and P30

first: Yuxuan

state: MA

summary: Compare transcriptome between P6 and P30 cardiomyocytes in mouse.

overall_design:
Rosa-Tom or Rosa-Cas9 mice were injected with AAV9-cTNT-Cre at P1. cardiomyoytes were isolated at P6 or P30.
In each experiment, cardiomyocytes were isolated by retrograde collagenase perfusion and purified by fluorescence activated cell sorting.
Total RNA was extracted from FACS sorted cells. RNA-seq libraries were generated using SMART-seq and Nextera kits and were sequenced on a NextSeq500 sequencer. FASTQ Data were aligned by STAR and count matrix generated by FeatureCounts.

first: William

last: Pu


title: Toxicity and mechanisms of atrazine to the photosynthetic physiology and central carbon metabolism of Phaeodactylum tricornutum, at environmental dose

city: Qingdao

first: liqiang

last: yang

address: No.189 Songling Road, Laoshan District, Qingdao

institute: Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences

summary: Atrazine is one of the most commonly used herbicide and has been frequently detected in estuarine and offshore waters worldwide. As a photosystem Ⅱ inhibitor, atrazine may inhibit phytoplankton from fixating of CO2 and alter its carbon metabolism, which will undoubtedly have negative effect on the primary productivity and carbon sequestration capacity of coastal waters. However, the existing reports mainly focused on agriculture and freshwater ecosystems and are mostly toxicity test with high-dose of atrazine, which have little concern about the negative effects of atrazine on the carbon metabolism of phytoplankton and can’t reflect the actual toxic situation in offshore water. Diatoms are widely distributed in freshwater and oceans and contribute at least 20% of the global CO2 assimilation, which is an ideal model group to assess the ecological risk of atrazine. Here we present a comprehensive analysis of the physiological and genome-wide gene expression characteristics of the diatom P. tricornutum Pt-1 (CCMP 2561) treated with environmental dose of atrazine at different stress stages.

overall_design: 18 samples were analysed as following:  1) D1-C,  P. tricornutum Pt-1 inoculated in uncontaminated culture medium for 12 hours; 2) D1-T,  P. tricornutum Pt-1  inoculated in atrazine-contaminated culture medium for 12 hours;  3) D2-C,  P. tricornutum Pt-1  inoculated in uncontaminated culture medium for 2 days ; 4)D2-T,  P. tricornutum Pt-1  inoculated in atrazine-contaminated culture medium for 2 days; 5)  D7-C,  P. tricornutum Pt-1  inoculated in uncontaminated culture medium for 7 days ;  6) D7-T,  P. tricornutum Pt-1  inoculated in atrazine-contaminated culture medium for 7 days. Three replicates were set up for each treatment.

first: Liqiang

last: Yang

first: Hongmei

last: Li

first: Ruoyu

first: Yongyu


title: Stomatin-like protein 2 induces metastasis by regulating the expression of a rate-limiting enzyme of the hexosamine biosynthetic pathway in pancreatic cancer

status: Public on Dec 11 2020

city: Sendai

first: Kyohei

last: Ariake

address: 1-1, Seiryo-machi, Aoba-ku

department: Department of Surgery

institute: Tohoku university

summary: Stomatin-like protein 2 (SLP-2) is associated with poor prognosis in several types of cancer, including pancreatic cancer; however, the molecular mechanism of its involvement remains elusive. This study aimed to elucidate the role of this protein in the development of pancreatic cancer. Human pancreatic cancer cell lines AsPC-1 and PANC-1 were transfected by a vector expressing SLP-2 shRNA. Analyses of cell proliferation, migration, invasion, chemosensitivity, and glucose uptake were performed, while a mouse xenograft model was used to evaluate the functional role of SLP-2 in pancreatic cancer. Immunohistochemical analysis was retrospectively performed on human tissue samples to compare expression between the primary site (n=279) and the liver metastatic site (n=22). Furthermore, microarray analysis was conducted to identify genes correlated with SLP-2. In vitro analysis demonstrated that cells in which SLP-2 was suppressed showed reduced cell motility and glucose uptake, while in vivo analysis showed a dramatic decrease in the number of liver metastases. Immunohistochemistry revealed that SLP-2 was elevated in liver metastatic sites. Microarray analysis indicated this protein regulated the expression of glutamine-fructose-6-phosphate transaminase 2 (GFPT2), a rate-limiting enzyme of the hexosamine biosynthesis pathway. SLP-2 contributes to the malignant character of pancreatic cancer by inducing liver metastasis. Cell motility and glucose uptake may be induced via the hexosamine biosynthesis pathway, through the expression of GFPT2. This reveals a new mechanism of liver metastasis and implies that SLP-2 and its downstream pathway could provide novel therapeutic targets for pancreatic cancer.

overall_design: This study aimed to elucidate the role of SLP-2 in the development of pancreatic cancer. Human pancreatic cancer cell lines AsPC-1 were transfected by a vector expressing SLP-2 shRNA. Microarray analysis was conducted to identify genes between SLP-2 control cells (AsPC-1cont) and ASPC-1 SLP-2 suppressed cells (AsPC-1sh1, AsPC-1sh2).

first: Dang

last: Chao


title: Macrophage heterogenity in liver and adipose during obesity

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

summary: Liver and adipose tissue undergo dynamic inflammatory changes during the progression of obesity.  This study was designed to evaluate the changes in gene expression profile and function of subpecific macophage subsets.

overall_design:
Cx3Cr1-GFP mice were fed a STD or high fat, high sucrose diet for 16 weeks after which macrophages were isolated from the adipose tissue and liver.  Flow sorting was utilized to divide liver macrophages into F4/80hi cells expressing TIM4 [i.e., STD KC, HFD KC] or those expressing Cx3cr1 (i.e., GFP positive) [Cx3cr1pos macs-HFD].  In the adipose tissue, high fat diet ATMs were flow sorted based on their expression of F4/80 and CD64 [i.e., ATMs-HFD].
A total of 3 samples from STD KC, 5 samples from HFD KCs, 4 samples of Cx3cr1 Macs, and 5 ATM samples on HFD were collected.

first: Sabine

last: Daemen

first: Anastasiia

last: Gainullina

first: Gowri

last: Kalugotla

first: Li

last: He

first: Mandy

last: Chan

first: Joseph

middle: W

last: Beals

first: Kim

last: Liss

first: Samuel

last: Klein

first: Ariel

middle: E

last: Feldstein

first: Brian

last: Finck

first: Joel

last: Schilling


title: Time resolved and interorgan response of mice to systemic energetic starvation

city: kyoto

first: Yusuke

last: Morita

state: kyoto

address: kyoto

institute: kyoto university

summary: The effects of fasting have been studied extensively, predominantly on isolated processes, within a specific organ. No comprehensive study of the adaptations was available for different organs including heart.The gene expression profiles of heart, liver, and muscle were investigated in this experiments.

overall_design: 6 week-old mice were fasted for 0,24,and 48 hours before sacrifice (n = 5 per group)

first: Eri

last: Minamino-Muta

first: Yohei

last: Tanada

first: Tetsuo

last: Shioi

first: Takao

last: Kato