title: Gene expression profiling predicts sensitivity of chronic lymphocytic leukemia cells to dasatinib

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumor Immunology

country: Germany

institute: Charité University Medicine

summary: In this study, we used RNA-sequencing to characterize the gene-expression profiles of CLL cells sensitive and resistant to dasatinib and define a specific gene-expression signature associated with drug sensitivity. Specifically, cells were isolated from the blood of 16 newly diagnosed, unselected CLL patients prior to any treatment and classified as responders or non-responders based on in vitro drug cytotoxicity assays. RNA-sequencing analysis of both treated and untreated samples revealed 154 genes differentially expressed between responders and non-responders and, among these, 31 genes were predictive of response in untreated samples. Cells sensitive to dasatinib exhibit increased expression of genes associated with stress signaling, metabolic pathways, including glycolysis, and immune response, including proinflammatory components. Neither of the responder and non-responder groups was enriched for any of the genetic aberrations commonly associated with CLL, as determined by gene mutation and copy-number analysis. We employed the Library of Integrated Network-Based Cellular Signatures (LINCS) database for validation of the obtained gene expression profiles and show, in sum, that dasatinib may represent a viable therapeutic option in a group of CLL patients preselected by gene-expression profiling.

overall_design: RNA-sequencing was performed for peripheral blood lymphocytes of 16 newly diagnosed, untreated and unselected CLL patients, cultured in-vitro with and without dasatinib.

first: Tamara

middle: J

last: Blätte

first: Marcin

middle: M

last: Machnicki

first: Eliza

last: Glodkowska-Mrowka

first: Anna

last: Dolnik

first: Marta

last: Karp

first: Agnieszka

last: Karczmarczyk

first: Krzysztof

last: Giannopoulos

first: Tomasz

last: Stoklosa


title: Epigenome analysis of normal PBMC and co-cultured PBMC with human colorectal adenocarcinoma cell lines using DNA microarray

status: Public on Dec 29 2020

city: Bangkok

first: Nakarin

last: Kitkumthorn

address: Yothee road

department: Oral Biology

country: Thailand

institute: Mahidol University

type: Methylation profiling by genome tiling array

summary:
The goal of this study is to investigate the secretion from human colorectal adenocarcinoma cell, which effect to peripheral blood mononuclear cell (PBMC).
Genome wide DNA methylation profiling of co-cultured PBMC without human colorectal adenocarcinoma cell lines and co-cultured PBMC with human colorectal adenocarcinoma cell lines were generated datas by microarray technology. The Illumina Infinium MethylationEPIC BeadChip was used to obtain DNA methylation profiles across approximately 850,000 CpGs in enhancer regions, gene bodies, promoters and CpG islands. Samples included duplicate PBMC of female control, duplicate PBMC of male control, duplicate PBMC of female were co-cultured with HT29, and duplicate PBMC of male were co-cultured with SW480.

overall_design:
Genome wide DNA methylation profiling of co-cultured PBMC without human colorectal adenocarcinoma cell lines and co-cultured PBMC with human colorectal adenocarcinoma cell lines.
Bisulphite converted DNA from the 8 samples were hybridized to the Illumina Infinium MethylationEPIC BeadChip.

first: Papatson

last: Boonsongserm

first: Apiwat

last: Mutirangura


title: Gene expression profiling in Col-0 and ein2-5 seedlings under glucose depletion and glucose recovery conditions

city: Shanghai

first: Renyi

last: Liu

state: Shanghai

address: 3888 Chenhua Road

department: Bioinformatics

country: China

institute: Shanghai Center for Plant Stress Biology

type: Expression profiling by high throughput sequencing

summary: We aimed to compare the differences in gene expression in Col-0 and ein2-5 seedlings under glucose depletion and glucose recovery conditions. Col-0 and ein2-5 seedlings were germinated in liquid 1/2 MS medium without glucose for 4 days and were then treated with or without glucose for 2 hours. mRNA seq was performed to make the comparisons.

overall_design: Col-0 and ein2-5 seedlings were grown in liquid 1/2 MS medium without glucose for 4 days, and were then treated with or without 15 mM glucose for 2 hours. RNA was isolated and mRNA-seq was performed to compare the differences in gene expression in Col-0 and ein2-5 seedlings.

first: Liwen

last: Fu

first: Yanlin

first: Guochen

last: Qin

first: Ping

last: Wu

first: Shuhui

last: Yang

first: Sang-Dong

last: Yoo

first: Yan

last: Xiong


title: Expression data from sevoflurane anesthesia treated rat

city: Beijing

first: Cheng

last: Ni

state: Beijing

address: No.49 North Garden Road

institute: Peking University Third Hospital

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

summary:
Long noncoding RNAs (lncRNAs) play important roles in brain function modulation and neurodegenerative diseases. However, whether lncRNA regulations are involved in the mechanisms of perioperative neurocognitive disorders (PNCD), especially in anesthesia related brain dysfunction, remains unknown.
We explored the expression and regulation pattern profiles of lncRNAs in the hippocampus of aged rats after sevoflurane anesthesia with microarrays.

overall_design: We focused on lncRNA and gene expression patterns in the hippocampus of aged rats after sevoflurane anesthesia. And we established functional annotation of differentially expressed (DE)-lncRNAs and their potential target genes, as well as lncRNA-mRNA co-expression network to reveal the role of lncRNAs in sevoflurane anesthesia related brain function modulation.

first: Yinyin

last: Qu

first: Min

last: Qian

first: Yujie

last: Wang

first: Ning

first: Liwei

first: Dengyang

last: Han

first: Jun

first: Xiangyang

last: Guo


title: Transcriptional profiling of WT-ProB, WT-PreB and ProB cells from Rag1ko/ko, IghTer5H/Ter5H, IghTer5 /wt;Rag1ko/ko , IghTer5H∆TM/ Ter5H∆TM and IghTer5H∆TM/ Ter5H∆TM ;Rag1ko/ko mice

city: Amsterdam

first: Heinz

last: jacobs

address: Plesmanlaan 121

country: Netherlands

institute: NKI

summary: We studied the role of the stable Igh mRNA in Igh chain check point. Here we generated RNA-seq data from sorted ProB (CD19+B220+c-Kit+CD25-) and PreB (CD19+B220+c-Kit-CD25+) populations from Bone marrow of mice.

overall_design: RNA-seq from sorted Pro and PreB cell populations from WT and Rag1ko/ko, IghTer5H/Ter5H, IghTer5 /wt;Rag1ko/ko , IghTer5H∆TM/ Ter5H∆TM and IghTer5H∆TM/ Ter5H∆TM ;Rag1ko/ko mice mice


title: Mesenchymal stromal cells orchestrate the overhaul of leukemia bone marrow microenvironment via educating macrophages [in vitro]

city: Guangzhou

first: Xia

last: Chengxiang

state: Guangdong

address: Kai Yuang Road 190

institute: GIBH

summary: RNAseq were performed to analyze the transcriptomic differences between macrophages and MSC-educated macrophages in vitro.

overall_design: RNAseq: Four macrophage samples and four MSC-educated macrophage samples.

first: Chengxiang

last: Xia

first: Qitong

last: Weng

first: Jinyong


title: Mesenchymal stromal cells orchestrate the overhaul of leukemia bone marrow microenvironment via educating macrophages

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

overall_design: Refer to individual Series


title: Mesenchymal stromal cells orchestrate the overhaul of leukemia bone marrow microenvironment via educating macrophages [in vivo]

summary: RNAseq were performed to analyze the transcriptomic differences between macrophage and MSC-educated macrophages in vivo.

overall_design: RNAseq: Six macrophage samples and six MSC-educated macrophage samples from two individual mice.


title: Circulating long noncoding RNAs associated with hypertrophic cardiomyopathy

first: Qi

address: Yanjiangxi Road

institute: Sun Yat-sen University

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

summary: Plasma lncRNA expression profiles were acquired by using a human lncRNA microarray.

overall_design: Whole blood was collected in venous blood collection tubes containing EDTA after fasting overnight, and plasma was separated by centrifugation.

first: Junjie

first: Runlu

last: Sun

first: Wenli

last: Gu

first: Zhijian

last: He

first: Qian

last: Chen

first: Wenhao

last: Liu

first: Yangxin

first: Jingfeng

first: Yuling

last: Zhang


title: Expression data from PSAT1 overexpression in CL1-0 lung cancer cell line and PSAT1 knockdown in CL1-5 lung cancer cell line.

city: Taipei

first: Michael

last: Hsiao

address: Academia Road, Section 2, Nankang, Taipei, 115, Ta

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

summary:
We demonstrate that PSAT1 down-regulation shRNAs significantly reduced cell migration and invasion in highly invasive lung cancer cell lines in vitro, as well as in lung metastases in vivo
We used microarrays to analyze the PSAT1 regulated gene expression underlying invasion-metastasis cascade.

overall_design: CL1-0 lung adenocarcinoma cells with PSAT1 overexpression and CL1-5 cells with PSAT1 knockdown were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Yu-Chan

last: Chang


title: Structural Basis for Bacterial Ribosome-Associated Quality Control by RqcH and RqcP

status: Public on Dec 28 2020

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

institute: Universitaet Hamburg

summary: In all branches of life, stalled translation intermediates are recognized and processed by ribosome-associated quality control (RQC) pathways. RQC begins with the splitting of stalled ribosomes, leaving an unfinished polypeptide still attached to the large subunit. Ancient and conserved NEMF family RQC proteins target these incomplete proteins for degradation by the addition of C-terminal "tails." How such tailing can occur without the regular suite of translational components is, however, unclear. Using single-particle cryo-electron microscopy (EM) of native complexes, we show that C-terminal tailing in Bacillus subtilis is mediated by NEMF protein RqcH in concert with RqcP, an Hsp15 family protein. Our structures reveal how these factors mediate tRNA movement across the ribosomal 50S subunit to synthesize polypeptides in the absence of mRNA or the small subunit.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: B. subtilis cell lysate and RqcH-bound (i.e. immunopreciptated, RqcH-IP) tRNAs used for tRNA microarrays to measure tRNA abundance - 4 biological replicates in total; 3 - RqcH-IP and 1 - total tRNA (lysate)

first: Hiraku

last: Takada

first: Caillan

last: Crowe-McAuliffe

first: Christine

last: Polte

first: Daniel

middle: N

last: Wilson

first: Vasili

last: Hauryliuk


title: Effects of an environmentally relevant mixture of organophosphate esters derived from house dust on endochondral ossification in murine limb bud cultures

city: Montreal

first: Barbara

middle: F.

last: Hales

state: QC

address: 3655 Prom. Sir William Osler, room 110

department: Pharmacology and Therapeutics

country: Canada

institute: McGill University

summary: Organophosphate esters (OPEs) are used widely as flame retardants and plasticizers but much remains unknown about their potential toxicity. Previously, we reported that four individual OPEs suppress endochondral ossification in murine limb bud cultures. However, real-life exposure is to complex OPE mixtures. In the present study, we tested the hypothesis that a Canadian household dust-based OPE mixture will affect endochondral ossification in gestation day 13 CD1 mouse embryo limb buds expressing fluorescent markers for the major cell populations involved in the process: COL2A1-ECFP (proliferative chondrocytes), COL10A1-mCherry (hypertrophic chondrocytes), and COL1A1-YFP (osteoblasts). Limbs were cultured for six days in the presence of vehicle or dilutions of the OPE mixture (1/1,000,000, 1/600,000, and 1/300,000). All three OPE mixture dilutions affected cartilage template development and the progression of endochondral ossification, as indicated by the fluorescent markers. The expression of Sox9, the master regulator of chondrogenesis, was unchanged, but the expression of Runx2 and Sp7, which drive chondrocyte hypertrophy and osteoblastogenesis, was dilution-dependently suppressed. RNA sequencing revealed that exposure to the 1/300,000 dilution of the OPE mixture for 24 h downregulated 153 transcripts and upregulated 48 others by at least 1.5-fold. Downregulated transcripts were enriched for those related to the immune system and bone formation. In contrast, upregulated transcripts were enriched for those with stress response functions known to be regulated by ATF4 activation. Thus, exposure to the mixture of OPEs commonly found in house dust may have adverse effects on bone formation.

overall_design: Forelimb buds collected from gestation day 13 CD1 mouse embryos were cultured for 24 hours in the presence of vehicle (DMSO) or 1 in 300,000 dilution of our Canadian house dust based OPE mixture; n = 4.

first: Yan

last: Han

middle: F


title: Genome-wide occupanies of Ssu72, Pol II, pSer2, pSer5, pSer7 and pThr4 of Ssu72 Wild Type and Knock-out MEFs and hepatocytes

city: Suwon

first: Hyun-Soo

last: Kim

address: 2066, SEOBU-RO, JANGAN-GU, SUWON-SI, GYEONGGI-DO

department: School of medicine

country: South Korea

institute: SUNGKYUNKWAN UNIVERSITY

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report the genome-wide occupanies for high-throughput profiling of Pol II and Pol II CTD phosphorylation modifications in mammalian cells and tissues. By obtaining over three billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, embryonic fibroblasts and primary hepatocytes. Loss of mammalian Ssu72 was found to be related to defect of transcriptional elongation though the defects of Pol II CTD phophorylational dynamics. In addition, depletion of Ssu72 resulted in defects of Pol II elongation by reducing CTD Ser2 and Thr4 phosphorylation which induced Pol II accumulation at the proximal promoter region by increasing CTD Ser5 and Ser7 phosphorylation of transcriptionally active genes in a tissue-specific manner. Our results revealed a fundamental role of mammalian Ssu72 in regulating RNA Pol II-mediated transcriptional plasticity for cell-type-specific homeostatic maintenance.

overall_design: Examination of Ssu72, Pol II and CTD modifications in 3 cell types.

first: Chang-Woo

last: Lee


title: Comprehensive Tissue Transcriptome of Bombina orientalis

status: Public on Dec 27 2020

city: Ulsan

first: Taejoon

last: Kwon

address: 50 Unist-gil

department: Department of Biomedical Engineering

institute: Ulsan National Institute of Science and Technology

summary: To construct the reference transcriptome of B. orientalis, we collected mRNAs of multiple tissues from adult animal.

overall_design: We sampled each tissue for two or three individual adult animals.

first: Hee-Sun

last: Yang

first: Hyo

last: Sim

first: Hanna

last: Cho

first: Woo

middle: Y

last: Bang

first: Ha

middle: E

first: Tae

last: Park


title: Transcriptomic analysis and dynamic expression of genes revealed flavonoid synthesis in Scutellaria viscidula

city: Xi'an

first: Bo

last: Cao

state: Shaanxi

address: 620 West Chang'an Road, Changan District

institute: Shaanxi Normal University

summary: Scutellaria viscidula Bunge (Labiatae), a perennial herb, is an important medicinal plant that possesses broad pharmacological actions. S. viscidula contains flavonoids with good bioactivities (e.g. baicalin, wogonoside, baicalein and wogonin) mainly in its dry root, which is used as alternative to Scutellaria baicalensis in the north of China. Furthermore, S. viscidula also has flavones with interesting diverged structures such as panicolin, viscidulin I, viscidulin II and viscidulin III. Tracing the dynamic process of gene expression will help reveal the mechanism of flavonoid synthesis in S. viscidula, as well as the 4'-deoxyflavone biosynthesis in S. baicalensis. One way is to generate and analyze the expressed sequence tags (ESTs). However, little is known on the transcriptome information of S. viscidula, particularly the key genes involved in flavonoid biosynthesis. In this study, we conducted de novo transcriptome analysis of S. viscidula and obtained 42,310,834 reads and 40,052 unigenes, respectively. We revealed 177 genes relating to flavonoid biosynthesis, where 23 key enzyme encoding genes including CHS, CHI, F3H, PAL and 4CL were annotated. Furthermore, we investigated the dynamic expression of CHS, CHI, F3H, MYB2, and bHLH of stem, root and leaf of S. viscidula in May, July and September. Our results showed that these key genes had important regulatory function and exhibited positive correlation with total flavonoid content in different growth stages of S. viscidula. Collectively, this study provides high-quality transcriptome data of S. viscidula, and further gives significant information for understanding the molecular mechanism of gene expression and active ingredients in Scutellaria plants.

overall_design: Root mRNA profiles of Scutellaria viscidula Bunge collected in June were generated by deep sequencing, in a mixture of three samples, using Illumina® Hiseq 2000 platform.qRT–PCR validation was performed using SYBR Green assays.

first: Bai

last: Chengke

first: Xu

last: Jun

first: Cao

last: Bo

first: Li

last: Guishuang


title: Single cell RNA sequence discover the musculoskeletal tissue cell atlas during limb development

city: Hangzhou

first: Zi

last: Yin

address: YuHangTang Road N0.866

institute: Zhejiang University

summary:
By using single cell RNA-seq,We dissect the cellular heterogeneity and transcriptome profiles during limb development, and reveal the characteristic features of limb development and musculoskeletal stem/progenitor cell populations involved in limb lineage development.
Our study therefore systematically decoded molecular markers and cellular program of limb development that would shed lights on limb developmental biology.

overall_design: We performed high throughput single-cell RNA sequencing on cells from E10.5, E12.5 and E15.5 murine limbs to dissect the cellular heterogeneity and transcriptome profiles during limb development.

first: Hongwei

last: Ouyang


title: TET1 regulates reprogramming with Vitamin C and relatively small molecules

first: zheng

last: hui

address: Kaiyuan av.190

summary: We found a small molecule-DKG, relative to Vitamin C, could replace the function of Viamin C during reprogramming. After comparing transcriptome profiling (RNA-seq) of  this molecule to vitamin C, it could provide a framework for more mechanism.

overall_design: mRNA profiles of day 3 and day8 during reprogramming with DMSO or Vitamin C or DKG infected Flag or Tet1CD virus.

first: Yixin

last: Zhang

first: Zheng

last: Hui


title: Transcriptional profiling of adult retinal ganglion cells during optic nerve regeneration

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

country: USA

institute: University of California Los Angeles

summary: Objective: To identify genes that are differentially expressed in retinal ganglion cells undergoing axon regeneration after optic nerve injury. Adult mice that express cyan-fluorescent protein (CFP) in RGCs were treated with pro-regenerative treatment after optic nerve injury. The treated RGCs were selected by FACS (CFP+mcherry) and their RNA profiles were analyzed.

overall_design: Adult CFP mice received AAV2-shPten-mcherry or AAV2-mcherry virus 2 weeks before optic nerve crush. Immediately after nerve injury, AAV2-shPten-injected mice received recombinant oncomodulin plus CPT-cAMP (T) and AAV2-mcherry-injected mice received saline intraocularly (C). RGCs were selected by FACS 1, 3, 5 days (D1, D3, D5) after nerve crush and treatment. Normal RGCs (Nor.) received AAV2-mcherry only. To find distinctive regulation after pro-regenerative treatment, samples from the treatment group were compared with that of same time point control group: D1.C vs. D1.T; D3.C vs. D3.T; D5.C vs. D5.T. All of the nerve-injured samples were also compared with normal RGCs.

first: Yuyan

last: Cheng

first: Yuqin

first: Alice

first: Zlexander

last: Bernstein

first: Kun

last: Gao

first: Kyra

last: Potter

first: Yan

last: Ao

first: Hui

last: Gilbert

first: Jing

last: Ou

first: Catherine

last: Fricano-Kugler

first: Jeffery

middle: L

last: Goldberg

first: Clifford

last: Woolf

first: Micahel

middle: V

last: Sofroniew

first: Larry

middle: I

last: Benowitz

first: Daniel

middle: H

last: Geschwind


title: Transcriptomic insight into molecular processes of dorsal muscle remodeling during Microhyla fissipes metamorphosis

status: Public on Dec 26 2020

city: Chengdu

first: xungang

last: wang

address: No.9 Section 4, Renmin Nan Road

institute: Chengdu Institute of Biology, Chinese Academy of Sciences

summary: We generated 120 Gb of raw sequencing data (~10 Gb per sample) and catalogued the expression profiles of 55106 annotated unigenes.We identified numerous differentially expressed genes that exhibited distinct expression patterns, and tight junction that were highly differentiated between S40 and S45, as well as between S36 and S43, S45. And genes related to glycolysis and pancreatic secretion were significantly enrichement beweent S43 and S45, these genes have known or potential roles in defense response and were enriched in functional gene categories potentially responsible for cucumber resistance.These results indicated that there are two process during metamorphosis, first one from S36-S43 is the larvel muscle development and apopsist, and the second from S43-S45 is the adult muscle development.  Therefore, they are appealing candidates for further investigation of the gene expression and associated regulatory mechanisms related to muscle remodeling during metamorphosis.

overall_design: Microhyla fissipes dorsal muscle mRNA profiles of four different development stage during metamorphosis were generated by deep sequencing with three biological replicates, using Illumina HiSeq4000.

first: Lusha

last: Liu

first: Wei

last: Zhu

first: Xungang

last: Wang

first: Jianping

last: Jiang


title: Gene expression after low dose irradiation in pluripotent stem cells developing to retinal ganglion cells

city: 4-6-1, Komaba, Meguroku

first: Takahide

last: Kohro

state: Tokyo

country: Japan

institute: LSBM, RCAST

summary: The effects of low dose irradiation on the gene expression on the neural cell development using human induced pluripotent stem cells (hiPS cells).

overall_design: We irradiated 30 and 180 mGy of radiation on hiPS cells between day 4 and 5 of differentiation to determine alteration of genome-wide gene expressions on day 6, 10, 17 and 35 of development. Activated and inactivated canonical pathways were identified by ingenuity pathway analysis and upstream molecules, diseases and functions were predicted.

first: Mari

last: Katsura

first: Urade

last: Yoshihiro

first: Hiroko

last: Nansai

first: Mika

last: Kobayashi

first: Akashi

last: Taguchi

first: Yukiko

last: Ishikawa

first: Tomohiro

last: Ito

first: Hisako

last: Fukunaga

first: Hideto

last: Tozawa

first: Yoko

last: Chikaoka

first: Ryo

last: Nakaki

first: Akinobu

last: Echigo

first: Hideko

last: Sone

first: Youichirou

last: Wada


title: Genome-wide profiling of histone chaperone FACT in Saccharomyces cerevisiae

city: Hyderabad

first: Ashutosh

last: Shukla

state: Telangana

address: Habsiguda X Road

country: India

institute: CSIR-Centre for Cellular and Molecular Biology

summary: Spt16-TAP ChIP-seq

overall_design: Spt16-TAP ChIP-seq single end sequencing on Illumina GAII. 2 biological replicates of each IP samples, 1 Input sample and 1 mock sample. Done in under normal growth and nutrient deprivation (2 hours)

first: Purnima

last: Bhargava


title: Divergent role for STAT5 in the adaptive responses of natural killer cells

city: Ithaca

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

institute: Cornell University

summary: Natural killer (NK) cells are innate lymphocytes with the capacity to elicit adaptive features, including clonal expansion and immunological memory. Because signal transducer and activator of transcription 5 (STAT5) is essential for NK cell development, the role of this transcription factor and its upstream cytokines IL-2 and IL-15 during infection have not been carefully investigated. In this study, we investigate how STAT5 regulates transcription during viral infection. We demonstrate that STAT5 is induced in NK cells by IL-12 and STAT4 early after infection, and that partial STAT5 deficiency results in a defective capacity of NK cells to generate long-lived memory cells. Furthermore, we find a functional dichotomy of IL-2 and IL-15 signaling outputs during viral infection, whereby both cytokines drive clonal expansion, but only IL-15 is required for memory NK cell survival. We thus highlight a novel role for STAT5 signaling in promoting an optimal antiviral NK cell response.

overall_design: RNA-seq was performed on Ly49H+ NK cells harvested during in vivo MCMV infection.

first: Joseph

middle: C

last: Sun


title: Effects of mitochondria-targeted antioxidant SS-31 on cigarette smoke-induced airway inflammation and oxidative stress in a mouse model

status: Public on Dec 25 2020

first: Yongchun

last: Shen

address: Medical clinic 37 Guoxue Alley

institute: West China Hospital of Sichuan University

summary: This study investigated whether mitochondria-targeted peptide SS-31 played a protective role in cigarette smoke (CS)-induced airway inflammation and oxidative stress in mice. Mice were exposed to CS for 4 weeks to establish a CS-induced airway inflammation model, then treated with SS-31. Pathological changes and oxidative stress in lung tissue, inflammatory cell counts and pro-inflammatory cytokines in bronchoalveolar lavage fluid (BALF) were examined. RNA sequencing from lung tissue and western blotting were conducted to investigate mechanisms. SS-31 attenuated CS-induced inflammatory injury of the airway. Numbers of total cells, neutrophils, and macrophages and levels of tumor necrosis factor α, interleukin 6, and matrix metallopeptidase 9 in BALF were markedly reduced by SS-31. SS-31 attenuated CS-induced oxidative stress by decresing malondialdehyde and myeloperoxidase levels, and increasing superoxide dismutase activity. It also reversed the expression of mitochondrial fission protein and optic atrophy 1 protein, and reduced cytochrome c release into the cytosol. RNA sequencing revealed that SS-31 changed CS-induced expression profiles and enriched MAPK pathway, western blotting confirmed that SS-31 inhibited the CS-activated MAPK pathway. SS-31 alleviates CS-induced airway inflammation and oxidative stress, possibly via the regulation of mitochondrial function and MAKP pathway, SS-31 may be a novel drug for CS-induced airway disorders.

overall_design: RNA-seq of CS vs SS-31H_CS in C57BL/6J mice

first: Deqing

last: Yang

first: Qiunan

last: Zuo

first: Tao

last: Wang

first: Dan

last: Xu

first: Lian

last: Liu

first: Lijuan

last: Gao

first: Chun

last: Wan

first: Lei

last: Chen

first: Fuqiang

last: Wen


title: Age-related gene changes of naïve and memory T cells in a mouse age-tracking model

city: Xi’an

first: Anjun

last: Jiao

address: No. 28, Xianning West Road, Xi'an City, Shaanxi Province

institute: Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University

summary: The transcriptomic changes of young and aged T cells are still unknown. Our previous study successfully tracked aged T cells generated from one wave of developing thymocytes of young age by a lineage-specific and inducible Cre-controlled reporter (TCRδCreERR26ZsGreen mouse strain). We used this transgenic mice and RNA-Seq to study the immunosenescence of naïve and memory T cell populations. A large number of genes involved in cellular and molecular functions, protein activity, cell cycle, cell adhesion, and immune functions were identified as having altered expression during aging. Our work revealed aged CD8 memory T cells with increased T cell activation and immunity genes, yet high expression of immunosuppressive checkpoints and resistance to cell death, implying aberrant T cell immunity in old mice. These feature genes identified in the current study serve as new therapeutic targets for correcting age-related defects.

overall_design: The differential features of gene expression levels in young and old T cells.

first: Baojun

last: Zhang

first: Xiaofeng

first: Xin


title: Regulation of electro-acupuncture(EA) and astragalus membranaceus (AM) on genes in bone marrow

city: Tianjin

first: Jin

last: Huang

address: No.10 Poyang Lake Road, Tuanbo new town, Jinghai District

institute: Tianjin University of Traditional Chinese Medicine

summary:
A large number of clinical trials have shown that acupuncture is effective in improving leukopenia after chemotherapy. Our study has shown that electroacupuncture can effectively improve the hematopoietic function of bone marrow in chemotherapy-induced  leukopenia mice. Therefore, we want to further observe the key signal pathway of bone marrow of electroacupuncture to improve leukopenia after chemotherapy.
We used microarray to detail the expression of  hematopoiesis related genes in bone marrow.

overall_design: The bone marrow samples (n=6) were mixed, extracted, purified, whose qualities were tested for total RNA with a standard Affymetrix protocol according to Shanghai Biotechnology Corporation (Shanghai, China) as reported previously.

first: Zhifang


title: Development of microRNA signatures for acute rejection after liver transplantation using rat model

city: Shanghai

first: jie

last: hu

address: 180 Fenglin Road

institute: Zhongshan hospital, Fudan University

summary: To find out acute rejection (AR) associated  microRNAs, we have employed Agilent microRNA microarray as a discovery platform to identify microRNAs with the potential to distinguish AR from controls. We first established a rat Orthotopic liver transplantation (OLT) model with AR, using Brown Norway (BN) rats that received OLT with liver grafts from Lewis rats (Lewis to BN). OLT with BN rats as the donors and recipients were also performed (BN to BN), and these rats served as the control group (non-rejection group, NR group). Then, global microRNA expression profiles of the plasma and grafts were evaluated and validated with high throughout microarray and RT-qPCR.

overall_design: Lewis to BN (AR group) and BN to BN (control) OLT were carried out with 4 rats in each group. All the 8 rats were sacrificed on the 7th day after OLT. Plasma and liver grafts were obtained and RNA were extracted for microarray hybridization. The differential expression profiles of plasma level and graft level were obtained via group comparision.

first: Jie

last: Hu

first: Zheng

first: Jian

last: Zhou

first: Jia

last: Fan


title: Single cell RNA-sequencing of human omental adipose tissue mesothelial cells

city: Durham

first: Rana

middle: K

last: Gupta

state: North Carolina

address: Carmichael Building, 300 North Duke St.

department: Duke Molecular Physiology Institute

institute: Duke University

summary: We assessed the heterogeneity of mesothelium-associated cells from omental adipose tissues from three individuals with obesity.

overall_design: We isolated mesothelium-associated cells  from human omental adipose tissue. Single cell library preparation was performed using the 10X Genomics Single Cell 3 v3 according to the manufacturers instructions.

first: Olga

middle: T

first: Lavanya

last: Vishvanath


title: RNA sequencing of Human Cortical Organoids diffrentiated for extended periods of time

first: Aaron

last: Gordon

address: 695 Charles E. Young Drive South, Gonda 2306, Los Angeles, CA  90095-1761

department: Neurology

institute: UCLA

summary: Assesing gene  expression in human cortical organoids during long term (>600 days) maturation.

overall_design:
62 samples collected during long term maturation of human cortical spheroids
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Authors state "Due to HIPPA compliance issues, submitters are unable to provide raw data".

first: Se-Jin

last: Yoon

first: Sergiu

middle: P

last: Pasca

first: Daniel

last: Geschwind


title: Brain tumor stem cell dependence on glutaminase reveals a metabolic vulnerability through the amino acid deprivation response pathway

city: Calgary

first: Ian

middle: James

last: Restall

state: Alberta

address: 3330 Hospital Drive NW

institute: University of Calgary

summary: Cancer cells can metabolize glutamine to replenish TCA cycle intermediates, leading to a dependence on glutaminolysis for cell survival. However, a mechanistic understanding of the role that glutamine metabolism has on the survival of glioblastoma (GBM) brain tumor stem cells (BTSCs) has not yet been elucidated. Here we report that, across a panel of twenty glioblastoma BTSC lines, glutaminase (GLS) inhibition showed a variable response – from complete blockade of cell growth to absolute resistance. Surprisingly, BTSC sensitivity to GLS inhibition was a result of reduced intracellular glutamate triggering the amino acid deprivation response (AADR) and not due to the contribution of glutaminolysis to the TCA cycle. Moreover, BTSC sensitivity to GLS inhibition negatively correlated with the expression of the astrocytic glutamate transporters EAAT1 and EAAT2. Blocking glutamate transport in BTSCs with high EAAT1/EAAT2 expression rendered these cells susceptible to GLS inhibition, triggering the AADR, and limiting cell growth. These findings uncover a unique metabolic vulnerability in BTSCs, support the therapeutic targeting of the upstream activators and downstream effectors of the AADR pathway in GBM, and demonstrate that gene expression patterns reflecting the cellular hierarchy of the tissue of origin can alter the metabolic requirements of the cancer stem cell population.

overall_design: Two cell lines (BT67 and BT89), treated with either the vehicle control DMSO or the GLS inhibitor CB-839. Three biological replicates of each sample, six samples per cell line, 12 samples total.

first: Hema

middle: A

last: Luchman

first: Samuel

last: Weiss


title: Characterization of growth-phase dependent expression of host factors that modulate mutagenic retrohoming in Legionella pneumophila through RNA-Seq analysis

first: Diego

last: Arambula

address: 615 Charles E Young Dr. South

summary: Diversity-generating retroelements (DGRs) function through a mutagenic retrohoming mechanism that introduces localized nucleotide substitutions in genes. Throught transcriptional profiling of the DGR genes and host global regulatory networks, here we probe how tight host-control over DGR activity balances the benefit of localized protein diversification with the potential loss of fitness from unbridled mutagenesis.

overall_design: Differential expression transcriptional profiling of Legionella pneumophila wt and regulatory mutants.

first: Serghei

last: Mangul


title: CBX8-PRC1 regulates adult olfactory neurogenesis and epithelial homeostasis

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

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

overall_design: Refer to individual Series


title: Whole-transcriptome profiling of regenerating olfactory epithelium following loss of CBX paralogs

summary: The polycomb group protein, CBX8, is a neuron-specific component of Polycomb repressive complex 1 (PRC1) in the adult olfactory epithelium. We performed loss of function assays in an in vitro model of the regeneratng olfactory epithelium to determine the role of CBX8 in adult olfactory neurogenesis. Whole-transcriptome analysis highlighted the importance of CBX8-PRC1 in the regulation of adult neurogenesis in the olfactory epithelium.

overall_design: Examination of cells treated with lentivirus-packaged short hairpin construct against non-targeting control (shCTR), Cbx7 (shCbx7), and Cbx8 (shCbx8); 3 biologic replicates per treatment.

first: Bradley

middle: J

last: Goldstein

first: Rhea

last: Choi


title: Single-cell transcriptomic analysis of rice root tips

city: Beijing

first: Xiaofeng

last: Gu

address: Zhongguancun south street

institute: Chinese Academy of Agricultrual Sciences


title: Identification of neuron lineage-specific PRC1 targets in olfactory neuron precursors

summary: The polycomb group protein, CBX8, is a neuron-specific component of Polycomb repressive complex 1 (PRC1) in the adult olfactory epithelium. We performed ChIP-seq to identify genes occupied by CBX8-PRC1.

overall_design: Examination of 2 PRC1 components, CBX8 and RING1B, and 2 histone marks, H3K27me3 and H3K27ac, in purified olfactory sensory neuron precursors; two biologic replicates per ChIP; input sequenced for every biologic replicate


title: Single-cell transcriptomic analysis of rice root tips [bulk RNA-seq]

summary: There are two main types of root systems in flowering plants, which are taproot systems in dicot and fibrous root systems in monocot. The cellular and molecular mechanism involved in root development are mainly from the study of dicot model Arabidopsis thaliana. However, mechanisms of root development and their conservation and divergence in monocot, which including the major crops, remain largely elusive. Here we profile the transcriptomes of more than 20,000 single cells in the root tips of two rice cultivars, Nipponbare (Nip; Japonica) and 93-11 (Indica). Single-cell analysis coupled with in situ hybridization identify the cell type-specific marker genes and annotate all the clusters. Comparison of single-cell transcriptome and analysis of mark gene expression suggest well-conserved molecular landscape between rice Nip and 93-11. Moreover, our analysis suggests specific functions gene expression patterns for each cell type cluster, including the hormone genes. Comparison to Arabidopsis single-cell RNA-sequencing dataset reveals extensive differences between Arabidopsis and rice cell types, and species-specific features emphasize the importance of directly studying rice root.  Our study reveals transcriptome landscape of major cell types of rice root in singe-cell resolution and provides molecular insight of the cell type morphology of cell type evolution in plants.

overall_design:
Bulk RNAseq of protoplast from rice root tips
Please note that each processed data file was generated from both replicates and is linked to the corresponding rep.1 sample records.

first: Qing

last: Liu

first: Zhe

last: Liang


title: DNA methylation dynamics of oocyte in follicular maturation (RNA-Seq data set)

city: Memphis

first: Xiaolong

last: Chen

state: TN

address: 262 Danny Thomas Pl

institute: St Jude Children's Research Hospital

summary: Folliculogenesis in mammals is a cyclic and hierarchical process that the ovarian follicles undergo dramatic changes in the shape and number of granulosa cells accompanied by gradually enlarged immature oocyte. Here we show a thorough and high-resolution view of DNA methylation maps in oocyte free of somatic cells present at each distinct follicular development stages. We found that global DNA establishment occurs in Type5b follicles, the final stage of pre-antral follicles, and that the acquisition of DNA methylation at different trans-regulatory elements couples with different chromatin modifiers. Besides, we showed that Dnmt1 as well as Uhrf1 also play critical roles in requiring and retaining of de novo methylation statue, typically at LINE and LTR elements, in these immature oocytes, which successfully escape DNA replication. Our study thus refined the current knowledge on the establishment of unique DNA methylation profile in mammalian oocytes, and provide a valuable resource for further studies on female gametogenesis.

overall_design: We collected oocytes from detailed 9 stages of folliculogenesis stages and conduct RNA-seq. Each stage contains 3-5 replicates.

first: Rui

last: Gao

first: Chuan

first: Yuanlin

last: He

first: Xiaochen

last: Kou

first: Yanhong

last: Zhao

first: Jing

last: Li

first: Yawei

first: Cizhong

last: Jiang

first: Shaorong


title: DNA methylation dynamics of oocyte in follicular maturation (ChIP-Seq data set)

overall_design: We collected oocytes from detailed 9 stages of folliculogenesis stages and conduct NChIP-seq , each stage contains 1-2 replicates.


title: DNA methylation analysis of porcine blastocysts form cumulus oocyte complexes matured in coculture with porcine luteal cells

status: Public on Dec 24 2020

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

institute: Université Laval

summary: The DNA methylation pattern in blastocysts that developed from cumulus oocyte complexes matured in coculture with porcine luteal cells was investigated. Genome-wide DNA methylation analysis was performed by micro array using EDMA platform.

overall_design: Two condition experiment,  4 pools of 10 blastocysts, collected on Day 7 and Day 8

first: Gabriela

last: Teplitz


title: Expression data from C2C12 cells after knocking-down lncRNA-MEG3

city: shenzhen

first: zishuai

last: wang

address: pengfei road

institute: CAAS

summary:
The expression level of mRNA after knocking-down lncRNA-MEG3 showed a great significance.
We  performed microarray and transcriptome profiling in C2C12 cells after transfection lncRNA-MEG3 48 hours later to detail the expression of mRNA after knocking-down lncRNA-MEG3.

overall_design: lncRNA-MEG3 was knocked down in C2C12 cells . MRNA was extracted for microarray each for 3 replicates.

first: Yao

last: Long

first: Wang

middle: Z

last: Shuai

first: Chen

last: Yun

first: Tang

last: Lin


title: Single-cell transcriptomic analysis of rice root tips [scRNA-seq]

first: Xiaofeng

last: Gu

overall_design: Single-cell RNAseq of rice root tips

first: Qing

first: Zhe


title: RNA-seq in Hs578T cells stimulated with TGF-β

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

institute: University of Tokyo

summary: Transforming growth factor-β (TGF-β) comprises a key component in the tumor microenvironment. It is reported that TGF-β can be pro-tumorigenic or anti-tumorigenic depending on various contexts. Some of the triple negative breast cancers highly express TGF-β, but pro-tumorigenic function of TGF-β in triple negative breast cancer cells is not fully known. Therefore, we analyzed genome-wide gene expression changes after stimulation with TGF-β in a triple negative breast cancer cell line, Hs578T cells.

overall_design: Expression of mRNA in Hs578T cells stimulated with TGF-β.

first: Yusuke

last: Tamura

first: Kohei

last: Miyazono


title: Co-expression Network analysis of LncRNA associated with overexpression of DNMT1 in esophageal epithelial cells

city: Jiaxiang

first: Yi

last: LEI

state: Zhejiang

address: NO. 118 of Jia hang Road,Jiaxing

institute: Jiaxing Unviersity

summary: Screening and preliminary identification of DNMT1 high expression related LncRNA, which is involved in various inter-related signaling pathways, has revealed a theoretical basis for various types of disease mechanisms.

overall_design: The experimental groups chosen expression DNMT1 cell line , which was developed following transfection of a WV0132 plasmid using TALE technology. The control group was a normal esophageal epithelial cell line HEEC.

last: Lei

last: Zhang

last: Xu

first: Xu-feng

last: LI

first: Yan

last: Chen


title: EIF2S3 suppresses proliferation and regulates cell cycle  in HL60 cells.

status: Public on Dec 23 2020

city: Guangzhou

first: Lihua

address: 151 Yanjiang West Road, Yuexiu, Guangzhou, Guangdong, China

institute: The First Affiliated Hospital of Guangzhou Medical University

summary: The expression of Eukaryotic translation initiation factor 2 subunit 3 (EIF2S3/eIF2γ) in patients with non-small cell lung cancer and colorectal cancer is lower than that in healthy people, but its functions and mechanisms are still unclear, and the study of EIF2S3 in adult leukemias has not been reported. The expression of EIF2S3 in acute myeloid leukemia (AML) patients was lower than that in patients with complete remission (CR) and significantly associated with clinicopathological parameters and prognosis. EIF2S3 overexpression inhibited cell proliferation, blockaded the progression of cell cycle from G0/1 to S phase, inhibited the tumorigenicity and decreased the phosphorylation level of ERK protein in AML cells. In conclusion, EIF2S3 could be expected to be a novel therapeutic target in AML.

overall_design: We used Retro-X Tet-Off Advanced doxycycline (DOX) inducible expression system to generate stable EIF2S3 overexpressed cell (HL60-EIF2S3). The targeted gene, EIF2S3, was suppressed in the presence of DOX.

first: Yawei

last: Zou

first: Jielun

last: Lu

first: Shuyi


title: Loss of the Tumor Suppressor FLCN Promotes Breast Tumor Growth by Inducing a TFE3-Dependent Program Driving Warburg Effect and Angiogenesis

city: Montreal

first: Alain

last: Pacis

address: 740 Dr Penfield Ave

institute: Canadian Centre for Computational Genomics (C3G)

summary: Growing tumors exist in metabolically compromised environments that require activation of multiple pathways to scavenge nutrients to support accelerated rates of growth. The FLCN tumor suppressor complex (FLCN, FNIP1, FNIP2) has been implicated in the regulation of energy homeostasis via two metabolic master kinases: AMPK and mTORC1. Loss-of-function mutations of the FLCN tumor suppressor complex have only been reported in renal tumors in patients with the rare Birt-Hogg-Dube syndrome. Here we reveal that FLCN, FNIP1, and FNIP2 are downregulated in many human cancers including poor prognosis invasive basal-like breast carcinomas where AMPK and TFE3 targets are activated compared to the luminal, less aggressive subtypes. We show that FLCN loss in luminal subtypes promotes tumor growth through TFE3 activation and subsequent induction of several pathways including autophagy, lysosomal biogenesis, aerobic glycolysis, and angiogenesis. Strikingly, induction of aerobic glycolysis and angiogenesis in FLCN deficient cells was dictated by the activation of PGC-1⍺/HIF-1⍺ pathway, which we show to be TFE3-dependent, directly linking TFE3 to Warburg metabolic reprogramming and angiogenesis. Thus, FLCN loss induces TFE3-dependent breast tumor growth through activation of multiple mechanisms, including previously unreported roles in aerobic glycolysis and angiogenesis. These findings could point to a general role of a deregulated FLCN/TFE3 tumor suppressor pathway in human cancers.

overall_design: RNA sequencing data from MCF7 mammary fat pad resected tumors derived from either Wildtype (WT) or FLCN KO cells

first: Leeanna

last: El-Houjeiri

first: Marco

last: Biondini

first: Mathieu

last: Paquette

first: Helen

last: Kuasne

first: Morag

last: Park

first: Peter

middle: M

last: Siegel

first: Arnim

last: Pause


title: Low avidity T cell responses to SARS-CoV-2 in unexposed individuals and severe COVID-19

city: Kiel

first: Daniela

last: Esser

address: Arnold-Heller-Str. 3

department: Institute of Clinical Chemistry

institute: University Hospital Schleswig-Holstein

summary: Pre-existing memory T-cells against SARS-CoV-2 are present in a fraction of unexposed individuals and their induction by common cold corona viruses (CCCoVs) infection is suggested. Here we demonstrate that SARS-CoV-2-reactive T-cells were present in the memory compartment of virtually all unexposed individuals but possessed only low functional avidity. They harbored multiple, highly variable cross-reactivities that were not restricted to CCCoVs. Cross-reactivity to CCCoV was almost absent in COVID-19 patients. This was irrespective of strong T-cell memory against CCCoV in all donors. In severe but not mild COVID-19, SARS-CoV-2-specific T-cells also displayed low functional avidity and reduced clonal expansion, despite strongly increased frequencies. Our data question a major protective role of CCCoV for COVID-19. Instead, we suggest that a low avidity pre-existing T-cell memory may contribute to the excessive but low avidity T-cell responses, which we identified here as a hallmark of severe COVID-19.

overall_design: Single-cell sequencing of 6 unexposed and 14 COVID-19 patients

first: Petra

last: Bacher

first: Elisa

last: Rosati

first: Gabriela

last: Rios Martini

first: Carina

last: Saggau

first: Esther

last: Schiminsky

first: Justina

last: Dargvainiene

first: Ina

last: Schröder

first: Imke

last: Wieters

first: Yascha

last: Khodamoradi

first: Fabian

last: Eberhardt

first: Maria

last: Vehreschild

first: Holger

last: Neb

first: Michael

last: Sonntagbauer

first: Claudio

last: Conrad

first: Florian

last: Tran

first: Philip

last: Rosenstiel

first: Robert

last: Markewitz

first: Klaus-Peter

last: Wandinger

first: Max

last: Augustin

first: Jan

last: Rybniker

first: Matthias

last: Kochanek

first: Frank

last: Leypoldt

first: Oliver

last: Cornely

first: Philipp

last: Koehler

first: Andre

last: Franke

first: Alexander

last: Scheffold


title: The Aim2 inflammasome exacerbates atherosclerosis in Jak2 clonal hematopoiesis bulk Cd11b+ cell RNA-Seq

city: New York

first: David

middle: G

last: Thomas

state: NY

department: Medicine

institute: Columbia University

summary: Bulk-cell RNA-Sequencing of CD11b+ cells harvest from spleens from wild-type or ldlr-/- mice harboring bone marrow with Jak2V617F mutations

overall_design: Wild-type C57b6 mice with bone marrow from littermate control or mice with and Mx1-Cre drivin Jak2V617F expression were harvested and CD11b cells from spleens were isolated using magnetic beads and sequenced. In parallel ldlr-/- mice with bone marrow from littermate control or Mx1-Cre Jak2V617F were subjected to a seven week western type diet to induce hypercholesteremia, then CD11b cells were harvested from spleens and sequenced.

first: Trevor

last: Fidler

first: Alan

middle: R

last: Tall

last: Wang


title: Albumin-mediated Delivery of Therapeutic Peptides for Pancreatic Cancer Therapy

city: Zhengzhou

first: Yue

last: Du

address: No.1 Jianshe East Road

institute: The First Affiliated Hospital of Zhengzhou University

summary: Bioactive peptides are promising agents for therapeutic applications, however their small size results in poor stability, low bioavailability and rapid renal clearance, so its widespread use is limited. To address these issues, fusing or conjugating peptides to suitable molecular scaffolds is required. In this study, human serum albumin (HSA) is used as a delivery carrier for human β-defensin-2 peptides (HBD2) in the production of HSA-delivered defensin complex (ADDC) to facilitate its cellular uptake and transport to intracellular targets. Conjugation can improve the stability of HBD2, while extend the circulation time and promote its accumulation within tumor, thereby improving the therapeutic efficacy. Herein, ADDC provides a protective structure against the harsh external environment and serves as a passive tumor-targeted system. Our data showed that the combination of ADDC with clinically relevant drugs, such as Doxorubicin, Gemcitabine, Cisplatin, and Cetuximab can significantly increase the cytotoxicity of ADDC on human pancreatic cancer cells. The results of bioinformatics analysis also revealed that ADDC may affect the metabolic processes, gene transcription and apoptosis of pancreatic cancer cells. Collectively, ADDC exhibited specific tumor targeting capabilities, low systemic toxicity, and enhanced antitumor efficacy in a mouse model of pancreatic cancer.

overall_design: The whole genome microarray expression profiling was employed to  research the molecular mechanism of ADDC action and identify its target genes, thereby facilitating ADDC development. The gene expression of MIA PaCa-2 cells treated with 15 μM ADDC, HSA, or HBD2 was analyzed, untreated cells served as a vehicle control.

first: Boyang

last: Shang

first: Hongfei

last: Yi

first: Yongliang

last: Yuan

first: Yongsu

last: Zhen

first: Jian

last: Xu


title: RNA Sequencing of cardiomyocytes from different treatment conditions

first: Kelly

middle: Madigan

last: Banks

address: 1300 York Ave, LC711

department: Surgery

institute: Weill Cornell Medicine

summary: We report MPTD treatment produces more mature cardiomyocytes

overall_design: We sequenced negative control, T3/Dexamethasone, and MPTD treated cardiomyocytes 10 days after treatment

first: Zohreh

middle: S

last: Badieyan

first: Loretta

last: Lacko

first: Hayley

last: Nicholls

first: Romulo

last: Hurtado

first: Robert

last: Shwartz

last: Cohen

first: Shuibing

last: Chen

first: Todd

last: Evans


city: Gothenburg

first: Subazini

last: TK

address: Medicineragatan 9A

country: Sweden

institute: Gothenburg university

summary:
Gene expression after treatment with Nutlin 3a (Nut) and Selinexor (Sel) in Neuroblastoma Cells
RNA from NBAT1 knockdown and its respective control (Csh) SH-SY5Y cells after nutlin-3a (10 uM) or DMSO treatement were isolated and sequenced using  BGI DNBseq.  IMR32 cells were treated with either DMSO, Nut, Sel and with both Nul and Sel and RNA was isolated following treatemnet
We observed that knowndown of the NBAT1 lncRNA in NB cells leads to perturbation of the P53 mediated gene expression. Combination treatment with with Nul and Sel in IMR32 cells leads to higher P53 mediated gene expression.

overall_design: Nutlin 3a treatment after known down of lncRNA NBAT1 in SHSY-5Y cells. IMR32 cells were treated with either Nut or Sel or combination of both the drugs.

first: Sanhita

last: Mitra

first: Tanmoy

last: Mondal

last: Kosalai

first: Chandrasekhar

last: Kanduri


title: GEP signatures in tumors from women with high grade early breast cancer

city: Milan

first: Marco

last: Silvestri

state: ITALY

address: Via Amadeo 42

department: Department of Applied Research and Technological Development

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori di Milano

summary:
Several molecular signatures are able to predict the activity of adjuvant chemotherapy in breast cancer patients. However, no molecular data are already available to detect microenvironment molecular signature that can identify patients who are good candidates for treatment with immune checkpoint inhibitors (ICIs). For this reason, in a series of women with operable high grade breast cancer (HGBC), we tried to combine the ECM3 and IFN molecular signatures reflecting different aspects of tumor microenvironment that can better draw the picture of the tumor microenvironment in which the immune cells are in close contact with extracellular matrix.
Subgroup of G3 tumors extracted from the ECTO1 study (Gianni L. et al, JCO 2009)

overall_design: All gene expression data considered were from previously untreated patients. Cox regression and Kaplan-Meier analysis were used to assess associations with Overall Survival (OS). Characterization of the tumor immune microenvironment was achieved evaluating gene expression patterns scores of tumor infiltrating lymphocytes and their phenotypes as assessed by immunohistochemistry.

first: V

last: Cappelletti


title: Transcriptome regulation by ALK in cerebral organoids revealed by single-cell RNA sequencing

city: Shanghai

first: Zikai

last: Zhou

state: Shanghai

address: 600 Wan Ping Nan Road

department: Research Center

institute: Shanghai Mental Health Center

summary: Cerebral organoids derived from human pluripotent stem cells has been used as a model to study the development of mammalian brain. In this study, we employed 10x genomic single-cell RNA sequencing analysis to gain mechanical insight into the transcriptional changes of cells in cerebral organoids subject to the regulation by anaplastic lymphoma kinase (ALK) pathway. Based on the marker genes that most strongly contribute to the clusters, we annotated each cluster to cell types including radial glial cells (RGCs, SOX2 dominant), RGCs and intermediate progenitors (IPs, both SOX2 and EOMES positive), proliferating cells (Ki67 positive), early-born neurons (TBR1 and BCL11B dominant) and immature neurons (both SOX2 and TBR1/BCL11B/POU3F2 positive). Then we compared the cell compositions of the ALK inhibitor and vehicle treated groups in annotated clusters. The results show that transient ALK inactivation significantly reduced the number of proliferating NPCs and early-born neurons, with more cells being entrapped at the RGC stage, indicating a delayed development course from NPCs to neurons after ALK inhibition. By characterizing cell-type-specific transcriptomes, we found that transient ALK inactivation in cerebral organoids cause altered transcription of several genes including claudin 5 (CLDN5), transthyretin (TTR), inhibitor of DNA-binding proteins (IDs), Purkinje cell protein 4 (PCP4), transient receptor potential cation channel subfamily M member 3 (TRPM3), 5-HT2C receptor (HTR2C) and pro-melanin concentrating hormone (PMCH). These genes were significantly down-regulated in response to ALK inhibition in RGCs. Interestingly, the same set of genes were significantly up-regulated in proliferating cells in ALK inhibition group. These results revealed transcriptome regulation by ALK pathway in cerebral organoids.

overall_design: Single-cell RNA sequencing was performed to dissect the cell compositions and transcriptional landscapes in two sets of human cerebral organoids (35 days in vitro) at 12 days post ALK inhibitor or vehicle treatment. 12,606 cells pooled from 10 ALK inhibitor treated organoids and 10,736 cells pooled from 8 organoids in the vehicle group were analyzed.

first: Rui

last: Mao


title: Genes enhancing disease resistance in Aleutian disease virus (ADV) infected American mink (Neovison vison)

status: Public on Dec 22 2020

city: Frederiksberg C

first: knud

middle: arnbjerg

last: christensen

address: Grønnegårdsvej 3,

department: Department of Veterinary Clinical Sciences, Animal Genetics, Bioinformatics and Breeding,

country: Denmark

institute: University of copenhagen

type: Genome variation profiling by high throughput sequencing

summary: Two groups of serologically confirmed ADV infected mink were used to analyze the association of  Single Nucleotide Polymorphisms with Aleutian disease (AD) resistance. Group I (n=97) was comprised of disease susceptible (ADS) animals, with disease related hyper-gammaglobulinemia confirmed by the lowered albumin: IgG ratio (A: IgG); and Group II (n=97) contained disease resistant (ADR) animals with normal A: IgG ratio. The phenotypic assignment into the groups was done according to previously validated MALDI-TOF A: IgG ratio of high reproducibility in ADV infected animals. Illumina Hiseq 2500 sequencing was used to produce sequence libraries which were biocomputationally analyzed the genome wide spread SNPs where then associated with the disease susceptible and resistant groups of animals. There was a clear over-dominance for the GATOR complex protein NPRL3 isoform X6, with a very strong effect on the differences between the animals of ADS and the ADR groups. A minor effect was observed around the HLA complex, however scattered over more genes in this area. The Protocadherin Fat 3 (FAT3) or it neighborhood could also be regarded as a candidate aerea influencing the outcome of the infection. In the absence of vaccination, and in the light of eradication failures, the results provide the foundation for the development of genomic tests, as the basis for assisted breeding for disease resistance. Additionally, the results could be useful in investigations of genetic basis of the resistance of animal infections of major economic importance, e.g. African swine fever (ASF).

overall_design: Group A (n=97) was comprised of disease susceptible (ADS) animals, with disease related hyper-gammaglobulinemia and Group B (n=97) contained disease resistant (ADR) animals with no symtos

first: A

last: Cepica

first: R

last: Anistoroaei

first: T

last: Iwamoto

first: KA

last: Christensen


title: Defining the activated FABP7 satellite myogenic cells in pleuropulmonary blastoma using single cell sequencing

first: rui

last: Dong

address: 399 Wan Yuan Road

institute: Department of Pediatric Surgery, Children’s Hospital of Fudan University, and Shanghai Key Laboratory of Birth Defect

summary:
Background: Pleuropulmonary blastoma (PPB) is a rare lung malignancy in children. Here, we classified PPB subpopulations with Single-cell RNA sequencing.
Methods: This study included 10,007 single cells from a girl with PPB. After choosing malignant tumor cells with an inferring copy number variation, we used non-negative matrix factorization and Seurat analysis to cluster the cells and divided the subgroups by their differentially expressed genes and Gene Ontology enrichment analysis. Additionally, pseudotime trajectory analysis of PPB was conducted with Monocle.
Results: Tumor cells were divided into muscle (DEShiTNNT1hiTNNI1hi) and cartilage (TWIST1hiHTRA1hiBMP4hi). In cartilage, SOX9hiPAX1hiPAX9hi prechondrocytes, OGNhiMGPhi chondrocytes and DKK2hi chondrocytes were defined. In muscle lineage, PAX7hiMYF5hi satellite myogenic cells and MYOGhiMEF2ChiMYOD1hi myocytes were defined. And a new undefined FABP7hi satellite cells subset was found to function like another known ITM2Ahi satellite cells subset. As the promoters of muscle cell development, both were responsible for establishing membrane protein and proliferating.
Conclusions: Our results roughly defined muscle heterogeneity in PPB and found activated and proliferating FABP7 satellite myogenic cells. And these satellite cells might be activated by microRNA regulation induced by the mutation of PPB classic mutation gene DICER1.

overall_design: one sample from human pleuropulmonary blastoma tissue

first: Zhi-Xue

first: Wen-Bo

last: Zhang

first: Chun-Jing

last: Ye

first: Yong

last: Zhan

first: Ran

last: Yang

first: Jia

last: Liu

first: Yi

last: Li

first: Bo

last: Hong

last: Wang

first: Wei-Qiang

last: Tan

first: Xiao

last: Shen

first: Ming


title: Regulation of carbon reserve use in olive trees under heat, drought, and recovery

city: Rehovot

first: Ester

last: Feldmesser

state: Rehovot

address: POB 25

department: Life Science Core Facilities

country: Israel

institute: Weizmann Institute

summary:
Purpose: Nonstructural carbohydrates has a major impact on trees response to meteorological conditions. The goals of this study were to define which changes in gene expression are linked to possible mechanisms used by the plant to buffer the decline in carbon source during gradual soil drying, an intensive abrupt heat wave, and recovery from drought?
Methods: We combined measurements of nonstructural carbohydrates (NSC), tree physiology and expression of genes encoding starch metabolism enzymes. The experiment was conducted on potted olive (Olea europaea) trees, half of them under 28 days of soil drought.
Results: We identified the gene family members relevant either to long-term or stress-induced carbon storage. Partitioning of expression patterns among β amylase’s and starch synthase’s family members were identified, with some members upregulated throughout drought while other members in recovery. The daily starch metabolism machinery was different from the stress-mode starch metabolism machinery when some genes are unique to the stress-mode response.

overall_design: RNA-Seq of 6 branches of 6 different olive trees, 3 samples of watered trees and 3 samples of dried trees.

first: Mor

last: Tsamir

first: Shifra

last: Ben Dor

first: Yaara

last: Openheimer-Shaanan

first: Rakefet

last: David-Schwartz

first: Alon

last: Samach

first: Tamir

last: Klein


title: Gene expression data from activity dependent genes in post mitotic-neurons

city: Maebashi

first: Yuichi

last: Uosaki

state: Gunma

address: 3-39-22 Showa-machi

department: Pediatrics

institute: Gunma university

summary:
Neurons express numerous genes in response to environmental stimuli. This activity-dependent transcription is vital for neurons to function and hence for the brain to exert its complex processes. Post translational modifications of core histones have been implicated in the regulation of neuronal activity-dependent transcription. On the other hand, transcription and repair also involves the exchange of core histones, which regulates histone metabolism, but its involvement in neural activity-dependent transcription is currently well unknown. Here, in mature postmitotic neurons derived from mouse hippocampus, a Hist1h3f gene, which encodes replication-dependent histone H3.2, is expressed upon stimulation to glutamine receptors. Salt extraction and metabolic labeling of newly synthesized proteins in neurons revealed that core histone proteins are increased at protein levels in response to glutamine receptor stimulation. These results suggest that newly synthesized replication-dependent histone play a role in post-mitotic neurons.
We performed microarrays to investigte the global transcriptional profiles of activity-dependent gene expression and identified two class of up-regulated genes during this process.

overall_design: Using Affymetrix Mouse Gene ST 1.0 array, we compared global gene expression profiles among of  four time points; 0 min, 30 min, 180 min, and 300 min with bicuculline stimulation.

first: Takumi

last: Takizawa


title: Cdkn2a loss in a model of neurofibroma demonstrates stepwise tumor progression to atypical neurofibroma and MPNST

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

summary: Plexiform neurofibromas (PN) are benign nerve sheath Schwann cell tumors, common in patients with neurofibromatosis type 1 (NF1), that are characterized by biallelic mutations in the NF1 tumor suppressor gene. Atypical neurofibromas (ANF) show additional frequent loss of CDKN2A/Ink4a/Arf and may be precursor lesions of aggressive malignant peripheral nerve sheath tumors (MPNST). We combined loss of Nf1 in developing

overall_design:
Schwann cells with global Ink4a/Arf loss and identified paraspinal PN and ANF.
Confirming susceptibility to transformation, upon transplantation the ANF generated GEM-PNST similar to human MPNSTs, and tumors showed reduced p16INK4a protein and reduced senescence markers. Superficial GEM-PNST contained regions of nerve-associated PN or ANF and grew rapidly on transplantation. Transcriptome analyses showed similarities to corresponding human tumors.  Thus, we recapitulate nerve tumor progression in NF1 and provide preclinical platforms for testing therapies at each tumor grade. The results support a tumor progression model in which NF1 loss in Schwann cells drives PN formation, additional Ink4a/Arf loss contributes to ANF formation, and further changes underlie transformation to MPNST.

first: Katherine

middle: E

last: Chaney

first: Melissa

last: Perrino

first: Leah

last: Kershner

first: Nancy

last: Ratner


title: Gene expression profiling of human-derived primary cardiomyocytes with lncRNA ZNF593-AS 5‘ end overexpression under phenylephrine stimulation

city: Wuhan

first: rong

last: xie

state: Hubei

address: Jiefang Ave.

institute: Huazhong university of science and technology

summary: The aim of this study is to investigate molecular mechanisms underlying the function of lncRNA ZNF593-AS in cardiomyocyte under phenylephrine stimulation in vitro.

overall_design: Human-derived primary cardiomyocytes were transfected with pcDNA3.1 or ZNF593-AS 5' end, the functional fragment of ZNF593-AS under the stimulation of phenylephrine. We extracted the total RNA 48h after the transfection and perform RNA-seq using Illimina platform.

first: Jiahui

last: Fan

first: Huaping

last: Li

first: Rong

last: Xie


title: Detecting lncRNA fusion events in breast cancer cells

first: YY

last: Xiong

address: Xingangxi Rd

department: School of Life Sciences

institute: Sun Yat-sen University

summary: We deep-sequenced the breast cancer cell line SKBR3 to detect fusion events involving lncRNAs for experimental validation

overall_design: detecting fusion events involving lncRNAs for experimental validation

first: M

last: Guo

first: Z

last: Xiao

first: Y


title: Transcriptome profiling (RNA-seq)  analysis of  NaIO3-induced RPE cells with or witout CaPB treatment

first: Gu

last: Ping

address: Manufacturing Road, 833

department: Department of Ophthalmology

institute: Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

summary:
Purpose:  The goal of this experiment is to investigate the role of CaPB in  NaIO3-induced RPE cells
Methods: RPE cell mRNA profiles were generated by deep sequencing, in triplicate, using Illumina  HiSeq 4000.
Results: According to the differential expressions of mRNA genes, among which 463 genes were upregulated and 397 genes were downregulated with significance in NaIO3-induced RPE cells after CaPB treatment . From the Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, it has been identified that ferroptosis ranked as the most downregulated pathway upon CaPB treatment.
Conclusions: Our study represented that CaPB against NaIO3-treated RPE cell death via ferroptosis inhibition

overall_design: NaIO3-treated RPE with or without CaPB treatment were collected by deep sequencing, in triplicate, using Illumina HiSeq 4000.

first: Zhimin

last: Tang

first: Ping

last: Gu


title: Super-enhancer LncRNA expression profile in human bladder cancer cell line and human urothelial immortalized cell line

city: Nanning

first: Aruo

state: Guangxi

address: Guangxi Medical University, Nanning 530021, Guangxi, China

institute: Guangxi Medical University

summary: To further explore the differential expression profile of super-enhancer long noncoding RNA (LncRNA) in human bladder cancer, we have employed super-enhancer lncRNA microarray expression profiling as a discovery platform to identify potential differential expression profile of super-enhancer lncRNA between human bladder cancer cell (UM-UC-3 cell) and urothelial immortalized cell (SV-HUC-1 cell). Results showed that a large number of differentially expressed super-enhancer lncRNA were found between UM-UC-3 cell and SV-HUC-1 cell. In this study, We verified 5 up-regulated differentially expressed super-enhancer lncRNAs using qPCR, of which the highest fold change is LINC00162. Then we further explored the biological function and mechanism of LINC00162 in bladder cancer in this study.

overall_design: In the initial stage, we conducted a super-enhancer LncRNA microarray analysis using human urothelial immortalized SV-HUC-1 cells as a control group and human bladder cancer UM-UC-3 cells as an experimental group. Then we find out the differentially expressed super-enhancer LncRNAs, and explore its function and mechanism of action through molecular biology experiments in vivo and in vitro.

first: Xin

last: Wang

first: Ruirui

last: Zhang

first: Shuilian

last: Wu


title: Gene expression dynamics in rice peduncles at the heading stage

city: New Delhi

first: Rita

last: Sharma

state: Delhi

address: SCIS, JNU

department: School of Computational & Integrative Sciences

institute: Jawaharlal Nehru University

summary: We report transcriptome profiling of elongating and non-elongating peduncles of rice in two Indian cultivars, Swarna and Pokkali at the time of heading. Sequencing of twelve libraries (three replicates from each stage) yielded >6.9 billion paired-end reads.

overall_design: Examination of elongating and non-elongating peduncles in two Indian cultivars, Swarna and Pokkali

first: Manu

last: Kandpal

first: Chandrapal

last: Vishwakarma

first: Kushagra

last: Krishnan

first: Viswanathan

last: Chinnusamy

first: Ashwani

last: Pareek

first: Manoj


title: Transcriptome sequencing reveals potential roles of ICOS in primary Sjögren’s syndrome

city: Wenzhou

last: Liao

address: Wenzhou Medical University, University Town, Chashan, Wenzhou, Zhejiang, P.R China

department: Institute of Genomic Medicine

institute: Wenzhou Medical University

summary: Primary Sjögren’s syndrome (pSS) is a chronic systemic autoimmune disease characterized by exocrine glands damage and extraglandular manifestations. To identify potential biomarkers for the early diagnosis of pSS and further investigate the potential mechanisms in progression of the disease, we combined our previous RNA- sequencing study and four microarrays data to conduct integrative transcriptome analyses in salivary glands (SGs) between the pSS and non-pSS. Differential gene expression analysis, gene co-expression network analysis and pathway analysis were conducted to detect hub gene, which was subsequently validated in peripheral blood. Correlation analysis, single-gene Gene Set Enrichment Analysis (GSEA) and receiver operating characteristic (ROC) curve were applied to investigate the role of ICOS in pSS and its classification capacity for pSS.

overall_design: A total of 16 pSS patients and 13 non-pSS subgroups were recruited to conduct RNA-sequencing with salivary glands

first: Jing

last: Luo

first: Suxian

last: Lin

first: Xiaobing


title: The molecular landscape and biological alterations induced by PRAS40-knockout in head and neck squamous cell carcinoma.

city: Changsha

first: Gangcai

last: Zhu

state: M

address: Remin Road 132

institute: The Second Xiangya Hospital, Central South University

summary: PRAS40 (Prolin-rich Akt substrate of 40 kDa) is a critical protein that directly connects PI3K / Akt and mTORC1 pathway. It plays an indispensable role in the development of many diseases. However, the relationship of PRAS40 and head and neck squamous cell carcinoma (HNSCC) remains unclear. Here, our study indicated that high expression of PRAS40 mRNA is a favorable prognosis factor in HNSCC patients by analyzing 498 clinical and mRNA data. Moreover, we confirmed that CRISPR/Cas9 induced PRAS40-knockout would promote cell colony formation, migration, and invasion in several HNSCC cell lines. RNA-seq was employed to investigate the further possible mechanisms involving in the above regulations by PRAS40 in HNSCC cells. The molecular landscape contributed by 253 differential expressed mRNA after PRAS40-knockout were enriched in TGF-beta, PI3K-Akt, P53, mTOR, NF-kB signaling pathway. Partial molecular alternations within these pathways were validated by PCR or western blot. Besides, we found that high expression of PRAS40 in HNSC patients would present more CD8+ T and T follicular helper cells, but less Th17 cells than the patients with low expression of PRAS40. The altered molecular pathways and immune infiltrating cells might associate with the mechanism of PRAS40 being a suppressor in HNSCC cells, which would provide a potential prognosis predictor and therapeutic target in HNSCC patients.

overall_design: Examination of 2 PRAS40 knockout HNSCC 6-10b cells and corresponding wildtype cells

first: Chen

last: Gang

first: Li

last: Zhexuan

first: Zhang

last: Xin

first: Zhu

last: Gangcai


title: Aurora kinase A phosphorylates histone methyltransferase NSD2 to promote drug resistance in multiple myeloma [RNA-Seq]

city: Tianjin

first: Liu

last: Zhiqiang

address: 22 Qxiangtai Rd

institute: Tianjin Medical University

summary: The epigenetic plasticity, such as DNA methylation and histone modification, has been suggested to be a potential mechanism controlling MM progression and drug resistance, but the underlying mechanisms are not fully understood. Here we demonstrate that some drug resistant genes were activated during myeloma resistance to bortezomib.  Mechanistically, Aurora A can interact with NSD2, whose SET domain is responsible to H3K36me2 to enhance the transcriptional activity of Aurora A target gene. Once Aurora A is knocked out, H3K36me2 activity will change, changing the transcription activity of those drug resistant genes.

overall_design: LP-1 was infected by virus packging sgRNA targeting AURKA gene (Aurora A-KO) while the non-target control (NT Ctrl) was defined as control. Cells were harvested for gene expression profiling when AURKA was knocked out. Three replicates were performed.

first: Hongmei

last: Jiang


title: ELL facilitates RNA Polymerase II mediated transcription of human epidermal proliferation genes

city: San Diego

first: George

last: Sen

state: CA

address: 9500 Gilman Drive

institute: UCSD

summary: ELL plays an essential role in human epidermal proliferation by binding to proliferation genes and facilitating the stabilization of RNA Polymerase II at the TSS to sustain their gene expression

overall_design: ChIP-seq and RNA-seq

first: Jingting

last: Li


title: A comparison of transcriptome between Drosophila S2R+ cell line cultured in M3 media supplemented with fly extract and S2R+ cell line cultured in M3 + BPYE + 10% FCS

city: Bloomington

first: Andrew

last: Zelhof

state: IN

address: 1001 East Third St

institute: Indiana University

summary: We report the transcriptome analysis of Drosophila S2R+ cells cultured in media lacking vertebrate fetal bovine serum during log-phase of growth. The three media conditions are:  (1) M3 BPYE 10% FCS (2) M3 + 10% Fex and (3) M3 + 2.5% Fex.

overall_design: A comparison of transcript profiles of Drosophila S2R+ cell line cultured in three distinct growth media : (1) M3+BPYE+10% FCS, (2) M3+10% fly extract and (3) M3 + 2.5% fly extract.

first: Arthur

last: Luhur

first: Daniel

last: Mariappa

first: Kristin

last: Klueg


title: GEP signatures in tumors from women with high grade early breast cancer [PrimitiveTumor].

first: Marco

last: Silvestri

address: Via Amadeo 42

institute: Fondazione IRCCS Istituto Nazionale dei Tumori di Milano

summary:
Several molecular signatures are able to predict the activity of adjuvant chemotherapy in breast cancer patients. However, no molecular data are already available to detect microenvironment molecular signature that can identify patients who are good candidates for treatment with immune checkpoint inhibitors (ICIs). For this reason, in a series of women with operable high grade breast cancer (HGBC), we tried to combine the ECM3 and IFN molecular signatures reflecting different aspects of tumor microenvironment that can better draw the picture of the tumor microenvironment in which the immune cells are in close contact with extracellular matrix.
Grade 3 primary tumors

overall_design: All gene expression data considered were from previously untreated patients. Cox regression and Kaplan-Meier analysis were used to assess associations with Overall Survival (OS). Characterization of the tumor immune microenvironment was achieved evaluating gene expression patterns scores of tumor infiltrating lymphocytes and their phenotypes as assessed by immunohistochemistry.

first: Massimo

last: Di Nicola

first: Vera

last: Cappelletti


title: Chitin attenuates virulence gene expression of Listeria monocytogenes in vitro

city: Cork

first: Miguel

last: Villoria Recio

address: Gaol walk

department: Alimentary Pharmabiotic Centre

country: Ireland

institute: University College Cork

summary: External signals are key for bacteria to sense their immediate environment and fine-tune gene expression accordingly. The foodborne pathogen Listeria monocytogenes senses a range of environmental cues in order to activate or deactivate the virulence-inducing transcriptional factor PrfA during transition between infectious and saprophytic lifecycles. Chitin is an abundant biopolymer formed from linked β-(1–4)-N-acetyl-D-glucosamine residues associated with fungi, the exoskeleton of insects and often incorporated into foods as a thickener or stabiliser. L. monocytogenes evolved to hydrolyse chitin, presumably, to facilitate nutrient acquisition from competitive environments such as soil where the polymer is abundant. Since mammals do not produce chitin, we reasoned that the polymer could serve as an environmental signal contributing to repression of L. monocytogenes PrfA-dependent expression outside the host. This study shows a significant downregulation of the core PrfA-regulon during virulence-inducing conditions in vitro in the presence of chitin. Our data suggest this phenomenon occurs through a mechanism that differs from PTS-transport of oligosaccharides generated from either degradation or chitinase-mediated hydrolysis of the polymer. Importantly, an indication that chitin can repress virulence expression of a constitutively active PrfA* mutant is shown, possibly mediated via a post-translational modification inhibiting PrfA* activity. To our knowledge, chitin as a molecule with anti-virulence properties against a pathogenic bacterium has not been previously reported. Thus, our findings identify chitin as a signal which may downregulate the virulence potential of the pathogen and may provide an alternative approach towards reducing disease risk.

overall_design: Comparison of the transcriptomic profile of L. monocytogenes under virulence inducing conditions with and without chitin.

first: Bo

last: Lee

first: Eva

last: Sternkopf Lillebæk

first: Vanessa

last: Las Heras

first: Birgitte

last: Kallipolitis

first: Cormac

last: Gahan

first: Hanne

last: Ingmer

first: Marianne

last: Halberg Larsen


title: Activation of LINE-1 antisense promoter stimulates the growth of cultured cells

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Long interspersed element 1 (LINE-1, or L1) is a retrotransposon that constitutes ~17% of the human genome. Although ~6,000 full-length L1s spread throughout the human genome, their biological significance remains undetermined. L1 5’ untranslated region has a bidirectional promoter activity with a sense promoter, driving L1 mRNA, and an antisense promoter (ASP), driving L1-gene chimeric RNAs. Here, we stimulated L1 ASP activity using the CRISPR-Cas9 system to evaluate its biological impacts. Activation of L1 ASP enhances L1 retrotransposition and cell growth. Conversely, we identified epigallocatechin gallate (EGCG) as an inhibitor of L1 ASP. The inhibition of L1 ASP by EGCG decreased cell growth but did not affect L1 retrotransposition. Collectively, these results indicate that activation of L1 ASP activity fuels cell growth. To our knowledge, this is the first report demonstrating the role of L1 ASP in the biological process. Considering that L1 sequences are de-silenced in various tumor cells, activation of L1 ASP may be a cause of tumor growth and interfering with L1 ASP activity will be a potential strategy to suppress the growth.

overall_design: We compared transcriptome of cells co-expressed dCas9-VP64 with Mock (Control), sgL1ASP #1 (sg1), or #3 (sg3).

first: Tomoyuki

last: Honda


title: Embryonic stem cell differentiation is regulated by SET through interactions with p53 and β‐catenin

city: Jerusalem

first: Eran

last: Meshorer

address: Institute of Life Sciences, The Hebrew University of Jerusalem Edmond J. Safra Campus, Givat Ram

department: Department of Genetics

institute: The Hebrew University of Jerusalem

summary: The multifunctional histone chaperone, SET, is essential for embryonic development in mouse. Previously, we identified SET as a factor that is rapidly downregulated during embryonic stem cell (ESC) differentiation, suggesting a possible role in the maintenance of pluripotency. Here, we set out to explore SET’s function and its mechanism in early differentiation. Using liquid chromatography tandem mass spectrometry (LC‐MS/MS), we uncover the factors and complexes, including P53 and β-catenin, by which SET regulates lineage-specification. SET knockout (KO) and shRNA-knockdown experiments for both P53 and β-catenin in SET-KO ESCs reveal that P53 knockdown partially rescues lineage-marker misregulation during differentiation. β-catenin depletion, on the other hand, rescues the elevated Wnt gene expression observed in SET-KO ESCs. Integration of multiple ChIP-seq and RNA-seq datasets reveals a predominantly activating function of SET in gene regulation. Moreover, further analysis reveals a co-regulatory relationship between SET and TCF3, a downstream effector of Wnt-signalling. Overall, we discover a role for both P53 and β-catenin in SET-regulated early differentiation and uncover a potential mechanism for SET function at the β-catenin-TCF regulatory axis.

overall_design: RNA-seq of Wt and SET KO ESCs and before and after 4d RA treatment in R1 background. In addition, RNA-seq performed with and without addition of Dox in KH2 ESCs with Dox-inducible SETa expression.

first: Patrick

last: Lim


title: Integrated gene expression analysis of blood and liver tissue in precancerous condition [miRNA]

city: Tokyo

first: Y-H.

last: Taguchi

state: Non-US/Canada

address: 1-13-27 Kasuga,Bukyo-ku

department: Physics

institute: Chuo University

type: Non-coding RNA profiling by high throughput sequencing

summary: Patients with diabetes mellitus (DM) have an epidemiologically higher risk for hepatocellular carcinoma (HCC). In mouse models, administration of streptozotocin (STZ) induces insulin-dependent DM by causing islet beta-cell dysfunction and also induced hepatocellular carcinoma (HCC) after 12 weeks. We attempted to elucidate the carcinogenic mechanism in the precancerous state by using hepatic miRNAs and create precancerous marker using exosomal miRNA.  Serum and liver tissues were collected from STZ mice and non-treated mice (CTL mice) at 6, 10 and 12W. Total RNA in liver and exosome were extracted. Histological examination in liver in HE stain and hepatic and exosomal miRNA analysis were serially performed. miRNA and mRNA was analyzed by next-generation sequencing (NGS). The raw data of NGS was analyzed by Principal Component analysis.  No inflammation or fibrosis was found in the liver in CTL mice during the observation period. In STZ-treated mice, regeneration and inflammation of hepatocytes was found at 6W and then nodules of atypical hepatocytes were found at 10 and 12 W. Expression of let-7f-5p, miR-21a-5p, 22-3p, and 26a-5p in liver of STZ mice was significantly increased during 6-10W, and these miRNAs controlled several tumor suppressor genes as target genes. We also identified six novel miRNAs associated with precancerous status. Furthermore, miR-122-5p and miR-192-5p in exosome were significantly upregulated in STZ mice in precancerous state.  The expression of miRNAs that regulate tumor suppressor genes was enhanced even before carcinogenesis, and the expression of these miRNAs was not affected by liver fibrosis. In addition, the expression pattern of miRNAs in exosome is expected to be a marker for predicting carcinogenesis.   Patients with diabetes mellitus (DM) have an epidemiologically higher risk for hepatocellular carcinoma (HCC). In mouse models, administration of streptozotocin (STZ) induces insulin-dependent DM by causing islet beta-cell dysfunction and also induced hepatocellular carcinoma (HCC) after 12 weeks. We attempted to elucidate the carcinogenic mechanism in the precancerous state by using hepatic miRNAs and create precancerous marker using exosomal miRNA.  Serum and liver tissues were collected from STZ mice and non-treated mice (CTL mice) at 6, 10 and 12W. Total RNA in liver and exosome were extracted. Histological examination in liver in HE stain and hepatic and exosomal miRNA analysis were serially performed. miRNA and mRNA was analyzed by next-generation sequencing (NGS). The raw data of NGS was analyzed by Principal Component analysis.  No inflammation or fibrosis was found in the liver in CTL mice during the observation period. In STZ-treated mice, regeneration and inflammation of hepatocytes was found at 6W and then nodules of atypical hepatocytes were found at 10 and 12 W. Expression of let-7f-5p, miR-21a-5p, 22-3p, and 26a-5p in liver of STZ mice was significantly increased during 6-10W, and these miRNAs controlled several tumor suppressor genes as target genes. We also identified six novel miRNAs associated with precancerous status. Furthermore, miR-122-5p and miR-192-5p in exosome were significantly upregulated in STZ mice in precancerous state.  The expression of miRNAs that regulate tumor suppressor genes was enhanced even before carcinogenesis, and the expression of these miRNAs was not affected by liver fibrosis. In addition, the expression pattern of miRNAs in exosome is expected to be a marker for predicting carcinogenesis.   Patients with diabetes mellitus (DM) have an epidemiologically higher risk for hepatocellular carcinoma (HCC). In mouse models, administration of streptozotocin (STZ) induces insulin-dependent DM by causing islet beta-cell dysfunction and also induced hepatocellular carcinoma (HCC) after 12 weeks. We attempted to elucidate the carcinogenic mechanism in the precancerous state by using hepatic miRNAs and create precancerous marker using exosomal miRNA.  Serum and liver tissues were collected from STZ mice and non-treated mice (CTL mice) at 6, 10 and 12W. Total RNA in liver and exosome were extracted. Histological examination in liver in HE stain and hepatic and exosomal miRNA analysis were serially performed. miRNA and mRNA was analyzed by next-generation sequencing (NGS). The raw data of NGS was analyzed by Principal Component analysis.  No inflammation or fibrosis was found in the liver in CTL mice during the observation period. In STZ-treated mice, regeneration and inflammation of hepatocytes was found at 6W and then nodules of atypical hepatocytes were found at 10 and 12 W. Expression of let-7f-5p, miR-21a-5p, 22-3p, and 26a-5p in liver of STZ mice was significantly increased during 6-10W, and these miRNAs controlled several tumor suppressor genes as target genes. We also identified six novel miRNAs associated with precancerous status. Furthermore, miR-122-5p and miR-192-5p in exosome were significantly upregulated in STZ mice in precancerous state.  The expression of miRNAs that regulate tumor suppressor genes was enhanced even before carcinogenesis, and the expression of these miRNAs was not affected by liver fibrosis. In addition, the expression pattern of miRNAs in exosome is expected to be a marker for predicting carcinogenesis.

overall_design: Examination of circulating and hepatic miRNA in pre-cancer state of liver

first: Tomohiro

last: Umezu

first: Koichi

last: Tsuneyama

first: Kohsuke

last: Kanekura

first: Michiyo

last: Hayakawa

first: Toshihito

last: Tanahashi

first: Mitsuoki

last: Kawano

first: Y-h

first: Hidenori

last: Toyoda

first: Akihiro

last: Tamori

first: Masahiko

last: Kuroda


title: Gene expression change of MDCK cells expressing scribble shRNA in a tetracycline-inducible manner (scribKD cells)

city: Bunkyo-ku

first: Motoyuki

last: Ogawa

state: Tokyo

department: Graduate School of Pharmaceutical Sciences

institute: The University of Tokyo

summary:
Cell competition is a social cellular phenomenon in which unfit cells are selectively eliminated by wild-type (WT) cells. Although recent studies show that mechanical forces induce competitive cell-cell interactions, it remains largely unknown how unfit cells are sensed and mechanically eliminated. Here, we report that MDCK cells depleted of the polarity gene scribble (scribKD cells) secrete FGF21 to drive cell competition. Knockdown of FGF21 in scribKD cells or loss of FGFR1 in WT cells increases the survival rate of scribKD cells in cell competition, suggesting that WT cells recognize scribKD cells through FGF21. Moreover, FGF21 promotes the compression and elimination of scribKD cells by attracting surrounding WT cells. We also demonstrate that activation of the ASK1-p38 pathway in scribKD cells induces FGF21 to drive cell competition. Our findings reveal a mechanism whereby WT cells mechanically eliminate scribKD cells and propose a new function for FGF21 in cell-cell communication.
We performed  DNA microarray analysis to search for the genes responsible for cell competition.

overall_design: mRNA of scribKD cells were extracted at 30, 45 and 60 hours after treatment with or without tetracycline (Tet).

first: Yosuke

last: Kawarazaki

last: Ichijo


title: Mesenchymal stromal cells orchestrate the overhaul of leukemia bone marrow microenvironment via educating macrophages

city: Guangzhou

first: Xia

last: Chengxiang

state: Guangdong

address: Kai Yuang Road 190

institute: GIBH

summary: RNAseq were performed to analyze the transcriptomic differences between healthy homeostatic MSC, pre-leukemic MSC and recovered MSC.

overall_design: RNAseq: Three healthy homeostatic MSC samples, six pre-leukemic MSC samples and four recovered MSC samples .

first: Chengxiang

last: Xia

first: Yong

last: Dong

first: Jinyong

last: Wang


title: Gene expression of breast cancer stem cells.

city: Nagoya

first: Nishimura

last: Tatsunori

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Graduate School of Medicine

institute: Nagoya University

summary: Metastatic progression remains the major cause of death in human breast cancer. Cancer cells with cancer stem cell (CSC) properties drive initiation and growth of metastases at distant sites. We have previously established the breast cancer patient-derived tumor xenograft (PDX) mouse model in which CSC marker CD44+ cancer cells formed spontaneous microscopic metastases in the liver. In this PDX mouse, the expression levels of S100A10 and its family proteins were much higher in the CD44+ cancer cells metastasized to the liver than those at the primary site.

overall_design: Duplicated analyses of gene expression of the cancer stem cell marker CD44-positive breast cancer patient-derived xenograft (PDX) cells collected separately from the two breast cancer PDX mice.

first: Yohei

last: Shimono

first: Tatsunori

last: Nishimura

first: Noriko

last: Gotoh


title: Integrated gene expression analysis of blood and liver tissue in precancerous condition

first: Y-H.

last: Taguchi

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

overall_design: Refer to individual Series


title: Integrated gene expression analysis of blood and liver tissue in precancerous condition [mRNA]

overall_design: Examination of  hepatic mRNA in pre-cancer state of liver

first: Tomohiro

last: Umezu

first: Koichi

last: Tsuneyama

first: Kohsuke

last: Kanekura

first: Michiyo

last: Hayakawa

first: Toshihito

last: Tanahashi


title: Hepatocyte CB1R nullification mitigates acute liver damage by mediating NF-κB signaling

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Cannabinoid 1 receptor (CB1R) expression is upregulated in hepatocytes during viral hepatitis, cirrhosis, and both alcoholic and non-alcoholic fatty liver disease (FLD), whereas its expression is muted under usual physiological conditions. Inhibiting CB1R has been shown to be beneficial in preserving hepatic function in FLD but it is unclear if inhibiting CB1R during an inflammatory response to an acute hepatic injury, such as toxin - induced injury, would also be beneficial. We tested if nullification of hepatocyte-specific CB1R (hCNR1-/-) in mice protects against concanavalin A (Con A) - induced liver injury. We looked for evidence of liver damage and markers of inflammation in response to Con A by measuring liver enzyme levels and proinflammatory cytokines (e.g., TNF-α, IL-1β, IL-6, IL-17) in serum collected from hCNR1-/- and control mice. We observed a shift to the right in the dose-response curve for liver injury and inflammation in hCNR1-/- mice. We also found less inflammatory cell infiltration and focal necrosis in livers of hCNR1-/- mice compared to controls, resulting from downregulated apoptotic markers. This anti-apoptotic mechanism results from increased activation of nuclear factor kappa B (NF-κB), especially membrane-bound TNF-α, via downregulated TNF-α receptor 2 (TNFR2) transcription levels. We also found that CB1R in hepatocytes regulated liver inflammation - related gene transcription. Collectively, these findings provide insight into involvement of CB1R in the pathogenesis of acute liver injury.

overall_design: Total hepatocyte RNA was extracted for microarray analysis of four hepatocyte-specific Cannabinoid 1 Receptor conditional  knock-out mice (hCNR1-/-) and four control wildtype (hCNR1+/+)  mice.

first: Yoo

last: Kim

first: Sudeep

last: Gautam

first: Jaekwan

first: Prabha

last: Chandrasekaran

first: Paritosh

last: Ghosh

first: Máire

last: Doyle

first: Ashley

last: Appleton

first: Doyle

middle: L

last: Lang

first: Elin

last: Lehrmann

first: Qing-Rong

last: Liu

first: Qinghua

last: Chen

first: Jennifer

middle: F

last: O’Connell

first: Josephine

last: Egan