title: Genomic profiles of ultraviolet-induced 6-4PP susceptibilities and potential new roles in melanoma development

status: Public on Dec 31 2020

city: Stanford

first: Brian

last: Perez

state: California

address: Gilbert Biology Building, 371 Serra Mall

department: Biology

country: USA

institute: Stanford University

summary: In this study we generated a genome map of 6-4PP lesion abundance in primary cells and conducted a comprehensive analysis to determine the epigenetic and genomic factors regulating 6-4PP susceptibility across the genome. We found that 6-4PP distribution across the genome is very similar to CPD, highest in heterochromatin regions near the nuclear periphery. Interestingly, we identified regions more susceptible to 6-4PP, but not CPD, located in bivalent and polycomb repressed chromatin states found closer to the center of the nucleus. Genes and enhancers in regions with the highest 6-4PP susceptibility are more mutated and have lower repair activity. However, these differences were not observed for genes located in regions more susceptible to 6-4PP and not CPD. Functional analysis of genes in these regions are involved in essential cellular processes required for cell growth and proteins localized to the cell membrane. This study reveals new insights into the genomic factors regulating 6-4PP susceptibility and suggest a novel role for 6-4PP lesions in skin cancer development.

overall_design: IP of 6-4PP lesions, followed by in-vitro repair and next-generation sequencing.


title: Small-hairpin RNAs cause target-independent microRNA dysregulation in neurons and elicit global transcriptomic changes (miRNA-seq)

city: Ann Arbor

first: Michigan

middle: CDB

last: Bioinformatics

state: MI

address: 109 Zina Pitcher Pl

department: Cell & Developmental Biology

institute: University of Michigan

type: Non-coding RNA profiling by high throughput sequencing

summary: Small RNA was isolated from neuronal cultures transduced with different shRNA constructs direct against shNogoA with and without mismatches in the seed region

overall_design: 4 replicates each of empty vector, shRNA, shRNA with 2 point mutation, shRNA with 5 point mutation

first: Rafi

last: Kohen

first: Craig

middle: N

last: Johnson

first: Roman

last: Giger


title: Tissue-resident PSGL1loCD4+ T cells promote B cell differentiation and chronic graft-versus-host-disease-associated autoimmunity

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

type: Expression profiling by high throughput sequencing

summary: We report application of RNA-seqencing to investigate PSGL1hi and PSGL1lo CD4+T cells transcriptional difference in the GVHD target tissues of spleen, liver and lung at day 30 after HCT.

overall_design: RNA profile of PSGL1lo and PSGL1hi CD4+ T cells in the spleen, liver and lung of cGVHD and GVHD-free mice.

first: Defu

last: Zeng

first: Xiaohui

last: Kong


title: Transcriptional profile of T, ITNK and NK cells

city: Guangzhou

first: zhiwu

last: jiang

address: 190 Kai Yuan Avenue, Science Park

country: China

institute: GIBH

summary: To further characterize the global gene expression profiles of ITNKs, we conducted RNA-sequencing analysis of T cells, ITNKs (CD3+NKp46+) and NK cells (CD3-CD56+) (both the CB and the PBMC origins with > 90% purity) from the CB and PBMC . Principal component analysis (PCA) and unsupervised hierarchical cluster analysis revealed that ITNKs had transcriptomic features of both T cells and NK cells

overall_design: mRNA from sorted T, ITNK and NK cells was prepared according to the TruSeqTM RNA Sample Preparation Guide, and sequencing was performed on a BGISEQ-500

first: Zhiwu

last: Jiang

first: Peng

last: Li


title: Myeloid-derived suppressor cells promote epithelial ovarian cancer cell stemness by inducing the CSF2/p-STAT3 signalling pathway

city: Shanghai

first: Xiaoqing

last: Guo

address: 2699 west gaoke road

department: Obstetrics and Gynecology

institute: Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine

summary: Myeloid-derived suppressor cells (MDSCs) are known to contribute to tumour immune escape, studies have verified that MDSCs can induce cancer stem cells (CSCs) and promote tumour immune evasion in breast cancers, cervical cancers and glioblastoma. However, the potential function of MDSCs in regulating CSCs in epithelial ovarian cancer (EOC) progression is unknown. Our results indicated that compared to nonmalignant ovarian patients, EOC patients showed a significantly increased proportion of MDSCs in the peripheral blood. In addition, MDSCs dramatically promoted tumour sphere formation, cell colony formation and CSC accumulation, and MDSCs enhanced the expression of the stemness biomarkers NANOG and c-MYC in EOC cells during co-culture. Moreover, the mechanisms by which MDSCs enhance EOC stemness were further explored, and 586 differentially expressed genes were found in EOC cells co-cultured with or without MDSCs; during co-culture, the expression level of colony stimulating factor 2 (CSF2) was significantly increased in EOC cells co-cultured with MDSCs. Furthermore, the depletion of CSF2 in EOC cells was successfully performed, the promotive effects of MDSCs on EOC cell stemness could be markedly reversed by downregulating CSF2 expression, p-STAT3 signalling pathway molecules were also altered, and the p-STAT3 inhibitor could markedly reverse the promotive effects of MDSCs on EOC cell stemness. In addition, the CSF2 expression level was correlated with EOC clinical staging. Therefore, MDSCs enhance the stemness of epithelial ovarian cancer cells by inducing the CSF2/p-STAT3 signalling pathway. Targeting MDSCs or CSF2 may be a reasonable strategy for enhancing the efficacy of conventional treatments.

overall_design: After 24 h co-culture with MDSCs, SKOV3 gene expression was different in the presence or absence of MDSCs

first: Li

last: Xiaofeng


title: Loss of Ikaros promotes oncogene independence in a model of Lmo2-induced T-cell acute lymphoblastic leukemia

city: Clayton

first: Nicholas

middle: C

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

country: Australia

institute: Monash University

summary: LMO2 is an oncogenic transcription factor that is frequently overexpressed due to chromosomal abnormalities in T-cell acute lymphoblastic leukemia (T-ALL). In transgenic mouse models, Lmo2 overexpression causes thymocyte self-renewal resulting in T-cell leukemia with long latency. However, the requirement for Lmo2 for leukemia maintenance is poorly understood. To study this, we developed a Tetracycline-regulated knock-in mouse model that reversibly expresses Lmo2 throughout the haematopoietic system. This led to a specific impairment of T-cell development and the development of self-renewing preleukemic stem cells (pre-LSCs) in the thymus, followed by the development of fully penetrant T-lymphoblastic leukemia resembling human T-ALL. In preleukemic mice, repression of Lmo2 overcame the LMO2-induced thymocyte developmental block, reversed Lmo2-induced gene expression changes and eliminated self-renewing pre-LSCs in vivo. In contrast, overt T-lymphoblastic leukemias arising in this model were either immature, Lmo2-dependent leukemias resembling human ETP-ALL, or mature leukemias which were Lmo2-independent. Genomic analyses identified frequent loss of tumour suppressor genes in Lmo2-independent T-ALLs. Deletion of one of these, Ikaros (Ikzf1), was sufficient to transform Lmo2-dependent tumours to Lmo2-independence. Together these results indicate an evolution of oncogene addiction in T-ALL and that loss of Ikaros can promote self-renewal of T-ALL lymphoblasts in the absence of initiating oncogenes.

overall_design: Lmo2-dependent, Evolving and Lmo2-independent T-ALL cells from recipient mice were subjected to RNA Seq before and after Dox activation. The study comprised of two LMO2 dependent T-ALL, three evolving and three LMO2 independent T-ALL samples before and after Dox activation.

first: Anh

last: Vo

first: Benjamin

middle: J

last: Shields

first: Matthew

middle: P

last: McCormack


title: Combination of drought and heat in soybean plants

city: Memphis

first: Soham

last: Sengupta

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

summary: Transcriptomic response of soybean plants subjected to drought, heat and their combination

overall_design: Soybean plants were subjected to a combination of drought and heat stress

first: Itay

last: Cohen

first: Sara

middle: I

last: Zandalinas

first: Rajeez

middle: K

last: Azad

first: Felix

middle: B

last: Fritschi

first: Ron

last: Mittler


title: Compared chromatin state of  T and INTK cells

type: Genome binding/occupancy profiling by high throughput sequencing

summary: KEGG analysis showed that peaks of open chromatin of NK signature associated genes were enriched in ITNK cells compared to T cells

overall_design: Examination of NK sigature genes locus  in T and ITNK cell types.


title: Small-hairpin RNAs cause target-independent microRNA dysregulation in neurons and elicit global transcriptomic changes

first: Michigan

last: Bioinformatics

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

overall_design: Refer to individual Series


title: Single cell transcriptomic analysis (10x Genomics) of mouse colon LP CD4+ Tcells cells isolated from mouse under different infection conditions [bulk RNA]

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: To determine the states that Teff actually adopt in frontline tissues in vivo, we applied single-cell transcriptome and chromatin analysis on colonic Teff cells, in germ-free or conventional mice, or after challenge with a range of Teff subset-biasing microbes. Subsets were marked by expression of interferon-signature or myeloid-specific transcripts, but transcriptome or chromatin structure could not resolve discrete Th clusters. At baseline or at different times of infection, transcripts encoding cytokines or proteins commonly used as Teff markers distributed in a polarized continuum, which was also functionally validated. Clones derived from single progenitors gave rise to both IFN-γ and IL17-producing cells. Most transcriptional variance was tied to the infecting agent, independent of the cytokines produced, and chromatin variance primarily reflected activity of AP1 and IRF transcription factor families, not the canonical subset master regulators T-bet, GATA3, RORγ.

overall_design: Single cells were sorted by flow cytometry for ultra low input RNAseq library preparation

first: Evgeny

last: Kiner

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: RNA-sequence analysis of mouse AAA samples obtained from wild type mice and PSGL-1-/- mice induced by DOCA plus salt or not

city: Beijng

first: Xianxian

last: Wu

address: 5 Panjiayuan Nanli Chaoyang District

institute: Institute of laboratory animal sciences, CAMS, PUMC

summary: We report the transcriptomic analysis of RNA-seq of abdominal aortas isolated from WT and PSGL-1-/- mice exposed to deoxycorticosterone acetate (DOCA) plus salt to uncover the mechanisms underlying the undefined role of PSGL-1 in abdominal aortic aneurysm (AAA)

overall_design: Comparison of mouse abdominal aortic samples obtained from WT mice in the absence and presence of DOCA plus sat, and PSGL-1-/- mice in the presence of DOCA plus salt


title: long noncoding RNAs expression in mature and immature dendritic cells-derived exosomes

city: Shenzhen

first: Guohua

last: Lai

state: Guangdong

address: NO.1333,Xinhu Road,Baoan District

institute: Shenzhen Hospital,Southern Medical University

summary: Dendritic cells release bioactive exosomes that are involved in immune regulation. Long non-coding RNAs (lncRNAs) have been demonstrated to be implicated in many immunoregulatory mechanisms. However, the roles of lncRNAs in dendritic cells-derived exosomes remain unknown. To investigate the roles of lncRNAs in mature and immature dendritic cells-derived exosomes and find specific lncRNAs with immunoregulatory function, this study showed the expression profiles of lncRNAs in bone marrow dendritic cells-derived exosomes from C57 mice.

overall_design: We compared lncRNA profiles in two kinds of exosomes derived from immature and mature bone marrow dendritic cells. There are three replicates in each group.

first: Jiachang

first: Renli

last: Zhao

first: Hongxun

last: Sang


title: RNA-Seq in Drosophila melanogaster S2 cells

city: Moscow

first: Nickolai

last: Tchurikov

address: 32, Vavilova str.

department: Department of Epigenetic Mechanisms of Gene Expression Regulation

country: Russia

institute: Engelhardt Institute of Molecular Biology

summary: RNA-Seq procedure was used for analysis of expression in S2 cells.

overall_design: Analysis of S2 gene expression levels by RNA-Seq. Two replicates non-stressed and two replicates of heatshock-stressed cells.

middle: A

first: Yuri

middle: V

last: Kravatsky

first: Olga

last: Kretova


title: Maintenance of cell fate by the Polycomb Group gene Sex combs extra enables a partial epithelial mesenchymal transition in Drosophila (Pol2 dataset)

city: Melbourne

first: Michael

middle: Joseph

last: Murray

state: VIC

address: Parkville

department: School of BioSciences

institute: University of Melbourne

summary: Epigenetic silencing by Polycomb group (PcG) complexes can promote epithelial-mesenchymal transition (EMT) and stemness and is associated with malignancy of solid cancers. Here we report a role for Drosophila PcG repression in a partial EMT event that occurs during wing disc eversion, an early event during metamorphosis. In a screen for EMT genes required for eversion we identified the PcG genes Sex combs extra (Sce) and Sex combs midleg (Scm). Depletion of Sce or Scm resulted in internalised wings and thoracic clefts, and loss of Sce inhibited the EMT of the peripodial epithelium and basement membrane breakdown, ex vivo. Targeted DamID (TaDa) using Dam-Pol II showed that Sce knockdown caused a genomic transcriptional response consistent with maintenance of an epithelial fate. Surprisingly only 17 genes were significantly upregulated in Sce-depleted cells, including Abd-B, abd-A, caudal, and nubbin. Each of these loci were enriched for Dam-Pc binding.  Of the four genes, only Abd-B was robustly upregulated in cells lacking Sce expression. RNAi knockdown of all four genes could partly suppress the Sce RNAi eversion phenotype, though Abd-B had the strongest effect. Our results suggest that in the absence of continued PcG repression peripodial cells express genes such as Abd-B which regulate epithelial state and thereby disrupt eversion.  Our results emphasise the important role that PcG suppression can play in maintaining cell states required for morphogenetic events throughout development and suggest that PcG repression of Hox genes may affect epithelial traits that could contribute to metastasis.

overall_design: Tada Dam-Pol2 and Dam-Pc on Drosophila Control and Sce RNAi wing disc peripodial cells


title: Small-hairpin RNAs cause target-independent microRNA dysregulation in neurons and elicit global transcriptomic changes (RNA-seq)

summary: Ribosomal-depleted total RNA was isolated from neuronal cultures transduced with different shRNA constructs direct against shNogoA with and without mismatches in the seed region

first: Rafi

last: Kohen

first: Craig

last: Johnson

first: Roman

last: Giger


title: Human lung organoid for modeling infection and disease conditions (Lung I)

city: La Jolla

first: Debashis

last: Sahoo

address: 9500 Gillman Drive

department: Pediatrics

institute: UCSD

summary: We sought to define the host immune response, a.k.a, the “cytokine storm” that has been implicated in fatal COVID-19 using an AI-based approach. Over 45,000 publicly available transcriptomic datasets of viral pandemics were analyzed to extract a 166-gene signature using ACE2 as a ‘seed’ gene; ACE2 was rationalized because the receptor it encodes enables the virus that causes Covid-19, SARS-CoV-2, to enter host cells. The signature was surprisingly conserved in all viral pandemics, including COVID-19, inspiring the nomenclature ViP-signature. A subset of 20-genes classified disease severity in respiratory pandemics. The ViP signatures pinpointed airway epithelial and myeloid cells as the major contributors of an IL-15 cytokine storm, and epithelial and NK cell destruction as determinants of severity/fatality. They also helped formulate precise therapeutic goals to reduce disease symptoms and severity. Thus, the ViP signatures provide a quantitative and qualitative framework for titrating the immune response in viral pandemics and may serve as a powerful unbiased tool in our armamentarium to rapidly assess disease severity and vet candidate drugs.

overall_design: Human lung tissues and organoids were processed from two patient samples

first: Soumita

last: Das

first: Pradipta

last: Ghosh


title: Common and Unique Transcription Signatures of YAP and TAZ in Gastric Cancer Cells

city: Singapore

first: Rong

last: Li

address: 5A Engineering Drive 1

department: Mechanobiology Institute (MBI)

country: Singapore

institute: National University of Singapore

summary: To identify both common and unique transcriptional targets of YAP and TAZ in gastric cancer cells

overall_design: We carried out RNA-sequencing analysis of overexpressed YAP or TAZ in the corresponding paralogous gene-knockouts (KOs), TAZ KO or YAP KO, respectively.

first: Yaelim

last: Lee

first: Megan

last: Finch-Edmondson


title: Immune repertoire analysis using RNA for tumor milieu analysis

city: Seoul

first: Sungyoung

address: 101 Daehak-ro

department: Center for Precision Medicine

country: South Korea

institute: Seoul National University Hospital

summary: we suggest that TCR repertoire analysis be carried out through IR-seq to produce reliable and accurate results, along with the removal of single-read clonotypes, to conduct immune research in cancer using high-throughput sequencing.

overall_design: 31 Multiple Myeloma samples of RNA-seq and IR-seq


title: Maintenance of cell fate by the Polycomb Group gene Sex combs extra enables a partial epithelial mesenchymal transition in Drosophila


title: A constant pool of Lgr5+ intestinal stem cells is required for intestinal homeostasis

first: Si Hui

last: Tan

address: 8A Biomedical Grove #06-06 Immunos

institute: Institute of Medical Biology

summary: Lgr5+ crypt base columnar cells, the operational intestinal stem cells (ISCs), are thought to be dispensable for small intestinal (SI) homeostasis. Using a novel Lgr5-2A-DTR (Diphtheria Toxin Receptor) model which ablates Lgr5+ cells with near-complete efficiency and retains endogenous levels of Lgr5 expression, we show that persistent depletion of Lgr5+ ISCs in fact compromises SI epithelial integrity and reduces epithelial turnover in vivo. In vitro, Lgr5-2A-DTR SI organoids are unable to establish or survive when Lgr5+ ISCs are continuously eliminated when DT is in the media. However, transient exposure to DT at the start of culture allows organoids to form, and the rate of outgrowth reduces with increasing length of DT presence. Our results indicate that intestinal homeostasis requires a constant pool of Lgr5+ ISCs, which is supplied by rapidly reprogrammed non-Lgr5+ crypt populations when pre-existing Lgr5+ ISCs are ablated.

first: Si

middle: H

first: Phyllis

last: Phuah

first: Jasmine

last: Goh

first: Liang

middle: T

first: Swathi

last: Yada

first: Lucian

last: Tomaz

first: Magdalene

last: Chua

first: Esther

last: Wong

first: Ray

last: Dunn

first: Bernett

first: Nick

last: Barker


title: Prediction of Auxin-Ethylene Crosstalk Mediators Using Meta-Analysis of Hormone-Induced Transcriptome Data in Arabidopsis

city: Novosibirsk

first: Elena

last: Ubogoeva

address: Lavrentyeva 10

institute: Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences

summary: Plant hormones auxin and ethylene are the key regulators of plant growth and development, and their crosstalk is essential for numerous processes. Large-scale identification of new molecular targets in this crosstalk and their characterization is a tempting idea. To address this issue, we combined our own and publicly available Arabidopsis thaliana transcriptome data on auxin and ethylene treatments in a meta-analysis.

overall_design: mRNA profiles of 3-dag mock and 1h IAA treated Arabidopsis roots were generated by RNA sequencing, in triplicate, with two runs (technical replicates) for each biological replicate, using Illumina HiSeq2000 technology

first: Victoria

last: Mironova

first: Daria

middle: D

last: Novikova


title: Genome-wide contacts of rDNA genes detected by 4C procedure (4C-rDNA) in Drosophila melanogaster S2 cells

first: Nickolai

last: Tchurikov

summary: 4C-rDNA procedure was used for analysis of genomic contacts of rDNA units in D. melanogaster S2 cells.

overall_design: Analysis of rDNA genome-wide contacts in S2 cells using 4C approach. Two replicates non-stressed and two replicates of heatshock-stressed cells.

first: Yuri

last: Kravatsky

first: Olga

last: Kretova


title: Renal aging resembles a continuum between normal and diseased kidneys that potentiates inflammatory response to injury [diet]

first: Su Woong

last: Jung

address: 892, Dongnam-ro, Gangdong-gu

institute: Kyung Hee University Hospital at Gangdong

summary:
Kidney aging is an irreversible physiological process and some suggest that kidney aging is viewed as a pathological condition.
To enhance understanding of the molecular nature of renal aging, we performed whole kidney RNA sequencing in young mice (2-month-old) fed with standard diet versus those with adenine-enriched diet, and this bulk transcriptome was then compared with transcriptional changes with aging.

overall_design: Whole kidney RNA sequencing from 2-month-old mice fed with standard diet versus those with adenine-enriched diet

first: Sang

last: Lee


title: Longitudinal blood transcriptomic analysis to identify molecular regulatory patterns of Bovine Respiratory Disease in beef cattle

city: Edmonton

first: Graham

last: Plastow

state: Alberta

address: 1400 College Plaza, 8215 - 112 Street

department: Agricultural, Food & Nutritional Science

country: Canada

institute: University of Alberta

summary: We profiled blood transcriptomics of 24 beef steers at three important stages (Entry: on arrival at the feedlot; Pulled: when sickness is identified; and Close-out: recovered, healthy cattle at shipping to slaughter) to reveal the key biological functions and regulatory factors of BRD and identify gene markers of BRD for early diagnosis and potentially use in selection.

overall_design: Same 24 beef cattle in three time point: entry stage, pulled stage, and close-out stage


title: Invariant Differential Expression Analysis Reveals Mechanism of Cancer Resistance to Cell Cycle Inhibitors

first: Debashis

last: Sahoo

summary: Cell cycle inhibitors are commonly used drugs against cancer. However, mechanism of developing resistance to this class of drugs is unknown. Retinoblastoma (RB) is a good model to study this process because it is driven by mutations in the core components of cell cycle, i.e, Rb gene. However, there is limited gene expression dataset in RB and reproducibility in standard differential expression analysis is hampered by patient and environment specific variation. To get a diverse human dataset, we performed xenografts and cultured in two different conditions using NCC cell lines. Two different culture conditions were used to grow NCC cell lines: standard tissue culture plates and graphene sponge.

overall_design: Finally, the human dataset included normal retina, retinoblastoma, xenografts, and RB cell lines (Total n = 23; GSE125903 (self-reanalysis), retina n=3, RB, n=7; NCC Xenograft n=3; NCC tissue culture n=3; NCC graphene sponge n=3; GSE141327 (third party-reanalysis), Weri n = 2, Y79 n = 2).

first: Amit

last: Chatterjee

first: Sonalisa

last: Pandey

first: Ravikanth

last: Danda

first: R

last: Ranjith Kumar

first: S

last: Maheswari

first: Vikas

last: Khetan

first: Pukhraj

last: Rishi

last: Ramaprabhu

first: Sailaja

last: Elchuri


title: RNA Sequencing MDA-MB-231 Treared with TGFβ and Alisertib

city: Rochester

first: Mrunal

middle: Kishor

last: Dehankar

state: MN

address: 200 First St. SW

department: Computational genomics

institute: Mayo Clinic

summary: RNA sequencing was performed on MDA-MB-231 samples treated with TGFβ nad Alisertib to obtaine the TGFβ-mediated gene expression profile which is regulated by AURKA activity.

overall_design: Experiments were done on triplicate for each treatment condition including control, TGFβ, Alisertib, and Combination

first: Antonio

last: D'Assoro

first: Mohammad

last: Jalalirad


title: Analysis of differential gene expression in mutant and overexpressing lines of DNE1

city: Strasbourg

first: Damien

last: GARCIA

address: 12 rue du Général Zimmer

country: France

institute: CNRS

summary: Transcriptomic analysis of a dne1-1 mutant, two overexpressors of DNE1 (P35S-GFP::DNE1), an overexpressor of DNE1_D153N (35S:GFP-DNE1_D153N), and vcs-6. Biological triplicates of 14 days old seedlings were analyzed.

last: Garcia


title: Analysis of gene expression and genome-wide rDNA contacts in Drosophila S2 cells

first: Nickolai

last: Tchurikov

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


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type, serpini1-/- and Tg(serpini1) zebrafish Transcriptomes

city: SHANGHAI

first: SHA

last: HAN

state: SHANGHAI

address: 12 Wulumuqi Zhong Road,

department: Department of Neurology

institute: Huashan Hospital, Fudan University

summary: We performed RNA-sequencing on serpini1 deficient zebrafish by CRISPR/Cas9 technique and an inducible neuroserpin overexpression model under the Huc promoter in the zebrafish to further research on the loss and gain of function of neruoserpin.

overall_design: Gene expression of 7dpf zebrafish larvae in each group (n=30 per group) after serpini1 ko or inducibale overexpression.

first: sha

last: han

first: liang

last: wang


title: Maintenance of cell fate by the Polycomb Group gene Sex combs extra enables a partial epithelial mesenchymal transition in Drosophila (Pc dataset)

first: Michael

last: Murray


title: RNA-seq analysis after depletion of ALDH1A2 by enhancer blocking in Jurkat cells

first: Tze King

last: Tan

address: 14 Medical Drive

department: Cancer Science Institute

summary: RNA-seq analysis was performed in a T-cell acute lymphoblastic leukemia cell line (Jurkat) to analyze gene expression changes after ALDH1A2 depletion.

overall_design: The inducible single-guide RNA mediated dCas9-KRAB system was used to transcriptionally deplete ALDH1A2 gene expression. Jurkat cells expressing the catalytic dead Cas9 fused with KRAB peptide was first established.  The cells were then infected with lentivirus encoding an inducible sgRNA targeting the regulatory element of ALDH1A2 gene. Total RNA was harvested 72hrs upon induction of sgRNA and applied for RNA-seq analysis.

first: Chujing

last: Zhang

first: Tze

first: Takaomi

last: Sanda


title: Next Generation Sequencing Facilitates Quantitative Analysis of MYC+ and MYC+; SETD2-/- Renal Tubular Cells Transcriptomes

first: Hanyu

last: Rao

address: No.1954, hua shan Rd. Shanghai

institute: Shanghai Jiao Tong University

summary: To get an insight into the mechanism of how SETD2 ablation promotes ccRCC, we performed RNA-seq using the renal tubules isolated from MYC+; SETD2-/- mice compared with their control MYC+ littermates.

overall_design: Renal primary tubular epithelial cells mRNA profiles of 6- to 8-week-old SETD2FL/FL KSPCRE/+ and MYC+; SETD2FL/FL KSPCRE/+ mice were generated by deep sequencing, in triplicate, using   Illumina NextSeq 500.

first: Wei-Qiang

last: Gao


title: RNA-seq revealed counter effect of chitosan against Botrytis cinerea on grape berries

city: Nanjing

first: Tariq

last: Pervaiz

state: Jaingsu

address: wei Gang

department: Horticulture

institute: Nanjing Agricultural University

summary: Plants have great potential to protect against pathogens and other abiotic stress, and thus the interaction between signaling networks of defense is incredible. This can be activated and express with the application of growth elicitors and antimicrobial natural compounds. In the present study we used natural polysaccharide, Chitosan (15kDa) against Grey mold in two grape varieties (Shine-muscat and Kyoho). The finding depicted that the interaction of DEG and KEGG in control and treated samples of grapevine, which provides the evidence for selection of gray mold related defense genes and chitosan for subsequent grapevine production/postharvest programs.

overall_design: Two Grape verities (Shine-muscat and Kyoho) treated with resistance inducers chitosan, the physiological changes in the grape berry were analyzed at 80-90 % physiologically maturities, with commercial grade chitosan, formulations were applied by foliar spray: 15% (w/v) chitosan (15 kDa) (Fig.1). To prepare formulations, we used distilled water as control. Each berry of grapy is treated as one replication and each replication is repeated together and randomized 3 times. One day later, Botrytis cinerea spores with 104 /μl concentration was used. The gray mold fungus was grown on grape berries at 25 °C, and 95 % relative humidity.

first: Haifeng

last: Jia

first: Peian


title: MicroRNAs Expressed in Visceral Adipose Tissue from Mice Fed High-Fat Diets Supplemented with Eicosapentaenoic Acid (EPA)

city: Lubbock

first: Naima

last: Moustaid-Moussa

state: TX

address: 1301 Human Sciences, Rm 402

department: Department of Nutritional Sciences

institute: Texas Tech University

summary:
The goal of this subproject is to identify microRNAs (miRNAs) expressed in visceral (VIS) adipose tissue (gonadal fat from male C57BL/6 mice) and regulated by eicosapentaenoic acid (EPA). This will provide insight into microRNAs regulated by EPA and their potential role in obesity-associated inflammation.
We performed small RNA-sequencing of white (VIS) adipose tissue from high-fat diet (45% kcal from fat) supplemented with EPA (45% Kcal from fat, 6.75% EPA).
Using the Gunaratne Next-Generation pipeline (published in Creighton et al. 2009), miRNA expression profiles were identified. Counts of each unique read were normalized to total usable reads, and had 40 counts added. We mapped about 13.8 million sequence reads per sample to the Mus musculus genome (build mm 10). We are specifically interested in those miRNAs expressed in VIS fat from EPA-fed mice compared to HF-fed mice.

overall_design:
Method: We performed small RNA-sequencing of VIS fat from mice fed high-fat diet supplemented with EPA (45% Kcal from fat, 6.75% EPA).
Results: Using the Gunaratne Next-Generation pipeline (published in Creighton et al. 2009), miRNA expression profiles were identified. Counts of each unique read were normalized to total usable reads, and had 40 counts added. We mapped about 13.8 million sequence reads per sample to the Mus musculus genome (build mm 10).
Conclusion: Specific miRNAs are expressed in white adipose tissue from mice fed EPA-supplemented HF diets.

first: Mandana

last: Pahlavani

first: Nishan

middle: S

last: Kalupahana

first: Preethi

last: Gunaratne

first: Cristian

last: Coarfa

first: Kimal

last: Rajapakshe


title: MC-LR induced piRNA changes in mouse sperm

first: Xiannan

last: Meng

address: Hankou Road 22

institute: Nanjing University

summary: The expressions of piRNA in mouse sperm were altered by MC-LR-exposure or Hsp90aa1 shRNA. MC-LR could induce intergenerational toxicity.

overall_design: Examination of 2 different doses of MC-LR exposure to sperm

first: Ling


title: MiRNA-mRNA expression profiles and functional network after injection of botulinum toxin type A into submandibular gland [miRNA-Seq]

city: Beijing

first: Mao

last: Qianying

address: No. 22 Zhong Guan Cun South Street, Haidian District,

department: Oral and Maxillofacial Surgery

institute: Peking University School and Hospital of Stomatology

summary:
Backgroud: Botulinum toxin type A (BTXA) is widely used for the treatment of sialorrhea and other glandular hypersecretion diseases. Micro ribonucleic acid (miRNA) plays an important role in the occurrence and development of salivary diseases, but it is still unclear which role miRNA plays during the inhibition of salivary secretion triggered by BTXA. This work was aimed to explore the miRNA-mRNA expression profiles and functional network after injection of BTXA into submandibular gland.
Methods: The differentially expressed (DE) miRNAs and mRNAs between the control group and BTXA group were identified through high-throughput sequencing and bioinformatic analyses and were confirmed by qRT-PCR. Bioinformatic analyses were performed to identify the critical biological functions and signalling pathways and established the functional network.
Results: A total of 19 DE miRNAs and 1072 DE mRNAs were identified between the control group and BTXA group. We confirmed 6 DE miRNAs through the qRT-PCR validation. Bioinformatic analysis identified that several pathways may be associated with the inhibition of salivary secretion, such as MAPK signaling pathway, Tight junction and Cytokine-cytokine receptor interaction. We predicted the target genes of these 6 DE miRNAs and established the miRNA-mRNA interaction network. The intersection of DE mRNAs and target genes was performed and finally obtained 7 mRNAs: EGR2, PAQR9, ZKSCAN1, USP6N, lCYB561A3, ZFHX4 and CLIC5.
Conclusions: Our study describes the miRNA and mRNA expression profiles and functional network after injection of BTXA into submandibular gland. These findings explore the mechanism of BTXA in inhibiting salivary secretion, and probably provide a new idea for the clinical application.
Key words: miRNA-mRNA, BTXA, submandibular gland

overall_design: Detection of expression profiles of miRNA and mRNA in submandibular glands of control group and BTXA group, and analysis of GO and KEGG pathways.

first: Ruolan

last: Xiang

first: Qianying

last: Mao


title: Time course transcriptome of wild type hESC and hESC treated with small molecule inhibitors SB431542 (TGF-ß pathway), SU5402 (FGF pathway) or DMSO (drug solvent control) over 9h hours, extracting samples every 3 hours

city: Zurich

first: Constance

last: Ciaudo

state: Zurich

address: Otto-Stern-Weg 7, HPL G.31

department: D-BIOL

country: Switzerland

institute: ETH Zurich

summary: Purpose:  The goals of this study was to identify direct targets of the FGF and TGF-ß pathway and novel crosstalk candidates

overall_design: mRNA profiles of H1 hESCs were generated by deep sequencing, in triplicates, using Illumina HiSeq2000.

first: Tobias

last: Beyer


title: Molecular mechanism of SHP/REV-ERBalpha/CYP4A axis in mediating alcohol-induced livery injury

city: Durham

first: Integrative

last: Bioinformatics

state: NC

address: 111 TW Alexander Drive

department: BCBB

institute: NIEHS

summary: The molecular mechanisms of CYP4A in ALD pathogenesis has not been elucidated. In the current study, we found that hepatic Cyp4a10 and Cyp4a14 expression were significantly upregulated in WT, but not in Shp-/- mice fed with ethanol.

overall_design: SHP knockout and wild type mice were fed 5% Lieber-DeCarli ethanol liquid diet (Bio-Serv; #F1258SP) or maltose control for 10 days followed by a binge of alcohol (5g/kg body weight) or isocaloric maltose dextrin (9g/kg body weight) at 9am on day 11. Liver samples were collected from groups of 3 control or ethanol fed mice serially post gavage at 6pm, 12am, 6am or 12pm over a 24-hour period.

first: Rana

last: Smalling

first: Li

last: Wang


title: Transcriptomic Analysis on Lipid Loaded HepaRG Model for Steatosis Reveal the Influence on the Regulation of Drug Metabolizing Enzymes and Transporters

city: Kingston

first: Fatemeh

last: Akhlaghi

state: RI

address: 7 Greenhouse Road

department: College of Pharmacy

institute: University of Rhode Island

summary: The present study was aimed to mimic steatosis in in-vitro HepaRG model and test the effect of lipid loading on drug metabolizing enzymes and transporters (DMET) in steatosis.  HepaRG cells, differentiated in-house were exposed to mixture of saturated and unsaturated fatty acids, 0.5 mM palmitate and oleate (1:2) conjugated to BSA (0.02%) for 72h.  Following the incubation, the model system was characterized using ORO staining for neutral lipids, tested for toxicity with WST-1 assay and triglyceride (TAG) accumulation was measured using TAG calorimetric assay.  Increased lipid accumulation and 6-fold increase in TAG was observed (P < 0.05, n=4).  The whole transcriptome was analyzed using RNA sequencing.  Differentially expressed transcripts were identified upon FA treatment versus (vs.) control in HepaRG cell line (393 total transcripts, 89 up- and 304 downregulated).  Lipid loading, led to significant down-regulation in gene expression levels of various DMET, nuclear receptors and transcription factors such as CYP3A4, 1A2, 2B6, 2C8, 2C9 and 2C19, along with this UGT1A9, UGT1A6, ABCB1, NR1I2 and HNF4α (P < 0.05, n=3).  The accumulation of saturated and polyunsaturated fatty acids may selectively inhibit certain DME pathways.

overall_design: Examination of drug metabolizing enzymes dyregulation in the presence of Oleate and Palmitate (2:1) enriched media in HepaRG cells

first: Anitha

last: Saravanakumar

first: Xin

last: Bush

first: Wen

last: He

first: Cassandra

last: Tierney

first: Jillian

last: Johnson


title: soil mcirobial functional communities

first: fan

last: wu

address: NO.5 Yiheyuan Road Haidian District

institute: Peking university

summary: To study the soil mcirobial functional communities and the  nutrient cycles couplings changes after exposure to different contaminant

platform_organism: Bacteria Archaea Eukaryota Viruses

overall_design: 15 soil sample exposed to 30 and 300 mg/kg contaminant after 30 days incubation.Each treatment has 3 repetitions

first: Fan

last: Wu

first: Xilong


title: Tet2 is required for Socs activation in immune response cells [RNA-seq_human]

city: MARSEILLE

first: erinn

last: soucie

address: 27 Boulevard Lei Roure

institute: CRCM

summary: Purpose: Systemic mastocytosis is a rare and chronic disease with phenotypes ranging from indolent to severe. Prognosis for this disease is variable and very few biomarkers to predict disease evolution or outcome are currently known. We have performed comprehensive screening in our large cohort of systemic mastocytosis patients for mutations previously found in other myeloid diseases and that could serve as prognostic indicators. KIT, SRSF2-P95 and TET2 mutations were by far the most frequent, detected in 81, 24 and 21 percent of patients, respectively. To understand the molecular mechanisms that regulate the functional cooperation that we and others have described for oncogenic KitD816V and Tet2 loss-of-function mutations in aggressive mastocytosis, and as part of a larger study, we have sequenced the transcriptomes of mast cells sorted from bone marrow biopsies of 3 patients in our cohort with aggressive disease and KitD816V mutation and 3 patients with aggressive disease, KitD816V and Tet2 mutation.

overall_design: RNA-seq was performed on mast cells sorted from bone marrow biopsies of 3 patients in our cohort with aggressive disease and KitD816V mutation and 3 patients with aggressive disease, KitD816V and Tet2 mutation. Full patient profiles associated to each sample are published in Hanssens, K. et al. “SRSF2-p95 hotspot mutation is highly associated with advanced forms of mastocytosis and mutations in epigenetic regulator genes”. Haematologica 99, 830–835 (2014).

first: Patrice

last: Dubreuil

first: Rabie

last: Chelbi

first: Ghislain

last: Bidaut

first: Erinn

last: Soucie


title: Mediator12 and 13 act as conditional anti-silencing factors in Arabidopsis  [RNA-seq]

first: Qikun

last: Liu

state: Beijing

address: Haidian District, 5 Yiheyuan Rd., Zonghekeyan BLDG, Rm 502

department: School of Advanced Agricultural Sciences

institute: Peking University

summary: Mediator is a multi-protein complex which facilitates the initial steps of gene transcription. Mediator 12 (MED12) and MED13 are components of a module that reversibly associates with the core Mediator complex, and both positively and negatively regulates gene expression. Here, in an Arabidopsis mutant screen for factors that can bypass repressive epigenetic marks, we identified MED12 and MED13 as anti-silencing factors. Both are preferentially required for the expression of genes in the absence of H3K4me3, an activating chromatin mark. Thus, MED12 and MED13 respond to specific epigenetic states and can act as conditional positive gene regulators in Arabidopsis.

overall_design: In each experiments, a minimum of three replicates were analyzed. cct-2 and gct-2 mutants were compared to columbia-0. GFP-morc1/med12 and GFP-morc1/med13 were compared to GFP-morc1. GFP-morc1 was compared to GFP-wt. GFP-ddc/med12 and GFP-ddc/med13 were compared to GFP-ddc. GFP-ddc was compared to GFP-wt. Please also see description section of each individual sample.

first: Steven

middle: E

last: Jacobsen


title: Analysis of gene expression in co-culture of PBMCs with ovarian cancer cell lines by High-Throughput Sequencing

city: Bangkok

first: Nakarin

last: Kitkumthorn

address: Yothee road

department: Oral Biology

country: Thailand

institute: Mahidol University

summary:
(Objectives) The goal of this study is to investigate paracrine effect of peripheral blood mononuclear cells (PBMCs) on ovarian cancer cell lines.
(Methods) Transcription profiles of PBMC (control) and PBMC co-cultured with ovarian cancer cell lines (treatment) were generated by deep sequencing, in triplicate, using Illumina HiSeq X Ten.
(Results and Conclusions) Transcriptome analysis of PBMCs has revealed the expression change when co-cultured with EOC cell lines with significantly in up-regulated genes; CDKN1B, GIMAP8 and SNN. The qRT-PCR validation have indicated that GIMAP8 was high expressed in EOC patients when compared with healthy female. We summarized that PBMCs were changed their expression as a result of paracrine signals from ovarian cancer cells.

overall_design: Transcription profiles of PBMC (control) and PBMC co-cultured with cancer (treatment) were generated by deep sequencing, using Illumina HiSeq 4000.

first: Natthamon

last: Sonthi

first: Apiwat

last: Mutirangura


title: Differential expression of genes in Listeria monocytogenes under prolonged heat shock

city: Dallas

first: Palmy

middle: R

last: Jesudhasan

department: Microbiology

institute: University of Texas Southwestern Medical Center

summary: Microarray analysis was performed to identify the differentially expressed genes during heat stress by comparing the transcriptome of L. monocytogenes under optimal temperature (37°C), and prolonged heat shock (60°C for 9 minutes) conditions.

overall_design: A total of  5 microarray slides were used.  Two arrays for each biological replicate that including dye swap method.

first: Réka

last: Ágoston

first: Scot

last: Dowd

first: Suresh

last: Pillai


title: TTF1 and TKTL1 mRNAs in Extracellular Vesicles as a Blood Biomarker for Lung Adenocarcinoma

city: Seattle

first: Kai

last: Wang

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

summary: Lung cancer remains the greatest cause of cancer related deaths and Low Dosage Computerized Tomography (LDCT) has been shown to improve early detection of lung cancer and survival rate of high risk individuals. However, such imaging is limited by high rates of false positivity leading to unnecessary patient anxiety and invasive procedures. Complementary blood biomarkers could increase the accuracy of early detection. We conducted next generation sequencing on extracellular vesicles (EVs) in plasma in cohorts of smoking and age matched individuals with surgically documented solitary lung nodules that were either adenocarcinomas or benign granulomas, and identified a glucose regulation gene TKTL1 as the most upregulated mRNA between the two cohorts. Together with a previously identified gene, TTF1, we designed molecular beacons and used a novel and yet facile tethered lipoplex nanoparticle (TLN) nanochip to assess their performance in lung cancer detection.

overall_design: Three separate compartments of plasma (whole plasma, EV and EV-free plasma) from a small number of malignant intermediate pulmonary nodules (IPN) patients with benign (N=10) or malignant Stage IA/B IPNs (N=7)

first: Taek-Kyun

last: Kim

first: Xiaogang

first: Yuqing

last: He


title: Whole blood transcriptional profiling by RNA sequencing in healthy donors

city: Milano

first: Gualtiero

middle: Ivanoe

last: Colombo

address: Via Carlo Parea, 4

country: Italy

institute: Centro Cardiologico Monzino IRCCS

summary: We performed the gene expression profiling by RNA-seq in order to describe in depth the transcriptional landscape of peripheral blood and pinpoint sex-biased differences

overall_design: Whole blood poly(A)+ RNA profiles of 20 healty donors were generated through RNA-Seq using the SOLiD 5500xl system.

first: Luca

last: Piacentini

first: Mattia

last: Chiesa

first: Elisa

last: Bono


title: Tet2 is required for Socs activation in immune response cells [RNA-seq_mouse]

first: erinn

last: soucie

summary: Purpose: We have previously established an in vitro murine model that recapitulates the transformed phenotype of primary Tet2-/- mast cells expressing the Kit kinase domain mutant allele, D816V, that is both an oncogene and characterises patients with mastocytosis. To better understand the molecular basis of this cooperation and to further our understanding of role of Tet2 during inflammation and in other immune system disorders, we used this same in vitro primary cell system for genome wide studies to identify genes and genomic loci that are deregulated when these two mutations cooperate in mast cells.

overall_design: RNA-seq was performed on biological replicates for 4 paired samples: 1) GFP-negative/control and 2) GFP-positive/KitD816V infected Tet2+/+ mast cells, and 3) GFP-negative/control and 4) GFP-positive/KitD816V infected Tet2-/- mast cells. Biological replicates constitute primary mast cell cultures derived from two individual mice of each genotype, cultured in parallel.

first: Patrice

last: Dubreuil

first: Rabie

last: Chelbi

first: Ghislain

last: Bidaut

first: Erinn

last: Soucie


title: Analysis of gene expression in co-culture of PBMCs with colon cancer cell lines by High-Throughput Sequencing

first: Nakarin

last: Kitkumthorn

summary:
(Objectives) The goal of this study is to investigate paracrine effect of peripheral blood mononuclear cells (PBMCs) on colon cancer cell lines.
(Method) Transcription profiles of PBMCs (control) and PBMCs co-cultured with colon cancer cell lines (treatment) were generated by deep sequencing, in triplicate for SW480 and duplicate for HT29, using Illumina HiSeq 4000.
(Results and conclusion) Transcriptome analysis of PBMCs has shown the gene expression changed when co-cultured with colon cancer cell lines. The result revealed significantly up- and down-regulated genes.

overall_design: Transcription profiles of PBMC (control) and PBMC co-cultured with colon cancer cell lines (treatment) were generated by deep sequencing, in triplicate for SW480 and duplicate for HT29, using Illumina HiSeq 4000.

first: Papatson

last: Boonsongserm

first: Apiwat

last: Mutirangura


title: CsPID is required for lateral organ organogenesis and development  in cucumber

city: Shanghai

first: Renyi

last: Liu

state: Shanghai

address: 3888 Chenhua Road

department: Bioinformatics

institute: Shanghai Center for Plant Stress Biology

summary: Lateral organ development is important for cucumber yield, while the molecular mechanism controlling  leaf and floral organ development in cucumber remain elusive. In this report, a novel EMS-mutaginized mutant, round leaf (rl) was distinguished with remarkable round leaf shape, abnormal floral organ and inhibited tendril outgrowth in early development phase. Moreover, the ovule organogenesis disrupted completely in parthenocarpy fruit of rl. MutMap+ analysis revealed that RL encodes a protein kinase PINOID (CsPID, Csa1G537400). A non-synoymous SNP in the second exon of CsPID resulted in an amino-acid substitution from Arg in the wild type to Lys in the rl mutant. CsPID was down-regulated in rl mutant and preferentially expressed in young leaf, and flower buds. IAA quantification showed that rl plants exhibited a lower IAA content than wild type in ovary and blade edge. IAA immunolocalization results confirmed the IAA content alteration in rl plants. Transcriptome profile analysis further suggested  IAA biosynthesis, polar transport and signal transduction genes participated in the leaf and floral development process by CsPID. Biochemical analyses showed that CsPID may regulate leaf shape by interacting with CsREV. In conclusion, this study revealed that the extensive genetic architecture of lateral organ organogenesis and development via CsPID regulating auxin polar transport action in cucumber.

overall_design: RNA profiles of 2 cm long leaf and female bud of wild type (WT) and rl

first: Tao

last: Wu


title: Analysis of gene expression in co-culture of PBMCs with Head and Neck cancer cells line by High-Throughput Sequencing

summary:
(Objectives) The goal of this study is to investigate paracrine effect of Peripheral Blood Mononuclear Cells (PBMCs) on Head and Neck cancer cell lines.
(Method) Transcription profiles of PBMCs (control) and PBMCs co-cultured with Head and Neck cancer cell lines (treatment) were generated by deep sequencing, in triplicate for HN17 and duplicate for HN4, using Illumina HiSeq 4000.
(Results and conclusion) Transcriptome analysis of PBMCs has shown the gene expression changed when co-cultured with HN cell lines. The result revealed significantly down-regulated genes. On the other hand, up-regulated gene, ZCCHC6 were used to validated with qRT-PCR in HNSCC patient blood. The synopsis of this study demonstrates paracrine effect on PBMC of HNSCC patient to significantly up expression of ZCCHC6 gene when compared with healthy donors.

overall_design: Transcription profiles of PBMC (control) and PBMC co-cultured with Head and Neck cancer cell lines (treatment) were generated by deep sequencing, in triplicate for HN17 and duplicate for HN4, using Illumina HiSeq 4000.

first: Areeya

last: Arayataweegool


title: High-throughput tRF&tiRNA realtime PCR Array for 10 paired gastric cancer tissues and matched noncancerous tissues

status: Public on Dec 30 2020

city: Shenyang City

first: Zhenning

last: Wang

address: 155 North Nanjing Street

department: Department of Surgical Oncology and General Surgery

institute: The First Affiliated Hospital of China Medical University

summary: Total RNA was isolated from ten pairs of matched gastric cancer tissues and non-cancerous tissues. RNAs were then pretreated with rtStar™ tRF&tiRNA Pretreatment Kit (Cat# AS-FS-005, Arraystar) and reverse-transcribed with rtStar™ First-Strand cDNA Synthesis Kit. The synthesed cDNA was used for realtime PCR to detect the differential expression of 353 tRF&tiRNA.

overall_design: Ten pairs of matched gastric cancer tissues and non-cancerous tissues were used in current PCR array. Each sample was applied in realtime PCR for three replicate. The gatric cancer tissues were regarded as experimental group and the non-cancerous tissues are set for control groups. For realtime PCR experiment, three commonly used house-keeping genes (RNU6, SNORD43, SNORD95) were used as the internal reference.

first: Yongxi

last: Song


title: Bifidobacterium longum subsp. infantis (B. infantis) strain dependent utilization of human milk oligosaccharides

city: Amherst

first: Ezgi

last: Ozcan

state: MASSACHUSETTS

address: 424 Chenoweth Lab, 102 Holdsworth Way

institute: University of Massachusetts Amherst

summary: Bifidobacterium longum subsp. infantis (B. infantis) colonizes the infant gut microbiome with a 43-kb gene cluster that enables human milk oligosaccharide (HMO) utilization. Although there is relative genomic homogeneity in this regard, previous observations suggest that B. infantis strains may differ in their utilization phenotype. To test this hypothesis, a panel of B. infantis strains were evaluated for their ability to utilize pooled HMOs to yield differential phenotypes including biomass accumulation, HMO consumption glycoprofile, end-product secretion, and global transcriptomes. Two strains (ATCC 15697 and UMA301) efficiently consumed several HMO isomers/anomers that exhibit degrees of polymerization (DP) ³ 4. These same strains partially consumed the smaller DP HMOs including fucosyllactose and lactodifucotetraose isomers/anomers. In contrast, UMA299 efficiently utilized fucosylated small molecular weight HMOs (DP<4), and accumulated greater biomass on purified 2´FL with significantly higher 1,2-propanediol production. This study identifies several strain-dependent features in HMO utilization phenotypes that are consistent with metabolic variation within a bifidobacterial-dominated infant-gut microbiome.

overall_design: Gene expression of Bifidobacterium infantis strains while growing on human milk oligosaccharides

last: Özcan

first: Apichaya

last: Bunyatratchata

first: Liv

last: Dedon

first: Daniela

last: Barile

first: David

last: Sela


title: Identification of circulating protein biomarkers for pancreatic cancer cachexia

city: Portland

first: Teresa

last: Zimmers

state: OR

address: 3181 S.W. Sam Jackson Park Road

department: Cell, Developmental & Cancer Biology

institute: Oregon Health & Science University

summary: Over 80% of patients with pancreatic ductal adenocarcinoma (PDAC) suffer from cachexia, characterized by severe muscle and fat loss and yet, there are no biomarkers identified for this debilitating condition. Our objective was to identify circulating protein biomarkers using serum for human PDAC cachexia and understand their biological functions. Serum from 30 patients with PDAC was collected and protein profiles were generated using SOMAscan. The protein profiles were correlated with clinical variables such as Cancer associated weight loss (CAWL), body composition measurements of skeletal muscle index (SMI), skeletal muscle density (SMD), total adipose index (TAI) using Spearman’s correlation. Overall, 110 proteins of 1294 correlated with these clinical measures - 47 proteins for CAWL, 19 for SMI, 14 for SMD, and 30 for TAI (r-value 0.5, p<0.05). LYVE1, a homolog of CD44 implicated in tumor metastasis, was the top CAWL-associated protein (r= 0.67, p=0.0001). Protein co-expression network analysis identified immune system related pathways such as B-cell signaling, natural killer cell signaling, IL6 signaling in addition to identifying other known pathways in cachexia. Taken together, these data identify both immune system molecules and additional secreted factors and pathways not previously associated with PDAC and confirm the activation of previously identified pathways.

overall_design: Serum from 30 patients with PDAC were collected and subjected to protein profiling using SOMAscan

first: Safi

last: Shahda

first: Ashok

last: Narasimhan

first: Joshua

last: Kays

first: Susan

middle: M

last: Perkins

first: Lijun

last: Cheng

first: Katheryn

middle: N

last: Hannaford

first: Daniel

last: Schloss

first: Leonidas

middle: G

last: Koniaris


title: Drosophila Hox genes induce melanized pseudo-tumors when misexpressed in hemocytes

city: Hyderabad

first: Divya Tej

last: Sowpati

state: Telangana

address: Habsiguda

country: India

institute: CSIR Centre for Cellular and Molecular biology

summary: Hox genes are early determinants of cell identity along the anterior-posterior body axis across bilaterians. Several late non-homeotic functions of Hox genes have emerged in a variety of processes involved in organogenesis in several organisms, including mammals. Several studies have reported the misexpression of Hox genes in a variety of malignancies including acute myeloid leukemia. The Hox genes Dfd, Ubx, abd-A and Abd-B were overexpressed via the UAS-Gal4 system using Cg-Gal4, Lsp2-Gal4, He-Gal4 and HmlD3-Gal4 as specific drivers. Genetic interaction was tested by bringing overexpression lines in heterozygous mutant backgrounds of Polycomb and trithorax group factors. Larvae were visually scored for melanized bodies. Circulating hemocytes were quantified and tested for differentiation. Pupal lethality was assessed. Expression of Dfd, Ubx and abd-A, but not Abd-B in the hematopoietic compartment of Drosophila led to the appearance of circulating melanized bodies, an increase in cell number, cell-autonomous proliferation, and differentiation of hemocytes. Pupal lethality and melanized pseudo-tumors were suppressed in Psc1 and esc2 backgrounds while polycomb group member mutations Pc1 and Su(z)123 and trithorax group member mutation TrlR85 enhanced the phenotype. Dfd, Ubx and abd-A are leukemogenic. Mutations in Polycomb and trithorax group members modulate the leukemogenic phenotype.

overall_design: RNA was isolated from blood tissue of Cg-Gal4>CS and Cg-Gal4>UAS-abd-A larvae and total RNA profiles were generated using Illumina NextSeq 500 to obtain paired end libraries of read length 75 X 2 with at least 25 million reads per sample. There were two replicates from blood tissue of Cg-Gal4>CS and three replicates of Cg-Gal4>UAS-abd-A larvae.  The sequence reads were quality checked using FastQC, mapped to reference genome (dm6) using STAR, raw counts were calculated using HTSeq and differential expression was performed using DESeq2.

first: Titus

last: Ponrathnam

first: Ravina

last: Saini

first: Rakesh

last: Mishra


title: Zfp521 is essential for the quiescence and maintenance of adult hematopoietic stem cells under stress

city: Chongqing

first: Zhigang

last: Li

state: China

address: NO.30 GaotanYan  Street, Shapingba District

institute: Southwest Hospital, Army Medical University

summary: To further characterize Zfp521-dependent genes and the molecular pathways involved in the regulation of hematopoietic stem cell (HSC) function, we conducted RNA-Seq analysis of HSC sorted from Zfp521fl/fl and Zfp521-CKO chimeric mice 2 months after transplantation.

overall_design: Examination of mRNA profiles of HSCs sorted from Zfp521fl/fl and Zfp521-CKO chimeric mice 2 months after transplantation

first: Xuemei

last: Fu

first: Yu

last: Hou

first: Jieping

last: Chen


title: Bulk RNA-seq of mouse cells from the dorsal cerebral cortex during its formation, with knocked-out Ski gene

city: Basel

first: Verdon

last: Taylor

address: Mattenstrasse 28

department: Department of Biomedizin

institute: University of Basel

summary: From mice treated with knocked-out Ski gene. Dorsal cortices from embryonic day E11.5 to E18.5 were micro-dissected and dissociated into single cell suspensions using Papain and Ovo-mucoid mix. Cells were washed with L15 medium and FAC-sorted for GFP positive NSCs using FACSariaIII (BD Biosciences) derived from Hes5::GFP transgenic embryos for NSCs and Tbr2::GFP transgenic embryos for BPs and NBNs.

overall_design: 63 samples of Ski-KO neural stem cells, basal progenitors and newborn neurons, daily from embryonic days 11.5 to 18.5.

first: Tanzila

last: Mukhtar

first: Alice

last: Grison

first: Zahra

last: Karimaddini

first: Marcello

last: Boareto do Amaral

first: Jeremie

last: Breda

first: Pascal

last: Grobecker

first: Katja

last: Eschbach

first: Christian

last: Beisel

first: Dagmar

last: Iber

first: Erik

last: van Nimwegen

first: Suzana

last: Atanasoski


title: Global assessment of CD24Fc activity on human immune system

city: Baltimore

first: Xu

last: Wang

state: MD

address: 725 W Lombard St

institute: University of Maryland Baltimore

summary: CD24Fc is a recombinant fusion protein consisting of the extracellular domain of mature human CD24 linked to the human immunoglobulin G1 (IgG1) Fc domain. Preclinical studies have demonstrated that CD24Fc provide therapeutic effect for autoimmune diseases and graft-vs-host diseases. These studies prompted clinical development of CD24Fc for immunological diseases. As the first-in-human (FIH) study, CD24Fc was tested in a phase I, randomized, double-blind, placebo-controlled, single ascending dose study for safety and pharmacokinetics in healthy people. For global assessment of CD24Fc activity on host immune system, we collected the peripheral blood mononuclear cells (PBMC) from human subjects in CD24Fc phase I clinical study and performed RNA-sequencing for PBMC samples. We found that CD24Fc treatment significantly reduced the transcripts of genes encoding pattern recognition receptors, inflammatory cytokines, chemokines and their receptors.

overall_design: To investigate the role of CD24Fc on host immune system, we collected the PBMC from human subjects in CD24Fc phase I clinical study, then performed RNA-sequencing for PBMC samples obtained on Day -1 (pre-treatment) and Day 3 (post-treatment) from subjects receiving 240 mg of CD24Fc. Of the samples collected from 6 patients, 4 pairs of RNA samples passed quality control and were subject to RNAseq.

first: Mingyue

last: Liu

first: Pan

last: Zheng

first: Yang


title: RNA-seq analysis of mice hypothalamus tissues.

city: Guangzhou

first: Gan

last: Xihui

address: School of Life Sciences Building 438, No. 132 Waihuan East Rd., Guangzhou University City, Panyu District

department: School of Life Sciences

institute: Sun Yat-sen University

summary: Analysis of mice hypothalamus genes differentially expressed in in weightlessness, noise and low air pressure condition.

overall_design: Total RNA obtained from 144 two-month-old C57BL/6N male mice hypothalamus tissues, and samples from three mice with the same conditions and the same time were mixed.

first: Huan

last: Ma

first: Jinhu

last: Guo

first: Xihui

last: Gan

first: Xiaohong


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Otud1-/- distal colonic tissue Transcriptomes adjacent to tumors

city: beijing

first: Tongtong

address: Peking University Health Science Center, 38 Xueyuan Road, Haidian District, Beijing

summary: Conclusion: Otud1-/- mice are more sensitive to azoxymethane(AOM)-Dextran sulfate (DSS) induced colon tumorigenesis

overall_design: 6 weeks WT and Otud1-/- C57BL/6 male mice were Intraperitoneal injection AOM at the day 0, followed by 3 cycles of 4 days 1.5% DSS and 14 days water. At day 81, Then distal tumor-filled colon was taken out, then tumor were removed and the RNA of colon tissue adjacent to tumors is extracted by Trizol method, followed by eukaryotic RNA-seq and associated analysis

first: Fuping

last: You


title: Telomeres reforged with non-telomeric sequences in mouse embryonic stem cells (Iso-seq)

city: suwon

first: DAEUN

last: KIM

address: World cup-ro

institute: Ajou university

summary: Telomere maintenance is indispensable for perpetuated cell division, but telomeres are not necessarily composed of a fixed sequence. Here we report the establishment of a model for alternative lengthening of telomeres (ALT) in mouse embryonic stem cells (mESCs) in which telomeres are reconstructed with an internal ALT template. Longitudinal whole-genome analyses of ALT mESCs showed that pre-amplification of the template into a telomeric region was a prerequisite for ALT activation, and that extensive copy number variations became concentrated in subtelomeric regions. Epigenomic analysis revealed the heterochromatic structure of the ALT telomeres, except for an insulator region within the ALT template. Quantitative proteomics followed by single-cell RNA-sequencing and functional assays revealed that HMGN1 protected new telomeres by regulating telomere repeat-containing RNA transcription and R loop formation in ALT mESCs. These findings implicate an evolutionarily conserved ALT mechanism driven by an internal template and provide a molecular basis underlying telomere evolution.

overall_design: Gene expression profiling of Terc knock-out mouse Embryonic Stem Cell (mESC) by passage doubling

first: Chuna

last: Kim

first: Sanghyun

last: Sung

first: Yoonseok

last: Jung

first: Jenny

middle: J

last: Seo

first: V


title: Re-expression of SMARCA4/BRG1 in Small Cell Carcinoma of Ovary, Hypercalcemic Type (SCCOHT) promotes an epithelial-like gene signature through an AP-1-dependent mechanism [RNA-seq]

city: Chapel Hill

first: Bernard

middle: E.

last: Weissman

address: 450 West Drive

department: Pathology and Laboratory Medicine

institute: University of North Carolina at Chapel Hill

summary: Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is a rare and aggressive form of ovarian cancer. SCCOHT tumors have inactivating mutations in SMARCA4 (BRG1), one of the two mutually exclusive ATPases of the SWI/SNF chromatin remodeling complex. To address the role that BRG1 loss plays in SCCOHT tumorigenesis, we performed integrative multi-omic analyses in a SCCOHT cell line +/- BRG1 re-expression. BRG1 re-expression induced a gene and protein signature similar to an epithelial cell and gained chromatin accessibility sites correlated with other epithelial originating TCGA tumors. Gained chromatin accessibility and BRG1 recruited sites were strongly enriched for transcription factor binding motifs of AP-1 family members. Furthermore, AP-1 motifs were enriched at the promoters of highly upregulated epithelial genes. Using a dominant negative AP-1 cell line, we found that both AP-1 DNA binding activity and BRG1 re-expression are necessary for the gene and protein expression of epithelial genes. Our study demonstrates that the BRG1 re-expression drives an epithelial-like gene and protein signature in SCCOHT cells that depends upon by AP-1 activity.

overall_design: Four biological replicates of BIN67 cells were co-transfected (FuGENE 6, Promega #E269A) with either control (pCMV-neo or pCDNA3-neo) or BRG1 (PBJ5-BRG1) plasmids at a 10:1 ratio to a plasmid containing puromycin resistance (pBABE-puro). Twenty-four hours after transfection, cells were placed on 2 µg/ml puromycin for 3 days and then harvested for analyses. Samples from each biological replicate were divided equally and processed for ATAC-seq and RNA-seq

first: Krystal

last: Orlando


title: Re-expression of SMARCA4/BRG1 in Small Cell Carcinoma of Ovary, Hypercalcemic Type (SCCOHT) promotes an epithelial-like gene signature through an AP-1-dependent mechanism [ChIP-seq]

overall_design: BIN67 cells were co-transfected (FuGENE 6, Promega #E269A) with either control (pCDNA3-neo) or BRG1 (PBJ5-BRG1) plasmids at a 10:1 ratio to a plasmid containing puromycin resistance (pBABE-puro). Twenty-four hours after transfection, cells were placed on 2 µg/ml puromycin for 3 days and then harvested for ChIP-seq analyses. ChIP-seq was performed for BRG1 in BIN67 cells +/- BRG1 re-expression.

first: Jesse

last: Raab


title: Re-expression of SMARCA4/BRG1 in Small Cell Carcinoma of Ovary, Hypercalcemic Type (SCCOHT) promotes an epithelial-like gene signature through an AP-1-dependent mechanism [ATAC-seq]

overall_design: Four biological replicates of BIN67 cells were co-transfected (FuGENE 6, Promega #E269A) with either control (pCMV-neo or pCDNA3-neo) or BRG1 (PBJ5-BRG1) plasmids at a 10:1 ratio to a plasmid containing puromycin resistance (pBABE-puro). Twenty-four hours after transfection, cells were placed on 2 µg/ml puromycin for 3 days and then harvested for analyses. Samples from each biological replicate were divided and processed for ATAC-seq and RNA-seq.


title: Non-CG methylation is more potent than CG methylation in moss genome regulation [Athaliana RNA-Seq]

city: Tel-Aviv

first: Katherine

last: Domb

address: Haim Levanon st.

department: Gray Faculty of Medical and Health Sciences

country: Israel

institute: Tel Aviv University

summary: Cytosine methylation is commonly targeted to symmetrical CG sites, as well as to non-CGs, such as the symmetrical-CHG and asymmetric-CHH sites in plants (H= A, C or T). Thus far, depletion of CG methylation in plants was associated with ample transcriptional activation of transposons. Here, we profiled transcription in various context specific methylation mutants in the early-diverged plant, Physcomitrella patens. We discovered that specific elimination of CG methylation is fully complemented by non-CG methylation but not vice versa. Between the symmetrically-methylated sites, CHG methylation silenced transposons stronger than CG methylation did. Finally, non-CG methylation revealed as crucial for the silencing of CG depleted transposons. Our results suggest that non-CG methylation evolved to silence transposons due to functional limitations and/or rapid mutability of methylated-CGs.

overall_design: mRNA-sequencing of A. thaliana wild type and ddcc (drm1drm2cmt2cmt3) leaves samples

first: Aviva

last: Katz

first: Rafael

last: Yaari

first: Efrat

last: Kaizler

first: Vu

last: Hoang Nguyen

first: Uyen

last: Vu Thuy Hong

first: Ofir

last: Griess

first: Keith

last: Harris

first: Karina

last: Gitin Heskiau

first: Nir

last: Ohad

first: Assaf

last: Zemach


title: Non-CG methylation is more potent than CG methylation in moss genome regulation [Ppatens RNA-Seq]

overall_design: mRNA-sequencing of P. patens wild type and single and double DNMT mutant samples (drm1drm2, met, cmt, dnmt3b, met/dnmt3b, cmt/dnmt3b)


title: The role of MELK in melanoma progression

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

summary: Survival kinase MELK has been shown to be important for proliferation of several tumors such as brain, breast or prostate. MELK expression is elevated in cutaneous melanoma, therefore, we analyzed the role of MELK in melanoma. Inhibition of MELK in melanoma cell lines resulted in decreased proliferation, increased cell death and decreased invasion. MELK expression is regulated through MAP kinase pathway and inhibition of MAPK pathway leads to diminished MELK expression. Finally, inhibition of MELK reduces tumor size in nude mice.

overall_design: A375 cells stably expressing two individual inducible shRNAs against MELK were used to prepare the total RNA, which was then used to analyze for gene expression using Illumina expression array.

first: Radoslav

last: Janostiak

first: Jianhong

last: Ou

first: Zhu

last: Lihua


title: Re-expression of SMARCA4/BRG1 in Small Cell Carcinoma of Ovary, Hypercalcemic Type (SCCOHT) promotes an epithelial-like gene signature through an AP-1-dependent mechanism [AFOS RNA-seq]

first: Bernard

last: Weissman

overall_design: BIN67 pINDUCER20-FLAG-A-FOS cells incuded with 1 µg/µl of doxycycline (DOX) daily with media change for 48 hours prior to transfections. Cells were co-transfected (FuGENE 6, Promega #E269A) with either control (pCDNA3-neo) or BRG1 (PBJ5-BRG1) plasmids at a 10:1 ratio to a plasmid containing puromycin resistance (pBABE-puro). Twenty-four hours after transfection, cells were placed on 2 µg/ml puromycin for 3 days and then cell pellet were harvested for RNA-seq analysis. Cell pells were flash frozen and stored at -80°C until total RNA extraction. Standard library preparation and sequencng was performed by Novogene (Novogene Corporation Inc, Sacramento, CA)

first: Krystal

last: Orlando

first: Amber

middle: K

last: Douglas

first: Aierken

last: Abudu


title: Changes in mRNA Expression by schedule-dependent combination of 5-FU and selumetinib

city: Daejeon

first: Seung Jin

last: Lee

address: 99 Daehak-ro, Yuseong-gu

department: College of pharmacy

institute: Chungnam national university

summary:
Anti-tumor effect of the combination between 5-FU and selumetinib was treatment schedule-dependent in BRAF or KRAS mutant CRC cells. Treatment of 5-FU for 2 days followed by selumetinib for another 2 days exhibited synergism for cell viability, whereas single or reversely combined treatment showed antagonism
Microarray analysis revealed the distinct groups of genes underlying the efficacy for schedule-dependent treatment.

overall_design: The mRNA expression was analyzed in 5 groups of colo205 cells treated with DMSO(vehicle)(V), 5-FU (FX), selumetinib (AZD6244)(AX), 5-FU followed by selumetinib (FA), or selumetinib followed by 5-FU (AF). Triplicate samples were prepared for each treated group and vehicle-treated samples were used as control group.

first: Seung

middle: j

first: Hye

middle: y

last: Jang


title: Gene expression pattern upon deletion of IRE1 in Candida albicans

city: New Delhi

first: Sneh

middle: Lata

last: Panwar

state: Delhi

address: Lab No 106, School of life science, JNU New campus New Delhi

department: Life sciences

institute: Jawaharlal Nehru University New Delhi

summary: To elucidate role of IRE1 in Candida albicans, genome wide expressional profile change was compared  by microarray analysis between wild type (SC5314) and IRE1 mutant (ire1 DX) cells after successful RNA extraction. Expression of six genes (HWP1, ECE1, SOD3, AMS1, YWP1, SIT1 and FET34) was validated by qPCR and observed to have similar expression pattern when compared to their relative expression in microaaray data.

overall_design: Agilent Whole Genome Candida albicans 8x15k Gene Expression  (AMADID: 026377) designed by Genotypic Technology privatted Limited, Bangalore  , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

middle: L

last: Panwwar


title: mRNA array in liver tissue samples of Sprague-Dawley rats

city: Barcelona

first: Christian

middle: Griñán

last: Ferré

state: Barcelona

address: Joan XIII, s/n

department: Pharmacology, Toxicology and Therapeutic Chemistry

country: Spain

institute: University of Barcelona

summary: Non-alcoholic fatty liver disease (NAFLD) has increased over the last decades and may evolve into hepatocellular carcinoma (HCC). As HCC is challenging to treat, knowledge on the modifia-ble risk factors for NAFLD/HCC, (e.g. hypercaloric diets rich in fructose) is essential. We used a model of diethyl nitrosamine-induced hepatocarcinogenesis to investigate the liver cancer-promoting effects of a diet supplemented with 10% liquid fructose, administered to male and female rats for 11 months. A subset of the fructose-supplemented rats received resveratrol in the last 4 months of treatment. We observed metabolic abnormalities mainly in the female fructose-supplemented rats (increases in weight, adiposity, and plasma glucose and triglycerides, as well as liver triglycerides and a reduced insulin sensitivity index), which were partially reversed by resveratrol. The livers of fructose-supplemented rats showed no de visu or histological evi-dence of liver tumorigenesis. Targeted analysis of 84 cancer-related genes in the female liver samples revealed expression changes associated with cancer-related pathways, but individual genes indicated that some changes increased the risk of hepatocarcinogenesis (Sfrp2, Ccl5, Socs3, and Gstp1), while others exerted a protective/preventive effect (Bcl2 and Cdh1). In conclusion, our data do not clearly demonstrate that chronic fructose supplementation promotes HCC development in rats.

overall_design: The expression of 84 mature cancer mRNAs in the liver of Sprague-rats corresponding to the different syudy groups (Control CT, Fructose FRC and Fructose plus Resveratrol)

first: Juan

middle: C

last: Laguna

first: Nuria

last: Roglans

first: Marta

last: Alegret

last: Griñán-Ferré


title: Potential Onco-Suppressive Role of miR122 and miR144 in Uveal Melanoma through ADAM10 and C-Met Inhibition

status: Public on Dec 29 2020

city: Genoa

first: Adriana

middle: Agnese

last: Amaro

address: Largo Rosanna Benzi 10

department: Molecular Pathology

institute: IRCCS Ospedale Policlinico SAN MARTINO - IST - NATIONAL CANCER RESEARCH INSTITUTE

summary: Uveal melanoma (UM) is a rare tumor of the eye that leads to deadly metastases in about half of the patients. ADAM10 correlates with c-Met expression in UM and high levels of both molecules are related to the development of metastases. MiR122 and miR144 modulate ADAM10 and c-Met expression in di erent settings. We hypothesized a potential onco-suppressive role for miR122 and miR144 through modulation of ADAM10 and c-Met in UM. We analyzed the UM Cancer Genome Atlas data portal (TCGA) dataset, two other cohorts of primary tumors and five human UM cell lines for miR122 and miR144 expression by miR microarray, RT-qPCR, Western blotting, miR transfection and luciferase reporter assay. Our results indicate that miR122 and miR144 are expressed at low levels in the UM cell lines and in the TCGA UM dataset and were down-modulated in a cohort of seven UM samples, compared to normal choroid. Both miR122 and miR144 directly targeted ADAM10 and c-Met. Overexpression of miR122 and miR144 led to reduced expression of ADAM10 and c-Met in the UM cell lines and impaired cell proliferation, migration, cell cycle and shedding of c-Met ecto-domain. Our results show that miR122 and miR144 display an onco-suppressive role in UM through ADAM10 and c-Met modulation.

overall_design: miRNA Gene expression profiles of 19 unique samples from uveal melanoma patients were measured.

first: Amaro

last: Adriana

first: Croce

last: Michela

first: Ferrini

last: Silvano

first: Barisione

last: Gaia

first: Gualco

last: Marina

first: Perri

last: Patrizia

first: Pfeffer

last: Ulrich

first: Jager

last: J. Martine

first: Coupland

last: Sarah E.

first: Mosci

last: Carlo

first: Filaci

last: Gilberto

first: Fabbi

first: Queirolo

last: Paola

first: Gangemi

last: Rosaria


title: Differential expression of genes in HCMV-infected or zeocin-treated ARPE-19 cells

city: Princeton

first: Thomas

last: Shenk

state: New Jersey

address: 119 Lewis Thomas Laboratory, Washington Road

department: Molecular Biology

institute: Princeton University

summary: We studied changes in a whole transcriptome during HCMV infection or zeocin treatment.

overall_design: Retinal pigment epithelial (ARPE-19) cells were infected with HCMV or treated with zeocin and total RNA was isolated at 24 hpi. Total 8 individual samples were used. There were 2 replicates analyzed per individual sample.

first: M

middle: T

last: Nogalski

first: T


title: Gene Expression Profiling in progesterone-induced HGSC development.

city: Indianapolis

first: Jaeyeon

last: Kim

state: IN

address: 635 Barnhill Drive, MS4053

department: Department of Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

summary: Here we show that ovarian progesterone is a crucial endogenous factor inducing metastatic ovarian cancer in a mouse model of high-grade serous carcinoma (HGSC). To examine the molecular signaling pathways underlying progesterone (P4)-induced HGSC development, we performed gene-expression profiling using RNA sequencing.

overall_design: mRNA profiles of wild type (Ovid) mice, DKO (Dicer Pten conditional KO) mice and bilateral ovariectomy DKO mice, and  bilateral ovariectomy DKO mice with treated P4  were generated by RNA sequencing, in triplicate, using Illumina NextSeq500.

first: Eunyoung

last: Park


title: The role of Prokineticin 2 in endometrial decidualization

city: zhengzhou

first: Ma

last: Linna

address: East of Jianshe Road NO.1

department: Center for Reproductive Medicine

institute: The First Affiliated Hospital of Zhengzhou University

summary: Recurrent implantation failure(RIF) is an urgent problem to be solved in reproduction.Currently, endometrium decidualization damage is considered as one of the important causes, but the mechanism is still unclear. Prokineticin 2(PK2) is a newly discovered secreted protein with multiple biological functions, and its role in the endometrium is unknown.Our previous study showed that PK2 was significantly increased in RIF patients, but endometrial decidualization markers PRL and IGFBP1 were lower compared with the control group. We performed transcriptome sequencing, we found there were significant differences between the PK2 overexpression group and the control group. Differential genes mainly involved in decidualization process including adhesion, immunity, chemotaxis, ect.

overall_design: Gene expression profile of PK2 overexpression group through lentivirus infection compared with control group  in decidualized cells

first: Linna

last: Ma

first: Yue

first: Guidong

last: Yao

first: Xueshan

first: Jun

last: Zhai


title: Transcriptional profiling of BoNT/A-induced lung injury in mice

city: Beijing

first: Duo

last: Su

address: Street Dongdajie

institute: Beijing Institute of Microbiology and Epidemiology

summary: In this study, we performed time course RNAseq profiling on mouse lungs induced by  intratracheal inoculation of BoNT/A. We systematically identified the lung intrinsic responses related to pulmonary botulism. These data highlight the ability of BoNT/A to induce acute inflammatory respones

overall_design: Examination of the trascriptional altertions  in mice  lungs  after acute exposure a single dose of BoNT/A in a time-dependent manner.

first: Huiying

last: Yang


title: ZFP541 ChIP-seq targets during male meiotic prophase

city: Chuo-ku

first: Kei-ichiro

last: Ishiguro

state: Kumamoto

department: Institute of Molecular Embryology and Genetics

country: Japan

institute: Kumamoto university

summary: ZFP541 is assumed to possess putative DNA-binding domains and associated with histone deacetylases, implying it plays a role in regulation of transcription via modulation of chromatin status. Therefore, we used ChIP-seq to search for targets of ZFP541 in meiotic prophase of mouse spermatocytes.

overall_design: ZFP541 ChIP was performed using chromatin lysates, that were derived from wild type testes at postnatal day 18-19, and protein A Dyna-beads (Thermo-Fisher) coupled with 5 μg of rabbit anti-ZFP541-N antibodies (#1 and #2). ChIP-seq libraries were prepared using 20 ng of input DNA, and 4 ng of ZFP541 ChIP DNA with KAPA Library Preparation Kit (KAPA Biosystems) and NimbleGen SeqCap Adaptor Kit A or B (Roche) and sequenced by Illumina Hiseq 1500 to obtain single end 50 nt reads. ChIP-seq reads were trimmed to remove adapter sequence when converting to a fastq file.

first: Yuki

last: Takada

first: Makoto

last: Tachibana

first: Ryo

last: Maeda

first: Kumi

last: Matsuura

first: Kenichi

last: Horisawa


title: RNA-seq analysis of the gene expression profile in HES2 hESCs after MTA2 transcript was decreased

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

institute: Anhui University

summary: Purpose:The goals of this study is to analyze the downstream genes after MTA2 expression was downregulated in human embryonic stem cells (hESCs) with RNA-seq approach.

overall_design: HES2 human ESCs cultured in N2B27/KSR condition in the presence of 10 µg Activin A and 10 µg bFGF were collected by using Trizol. These samples were sent to GENERGY BIO (Shanghai, China) company to do deep sequencing by using illumina Hiseq.

first: Shoudong

last: Ye


title: Proton shifting induces cell growth and is exploited in leukemia by epigenetic enforcement of H+/lactate-cotransporter expression

city: Boston

first: Li

last: Jiang

state: MA

address: 360 Longwood Ave

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

summary: Ion balance is critical for membrane polarity, signaling and bioenergesis in cells. Here, we report that proton distribution resets metabolism and alters growth in hematopoietic cells. Multiple oncogenic mutations in acute myeloid leukemia utilize proton partitioning to enhance growth by epigenetically upregulating H+/lactate-co-transporter, MCT4, shuttling protons extracellularly to increase intracellular pH. Secondarily, activity of metabolic enzymes (hexokinase, pyruvate kinase and glucose-6-phosphate dehydrogenase) is increased, raising carbon flux through glycolysis and pentose phosphate pathway necessary for proliferation. MCT4-overexpression in normal hematopoietic stem and progenitor cells increases growth without malignant transformation. Yet, inhibiting MCT4 in AML decreases pHi and carbon flux that improves animal survival and, unexpectedly, elimination of leukemic initiating cells in vivo. AML with increased MCT4 expression have activating histone mark, H3K27ac, in MCT4 promoter where MLL-AF9 and BRD4 directly bind. These data demonstrate the sequential alteration of metabolism through epigenetic activation of proton regulator and point to cytoplasmic alkalization as a growth promoting strategy exploited by malignant cells. Inhibiting this process may diminish the competitive advantage of leukemia and potentially improve AML treatment.

overall_design: MCT4 was knock out by CRISPR-Cas9 in murine MLL-AF9 AML, with non-targeting gRNA as control. Upon induction of Cas9, AML was cultured in either 20% or 2% oxygen conditions. Total RNA was harvested and mRNA was extracted for high throughtput RNA sequencing.

first: David

last: Scadden

first: Cheuk

middle: H

last: Man


title: Combined heart-lung transplant for COVID-19

city: Nashville

first: Jonathan

middle: A

last: Kropski

state: TN

department: Medicine

institute: Vanderbilt University Medical Center

summary: Here we report single-cell RNA-sequencing generated from one COVID-19 lung removed at the time of organ transplant.

overall_design: scRNA-seq of unsorted single-cell suspension generated from one COVID-19 lung ~10 weeks after initial infection was performed using 10X Genomics 5' library prepration.

first: Ciara

last: Shaver

first: Nicholas

middle: E

last: Banovich


title: Gain-of-function MUC5B Promoter Variant, Strongly Linked to Idiopathic Pulmonary Fibrosis, Defines an Epigenetically Poised Enhancer (ATAC-seq)

city: Denver

first: Sarah

last: Sasse

state: CO

address: 1400 Jackson St., K720

institute: National Jewish Health

summary: The G/T transversion, rs35705950, located approximately 3 kb upstream of the MUC5B start site, is the cardinal risk factor for IPF. Here, we investigate the function and chromatin structure of this -3 kb region and provide evidence that it functions as a classically defined enhancer subject to epigenetic programming. We use nascent transcript analysis to show that RNA polymerase II loads within 10 bp of the G/T transversion site, definitively establishing enhancer function for the region. By integrating ATAC-seq analysis of fresh and cultured human airway epithelial cells with nuclease sensitivity data, we demonstrate that this region is in accessible chromatin that affects the expression of MUC5B. Through applying paired single nucleus RNA- and ATAC-seq to frozen tissue from IPF lungs, we extend these findings directly to disease, with results indicating that epigenetic programming of the -3 kb enhancer in IPF occurs in both MUC5B-expressing and non-expressing lineages. In aggregate, our results indicate that the MUC5B-associated variant, rs35705950, resides within an enhancer that is subject to epigenetic remodeling and contributes to pathologic misexpression in IPF.

overall_design: The Omni method for the Assay for transposase-accessible chromatin by sequencing (Omni-ATAC-seq) was performed in primary human airway epithelial cells cultured at air-liquid interface (ALI), cells from fresh bronchial brushes or BEAS-2B airway epithelial cells. All samples were sequenced in duplicate.

first: Fabienne

last: Gally

middle: S

last: Kurche

first: Margaret

last: Gruca

first: Tsukasa

last: Okamoto

first: Hong

middle: W

last: Chu

first: Xiaomeng

last: Hou

first: Olivier

middle: B

last: Poirion

first: Justin

last: Buchanan

first: Sebastian

last: Preissl

first: Bing

last: Ren

first: Sean

middle: P

last: Colgan

first: Robin

middle: D

last: Dowell

first: Ivana

middle: V

last: Schwartz

first: Anthony

last: Gerber


title: The IPF-associated variant in MUC5B, rs35705950, resides within an enhancer that is subject to lineage- and disease-dependent epigenetic remodeling

summary: Genetic polymorphisms account for over 30% of the risk for sporadic pulmonary fibrosis. Yet it remains unknown how the minor variant of rs35705950, the strongest driver of IPF genetic risk, mediates molecular changes to influence IPF development. In the parent publication we use chromatin immunoprecipitation, nuclease sensitivity, nascent transcript analysis, bulk RNA- and ATAC-seq from established cell lines, and finally, paired single-nucleus RNA- and ATAC-seq from IPF patients and controls to demonstrate that the variant rs35705950 resides within a classically defined enhancer of the MUC5B locus.

overall_design:
In this pilot study we used paired single nucleus RNA- and ATAC-sequencing on fresh frozen control and IPF lung tissue specimens obtaind through the Lung Transplant Research Consortium or our Systems Biology project (COMIRB #15-1147). Samples were stratified by rs35705950 genotype and IPF disease status and include 2 control specimens (1 homozygous nonvariant at rs35705950 (GG), one homozygous variant (TT)), and 2 IPF specimens (1 homozygous nonvariant at rs35705950 (GG), one homozygous variant (TT)). To minimize confounding variability with small sample size samples were age-, race-, and sex-matched.
**Unable to provide raw sequencing files due to conflict with privacy protection for human subjects**

first: David

middle: I

last: Yang

first: Jonathan

last: Cardwell


title: Gain-of-function MUC5B Promoter Variant, Strongly Linked to Idiopathic Pulmonary Fibrosis, Defines an Epigenetically Poised Enhancer

last: Sasse

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

overall_design: Refer to individual Series


title: Transcriptomics in whole-blood cells of Buruli ulcer patients identifies a signature of inflammation

city: Paris

first: Jeremy

last: Manry

address: 24 boulevard du Montparnasse

institute: INSERM, Institut Imagine

summary: Mycolactone, a lipid-like toxin, is the major virulence factor of Mycobacterium ulcerans, the etiological agent of Buruli ulcer. Its involvement in lesions development has been widely described in early stages of the disease, through its cytotoxic and immunosuppressive activities, but less is known about later stages. Here, we revisit the role of mycolactone in disease outcome and provide the first demonstration of the pro-inflammatory potential of this toxin. We found that the mycolactone-containing mycobacterial extracellular vesicles produced by M. ulcerans induced the production of IL-1β, a potent pro-inflammatory cytokine, in a TLR2-dependent manner, targeting NLRP3/1 inflammasomes. We showed our data to be relevant in a physiological context. The in vivo injection of these mycolactone-containing vesicles induced a strong local inflammatory response and tissue damages, which were prevented by corticosteroids. Finally, several soluble pro-inflammatory factors, including IL-1β, were detected in infected tissues from mice and Buruli ulcer patients. Our results revisit Buruli ulcer pathophysiology by giving a new insight, thus paving the way for development of new therapeutic strategies, taking account the pro-inflammatory potential of mycolactone.

overall_design: 29 patients diagnosed with Buruli ulcer and treated at the Centre de Diagnostique et de traitement de la Lèpre et de l’Ulcère de Buruli CDTLUB (Pobè, Benin) were enrolled for the study. 3 mL of whole blood from each subject into a Tempus tube (Applied Biosystem) at diagnosis (Day 0) and at the end of treatment (Day ≥ 56). For subjects remaining at the CDTLUB after the completion of their antibiotic treatment (e.g. for surgery), additional whole blood samples were collected. Total RNA was extracted with the Tempus Sample kit (Applied Biosystem). From the 29 patients, a total of 100 blood samples passed BioAnalyser (Agilent) quality control, with mean RNA integrity numbers above 8.7 (the lowest value being 6.5), indicating high quality RNA.

first: Jérémy

first: Estelle

last: Marion

first: Laurent

last: Abel

first: Alexandre

last: Alcaïs


title: Gcn5 transcriptional activation of Myc-induced genes promotes B-cell lymphomagenesis

city: Smithville

first: Sharon

middle: Roth

last: Dent

state: Texas

address: 1808 Park Road 1C

institute: Univ Texas M.D. Anderson Cancer Center

summary:
Purpose: In this study we sought to elucidate whether Gcn5 cooperates with Myc to induce the formation of lymphoma using an in vivo model, the Eµ-Myc mouse. In order to define the molecular mechanisms for how Gcn5 contributes to lymphoma development upon overexpression of Myc, we performed RNA-seq analyses on total RNA isolated from CD19+ B cells sorted from spleens of 5-6-week-old wild-type, Eµ-Myc, and Eµ-Myc; Gcn5Fx/Fx mice.
Conclusions: Loss of Gcn5 not only ameliorates dysregulation of the cell cycle caused by Myc overexpression, but also affects Myc-induced pathways related to cancer cell growth.

overall_design: mRNA profiles of CD19+ B cells of 5-6 week old WT, Eµ-Myc, and CD-19 Cre; Eµ-Myc; Gcn5 Fx/Fx and mice.

first: Aimee

last: Farria

middle: Y

first: Jianjun

last: Shen

first: Yue

last: Lu

first: Kevin

last: Lin


title: Transcriptomic responses predict the toxic effect of parental combined exposure to DBP and DiBP on the early development of zebrafish offspring

city: Zhenjiang

first: Hui

last: Chen

address: Xuefu Road

institute: jiangsu university

summary: Dibutyl phthalate (DBP) and diisobutyl phthalate (DiBP) have been reported to exhibit reproductive toxicity and may pose a threat to their offspring. However, the combined effect of DBP and DiBP on offspring remains unclear, especially for aquatic organisms. The aims of this study were to assess the effects of parental combined exposure to DBP and DiBP on early development of zebrafish offspring, and to explore the potential molecular mechanisms involved. The early developmental indicators and transcriptomic profiles of F1 larvae were examined after parental exposure to DBP, DiBP and their mixtures (Mix) for 30 days. Results showed that parental exposure to DBP and DiBP, alone or in combination, resulted in increasing hatchability at 48 hpf and heart rate at 96 hpf, and affected the malformation and mortality in F1 larvae. Generalized linear model (GLM) indicated that the interactive effects between DBP and DiBP on the mortality and malformation of F1 larvae was antagonistic. The transcriptomic analysis predicted that the molecular mechanisms of parental combined exposure were different from those of either chemical alone, disruption of the molecular function involving unfolded protein binding, E-box binding and photoreceptor activity in F1 larvae could be the mechanism of action after parental combined exposure.

overall_design: Larvae mRNA sequencing of 120 h post-fertilization offspring after parental single and combined exposure to DBP and DiBP for 30 days, in triplicate, using Illumina

first: Kun

first: Xuchun

last: Qiu

first: Hai

last: Xu

first: Weiwei

last: Feng

first: Guanghua

last: Mao

first: Ting

last: Zhao

first: Xiangyang

last: Wu

first: Liuqing


title: Mitochondrial transfer of the mutant human ND6T14484C gene causes visual loss and optic neuropathy

city: Provo

first: David

middle: Wayne

last: Sant

state: UT

address: 1712 South East Bay Blvd, Building 5 Suite 300

department: Biomedical Informatics

institute: Noorda College of Osteopathic Medic

summary: In this study we investigated the effects of mutant human ND6 on mouse optic nerves

overall_design: Optic nerves of mice with mutant human ND6

first: Hong

last: Yu

first: John

last: Guy


title: Gain-of-function MUC5B Promoter Variant, Strongly Linked to Idiopathic Pulmonary Fibrosis, Defines an Epigenetically Poised Enhancer (PRO-seq)

first: Sarah

last: Sasse

overall_design: Deep sequencing of nascent transcripts was performed using Precision Run-on sequencing (PRO-seq) in airway eptihelial cells including cancer-derived A549 and LC-2/ad cells, which express MUC5B under basal culture conditions, and BEAS-2B cells, which do not. All samples were sequenced in duplicate.

first: Fabienne

last: Gally

middle: K

first: Jonathan

last: Kurche

first: Margaret

last: Gruca

first: Tsukasa

last: Okamoto

last: Chu

first: Xiaomeng

last: Hou

first: Olivier

last: Poirion

first: Justin

last: Buchanan

first: Sebastian

last: Preissl

first: Bing

last: Ren

first: Sean

last: Colgan

first: Robin

last: Dowell

first: Ivana

last: Yang

last: Schwartz

first: Anthony

middle: N

last: Gerber


title: Transcriptomic response of Sclerotinia sclerotiorum after exposure to allyl-isothiocyanate and indol-3 carbinol

city: Pontevedra

first: Pilar

last: Soengas

state: Pontevedra

address: Palacio de Salcedo

department: Brassica Genetic and Biochemistry

institute: CSIC

summary: We performed a transcriptomic analysis of the necrorophic fungus Sclerotinia sclerotiorum exposed to two different isothiocyanates (allyl-isothiocyanate and indol-3-carbinol), searching for mechanisms of adaptation and detoxification of these chemicals.

overall_design: Three comparisons were performed: allyl-isothiocyanate vs control, indol-3-carbinol vs control and allyl-isothiocyanate vs indol-3-carbinol. Two repetitions of each treatment were performed.

first: Pari

last: Madloo

first: Margarita

last: Lema