title: Transcriptome profiling of in vitro cellular entities involved in lung tumour fusion events

status: Public on Aug 10 2020

city: Marburg

first: Leon

middle: Nicolas

last: Schulte

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

institute: Philipps-Universität Marburg

summary: Cell fusion theory for explaining metastasis origin has been hypothesised for almost one-hundred years, mainly availed with data coming from patients who received a bone marrow transplant and all had tumour cells with DNA from their cancer-free donors. In fact, colonisation of distant organs by an original tumour could be explained with the acquisition of hallmarks from both immune and tumour parents. Here, we systematically conducted in vitro fusions between CD14+human monocytes and GFP+H60 lung tumour cells. Transcriptome analysis of naïve monocytes, and sorted GFP+, CD14+ and CD14+GFP+ cells showed the latter sharing common pathways with both parental types, which sustain their in vivo metastatic characteristics, such as mobility and invasiveness. Altogether, our data demonstrates that differentially genes profile acquisition by hybrids enables them to drive metastasis.

overall_design: RNA-seq in biological replicates of four days in vitro fusions between human PBMC derived monocytes and GFP+CSC-H460 tumour cell line.

first: Eduardo

last: López-Collazo

first: Luis

last: Aguirre

middle: N


title: Differential gene expressions in dose-related radioresistant hypopharyngeal cancer cells

status: Public on Aug 11 2020

city: Chongqing

first: Liu

last: Chuan

address: No 1, Yixueyuan Road

department: Otorhinolaryngology

country: China

institute: Chongqing Medical University

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

summary: To explore the mechanisms underlying the radioresistance of hypopharyngeal carcinoma, we first established specifically radioresistant FaDu cell line (FaDu-RR cells) derived from FaDu cell lines by repeatedly exposing to different doses of ionizing radiation. Then, the aberrantly expressed mRNAs and IncRNAs were detected using microarrays and their bioinformatics were analyzed.

overall_design: Gene expressions of different radioresistant FaDu cells were measured after exposure to different doses of 0, 20, 40 and 60 Gy x-rays.

first: Hu

middle: G

last: Hua


title: Transcriptome profile after knockdown of a lncRNA EPEL in A549 lung cancer cells

status: Public on Aug 07 2020

city: Goyang

first: Seong-min

last: Park

address: Ilsan-ro

country: South Korea

institute: NCC

summary: Analysis of regulation of a lncRNA EPEL at gene expression level. The hypothesis tested in the present study is that EPEL regulates proliferation of lung cancer cells through up-regulation of E2F target genes. Results provide important information of the response of EPEL knockdown such as up-regulation of specific cell cycle-related E2F genes and the cellular functions.

overall_design: Total RNA samples were isolated from A549 lung cancer cells after treating with siRNAs for EPEL or a non-targeting control siRNA. The cRNA libraries were prepared from the total RNA samples, hybridized to the HumanHT-12 gene expression beachip (Illumina).

first: Seong-Min

first: Eun-Young

last: Choi

first: Youn-Jae

last: Kim


title: Genomic distribution of H3T3ph in Drosophila melanogaster S2 cells

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Drosophila Haspin kinase phosphorylates Histone H3 at threonine 3 at centromeric heterochromatin and either lamin- or polycomb-enriched euchromatic regions, being required for nuclear organization of interphase cells and polycomb-dependent gene silencing.

overall_design: ChIP-seq peak calling of H3T3ph against input sample in Drosophila melanogaster S2 cells

first: Ujué

last: Fresán

first: Maria

last: Rodríguez-Sánchez

last: Reina

first: M

middle: L

last: Espinàs


title: Long noncoding RNA DICER1-AS1 functions in methylation regulation on the multi-drugresistance of osteosarcoma cells via miR-34a-5p and GADD45A (mRNA-seq)

status: Public on Aug 20 2020

city: Hefei,

first: Youguang

last: Pu

state: Anhui

address: No. 96 Jinzhai Road, Hefei City, Anhui Province

institute: University of Science and Technology of China

type: Expression profiling by high throughput sequencing

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Methods: Total RNA was extracted by Trizol reagent, and DNA was produced by gene specific primers or random primers. Illumina-Hiseq 4000 system was used for RNA sequencing and Illumina-Hiseq 2000 system was used for library sequencing (BGI Technology Company). A single-ended library was prepared according to the Illumina-Truseq RNA sample preparation kit (Illumina) scheme The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: Using an optimized data analysis workflow, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to retinal function. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling.
Conclusions: Our study represents the first detailed generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: mRNA-seqs that were differentially expressed between DICER1-AS1-overexpression and control vector in SJSA-1 and MNNG/HOS cells


title: Integrative analysis of hepatic microRNA and mRNA to identify potential biological pathways associated with monocrotaline-induced liver injury in mice

status: Public on Aug 02 2020

city: Shanghai

first: Zhenlin

last: Huang

state: Shanghai

address: 1200 Cailun Road, Zhangjiang High Tech Park

department: Institute of Chinese Materia Medica

institute: Shanghai University of Traditional Chinese Medicine

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

summary:
In this study, the analysis of miRNA and mRNA expression profiles was used to identify the potential engaged biological signaling pathways involved in Monocrotaline-induced liver injury.
There were total 35 hepatic miRNAs differentially expressed in mice treated with  Monocrotaline (both 270 mg/kg and 330 mg/kg)

platform_organism:
Mus musculus
Murid betaherpesvirus 1
Murid gammaherpesvirus 4

overall_design:
[miRNA] In the study presented here, 9 liver samples from 3 groups (control group,270 mg/kg MCT group and 330mg/kg MCT group) were collected, each group contained 3 replicates, and were used to acquire expression profiles of a total of 1,177 unique miRNAs.
[mRNA] In the study presented here, 9 liver samples from 3 groups(control group,270 mg/kg MCT group and 330mg/kg MCT group)were collected, each group contained 3 replicates, and were used to acquire expression profiles of a total of 18,816 genes.

first: Lili

last: Ji


title: miRNA expression alterations in vildagliptin treated rats arota

status: Public on Aug 03 2020

city: Beijing

first: Qian

last: Zhang

address: No. 1 Shuaifuyuan, Dongcheng District

institute: Peking Union Medical College Hospital

summary: vildagliptin may distrub miRNA expression in diabetic rats arota

overall_design: miRNA array in vildagliptine-treated rat arota

first: Xinhua

last: Xiao

first: Jia

last: Zheng

first: Ming

last: Li

first: Miao

last: Yu

first: Fan

last: Ping

first: Cuijuan

last: Qi

first: Tong

last: Wang

first: Xiaojing

first: Liyuan

last: Zhou


title: Determination of dynamic changes in gene expression and chromatin accessibility during cellular reprogramming

status: Public on Aug 17 2020

city: Singapore

first: Chadi

last: El Farran

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: The circular RNA of peripheral blood mononuclear cells: hsa_circ_0005836 as a new diagnostic biomarker and therapeutic target of active pulmonary tuberculosis

status: Public on Aug 04 2020

city: dongguan

first: Hou-Long

last: Luo

state: Guangdong

address: No. 1 Xincheng Road

institute: Guangdong Medical University

summary: It has been reported that circular RNA (circRNA) is associated with human cancer. However, few studies have been reported in active pulmonary tuberculosis (APTB). The global circRNA expression was detected in the peripheral blood mononuclear cells (PBMCs) of APTB patients (n=5) and healthy controls (HC) (n=5) by using high-throughput sequencing. According to the systematical bioinformatics analysis, the basic content of circRNAs and their fold changes in the two groups were calculated. We selected 6 significant differentially expressed circRNAs, hsa_circ_0005836, hsa_circ_0009128, hsa_circ_0003519, hsa_circ_0023956, hsa_circ_0078768, and hsa_circ_0088452 and validated the expression in PBMCs from APTB (n=10) and HC (n=10) by real-time quantitative reverse transcription-polymerase chain reactions (qRT-PCRs). Further, the verification of these specific circRNAs (hsa_circ_0005836 and hsa_circ_0009128) between APTB (n=34) and HC (n=30) in PBMCs was also conducted by qRT-PCRs. The RNA-seq data showed the significant differential expression of the 523 circRNAs between the APTB and HC groups (199 circRNAs were significantly up-regulated and 324 circRNAs were down-regulated). Hsa_circ_0005836 and hsa_circ_0009128 expression was significantly down-regulated in the PBMCs of APTB (P< 0.05) in the samples of APTB compared to HC in our study. The gene ontology based enrichment analysis of the circRNA-miRNA-mRNAs network showed that cellular catabolic process (P=7.10E-08), regulation of metabolic process (P=2.10E-06), catalytic activity (P=3.67E-08), protein binding (P=1.71E-07), cell part (P=3.46E-06), intracellular part (P=1.71E-07), and intracellular (P=3.67E-08) were recognized in the comparisons between APTB and HC. Based on KEGG analysis, HTLV-I infection, regulation of actin cytoskeleton, neurotrophin signaling pathway and mTOR signaling pathway were relevant during tuberculosis bacillus infection. We found for the first time that hsa_circ_0005836 and hsa_circ_0009128 were significantly down-regulated in the PBMCs of APTB compared with HC. Our findings indicate hsa_circ_0005836 might serve as a novel potential biomarker for TB infection.

overall_design: Five RNA samples of the same group were pooled and aliquoted into two for sequencing.

first: JunFa

last: Xu

first: ZeGang

last: Zhuang

first: JunAi

first: HouLong

first: GanBin

last: Liu

first: YuanBin

last: Lu

first: NanHai

last: Ge

first: BiYing

first: RuiXi

first: Chen

last: Chen

first: Xin

first: YuQing

first: FengHui

first: Yong

first: XiaoZhen

last: Cai

first: ZhengW


title: Epigenetic and Expression Profiling of Tissue Selective Estrogen Compounds in Breast Epithelial Cell Lines

status: Public on Aug 01 2020

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

country: USA

institute: University of Vermont


title: Establishment and characterization of testicular cancer patient-derived xenograft (PDX) models

status: Public on Jul 29 2020

city: Groningen

first: Steven

last: de Jong

address: Hanzeplein 1

department: Medical Oncology

country: Netherlands

institute: University Medical Center Groningen


title: High-sensitive circulating microRNA panel for early detection of hepatocellular carcinoma

city: Kanagawa

first: Satoko

last: Takizawa

address: kamakurashi

country: Japan

institute: Toray industries inc

summary:
A serum miRNA combination could be a powerful classifier for the detection of hepatocellular carcinoma.

Keywords: Non-coding RNA profiling by array

overall_design: Serum microRNA profiles of 1817 samples, which consist of 345 with hepatocellular carcinoma,  46 patients with chronic hepatitis, 93 patients with liver cirrhosis, and 1033 non-cancer individuals.

first: Yusuke

last: Yamamoto

first: Shunsuke

last: Kondo

first: Juntaro

last: Matsuzaki

first: Minoru

last: Esaki

first: Takuji

last: Okusaka

first: Kazuaki

last: Shimada

first: Yoshiki

last: Murakami

first: Masaru

last: Enomoto

first: Akihiro

last: Tamori

first: Ken

last: Kato

first: Yoshiaki

last: Aoki

first: Hiromi

last: Sakamoto

first: Shumpei

last: Niida

first: Fumitaka

last: Takeshita

first: Takahiro

last: Ochiya


title: Epigenetic and Expression Profiling of Tissue Selective Estrogen Compounds in Breast Epithelial Cell Lines (ChIP-seq)

first: Jonathan

last: Gordon

summary: Current approaches to menopausal hormone therapy consist of compounds which provide tissue specific beneficial effects while working to minimize any increase in cancer risk associated with replacement therapy.  In this study, an examination of the genomic distribution of histone modification and expression changes in two breast epithelial cell lines, the normal MCF10A cell line and the MCF-7 breast cancer cell line, upon treatment with several of the current therapies used for treating post-menopausal symptoms is presented. Analysis of the observed changes upon treatment with either 17-estradiol (E2), a combined treatment with the top 10 most abundant Premarin chemical equivalents (EC10), the non-steroidal SERM, Bazadoxifene (BZA) and the TSEC; BZA combined with EC10 (Duavee) or BZA combined with E2 provides evidence of expression changes in genes involved in DNA replication, nucleosome assembly, RNA-splicing and processing, biological regulation and cell signaling, and many of the known steroid response genes.  There were distinct global changes in chromatin states observed that were specific to each of the breast epithelial cell type normal, basal MCF10A and ESR/PGR positive luminal breast cancer MCF7 cell lines and selective changes observed upon treatment with each of the treatment groups.  Specifically, we observed a global loss of H3K4ac upon treatment with BZA.  These changes were observed in both ESR1 bound and non-bound regions suggesting modifications in both promoters and enhancer regions.  The levels of H3K4ac upon treatment of BZA showed a decrease below basal non-treated H3K4ac levels in MCF7.  There was an increase observed with E2 and EC10 treatment in MCF7 that was mitigated by the addition of BZA to either steroid as a combined treatment.  This study provides a better understanding of the role of epigenetic modifications in endocrine responsiveness and provides evidence of an improved therapeutic profile for combined TSEC compounds for treating and managing the overall physiological effects of declining estrogen.

overall_design: 6 drug treatments in 2 cell lines with 2 biological replicates

first: Terri

last: Messier

first: Joseph

middle: R

last: Boyd

first: Gary

middle: S

last: Stein


title: Transcriptome analysis of SH-SY5Y neuroblastoma cells treated with copper and copper chelators (Dextran-Catechin - DC, and Tetraethylenepentamine pentahydrochloride - TEPA) in the presence or absence of interferon gamma

status: Public on Jul 28 2020

city: Bologna

first: Daniele

last: Mercatelli

address: Via Irnerio 45

department: Pharmacy and Biotechnology

country: Italy

institute: University of Bologna

summary: Therapeutic checkpoint antibodies blocking PD1/PD-L1 signaling have radically improved clinical outcomes in cancer. However, the regulation of PD-L1 expression on tumor cells is still poorly understood. Here we show that intra-tumoral copper levels influence PD-L1 expression in cancer cells. Copper supplementation enhanced PD-L1 expression at mRNA and protein levels in cancer cells and RNAseq revealed that copper regulates key signaling pathways mediating PD-L1-driven cancer immune evasion. Conversely, copper chelators inhibited phosphorylation of STAT3 and EGFR and promoted ubiquitin-mediated degradation of PD-L1. Overall, this study reveals an important role for copper in regulating PD-L1 and suggests that anti-cancer immunotherapy might be enhanced by pharmacologically reducing intra-tumor copper levels.

overall_design: The aim of our work was to study the effects of intra-tumoral copper regulation in neuroblastoma cells. 24 samples (each in triplicate) have been included. SH-SY5Y neuroblastoma cells were were harvested after 24h of drug treatment for Dextran-Catechin (DC), Tetraethylenepentamine pentahydrochloride (TEPA) and Interferon-gamma (IFN-g) or after 4h of copper chloride hydrate (CuCl2) treatment.

first: Florida

last: Voli

first: Emanuele

last: Valli

first: Luigi

last: Lerra

first: Kathleen

last: Kimpton

first: Federica

last: Saletta

first: Federico

middle: M

last: Giorgi

first: Jourdin

last: Rouaen

first: Sylvie

last: Shen

first: Jayne

middle: E

last: Murray

first: Aria

last: Ahmed-Cox

first: Giuseppe

last: Cirillo

first: Chelsea

last: Mayoh

first: Paul

middle: A

last: Beavis

first: Michelle

last: Haber

last: Trapani

first: Maria

last: Kavallaris

first: Orazio

last: Vittorio


title: Establishment and characterization of testicular cancer patient-derived xenograft (PDX) models [SNP array]

first: Steven

last: de Jong

summary: Testicular cancer (TC) is the most common solid tumour in young men. While cisplatin-based chemotherapy is highly effective in TC patients, chemoresistance still accounts for 10% of disease-related deaths. Pre-clinical models that faithfully reflect patient tumours are needed to assist in target discovery and drug development. Tumour pieces from eight TC patients were subcutaneously implanted in NOD scid gamma (NSG) mice. Three patient-derived xenograft (PDX) models of TC, including one chemoresistant model, were established containing yolk sac tumour and teratoma components. Whole-exome sequencing, copy number variation analysis and RNA-sequencing was performed on these TP53 wild type PDX tumours to assess the effects of passaging, showing high concordance of molecular features between passages.

overall_design:
Genomic DNA extracted from testicular cancer PDX tumors was genotyped using the Infinium Global Screening Array-24 v1.0 BeadChip (Illumina) with extra custom content.
10 samples

first: S


title: MYSM1 maintains ribosomal protein gene expression in hematopoietic stem cells to prevent hematopoietic dysfunction I.

city: MONTREAL

first: David

last: Langlais

state: QC

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

department: Human Genetics

country: Canada

institute: McGill University

summary: MYSM1 is a transcriptional regulator essential for HSC function and hematopoiesis. We established that HSC dysfunction in Mysm1-deficiency is driven by p53 stress response, however, the molecular function of MYSM1 as a transcriptional activator and its essential role in p53 stress response repression remain difficult to reconcile. Here, we performed genome-wide analyses of MYSM1-regulated genes in hematopoietic stem and progenitor cells (HSPCs). This included RNA-Seq of sorted Mysm1-deficient mouse HSCs and MPPs, and ChIP-Seq mapping of MYSM1 DNA-binding sites in hematopoietic progenitor cell lines. We demonstrate a direct role for MYSM1 in the regulation of genes encoding protein components of the ribosome (RP-genes) and other regulators of translation. Mechanistically, the dysregulation of RP-genes in Mysm1-deficiency was upstream of p53-activation and associated with reduced HSCs protein synthesis rates and p53-dependent anemia.

overall_design: To gain insight into the genomic regions directly regulated by MYSM1 in hematopoietic cells, we mapped MYSM1 DNA binding sites by ChIP-Seq. The experiments were carried out in two murine hematopoietic progenitor lines expressing triple-FLAG-tagged MYSM1: a multipotent progenitor line HPC7 widely used as a model to study transcriptional programs of hematopoiesis, and pro-B cell line Ba/F3 that was used in our previous work to model p53-activation and other molecular mechanisms of Mysm1-deficiency (Belle et al., 2016).

first: HanChen

last: Wang

first: Jad

last: Belle

first: Jessica

last: Petrov

first: Anastasia

last: Nijnik


title: MYSM1 maintains ribosomal protein gene expression in hematopoietic stem cells to prevent hematopoietic dysfunction II.

overall_design: We performed RNA-Seq transcriptional profiling of FACS-sorted primary HSC, MPP1, and MPP2 cells. Briefly, bone marrow cells were harvested from Mysm1 fl/fl CreERT2 mice following tamoxifen-induced Mysm1-deletion, and from tamoxifen-treated Mysm1 fl/+ CreERT2 and corn-oil vehicle-treated Mysm1 fl animals. The cells were sorted using FACS into primary HSC, MPP1, and MPP2 cells, gating on Lin-cKit+Sca1+CD150+Flt3-, and CD34-CD48- for HSCs, CD34+CD48- for MPP1, and CD34+CD48+ for MPP2 cells. RNA was isolated from the FACS-sorted cells using the MagMAX total RNA kit (Ambion, Life Technologies), and quality assessed using Bioanalyzer RNA Pico chips (Agilent). rRNA depletion and library preparation were performed using the SMARTer Stranded RNA-Seq kit (Takara Clontech). The libraries were sequenced on an Illumina HiSeq 2000 sequencer in paired-end 50bp configuration. Cells from multiple mice were pooled to achieve yields of >1ng of RNA per sample, and three independent samples were analyzed per genotype for each cell-type for tamoxifen-induced mice and two independent samples for vehicle-treated mice.


title: Identification of differentially expressed miRNAs of exosome-like microvesicles secreted from mouse colon cancer stem cells

status: Public on Jul 27 2020

city: Taipei

first: Wei-Lun

last: Hwang

address: No.155, Sec.2, Linong Street

department: Department of Biotechnology and Laboratory Science in Medicine

country: Taiwan

institute: National Yang Ming Chiao Tung University

summary: As accumulating evidence suggests cancer cells exhibit stem-like properties for advanced diseases and cancer stem cells (CSCs) have been identified in various tumor types, revisiting present knowledge toward CSCs is essential.  The identification of exosome-loaded miRNAs responsible for stemness and chemoradioresistance of CSCs should eventually leadd to development of novel therapeutic approaches.

overall_design: Expression profiles of miRNAs of purified exosome-like vesicles (ELVs) from parental mouse CT26 cells and CT26-derived cancer spheres were generated for identifying central miRNAs for CSC malignancy.

first: Wei-Chung

last: Cheng


title: Transcriptome and proteome analysis of resistant peanut pre-harvest seeds in response to Aspergillus flavus

city: Hangzhou

first: Jianning

last: Liu

address: 866 Yuhangtang Road

institute: Zhejiang University

summary: In this study, we used RNA-seq to obtain and compare transcriptomic profiles of a resistant genotype J11 in pre-harvest seeds, with A. flavus inoculation at the whole-genome level. The TMT method was also implemented to help further understand the molecular mechanism of peanut resistance to A. flavus invasion at proteome level. Meanwhile, we conducted a thorough research on a chitinase and a NBS-LRR gene, which were found in our data. This study is our first step towards a comprehensive genome-scale platform for developing Aspergillus resistant peanut cultivars through genetic engineering.

overall_design: Seed coat samples were pooled together for RNA isolation, and employed as a mixed stress library according to the strategy for preparing a pooled cDNA library (Eybishtz et al, 2009) which represented gene expression during the early stage of infection, whereas the samples without infection served as a control group. Each group comprised three biological replicates.

first: Xiaobo

last: Zhao


title: Differential miRNA expression profiles of human vascular endothelial cells (VECs) between Type-I pro-proliferative/pro-stenotic VECs and Type-II anti-proliferative/anti-stenotic VECs [Agilent-046064]

city: Shinjuku-ku

first: Kumiko

last: Saeki

state: Tokyo

address: 1-21-1 Toyama

department: Department of disease control

institute: National Center for Global Health and Medicine

summary: Human VECs are categorized into two groups according to their effects on the proliferation of vascular smooth muscle cells (in vitro) and the induction of stenosis in endothelia-removed arteries after transplantation (In vivo): pro-proliferative/pro-stenotic (Type-I) virsus anti-proliferative/anti-stenotic (Type-II) VECs. Since RGS5, which is a master gene responsible for aging- and oxidative stress-dependent Type-II to Type-I conversion, is the only protein-coding gene that shows differential expression profiles between Type-I and Type-II VECs, non-coding RNAs including miRNA should be working at the downstream of RGS5 for quality control of VECs.

overall_design: Totally 13 samples of Type-I VECs (HRMVEC, HCAEC, HMVEC, HBVEC, aged ES(KhES1)dEC, aged ES(KhES3)dEC) and Type-II VECs (young ES(KhES1)dEC, young ES(KhES3)dECs, SeViPS(BJ)dEC_lot1, SeViPS(BJ)dEC_lot2, SeViPS(HUVEC)dEC_lot1, SeViPS(HUVEC)dEC_lot2, SeViPS(HUVEC)dEC_lot3) ( (Nishio et al., World J Transl Med 4: 88-100. DOI:10.5528/wjtm.v4.i3.101) were subjected to the analyses.

first: Masako

last: Nakahara

first: Norihiko

last: Kobayashi

last: Oka


title: Gene expression profiles of mouse neutrophils stimulated with cancer stem cell-derived microvesicles

summary: Tumor-infilitrated myeloid cells have been implicated for tumor-host interaction and therapeutic resistance. However, impacts of tumor-secreted microvesicles on host neutrophils remain unknown. By examining transcriptome profiles of tumor exosome-stimulated neutrophils, key genes regulating tumor immunity will be elucidated to develope coping strategies for combating pathological tumor-host interaction.

overall_design: A colon cancer cell line, CT26, is used to enrich cancer stem cells by a defined stem cell medium (SCM) cultivation. The tumor exosomes of cancer stem cells are collected from SCM by ultracentrifugation for neutrophil treatment.


title: Sorafenib resistance related circRNAs

status: Public on Jul 25 2020

first: Xiujun

last: Cai

state: Zhejiang

address: 3 East Qingchun Road

department: Department of General Surgery

institute: Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine

summary: Sorafenib resistance up-regulated circRNA_104797 could be transmitted by exosomes and responsible for the spread of Sorafenib resistance among HCC cells. CircRNA_104797 was critical for Sorafenib resistance maintenance and silencing circRNA_104797 could substantially increase the efficacy of Sorafenib by inducing apoptosis. Mechanism dissection unveiled that circRNA_104797 could specifically sponge miR-103a-2-5p and miR-660-3p and act as a competing endogenous RNA (ceRNA), thus competitively activated wnt/β-catenin pathway and induced Sorafenib resistance. Meanwhile, LC-MS/MS also revealed that circRNA_104797 could specifically bind to translation related proteins, which might regulate downstream glycan biosynthesis and lipid metabolism, and finally induce Sorafenib resistance. In vivo experiments portrayed a promising clinical application by locally injection of in vivo-grade siRNA for circRNA_104797 by TACE or other manners, which could intensively enhance Sorafenib efficacy in HCC patients. The clinical application of in vivo-grade siRNA for circRNA_104797 in Sorafenib treated HCC patients might shed bright future for the management of advanced HCC.

overall_design: Arraystar Human circRNA Array analysis specifically for human circular RNAs splicing sites was used with six HCC cell samples (3 parental HepG2 samples and 3 Sorafenib resistant HepG2 samples) in the present study.

first: Junjie

last: Xu


title: HuR-dependent gene expression in brown adipose tissue

status: Public on Jul 22 2020

city: Columbus

first: Michael

last: Tranter

state: OH

address: 2255 Kenny Road

department: Molecular Medicine and Therapeutics

institute: The Ohio State University

summary: We utilized adipocyte-specific deletion of HuR followed by RNA-seq of total BAT mRNA to identify HuR-dependent gene expression within BAT

overall_design: RNA-seq from BAT from Adipocyte-specific HuR deletion and littermate controls

first: Tranter

last: Michael


title: Repression of p53-target gene Bbc3/puma by MYSM1 is essential for the survival of hematopoietic multipotent progenitors and contributes to stem cell maintenance

last: Langlais

summary: MYSM1 is a transcriptional regulator essential for HSC function and hematopoiesis. We established that p53 activation is a common mechanism mediating HSC dysfunction, MPP depletion, and lymphopenia in Mysm1-deficiency, however, the specific p53-induced effectors that trigger dysfunction in Mysm1-deficient HSPCs remain unknown. Here, we performed RNA-Seq of Lin-cKit+Sca1+CD150+ and CD150- HSPCs from Mysm1-/-Puma-/-, Mysm1-/-Puma+/-, Puma-/-, and wild-type mice; (Mysm1-/-Puma+/- phenocopies Mysm1-/-). We showed that Bbc3/PUMA is the primary non-redundant mediator of MPP depletion in Mysm1-deficiency and contributes to HSC dysfunction, whereas depletion of lymphoid-lineage cells involves PUMA-independent p53 activities. We also identified a broad downregulation of genes encoding protein components of the ribosome (RP-genes) and other regulators of translation in Mysm1-deficiency, and the downregulation persisted in Mysm1-/-Puma-/-.

overall_design: We performed RNA-Seq transcriptional profiling of FACS-sorted primary hematopoietic stem and progenitor cells. Briefly, bone marrow cells were harvested from Mysm1-/-Puma-/-, Mysm1-/-Puma+/-, Puma-/-, and wild-type mice; (Mysm1-/-Puma+/- phenocopies Mysm1-/-), and sorted using FACS into primary HSPCs, gating on Lin-cKit+Sca1+CD150+ and CD150-. RNA was isolated from the FACS-sorted cells using the MagMAX total RNA kit (Ambion, Life Technologies), and quality assessed using Bioanalyzer RNA Pico chips (Agilent). RNA (10 ng) was rRNA-depleted and used for library preparation with the SMARTer Stranded RNA-Seq kit (Takara Clontech, Mountain View, CA, USA) designed for low input. The RNA-seq libraries were sequenced on an Illumina HiSeq 2000 sequencer in a paired-end 50-bp configuration.


title: Taurine upregulated gene 1 functions as a master regulator to coordinate glycolysis and metastasis in hepatocellular carcinoma

status: Public on Jul 19 2020

city: Taoyuan

first: Yang-Hsiang

last: Lin

address: Wenhua 1st Rd., Guishan Dist.

department: Department of Biochemistry

institute: Chang Gung University

summary: to investigate differentially expressed lncRNAs and mRNAs in HCC specimens

overall_design: The goal of this study is to explore the fundamental knowledge of biological roles of lncRNAs in liver cancer. In the future, it will be used for effective diagnosis and prognosis, or novel therapeutic target development for HCC.

first: Kwang-Huei


title: Comparison of six methods for isolation of urinary microvesicles for miRNA profiling in proteinuria.

city: Nijmegen

first: Ilse

last: Rood

address: PO Box 9101

institute: Radboudumc

summary: Urinary extracellular vesicles (uEVs) are a promising source for biomarker discovery, including miRNAs. The optimal isolation method of uEVs for miRNA profiling in patients with proteinuria is unknown. Six different methods were compared for the isolation of microvesicles and these were compared to raw urine (method A). 2 methods failed and further analysis was performed with the following methods: ExoRNeasy (method C), modified protocol for ExoRNeasy (method E) and ultracentrifugation (method F). Different miRNAs are enriched by method C and F. No differences were observed between method C and E.

overall_design: 10 urine samples from patients with proteinuria

first: Thomas

last: Laufer

first: Jan

last: vandenBrand

first: Mustafa

last: Kahraman

first: Anna

last: Saiz

first: Hannah

last: Schrörs

first: Johan

last: vanderVlag

first: Jack

last: Wetzels

first: Jeroen

middle: J

last: Deegens


title: Establishment and characterization of testicular cancer patient-derived xenograft (PDX) models [RNA-seq]

first: Steven

last: de Jong

overall_design: 6 samples derived from TC PDX tumors at different mouse passages (untreated).

first: S


title: Ventricular T-box 5 in the adult heart ensures normal cardiac conduction and protects from pathologic cardiac remodeling [ChIP-seq]

city: Göttingen

first: Franziska

middle: Sophie

last: Rathjens

state: Niedersachsen

address: Robert-Koch-Straße 40

department: Institute of Pharmacology and Toxicology

country: Germany

institute: University Medical Centre Göttingen

summary: Sudden cardiac death is the number one cause of death worldwide. Major causes of sudden cardiac death include myocardial infarction and cardiomyopathies. To develop novel therapeutic strategies, we need to identify key factors that are required for proper cardiac function and are dysregulated in the diseased heart. Under this notion, we found T-box 5 (TBX5), a transcription factor regarded solely in the context of congenital heart disease, to be downregulated in human diseased left ventricles. To investigate the effects of TBX5 loss in the adult heart, we generated an inducible ventricular cardiomyocyte specific knock-out mouse model (vTbx5KO). We performed integrative genome-wide chromatin occupancy and transcriptomic analysis and identified 47 downregulated transcripts in vTbx5KO that contain TBX5 active enhancers. The TBX5 targets in the ventricle included genes implicated in cardiac conduction and contraction (Gja1, Kcnj5, Kcng2, Cacna1g, Chrm2), cytoskeleton organization (Fstl4, Pdlim4, Emilin2, Cmya5) as well as cardiac protection upon stress (Fhl2, Gpr22, Fgf16). In line with this analysis, vTbx5KO mice presented cardiac conduction defects and arrhythmias at baseline as well as exacerbated cardiac remodeling upon Angiotensin II-induced hypertrophy. In conclusion, this study uncovers a novel protective role of TBX5 upon cardiac remodeling and renders TBX5 as an interesting therapeutic target.

overall_design: Chromatin-Immunoprecipitation-Sequencing for TBX5 and IgG in adult mouse ventricular tissue; two biological replicate for each sample

first: Laura

middle: C

last: Zelarayán

first: Maria

middle: P

last: Zafeiriou


title: Dnmt1 binds and represses genomic retroelements via DNA methylation in mouse early embryos

city: Daejeon

first: Byungkuk

last: Min

address: 125 Gwahak-ro, Yuseong-gu

department: Development and Differentiation Research Center

institute: KRIBB

type: Methylation profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Next Generation Sequencing Facilitates Quantitative Analysis of Splenic Macrophage Subpopulations identified by Ly6c and F4/80 Transcriptomes in mouse T cell acute lymphoblastic leukemia

city: Tianjin

first: Guo Guang

last: Zheng

state: Tianjin

address: Blood Hospital,288 Nanjing Road,Heping District

department: Institute of Hematology & Blood Hospital

institute: Chinese Academy of Medical Science& Peking Union  Medical College

summary: The goals of this study aim to reveal functional and phenotypic diversity of Spleenic Macrophage subpopulations identified by Ly6c and F4/80  in response to the microenvironmental cues  in mouse T cell acute lymphoblastic leukemia

overall_design: Compare Transcriptomes of Splenic Macrophage Subpopulations identified by Ly6c and F4/80  in mouse T cell acute lymphoblastic leukemia

first: Feifei

last: Yang

first: GuoGuang


title: Transcriptome analysis of Human Cytomegalovirus (HCMV) infected nasal turbinate tissues

status: Public on Jul 16 2020

city: Jerusalem

first: Dana

last: Wolf

address: Ein Kerem

department: Dept. of clinical Microbiology & Infectious Diseases

country: Israel

institute: Hadassah University Hospital

summary: We report the application of RNA sequencing for transcriptome analysis of HCMV infected Human nasal turbinate tissues, enabling the study of tissue responses to HCMV infection

overall_design: Two pools of nasal turbinate tissues, from five individuals each, were either HCMV- or mock-infected and subjected to transcriptome analysis.

first: Or

last: Alfi


title: Ventricular T-box 5 in the adult heart ensures normal cardiac conduction and protects from pathologic cardiac remodeling [RNA-seq]

overall_design: Gene expression profiling from cardiac ventricles of 16 weeks-old vTBX5 KO and Flox mice


title: Differential miRNA expression profiles of human vascular endothelial cells (VECs) between Type-I pro-proliferative/pro-stenotic VECs and Type-II anti-proliferative/anti-stenotic VECs [Agilent-070156]

first: Kumiko

last: Saeki

first: Masako

last: Nakahara

first: Norihiko

last: Kobayashi

last: Oka


title: Differential miRNA expression profiles of human vascular endothelial cells (VECs) between Type-I pro-proliferative/pro-stenotic VECs and Type-II anti-proliferative/anti-stenotic VECs


title: Transcriptomic changes in parvalbumin positive interneurons from cortex and striatum.

city: Seville

first: Xavier

last: d'Anglemont de Tassigny

address: Hospital Universitario Virgen del Rocio. Calle Antonio Maura Montaner

department: Cell Neurobiology and Biophysics

institute: Instituto de Biomedicina de Sevilla (IBiS)

summary:
This experiment was designed to compare the transcriptomic differences between two parvalbumin (PV) interneuron population of the mouse brain. These two populations have the same embryological origin and share several neurochemical and electrophysiological properties, but differ in their ability to express the glial cell line-derived neurotrophic factor GDNF (negative in cortex and positive in striatum). Two different reporters for PV expressing cells were used: i) a constitutive tdTomato gene inserted in the Pvalb locus, and ii) a PV-Cre; tdTomato model in which fluorescent cells are PV cells expressing Cre recombinase. The comparative gene expression analysis between PV neurons captured from striatum and cortex allowed unraveling differential molecular characteristics of GDNF-synthesizing striatal PV interneurons and their potential role in endogenous GDNF modulation.
The specific expression of several genes of interest in the striatal PV interneurons has been validated by other methods (real-time RT-PCR, in situ hibridization, immunohistochemistry).

overall_design: Parvalbumin-positive interneurons were obtained from two postnatal day 30 mouse brains: PVCre; tdTomato (N = 4) or PV-tdTomato mice (N = 4). Cells from two different brain regions (CTX or ST) were mechanically and enzymatically dissociated and then sorted by FACS. RNA was extracted from 2000 cells / replicate. RNA was  amplified and hybridized with Affymetrix GeneChip Mouse Transcriptome 1.0 Arrays. Due to the low yield, cells from 2 to 4 mice were pooled to reach a total number of 2000 cells required for RNA isolation.

first: Daniel

last: Enterría-Morales

first: Ivette

last: López-López

first: José

last: López-Barneo


title: MYSM1

status: Public on Jul 24 2020

first: David

last: Langlais


title: Expression profiling of human neuroblastoma cells SK-N-SH after treatment with low dose of 2,3,7,8- tetrachlorodibenzo-p-dioxin

status: Public on Jul 12 2020

city: Beijing

first: Tuan

last: Xu

state: Beijing

address: 18 Shuangqing Road

department: Research Center for Eco-Environmental Sciences

institute: Chinese Academy of Sciences

summary:
Exposure to dioxins has been associated with impaired development of the nervous system and losses of brain functions. However, the precise cellular events and related molecular basis underlining these adverse effects has not been fully understood.
We aimed to reveal global alterations of mRNA expression and potential cellular events by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) exposure.

overall_design: Messenger RNA microarray analysis was employed on cultured human neuroblastoma cells SK-N-SH exposed to 10-10 M TCDD.Total RNA was extracted from cell samples using Trizol/Chloroform method, and then purified with magnetic beads of Agencourt Ampure (Beckman Coulter, Brea, CA, USA). Target preparation for microarray processing was carried out according to the GeneChip® WT PLUS Reagent Kit. In each preparation, 500 ng total RNA was used for a double-round of cDNA synthesis. After fragmentation of 2nd-cycle single-stranded cDNA, sample was labeled with biotin by terminal deoxynucleotidyl transferase (TdT). Then sample was hybridized to a GeneChip® Human Transcriptome Array 2.0 (HTA 2.0, Affymetrix) with 44699 annotated genes.

first: Heidi

middle: Q

last: Xie

first: Yingjie

last: Xia

first: Yunping

last: Li

first: Zhiling

last: Guo

first: Yangsheng

last: Chen

first: Li

first: Bin

last: Zhao


title: Expression data from mesenchymal stromal cells derived from pediatric leukemia patients and healthy pediatric controls

status: Public on Jul 13 2020

city: Utrecht

first: Judith

middle: M.

last: Boer

address: Heidelberglaan 25

institute: Prinses Maxima Centrum

summary: B-cell precursor acute lymphoblastic leukemia (BCP-ALL) cells reside in the bone marrow microenvironment, where they are protected against chemotherapeutic agents. Mesenchymal stromal cells (MSCs) are key components of this supporting framework. The present study aimed to unravel whether MSCs derived from pediatric BCP-ALL patients (leukemic MSCs) differ from MSCs derived from healthy pediatric donors (control-MSCs). Therefore, we studied their gene expression profiles.

overall_design: Microarray analyses were performed of primary MSCs derived from bone marrow samples collected at initial diagnosis (n=35; day0-leukemic-MSCs), after induction and consolidation therapy when patients are in remission of their leukemia (n=29; day79 remission-MSCs), and at Relapse (n=6; Relapse-MSCs). These profiles were compared to the gene expression profiles of 16 control-MSCs.

first: Elisabeth

last: Steeghs

first: Monique

last: den Boer


title: Epigenetic enhancer changes during oncogenic transformation

status: Public on Jul 11 2020

city: London

first: Paola

last: Scaffidi

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute


title: Circulating microRNA expression patterns and target prediction in sepsis development

city: Guangzhou

first: jiyou

last: yao

address: 1  Panfu Road

department: Department of HBP SURGERY I

institute: Guangzhou First People's Hospital, School of Medicine, South China University of Technology

summary:
To screen the circulating miRNAs which can be used to evaluate the diagnosis and prognosis of sepsis by gene microarray,and to predict its target gene and mechanism by bioinformatics analysis in sepsis.
To screen the circulating miRNAs which can be used to evaluate the diagnosis and prognosis of sepsis by gene microarray,and to predict its target gene and mechanism by bioinformatics analysis in sepsis.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: In this study, global microRNA (miRNA) expression profiling was performed for 3 sepsis patents, 3 septic shock patients and 3 normal controls’ plasma samples by microarray. MiRNA-targets were identified by integrating the miRNA expression profiles with mRNA expression profiles and bioinformatics analysis of the matched samples. At last, we used the miRanda and Targetscan target genes databases to predict target genes of miRNAs, also analyzed the pathway by the KEGG database.

first: C

last: Cai

first: J

last: Lv

last: Yao


title: Expression data from C6 glioma and small molecule induced glial cells (SMiG)

city: Seoul

first: Jinsoo

last: Oh

address: Yonsei-ro, Shinchon-dong, Seodaemoon-gu

department: Neurosurgery

institute: Yonsei University

summary:
Here we show that malignant glioma can be converted into benign glial cells through the combined action of small molecules.
Gene ontology related to myelination and glial differentiation were significantly up-regulated in SMiG.

overall_design: Our findings show the proof of concept that malignant gliomas can be reprogrammed to benign glial cells, using a combination treatment of small molecules, and their proliferation can be regulated by the differentiation.


title: Revisiting the putative role of heme as a trigger of inflammation

status: Public on Jul 10 2020

city: Zurich

first: Christian

middle: Andreas

last: Schaer

address: Raemistrasse 100

country: Switzerland

institute: University Hospital Zurich

overall_design: A two color common reference design was chosen with 4 independent biological replicates of each condition. Each experimental sample (Cy5 labeled) was hybridized against a non-treated reference sample (Cy3 labeled). To compensate for dye bias control arrays with competitively hybridized Cy3- and Cy5-labeled non-treated reference samples were used. The latter allowed for a very robust statistical analysis with pair-wise comparison of treatment array replicates versus the corresponding control array replicates.

first: Dominik


title: Ventricular T-box 5 in the adult heart ensures normal cardiac conduction and protects from pathologic cardiac remodeling

first: Franziska

last: Rathjens


title: Epigenetic enhancer changes during oncogenic transformation [ChIP-seq]

summary: Identification of differential enhancers active during oncogenic transformation, using FAIRE-seq and ChIP-seq for H3K4me1 and H3K27ac

overall_design: ChIP-seq analysis of biological replicates from SSEA1+ in vitro transformed human skin fibroblasts

first: M

last: Burney

first: P


title: Single cell reconstruction of human basal cell diversity in normal and IPF lung (single-cell RNAseq)

status: Public on Jul 09 2020

city: los angeles

first: Changfu

state: Ca

address: 8700 Beverly Blvd. AHSP Room A9401

department: Lung and Regenerative Medicine Institutes

institute: cedars-sinai medical center

summary: Declining lung function in patients with interstitial lung disease is accompanied by epithelial remodeling and progressive scarring of the gas-exchange region. There is a need to better understand the contribution of basal cell hyperplasia and associated mucosecretory dysfunction to the development of idiopathic pulmonary fibrosis (IPF). Single cell RNA sequencing was used to map epithelial cell types of the normal and IPF human airway. Organoid and ALI cultures were used to investigate functional properties of basal cell subtypes. We confirmed that Notch2 maintains undifferentiated basal cells and restrict basal-to-ciliated differentiation, and present evidence that Notch3 functions to restrain secretory differentiation. When characterizing single cell transcriptomes of the IPF lung we found a bias towards accumulation of the secretory primed basal cell subset.

overall_design: Single cell RNA-seq using 10x chromium system on  isolated epithelial cells (DAPI-,CD45-,CD31-,CD326+) from donor trachea, and IPF patients lung explant tissue. Due to the sample processing timing, samples are processed either v2 or v3 three prime mRNA kit. Similarly, sample was aligned either with cellranger 2 or cellranger 3. Thus in detail, sample dd09, ipf01, ipf02, ifp04, ifp07 and ipf1883 were processed using cellranger2, others are processed using cellranger3.For cc05, trachea, extralobar bronchi and dissected proximal intra-lobar bronchi with minimal connective distal tissue. TotalSeq-A human hashing antibodies (BioLegend,  394605 and 394607) are used to label cells from trachea, extralobar bronchi (TotalSeq-A0253, 394605) and proximal intra-lobar bronchi (TotalSeq-A0254, 394607) followed standard protocol.

first: Gianni

last: Carraro

first: Barry

last: Stripp


title: Human basal cell diversity in normal and IPF lung


title: Dysregulation of PDGFRB contributes to the pathogenesis of  LMNA-related dilated cardiomyopathy

status: Public on Jul 17 2020

city: Stanford

first: Joseph

last: Wu

state: Carlifornia

address: Stanford University School of Medicine

institute: Stanford University School of Medicine

summary:
Purpose: LMNA-DCM accounts for 5-10% of DCM cases and has an age-related penetrance whose onset typically appears between the ages of 30 and 40. However, the precise mechanisms linking the LMNA mutation to increased arrhythmogenicity are still unknown.
Methods: We utilized human iPSC-CMs, hESC-CMs, and cardiac tissues with RNA-seq, ChIP-seq, and ATAC-seq technologies.
Results: The electrophysiological studies of iPSC-CMs identify the LMNA mutation as a cause of increased arrhythmogenicity in mutant iPSC-CMs through abnormal calcium homeostasis. We find that the mutations in LMNA disrupt the global chromatin conformation, resulting in hyper-activation of the platelet-derived growth factor (PDGF) signaling pathway in LMNA-mutant iPSC-CMs. Inhibition of the PDGF signaling pathway can rescue the arrhythmic phenotype of mutant iPSC-CMs.
Conclusions: These findings were corroborated in cardiac tissues from healthy and LMNA-DCM patients, thus confirming a novel mechanism of LMNA-DCM pathogenesis both in vitro and in vivo.

overall_design: RNA-seq, ChIP-seq, and ATAC-seq of iPSC-CMs and hESC-CMs

first: Jaecheol

last: Lee

first: Vittavat

last: Termglinchan

first: Ning-Yi

last: Shao


title: Seasoning ingredients in a medium fat diet regulate lipid metabolism [Liver]

status: Public on Jul 07 2020

city: Bunkyo-ku

first: Tomiko

last: Asakura

department: Applied Biological Chemistry Graduate School of Agricultural and Life Sciences

institute: The University of Tokyo

summary:
Despite a variety of seasoning ingredients in diets, little is known about their cooperative effect on animal metabolism. We fed rats a diet containing 30 wt.% instant noodle with a 26% fat-to-energy ratio for 30 days (N-group). Compared with rats that were fed the same diet without seasonings (C-group), the N-group showed lower liver triacylglycerol levels and higher fecal cholesterol levels. To assess the mechanisms underlying this phenotype, we conducted transcriptome analyses of the hypothalamic–pituitary axis (HP), liver and white adipose tissue (WAT).
Our results suggest that these ingredients may affect lipid homeostasis via the HP axis.

overall_design: We fed rats a diet containing 30 wt.% instant noodle with a 26% fat-to-energy ratio for 30 days (N-group). For the control group, we used rats that were fed the same diet without seasonings (C-group), and the mRNA expression in the Liver was compared between the two groups.

first: Mitsuru

last: Tanaka

first: Akihito

last: Yasuoka

first: Haruka

last: Yoshinuma

first: Yoshikazu

last: Saito

first: Soichi

last: Tanabe


title: Seasoning ingredients in a medium fat diet regulate lipid metabolism [WAT]

overall_design: We fed rats a diet containing 30 wt.% instant noodle with a 26% fat-to-energy ratio for 30 days (N-group). For the control group, we used rats that were fed the same diet without seasonings (C-group), and the mRNA expression in the white adipose tissue was compared between the two groups.


title: Oral administration of vanillin improves imiquimod-induced psoriatic skin inflammation in mice: the involvement of interleukin-23/interleukin-17 axis

city: Taichung

first: Chien-Yun

last: Hsiang

address: 91 Hsueh-Shih Road

institute: China Medical University

summary: Vanillin is one of the most widely used flavouring products worldwide. Psoriasis is a chronic inflammatory skin disorder. Here we analyzed the effect of vanillin on imiquimod (IMQ)-induced psoriatic skin inflammation in mice.

overall_design: Mice were treated topically with IMQ and/or orally with 100 mg/kg vanillin for 7 consecutive days. RNA was extracted from skin tissues. The gene expression profiles were further analyzed by microarray.


title: Seasoning ingredients in a medium fat diet regulate lipid metabolism [hypothalamus]

overall_design: We fed rats a diet containing 30 wt.% instant noodle with a 26% fat-to-energy ratio for 30 days (N-group). For the control group, we used rats that were fed the same diet without seasonings (C-group), and the mRNA expression in the hypothalamus was compared between the two groups.


title: Human basal cell diversity in normal and IPF lung (bulk RNAseq)

last: Yao

summary: Declining lung function in patients with interstitial lung disease is accompanied by epithelial remodeling and progressive scarring of the gas-exchange region. There is a need to better understand the contribution of basal cell hyperplasia and associated mucosecretory dysfunction to the development of idiopathic pulmonary fibrosis (IPF).We confirmed that Notch2 maintains undifferentiated basal cells and restrict basal-to-ciliated differentiation, and present evidence that Notch3 functions to restrain secretory differentiation. When characterizing single cell transcriptomes of the IPF lung we found a bias towards accumulation of the secretory primed basal cell subset.

overall_design: We isolated basal cells from donor trachea based on expression of NGFR, then further  subset based on expression of CD66 into CD66 possitive and negative. We also put these two group of cells into organoid culture, then further subset  cells from these organoids for bulk RNAseq. 3 replicates per group.


title: Seasoning ingredients in a medium fat diet regulate lipid metabolism

overall_design: Refer to individual Series


title: Wound healing related cells: Control vs. SE-14000 stimulation

city: Tokyo

first: noriko

middle: muto

last: matsumoto

address: 1-1-5 Sendagi, Bunkyo-ku

department: Department of Plastic, Reconstructive and Regenerative Surgery

institute: Nippon Medical School

summary: Transcriptional profiling of SE-14000 stimulated wound healing associated cells (HaCat, NHDF, HMEC-1) comparing control untreated cells. Goal was to determine the effects of SE-14000 to the wound healing associated cells (HaCat, NHDF, HMEC-1).

overall_design: Two-condition experiment, Control vs. SE-14000 stimulated cells. Biological replicates 3 control cells, 3 stimulatred cells.

first: Masayo

last: Aoki

first: Noriko

last: Matsumoto


title: DNA hypomethylation confers enhanced immunity against parasitic nematodes in plants

city: Ghent

first: Jeroen

last: Galle

address: Coupure Links 653

department: Dept. Of Mathematical Modelling, Statistics and Bioinformatics

country: Belgium

institute: Ghent University

summary:
Background: Epigenetic processes play an important role in the plant response to adverse environmental conditions. A role for DNA hypomethylation has recently been suggested in the pathogenic interaction between bacteria and plants, yet it remains unclear whether this phenomenon reflects a conserved and general plant immunity response. We therefore investigated the role of DNA methylation in the plant defence against damaging parasitic nematodes.
Methods and results: Treatment of roots of rice (monocot plant) and tomato (dicot plant) by a nematode-associated molecular pattern (NAMP) from different parasitic nematodes revealed global DNA hypomethylation using ELISA based quantification, suggesting conservation among plants. Focusing on root-knot induced gall tissue in rice, the causal impact of hypomethylation on immunity was revealed by a significantly reduced plant susceptibility upon 5-Azacitidine treatment. Whole genome bisulfite sequencing revealed that hypomethylation was massively present in the CHH context, while absent for CpG or CHG nucleotide contexts. CHH hypomethylated regions were predominantly associated with gene promoter regions, which was not correlated with activated gene expression at the same time point, but rather showed a delayed effect on transcriptional gene activation. Finally, the relevance of CHH hypomethylation in plant defence was confirmed in rice mutants of the RNA-directed DNA methylation pathway (RdDM) and DDM1, which are known to be steering DNA methylation in CHH context.
Conclusions: We demonstrated that DNA hypomethylation confers enhanced defence in rice towards root-parasitic nematodes and is likely to be part of the basal NAMP-triggered immunity response in plants.

overall_design: Rice plants (Oryza sativa L. cv. Nipponbare) were infected with Meloidogyne graminicola. Three replicates were made per condition (non-infected and infected). Each sample was multiplexed in four subsamples.

first: Mohammad

last: Reza Atighi

first: Bruno

last: Verstraeten

first: Tim

last: De Meyer

first: Tina

last: Kyndt


title: Expression data of mesenchymal stromal cells after 40 hours of co-culture with primary B-cell precursor acute lymphoblastic leukemia cells

first: Judith

last: Boer

summary: B-cell precursor acute lymphoblastic leukemia (BCP-ALL) cells reside in the bone marrow microenvironment, where they are protected against chemotherapeutic agents. Mesenchymal stromal cells (MSCs) are key components of this supporting framework. The present study aimed to unravel whether MSCs derived from pediatric BCP-ALL patients (leukemic MSCs) differ from MSCs derived from healthy pediatric donors (control-MSCs). Therefore, we studied their gene expression profiles after 40 hours of co-culture with primary B-cell precursor acute lymphoblastic leukemia cells. MSCs were sorted using fluorescence-activated cell sorting (FACS).

overall_design: Six different primary mesenchymal stromal cells (MSCs) were cultured for 40 hours in the presence of primary B-cell precursor acute lymphoblastic leukemia cells (derived from 4 different pediatric BCP-ALL patients). Mesenchymal stromal cells were sorted from B-cell precursor acute lymphoblastic leukemia cells using a fluorescence-activated cell sorter (FACS). Microarray analyses were performed on these sorted MSCs. Limma analyses were performed to identify differentially expressed probesets in MSCs upon co-culture with BCP-ALL cells compared to mono-cultures of these MSCs. One sample was lost due to poor RNA quality.

first: Elisabeth

last: Steeghs

first: Monique

last: den Boer


title: Comparative transcriptomics in the Drosophila Auditory Organ

status: Public on Jul 05 2020

city: Leuven

first: Stein

last: Aerts

address: Herestraat 49

department: Center for Human Genetics

institute: KULeuven

summary: We use closely-related Drosophila species to understand mechanosensation and how hearing as a form of mechanosensation drives reproductive isolation and evolution. In particular, we performed RNA-seq to obtain the Johnston's Organ transcriptomes of six closely-related Drosophila species, namely, D.melanogaster, D.yakuba, D.pseudoobscura and D.persimilis.  Application of the Ornstein-Uhlenbeck model identified gene expression changes between the species' auditory structures. Motif discovery ( i-cisTarget and iRegulon) in differentially expressed genes in the oobscura group and melanogaster group on these transcriptomes identified thetranscription factor Hr39 as important for auditory differences among species. Hr39 is a nuclear hormone receptor important in song production and spermathecae development. Futher functional analyses Hr39 and many of its downstream targets are expressed in Johnston's Organ neurons. Hr39 mutants show sexually dimorphic defects in auditory mechanics and compound action potentials. These results indicate that Hr39 and its downstream regulon have a key role in Drosophila courtship behavior as a mechanism of reproductive isolation and evolution.

sample_organism:
Drosophila melanogaster
Drosophila persimilis
Drosophila pseudoobscura
Drosophila simulans
Drosophila yakuba

overall_design: RNA-seq in the Johnston's Organ of five Drosophila species, namely D.melanogaster, D.yakuba, D.pseudoobscura, D.simulans and D.persimilis.

first: Ryan

last: Kavlie

first: Marina

middle: N

last: Sanchez

first: Xiao

last: He

first: Gert

last: Hulselmans

first: Joerg

middle: T

last: Albert


title: Transcriptome profiling of breast cancer cells MDA-MB-231 overexpressing PD-L1 protein

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

summary: Effect of PD-L1 overexpression in MDA-MB-231 breast cancer cells

overall_design: Comparisons of genes regulated by human PD-L1 in MDA-MB-231 breast cancer cells

last: Quesnel


title: Expression data of two single colony (No.4 and No.8) derived from C6 glioma

first: Jinsoo

last: Oh

summary: The top 10 most-expressed genes in colony No. 8 were prkcb, postn, mpz, cd55, ct55, plxdc2, antxr1, fmr1nb, igfbp5

overall_design: Here we show that gene expression profiling of each single colony (No.4 and No.8) from C6 glioma is difference.


title: Association of microRNA-618 Expression With Altered Frequency and Activation of Plasmacytoid Dendritic Cells in Patients With Systemic Sclerosis

city: Verona

first: Marzia

last: Rossato

address: Strada Le Grazie 15

department: Biotechnology

institute: University of Verona

summary:
To identify potential dysregulation of miRNA expression in plasmacytoid dendritic cells from Systemic Sclerosis patients (SSc), miRNA profiling was performed in pDCs from healthy donors or patients with the most severe fibrotic cutaneous form of SSc, namely in dcSSc, with either disease duration shorter (edcSSc) or longer than two years (ldcSSc).
Plasmacytoid dendritic cells (pDCs) are a critical source of type I interferons (IFNs) that can contribute to the onset and maintenance of autoimmunity. Molecular mechanisms leading to pDC dysregulation and persistent type I IFN signature are largely unexplored, especially in systemic sclerosis (SSc), a disease in which pDCs infiltrate fibrotic skin lesions and produce higher levels of IFNa as compared to healthy controls. To investigate potential microRNA–mediated epigenetic mechanisms underlying pDC dysregulation and type I IFN production in SSc. microRNA expression profiling and validation was performed in highly purified pDCs obtained from the peripheral blood of 3 independent cohorts of healthy controls and SSc patients. Possible functions of miR-618 on pDC biology were identified by overexpression in healthy pDCs. miR-618 expression was upregulated in pDCs of SSc patients, including those in the early stage of disease onset and not presenting with skin fibrosis. IRF8, a crucial transcription factor for pDC development and activation, was identified as a target of miR-618. miR-618 overexpression reduced the development of pDCs from CD34+ cells in-vitro and enhanced their ability to secrete IFNα, mimicking the pDC phenotype observed in SSc patients. miR-618 upregulation suppresses pDC development and increases their ability to secrete IFNα, potentially contributing to the type I IFN signature observed in SSc patients. Considering the importance of pDCs in the pathogenesis of SSc and other diseases characterized by a type I IFN signature, miR-618 potentially represents an important epigenetic target to regulate immune system homeostasis in these conditions.

overall_design: BDCA-4+ pDC freshly isolated from pehripheral blood of 19 donors: 7 healthy (HC), 5 early diffuse cutaneous SSc patients (edcSSc) and 7 late diffuse cutaneous SSc patients (ldcSSc)

first: Timothy

last: Radstake


title: Transient expression of miRNA-203 strenghten stemness potential of pluripotent cells by modulating de novo DNA methylation

city: Madrid

first: Maria

last: Salazar

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Molecular Oncology

institute: CNIO

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


title: MiRNA expression data from TMZ-resistant GBM cell line

status: Public on Jul 04 2020

city: Nanjing

first: Yali

last: Zhou

address: 22 Hankou Road

institute: Nanjing University

summary:
Glioblastoma multiforme(GBM) is the most common and lethal malignant primary brain tumor. Temozolomide (TMZ) is a promising chemo-therapeutic agent to treat GBM. However, resistance to TMZ develops quickly with a high frequency. The mechanisms underlying GBM cells’ resistance to TMZ are not fully understood.
Non-coding RNAs are aberrantly expressed in many cancers and are highly involved in their pathogenesis including drug-resistence. In order to systematically study the role of miRNAs in GBM cells' resistence to TMZ , we built gene expression profiles of TMZ-resistant cell line and TMZ-sensitive cell line using miRNA gene expression microarrays.

overall_design: TMZ-resistant cell line and TMZ-sensitive cell line were used for RNA extraction and hybridization on microarrays. We sought to study the expression profiles of miRNA in GBM cell lines and to find potential core genes in the drug-resistance of this high malignant lethal disease.

first: Hao

last: Pan


title: MicroRNA-19a-PTEN axis is involved in the developmental decline of axon regenerative capacity in retinal ganglion cells

city: Hong Kong

first: Heather

middle: Kayew

last: Mak

address: 147K Argyle Street

department: Ophthalmology and Visual Sciences

institute: The Chinese University of Hong Kong

summary: Irreversible blindness from glaucoma and optic neuropathies is attributed to retinal ganglion cells (RGCs) losing the ability to regenerate axons. While several transcription factors and proteins have demonstrated enhancement of axon regeneration after optic nerve injury, mechanisms contributing to the age-related decline in axon regenerative capacity remains elusive. Here, we show that microRNAs are differentially expressed during RGC development, and identify microRNA-19a (miR-19a) as a heterochronic marker; developmental decline of miR-19a relieves suppression of PTEN, a key regulator of axon regeneration, and serves as a temporal indicator of decreasing axon regenerative capacity. Intravitreal injection of miR-19a promotes axon regeneration after optic nerve crush in adult mice, and increases axon extension in RGCs isolated from aged human donors. This uncovers a previously unrecognized involvement of the miR-19a-PTEN axis in RGC axon regeneration, and demonstrates therapeutic potential of microRNA-mediated restoration of axon regenerative capacity via intravitreal injection in patients with optic neuropathies.

overall_design: Freshly purified retinal ganglion cells (RGCs) from embryonic day 21 (E21), post-natal day 6 (P6), and post-natal day 30 (P30) Sprague Dawley rats using Neural Tissue Dissociation Kit Postnatal Neurons (Miltenyi Biotec, #130-094-802) and Retinal Ganglion Cell Isolation Kit (Miltenyi Biotec #130-096-209) were collected for detection of age-related changes in microRNA expression using microarray (SurePrint G3 Rat v16.0 miRNA Array Kit, Agilent). There were three biological replicates for E21 and P6 RGC samples each, and two biological replicates for P30 RGC samples. Expression values were extracted using Agilent Feature Extraction Software (v9.5.3.1) with the default protocols and settings for background subtraction and signal intensity processing. Non-uniform outliers were excluded. Data was further processed using GeneSpring GX Software (v11.5). The data set was normalized using a 75th percentile shift normalization method, and p-values were obtained using a moderated t-test with a Benjamini-Hochberg correction.

middle: K

first: Jasmine

last: Yung

first: Robert

last: Weinreb

first: Shuk Han

last: Ng

first: Xu

last: Cao

first: Tracy

middle: Y

last: Ho

first: Tsz Kin

first: Wai Kit

last: Chu

first: Wing-Ho

first: Kwong Wai

last: Choy

first: Chi-Chiu

last: Wang

first: Tin-Lap

last: Lee

first: Christopher

last: Leung


title: Systematic identification of Circular RNAs in pre-ovulatory ovarian follicles of goats

status: Public on Jul 03 2020

city: Wuhan

first: Hu

last: Tao

state: Hubei

address: Shizishan street

institute: Hubei Academy of Agricultural Sciences

summary: We deep sequenced and analyzed circRNA using deep RNA sequencing (RNA-seq) in pre-ovulatory follicle samples of Macheng black goats and Boer goats. We analyzed the RNA-seq data with 301 million reads and 288 million reads,  and reveal the expression profiles of circRNAs and predicted 13,950 circRNAs. 827 circRNA host genes, mostly related to transferase activity and metabolic process. Twenty-four circRNAs were upregulated and 13 were downregulated in the pre-ovulatory follicles of the Boer group compared to their expression in the Macheng group.

overall_design: Examination of circRNAs expression profile in pre-ovulatory follicle samples of Macheng black goats and Boer goats

first: Mingxin

last: Chen


title: Expression data from rat pituitary adenoma cells

first: Tang

last: Chao

address: 305 East Zhongshan Road, Nanjing,  China

institute: Jinling Hospital, School of Medicine, Nanjing University

summary:
Cabergoline (CAB) and bromocriptine (BRC) as first-line drug are recommended for treating patients with prolactinoma. Nonetheless, patients present with the differences of effective to CAB and BRC. The sensitivities of patients to the two drugs were different.
We used microarrays to detail the global programme of gene expression underlying in treatment of CAB and BRC, and identified distinct classes of up-regulated genes during this process.

overall_design: Rat pituitary adenoma cells  were treated with CAB and BRC for RNA extraction and high throughput sequencing on Affymetrix GeneChip® Rat Genome 230 2.0 Array . The  differential gene expression between the groups was analyzed. The groups as following：1. MMQ 2.MB (MMQ+BRC) 3.GH3 4.GC(GH3+CAB) 5.GB(GH3+BRC) 6.GCB(GH3+BRC+CAB) 7.MC(MMQ+CAB) 8.MCB(MMQ+CAB+BRC)

first: Chiyuan

last: Ma

first: Chao

last: Tang

first: Pengping

last: Li

first: Guodao

last: Wen

first: Chunyu

last: Zhong


title: Polaprezinc inhibits liver fibrosis and proliferation in hepatocellular carcinoma

status: Public on Jul 01 2020

city: hangzhou

first: jingjing

last: wang

address: WENYI  WEST road

summary: Hepatic fibrosis is defined as a pathological process, and activation of hepatic stellate cells (HSCs) is believed to be the key event of liver fibrosis. Additionally, activated HSCs may participate in the formation of the tumor microenvironment. Polaprezinc, a protector of the gastric mucosa, has been recently demonstrated to be an inhibitor of liver fibrosis in a mouse model.Proliferation and colony formation assays were performed to determinethe inhibitory effects of polaprezinc on the growth of LX-2 and hepG2 cells. A migration assay was used to evaluate the change in mobility of LX-2 cells and quantitative polymerase chain reactionwas performed to detect the expression levels of key markers of fibrosis. Finally, a gene chip assay for polaprezinc-treated hepG2 cells was performed to evaluate the effectof polaprezinc on the hepG2 gene expression profile.The proliferation assay indicated that polaprezinc  may inhibit the LX-2 cell proliferation and the migration assays confirmed the inhibition of mobility. The expression levels of fibrotic markers such as collagen I, fibronectin and α-smooth muscle actinweredownregulated followingpolaprezinc treatment. The proliferation activity of polaprezinc-treated hepG2 cells was reduced and the gene chip assay indicated that series of gene expression changes associated with cancer migration, cell skeletal organization and proliferation had occurred.In conclusion, polaprezinc treatment mayinhibit the proliferation of hepatocellular carcinoma cells and reverse liver fibrosis by deactivating HSCs. The present findings suggest that polaprezinc provides a novel treatment for patients with gastritis complicated with cirrhosis

overall_design: one sample was treatment with polaprezinc at 0 µg/ml ，and another was  treatment with polaprezinc at 16  µg/ml. The two samples were detected by Phalanx Human OneArray(®) Annotation HOA v7 release 1.0 with 31,741 mRNA probes and 20,672 genes in the  human genome

first: JUN

last: YE

first: ZHENGSEN

last: ZHANG


title: LncRNA and mRNA expression data from human glioblastoma multiforme

status: Public on Jun 30 2020

first: Yali

last: Zhou

summary:
Glioblastoma multiforme(GBM) is the most common and lethal malignant primary brain tumor. Long non-coding RNAs (lncRNAs) are aberrantly expressed in many cancers and are involved in their cell proliferation, apoptosis, angiogenesis, and invasion.
To systematically study the role of lncRNAs in GBM, we built gene expression profiles of GBM and non-tumor tissues using lncRNA and mRNA gene expression microarrays.

overall_design: GBM and non-tumor tissues were selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to study the expression profiles of lncRNA and mRNA in GBM and to find potential core genes in the pathogenesis of this high malignant lethal disease.


title: Comparison of sRNA populations obtained using HD or standard Illumina adapters in A thaliana, with or without TAP treatment

city: Norwich

first: Tamas

last: Dalmay

address: Earlham Road

department: School of Biological Sciences

institute: University of East Anglia

summary: The sRNA population (sequence identity and distribution of abundances) in A thaliana was assessed using High Definition (HD) [Sorefan et al 2012, Xu et al 2015] or standard Illumina adapters; the usage of HD adapters revealed a more diverse population of sRNAs (in particular, it revealed the presence of more unique 24mers)

overall_design: sRNA libraries from A thaliana leafs were created using HD and standard Illumina adapters, with or without a TAP treatment; the resulting libraries were compared side by side.

first: Ping

last: Xu

first: Irina

last: Mohorianu

first: Rachel

middle: R

last: Pilcher


title: Transcriptome analysis for human lung microvascular endothelial cells

city: Oralndo

first: Junko

last: Sawada

state: Florida

address: 6400 Sanger Rd

institute: SBP Discovery MRI

summary: RNA-seq was performed for the human lung microvascular endothelial cells (HMVEC-L)

overall_design: RNA was isolated from HUVEC-L, after podoplanin positive cells were removed by using FACS sorter. RNA- seq was performed to analyze transcriptome in HMVEC-L.

first: Masanobu

last: Komatsu


title: Transcriptional Sequencing of Epicardium-Derived Cells from the Mouse Embryo

status: Public on Jun 27 2020

city: Rochester

first: Eric

last: Small

state: NY

address: 601 Elmwood Avenue, Box CVRI

institute: University of Rochester

summary: The goal of this study was to perform transcriptional profiling of epicardium-derived cells, compared to non epicardium-derived cells, obtained from the  embryonic heart, to interrogate transcriptional mechanisms that control epithelial to mesenchymal transition.

overall_design: RNA sequencing was performed on epicardium-derived cells and non-epicardium derived cells isolated from E12.5 embryonic heart explants that were  transduced with  adenoviruss to delete MRTFA and MRTF B or SRF, with relevant controls as indicated below.

middle: M

first: Michael

last: Trembley


title: Whole genome expression profiling of Arabidopsis thaliana Di19 mutant vis-à-vis wild-type

status: Public on Jun 29 2020

city: New Delhi

first: Jitendra

middle: Paul

last: Khurana

address: Benito Juarez Road

department: Department of Plant Molecular Biology

country: India

institute: University of Delhi South Campus

summary: The Arabidopsis T-DNA insertion mutant of Di19-3 (SALK_072390) showed involvement in various physiological responses like photomorphogenesis, lateral rootgrowth and development. We identified that Di19 is also involved in auxin and ethylene mediated responses. Therefore, to identify the downstream pathways affected in the Di19 mutant, we performed transcriptome profiling of mutant vs wild type using Affymetrix microarray platform.

overall_design: Ten days old Arabidopsis seedlings for each genotype were grown on 1/2MS medium and 100 mg tissue was harvested, snap frozen in liquid nitrogen. Total RNA was isolated and hybridized on Arabidopsis GeneChips with two replicates for each genotype. Microarray using Affymetrix platform was performed for total of four samples, two for wild type and two for mutant.

first: Susmita

last: Maitra Majee

first: Brinderjeet

last: Singh


title: Analysis of the effect of androgen and androgen receptor on gene expression in CRPC model cell

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

institute: Tokyo Metropolitan Institute of Gerontology

summary: Androgen receptor (AR) belongs to a nuclear receptor superfamily and functions as a ligand-dependent transcription factor. AR-regulated transcriptional program is associated with various diseases, especially prostate cancer. Suppression of AR is an effective therapy for AR-dependent prostate cancer. However, in most of the cases it relapses as castration-resistant prostate cancer (CRPC), acquiring resistance to hormone therapy. We investigated the effect of androgen treatment and AR knockdown on gene expression by RNA-seq using CRPC model cells.

overall_design: We treated CRPC model cells with dihydrotestosterone (DHT) or vehicle (ethanol) and siRNA targeting AR or drug (ribavirin: R).


title: Gene expression signatures in anoikis-resistance of human prostate PC-3 cells

status: Public on Jun 26 2020

first: Peng

last: Zhang

address: 1277 Jiefang Ave.

department: Urology

country: China

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

summary: To investigate potential molecular targets that regulate metastasis and metabolism in anoikis-resistance of prostate cancer cells, we have establised anoikis-resistant prostate PC-3 cells with ultra-low attachment 6-well plates (Corning) and employed whole genome microarray expression profiling as a discovery platform to identify differentially expressed genes between anoikis-resistant PC-3 cells and corresponding parental cells.

overall_design: Prostate cancer PC-3 cells were continuously suspension cultured in ultra-low attachment 6-well plates for 7 days then transferred into normal plates with attachment culture for 2 days, and the re-adherent cells were regarded as anoikis-resistant. Three independent experiments were performed. Total RNA samples extracted from three independent anoikis-resistant cell samples and corresponding parental samples were applied for genome microarray expression profiling.

first: Yarong

last: Song

first: Xuechao

last: Li

first: Lifeng

last: Chen

first: Yadong

last: Sun

first: Yifei

last: Xing


title: Binding of guide piRNA triggers methylation of the unstructured N-terminal region of Aub leading to assembly of the piRNA amplification complex

status: Public on Jun 25 2020

city: pasadena

first: xiawei

last: huang

state: CALIFORNIA

address: 1200 E California Blvd

institute: caltech

summary: In Drosophila, Piwi proteins use guide piRNAs to repress selfish genomic elements, protecting the genomic integrity of gametes and ensuring the fertility of animal species. Efficient transposon repression depends on amplification of piRNA guides in the ping-pong cycle, which in Drosophila entails tight cooperation between two Piwi proteins, Aub and Ago3. Here we show that post-translational modification, symmetric dimethylarginine (sDMA), of Aub is essential for piRNA biogenesis, transposon silencing and fertility. Methylation is triggered by loading of a piRNA guide into Aub, which exposes its unstructured N-terminal region to the PRMT5 methylosome complex. Thus, sDMA modification is a signal that Aub is loaded with piRNA guide. Amplification of piRNA in the ping-pong cycle requires assembly of a tertiary complex scaffolded by Krimper, which simultaneously binds the N-terminal regions of Aub and Ago3. To promote generation of new piRNA, Krimp uses its two Tudor domains to bind Aub and Ago3 in opposite modification and piRNA-loading states. Our results reveal essential functions of post-translational modifications in unstructured regions of Piwi proteins and of Tudor domains capable of discriminating between modification states in piRNA biogenesis and silencing.

overall_design: Small RNA isolated from GFP-wtAub and GFP-mdAub in wt ovaries. Total small RNA from heterozygous ovaries, GFP-wtAub rescue ovaries, GFP-mdAub rescue ovaries as well as aub[HN]/[QC] mutant ovaries

first: Xiawei

last: Huang

first: Ravi

last: Sachidanandam

first: Alexei

last: Aravin


title: Illumina Bead expression array data from Human B cells treated with miR-29 over expression

status: Public on Jun 24 2020

city: London

first: David

middle: Jonathan

last: Fear

address: 5th Floor, Tower Wing, Great Maze Pond

department: Respiratory Medicine and Allergy

institute: Kings College London

summary: Human Tonsillar B cells were isolated and transfected with miR-29 mimic molecules or transfection controls. B cells were subsequently cultured in class switching media for 24 hours and subjected to transcriptome analysis using the Illumina HumanHT-12 v4 Expression BeadChip array platform.  B cells derived from 3 donors are submitted.

overall_design: Total B  cells were isolated from discarded tonsillar tissue from 3 donors following routine tonsillectomy (following informed consent) and transfected (nucleofection) with miR-29 mimic molecules or transfection controls prior to cultured in the presence of IL-4 and anti-CD40 stimulation. After 24 hours culture total RNA extracted. RNA was then reverse transcribed, amplified and biotin labelled prior to profiling on Illumina Human HT-12 v4 expression arrays.


title: Histone marks in C. elegans IKB mutants

city: Barcelona

first: Lluis

last: Espinosa

state: Barcelona

address: Dr. Aiguader 88

department: Institut Municipal d'Investigacions Mèdiques, (IMIM)

institute: Hospital del Mar

summary: Our study focuses in undersatnding the chromatin-associated function of the c. elegans IKB homologues nfki-1 and ikb-1. We this objective, we have generated different worm mutant strains and then analyzed by ChIP-seq possible changes in H3K36me3 and H3K27me3 marks in the WT , nfki-1, ikb-1 and double c elegans mutants.

overall_design: ChIP with commercial antibodies followed  by sequencing

middle: E

last: Blay

first: Julian

last: Ceron


title: LncRNA and mRNA expression data from TMZ-resistant cell line

first: Yali

last: Zhou

summary:
Glioblastoma multiforme (GBM) is the most common and lethal malignant primary brain tumor. Temozolomide (TMZ) is a promising chemo-therapeutic agent to treat GBM. However, resistance to TMZ develops quickly with a high frequency. The mechanisms underlying GBM cells’ resistance to TMZ are not fully understood.
Long non-coding RNAs (lncRNAs) are aberrantly expressed in many cancers and are highly involved in their pathogenesis including drug-resistence. In order to systematically study the role of lncRNAs in GBM cells' resistence to TMZ , we built gene expression profiles of TMZ-resistant cell line and TMZ-sensitive cell line using lncRNA and mRNA gene expression microarrays.

overall_design: TMZ-resistant cell line and TMZ-sensitive cell line were used for RNA extraction and hybridization on microarrays. We sought to study the expression profiles of lncRNA and mRNA in GBM cell lines and to find potential core genes in the drug-resistance of this high malignant lethal disease.

first: Hao

last: Pan


title: MNase seq data of primary, immortalized and transformed mouse skin fibdroblasts from Ssrp1fl/fl;CreERT2 mice

status: Public on Jun 16 2020

city: Buffalo

first: Katerina

last: Gurova

address: Elm and Carlton Str

department: Cell Stress Biology

institute: Roswell Park Cancer Institute

summary: Nucleosome distribution was compared between primary, immortalized and transformed mouse skin fibdroblasts with and without FACT using conditional knockout of Ssrp1 subunit of FACT

overall_design: Primary cells were isolated from mouse tails and used between passage 3 and 4, immortalized cells were transduced with p53 dominant negative inhibitor GSE56, transformed cells were obtained from immortalized by transduction with mutant HRasV12 oncogene. All cells were treated with tamoxifen for 4 days and after that used for MNase seq library preparation.

first: Jianmin

last: Wang


title: MS2-TRIBE evaluates both protein-RNA interactions and nuclear organization of transcription by RNA editing

status: Public on Jun 20 2020

city: New York

first: Jeetayu

last: Biswas

address: 417 East 68th St

department: Molecular Pharmacology

institute: Memorial Sloan Kettering Cancer Center

summary: Nearly every step of RNA regulation is mediated by binding proteins (RBPs). The most common method to identify specific RBP target transcripts in vivo is by crosslinking (“CLIP” and its variants), which rely on protein-RNA crosslinking and specific antibodies. Another recently introduced method exploits RNA editing, with the hyperactive mutant catalytic domain of ADAR covalently attached to a specific RBP (“HyperTRIBE”). Both CLIP and TRIBE approaches suffer from difficulties in distinguishing real RNA targets from false negative and especially false positive signals.  To critically evaluate this problem, we used fibroblasts from a mouse where every endogenous β-actin mRNA molecule was tagged with the bacteriophage MS2 RNA stem loops in the β-actin 3’ UTR; hence there is only a single bona fide target mRNA for the MS2 capsid protein (MCP). CLIP and HyperTRIBE (hereafter referred to as TRIBE) could both detect the single RNA target, albeit with some false positives (transcripts lacking the MS2 stem loops). Consistent false positive CLIP signals could be attributed to nonspecific antibody interactions. However, to our surprise the putative false positive TRIBE targets correlated with the location of genes spatially proximal to the β-actin gene. This result indicates that MCP-ADAR bound to β-actin mRNA contacted and edited nearby nascent transcripts, as evidenced by frequent intronic editing. Importantly, nascent transcripts on nearby chromosomes were also edited, agreeing with the interchromosomal contacts observed in chromosome paint and Hi-C.  These results were repeated in human osteosarcoma cells with a randomly integrated and inducible MS2 reporter and indicated that MS2-TRIBE can be applied to a broad array of cells and transcripts. The identification of nascent RNA-RNA contacts imply that RNA-regulatory proteins such as splicing factors can associate with multiple nascent transcripts and thereby form domains of post-transcriptional activity, which increase their local concentrations. These results indicate that TRIBE combined with the MS2 system, MS2-TRIBE, is a new tool to study nuclear RNA organization and regulation.

overall_design: We identifying the targets of RNA binding proteins by fusing the proteins to an the RNA editing enzyme adenosine deaminase (RBP-ADAR). Targets are read out by RNA sequencing where two replicates are compared to an mCherry-ADAR control. By concentrating fusions to a genomic locus we are able to edit nascent RNAs from nearby transcribing loci.

first: Robert

middle: H

last: Singer


title: Transcriptome of the Wistar audiogenic rat (WAR) strain following audiogenic seizures

status: Public on Jun 13 2020

city: Belo Horizonte

first: Samara

last: Damasceno

state: MG

address: Avenida Antonio Carlos 6627

department: General Biology

country: Brazil

institute: Universidade Federal de Minas Gerais

summary: The Wistar Audiogenic Rat (WAR) is a model whose rats are predisposed to develop seizures following acoustic stimulation. We aimed to establish the transcriptional profile of the WAR model, searching for genes that help in understanding the molecular mechanisms involved in the predisposition and seizures expression of this strain. RNA-Seq of the corpora quadrigemina of WAR and Wistar rats subjected to acoustic stimulation revealed 64 genes differentially regulated in WAR. We validated twelve of these genes by qPCR in stimulated and naive (nonstimulated) WAR and Wistar rats. Among these, Acsm3 was upregulated in WAR in comparison with both control groups. In contrast, Gpr126 and Rtel1 were downregulated in naive and stimulated WAR rats in comparison with the Wistar controls. Qdpr was upregulated only in stimulated WAR rats that exhibited audiogenic seizures. Our data show that there are genes with differential intrinsic regulation in the WAR model and that seizures can alter gene regulation. We identified new genes that might be involved in the epileptic phenotype and comorbidities of the WAR model.

first: Nathália

last: Bustamante de Menezes

first: Cristiane

last: de Souza Rocha

first: Alexandre

last: Berenguer de Matos

first: André

middle: S

last: Vieira

first: Márcio

middle: F

last: Dutra Moraes

first: Almir

last: Martins

first: Iscia

last: Lopes-Cendes

first: Ana

middle: L

last: Brunialti Godard


title: RNA expression profile comparison of HFKs expressing E6/E7 from beta-3 HPVs (49, 75, 76, 115) and from HR alpha HPV16 and beta-2 HPV38

city: LYON

first: Alexis

last: Robitaille

state: Rhône-Alpes

address: 150 Cours Albert Thomas

department: Section of Infections

institute: International Agency for Research on Cancer (IARC)

summary: Comparative analysis of RNA expression profiles of keratinocytes expressing E6/E7 from the different beta-3, with the RNA profiles of HPV16 and HPV38 E6/E7 HFKs reveals that HPV115 is the more divergent from the HR-mucosal type. Moreover beta-3 HPV 49, 75 and 76 E6/E7 HFKs show altered expression of genes involved in cell cycle regulation and DNA damage response which are also deregulated by expression of E6/E7 of HPV16.

overall_design: Total RNA obtained from Human Foreskin Keratinocytes (HFKs) expressing E6/E7 from 6 different HPV types (49, 75, 76, 115, 16, 38) compared to 2 controls (HFK and empty vector).

first: Rosita

last: Accardi-Gheit

first: Massimo

last: Tommasino

first: Lucia

last: Minoni

first: Florence

last: Le Calvez-Kelm


title: SREBF1 coordinates with master transcription factors in regulating lipid metabolism and cancer-promoting pathways in squamous cell carcinoma

status: Public on Jun 15 2020

city: Los Angeles

first: Qian

last: Yang

state: CA

address: 8700 Beverly Blvd

department: Department of Surgery

institute: CEDARS SINAI MEDICAL CENTER

summary: We profiled esophageal squamous cell carcinorma (ESCC) cell lines with chromatin immunoprecipitation sequencing (ChIP-Seq). Mathematically modeling was performed to establish (super)-enhancers landscapes and inter-connected transcriptional circuitry formed by master TFs. Coregulation and cooperation between master TFs was investigated by ChIP-Seq, RNASeq, 4C-Seq and luciferase assay. Biological functions of candidate factors were evaluated by measuring cell proliferation, colony formation, cell apoptosis and xenograft growth. Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. Here, we aim to compare of ESCC cells knock down SREBF1 with siRNA and negative control transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis. We also report the application of circular chromatin conformation capture (4C) sequencing technology for studying master transcription factor (SREBF1) in human ESCC cancer cell lines (TE5).

overall_design: Esophageal Squamous cell carcinomas cell lines were harvested, and ChIPseq was performed using transcription factor antibodies. KYSE150 and TE5 cells knock-down SREBF1 with siRNA and negative control were generated by deep sequencing, using Illumina GAIIx. 4C sequencing analysis in espohageal squamous cell carcinomas cell line.

first: Liyan

last: Li

first: Yanyi

last: Jiang

first: Wei

first: Yuan

first: Masaharu

last: Hazawa

first: Bo

last: Zhou

first: Xiang

first: Sigal

last: Gery

first: Lingwen

last: Ding

first: Allen

last: Ho

first: Zachary

last: Zumsteg

first: Mingrong

last: Wang

first: Yanbing

first: Stephen

middle: J

last: Freedland

last: Xu

first: Enmin

first: H

middle: P

last: Koeffler

first: Dechen

last: Lin


title: Changes in the transcriptome, proteome and phosphoproteome in a cardiomyocyte model of nitroxidative stress

status: Public on Jun 22 2020

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

summary:
Cells adapt to stress via changes in gene expression, protein degradation and PTMs. However, compared to regulations via PTMs and protein turnover, gene expression is a relatively slow process.
We used a multi-omic approach to investigate different dynamics of transcripts, proteins and phosphoproteins during nitroxidative stress.

overall_design: This study was performed in biological triplicates for rat cardiomyocytes

first: Eva

last: Griesser

first: Julia

last: Rauch

first: Marie

last: Narzt

first: Florian

last: Gruber

first: Ralf

last: Hoffmann

first: Maria

last: Fedorova


title: Muscle and blood RNA-seq in mdx and wt mice

city: Leiden

first: Pietro

last: Spitali

state: Zuid Holland

address: Postzone S4-P, Albinusdreef 2

department: Human Genetics

institute: Leiden University Medical Center

summary: RNAseq data from blood and muscle was obtained to study the association of blood markers with disease progressionin mdx mice and to study the association between muscle and blood gene expression

overall_design: Longitudinal design

first: Annemieke

last: Aartsma-Rus


title: BMP2 Signaling Activation Enhances Bone Metastases of Non-small-cell Lung Cancer

city: Fuzhou

first: Fei

last: Huang

address: No 20 Chazhong Road

institute: First Affiliated Hospital, Fujian Medical University

summary: Bone metastasis is one of the most frequent metastases of NSCLC and leads to poor prognosis. It has been reported that high expression of BMP2 in NSCLC indicates poor survival, but whether BMP2 contributes to NSCLC bone metastasis remains largely unknown.

overall_design: We injected the Lewis lung carcinoma cells (LLCs) into tail veins of C57/BL6 mice, resulting in lung metastases and bone metastases. RNA-seq was carried for bone metastasis tissues, lung metastasis tissues and parental Lewis lung cells to analyze the transcriptome differences.

first: Yaqiang

last: Cao