title: Changes in nuclear shape and gene expression in response to simulated microgravity are LINC complex-dependent

status: Public on Jan 31 2021

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

country: USA

institute: Case Western Reserve University

type: Expression profiling by high throughput sequencing

summary: Microgravity is known to affect the organization of the cytoskeleton, cell and nuclear morphology and to elicit differential expression of genes associated with the cytoskeleton, focal adhesions and the extracellular matrix. Although the nucleus is mechanically connected to the cytoskeleton through the LInker of Nucleoskeleton and Cytoskeleton (LINC) complex, the role of this group of proteins in these responses to microgravity has yet to be defined. Therefore, we used simulated microgravity achieved by growing cells on a 3d clinostat to investigate whether the LINC complex acts to mediate responses to the microgravity environment. We show that nuclear shape and differential gene expression are both responsive to simulated microgravity in a LINC-dependent manner and that this response changes with the duration of exposure to simulated microgravity. These LINC-dependent genes likely represent elements normally regulated by the mechanical forces imposed by gravity on Earth.

overall_design: Response of MCF 10A engineered cells to SMG

first: S

last: Neelam

first: B

last: Richardson

first: R

last: Barker

first: C

last: Udave

last: Gilroy

first: M

first: H

last: Levine

first: Y

last: Zhang


title: Cephalopod Neurogenomics

city: St Augustine

first: Leonid

middle: L

last: Moroz

state: FL

address: 9505 Ocean Shore Blvd

institute: University of Florida

summary: Transcriptome profiling of Octopus nervous systems and associated structures provides insights into the molecular organization of neuronal complexity and behavioral flexibility. RNA-seq also highlights molecular diversity in cell signaling pathways.

overall_design: Ninety five transcriptomes from Octopus bimaculoides tissues and cells are included. Sixty one transcriptomes are neuronal tissues, including individual lobes of the brain, the optic lobes, stellate ganglia, and arm cords. There are at least three replicates of each neural tissue, except for the subesophageal lobes, which wwas divided into anterior, middle, and posterior regions with a single replicate of each. Thirty four transcriptomes are from non-neuronal tissues including representatives from circulatory, digestive, endocrine, reproductive, integumentary, and visual systems/tissues. All transcriptomes were run on Illumina platforms: either HiSeq3000 or NextSeq500

first: Gabrielle

middle: C

last: Winters

first: Peter

last: Williams

first: Caleb

middle: J

last: Bostwick

first: Yelena

middle: V

last: Bobkova


title: Sensory profiles and immune related expression patterns of patients with and without neuropathic pain after peripheral nerve lesion

status: Public on Jan 30 2021

city: Würzburg

first: Richa

last: Bharti

state: Bavaria

address: Josef-Schneider-Straße 2 / Bau D15

department: IMIB,Core Unit Systemmedizin

country: Germany

institute: University of Wuerzburg

summary: We investigated systemic expression profiles of patients with painful and painless peripheral nerve lesion compared to control subjects

overall_design: We investigated n=14 samples, no replicates, comparison between two patient groups, and patient group with healthy controls. (NL-1) is with nerve lesion and (NL-0) is without neuropathic pain.

first: Nurcan

last: Üçeyler

first: Melissa

last: Held


title: Small RNA and Degradome Deep Sequencing Reveals the roles of microRNAs in Seed Expansion in Peanut (Arachis hypogaea L.)

city: Zhengzhou

first: Xingli

last: Ma

address: Wenhua Road 95

country: China

institute: Henan Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: Seed expansion in peanut is a complex biological process involving many gene regulatory pathways. MicroRNAs (miRNAs) play important regulatory roles in plant growth and development, but little is known about their functions during seed expansion, or how they contribute to seed expansion in different peanut lines. We examined seed miRNA expression patterns at 15 and 35 days after flowering ( DAF ) in two peanut 8th generation recombinant inbred lines (RIL8); 8106, a medium-pod variety, and 8107, a super-pod variety. Using high-throughput sequencing, we identified 1082 miRNAs in developing peanut seeds including 434 novel miRNAs. We identified 316 differentially expressed miRNAs by comparing expression levels between the two peanut lines. Interestingly, 24 miRNAs showed contrasting patterns of expression in the two RILs, and 149 miRNAs were expressed predominantly in only one RIL at 35 DAF. Also, potential target genes for some conserved and novel miRNAs were identified by degradome sequencing; target genes were predicted to be involved in auxin mediated signaling pathways and cell division. We validated the expression patterns of some representative miRNAs and 12 target genes by qPCR, and found negative correlations between the expression level of miRNAs and their targets. miR156e, miR159b, miR160a, miR164a, miR166b, miR168a, miR171n, miR172c-5p, and miR319d and their corresponding target genes may play key roles in seed expansion in peanut. The results of our study also provide novel insights into the dynamic changes in miRNAs that occur during peanut seed development, and increase our understanding of miRNA function in seed expansion.

overall_design: We examined seed miRNA expression patterns at 15 and 35 days after flowering (DAF) in two peanut 8th generation recombinant inbred lines (RIL8); 8106, a medium-pod variety, and 8107, a super-pod variety by using high-throughput sequencing

first: Dongmei

last: Yin


title: p53 binding in mouse embryonic stem cells treated with Nutlin

city: Bethesda

first: Jing

last: Huang

state: MD

institute: National Cancer Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The goal is to profile p53 binding sites in Nutlin-treated mouse embryonic stem cells.

overall_design: Fifty million of mES cells were treated with 20 uM Nutlin for 8 hours. Fixed cells were subject to ChIP-seq assay.


title: RNA-seq revealed many novel genes associated with Leishmania donovani persistence and clearance in host macrophage

city: Kolkata

first: Nahid

last: Ali

state: West Bengal

address: 4, Raja Subodh Chandra Mallick Rd, Poddar Nagar, Jadavpur,

country: India

institute: CSIR-Indian Institute of Chemical Biology

summary: Mouse models were infected with Leishmania donovani and the effects were observed over multiple passages to observe the macrophage-parasite interaction

first: Md

last: Shadab


title: Transcriptome-wide in vitro effects of aspirin on patient-derived normal colon organoids

city: Charlottesville

first: Matthew

last: Devall

state: Virginia

address: 1335 Lee Street

institute: University of Virginia

summary: Here, we used bulk RNA-seq data derived from healthy colon organoids (un)exposed to aspirin. Through the use of external single cell RNA-seq data, we estimate changes in cell composition. We extend this analysis by controlling for cell composition and performing WGCNA to identify modules of co-expression differentially affected by aspirin treatment in colon organoids.

overall_design: Analysis of the effects of aspirin treatment on gene expression in colon organoids

first: Graham

last: Casey


title: Anabolic effects of cheddar cheese consumption in human skeletal muscle

city: Salt Lake City

first: Michael

middle: T

last: Howard

state: UT

department: Human Genetics

institute: University of Utah

summary: The goal of this project was to use a randomized, cross over design to determine the amino acid blood and muscle response to the acute ingestion of cheddar cheese in comparison to that of bovine milk and to investigate the skeletal muscle mTORC1 response.

overall_design: Human muscle samples were analyzed, n=4. 3 samples per visit, two visits, so a total of 24 samples.

first: Micah

last: Drummond

first: Naomi

middle: M

last: de Hart

first: Ziad

middle: S

last: Mahmassani


title: Functional and structural basis of extreme conservation in vertebrate 5’ untranslated regions [icm2]

city: Stanford

first: Gun Woo

last: Byeon

state: CA

address: 279 Campus Dr., Beckman Center B309

institute: Stanford University

summary: The lack of knowledge about extreme conservation in genomes remains a major gap in our understanding of the evolution of gene regulation. Here, we reveal an unexpected role of extremely conserved 5’UTRs in non-canonical translational regulation that is linked to the emergence of essential developmental features in vertebrate species. Endogenous deletion of conserved elements within these 5’UTRs decreased gene expression, and extremely conserved 5’UTRs possess cis-regulatory elements that promote cell-type specific regulation of translation. We further developed in-cell mutate-and-map (icM2), a novel methodology that maps RNA structure inside cells. Using icM2, we determined that an extremely conserved 5’UTR encodes multiple alternative structures and that each single nucleotide within the conserved element maintains the balance of alternative structures important to control the dynamic range of protein expression. These results explain how extreme sequence conservation can lead to RNA-level biological functions encoded in the untranslated regions of vertebrate genomes.

overall_design: In-cell M2-seq (mutate-and-map sequencing)

first: Gun

middle: W

first: Elif

last: Sarinay Cenik

first: Lihua

last: Jiang

first: Hua

last: Tang

first: Rhiju

last: Das

first: Maria

last: Barna


title: Expression data from kidney tissues treated with vehicle, losartan and metformin

city: Kumammoto

first: Kohei

last: Omachi

address: 5-1, Oe-honmachi

department: Molecular Medicine

country: Japan

institute: Kumamoto University

summary:
Chronic kidney disease (CKD) is one of the major global health problems with high incidence, poor prognosis and high medical cost. However, few pharmacological options are available for CKD. Metformin is widely used for treatment of type-2 diabetes, but recent works showed that metformin ameliorates tumor progression, inflammatory disease and tissue fibrosis. Whether metformin ameliorates non-diabetic chronic glomerular disease and CKD is unexplored. Here we showed that metformin or losartan (used as control) has protective effects against CKD by suppressing proteinuria, renal inflammation, fibrosis and glomerular injury in Alport syndrome mouse model, which spontaneously manifests chronic glomerular and kidney disease. Transcriptome analysis showed that metformin and losartan influenced molecular pathways of metabolism and inflammation, respectively. While metformin specifically affected genes that were classified as metabolic regulators, losartan specifically altered genes that were classified as inflammatory regulators. Metformin also induced multiple signaling pathways not affected by losartan. Overall, metformin ameliorates non-diabetic chronic glomerular diseases, and could be considered a therapeutic option for CKD.
We used microarrays to investigate the global gene expression underlying the protective effects of metformin on Alport syndrome mice model

overall_design: Total RNA  were extracted from kidney tissues of wildtype and vehicle-treated Alport mice (Alport CON), losartan-treated Alport mice (Alport Losartan), metformin-treated Alport mice (Alport metformin). Extracted RNA samples were hybridized to Affymetrix Clariom S Arrays.

first: Hirofumi

last: Kai


title: DIMETHYLBENZANTHRACENE (DMBA) INDUCED MAMMARY CARCINOGENESIS IN MMTV-Neu and MMTV/p53 KO FEMALE MICE AND EFFECTS OF REXINOIDS

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: Murine models of mammary cancers have proven to be highly informative on numerous fronts including individual gene causation, microenvironmental analyses, and chemoprevention studies. The MMTV-Neu transgenic model of mammary cancer has proven to be a useful model and has been employed in several prevention studies.  However, there are certain practical drawbacks to its use including long tumor latencies and a tendency to develop mutations in the transmembrane domain of Neu (unlike human HER2/Neu overexpressing breast cancers).  Here we report modifications that were made in an attempt to optimize this mouse model for chemopreventive screening.  First, homozygous MMTV-Neu and homozygous P53 KO mice were crossed to create a MMTV-Neu/P53+/- strain (which more closely approximates the genetic make-up of most HER2+ human patients).  Second, to overcome the drawback of long tumor latencies, the mice were treated with DMBA for eight weeks.  DMBA treatment greatly decreased the latency of mammary carcinomas in the MMTV-Neu mice although the resulting tumors remained histopathologically similar to those from MMTV-Neu control mice.  Next, we examined gene expression in tumors derived from MMTV-Neu, MMTV-Neu/p53+/-, and DMBA treated mice.  It was found that the characteristic MMTV-Neu tumor-defined expression pattern was still the most prevalent feature of all the MMTV-Neu tumors despite their being crossed to the p53 null allele, treated with DMBA, or both.  However, tumors from the DMBA treated animals exhibited many unique gene expression changes including the high expression of stress response, defense, and inflammation genes.  Finally, we demonstrated that the RXR agonists UAB30 and Targretin, both inhibited mammary cancer formation in MMTV-Neu mice, including those treated with DMBA. These results demonstrate the potential utility of this murine model for additional chemoprevention studies.

overall_design: 19 samples

first: Jerry

last: Usary

first: Ronald

middle: A

last: Lubet


title: Transcriptome data of Hyphopichia burtonii and Hyphopichia pseudoburtonii when exposed to high osmosterss (1M NaCl) condtion at several time points.

city: Seoul

first: Dong Wook

last: Lee

address: 84, Heukseok-ro, Dongjak-gu

country: South Korea

institute: Chung-Ang university

summary:
The goal and objectives of this experiment are to find out the transcriptomic changes and differences when the two halotolerant yeast H. burtonii and H. pseudoburtonii isolated from Nuruk were exposed to high salt conditions over time. So the RNA-seq anaylsis was perfomred by setting up each time points (0, 5, 15, 30 min)
The sequencing data of RNAs obtained from yeast cells cultured in YPD + 1M NaCl at each time were analyzed using YPD condtions as acontrol

sample_organism:
Hyphopichia burtonii
Hyphopichia pseudoburtonii

overall_design: 4 conditions were analzyed duplicate : total 16 samples for two yeast species

first: DongWook

first: HyunAh

last: Kang


title: Analysis of lentiviral vector splicing events with nanopore sequencing

city: London

first: Chad

last: Swanson

state: Select...

address: Great Maze Pond

department: Infectious Diseases

country: United Kingdom

institute: King's College London

summary: All lentiviral vectors derived from HIV-1 have the major splice donor (SD1) in the 5’ leader region and splice acceptor 7 (SA7) within the env region. Splicing events decrease the amount of full-length RNA available for packaging into virions and could lead to packaging of genomes containing internal deletions. Because there are splice sites or splicing enhancer/silencer elements in both gag and env, we compared how deleting each region affected intracellular genomic RNA splicing in RNA isolated from transfected HEK293Tsa cells. Oxford Nanopore direct cDNA sequencing was used to characterize the splice variants because the long-read length allows full-length transcripts to be analyzed. We show that deleting 507 nt of env, including the SA7, decreased the number of splicing events per transcript and increased the proportion of unspliced genomic RNAs ~3-fold in the cell.

overall_design: The usage of canonical and cryptic splice sites in wildtype lentiviral vector and four mutant vectors was evaluated

first: Helin

last: Sertkaya


title: Selective inhibition of the second bromodomain of BET family proteins results in robust antitumor activity in preclinical models of acute myeloid leukemia

city: North Chicago

first: Xin

last: Lu

state: IL

address: 1 North Waukegan Rd

department: Oncology Discovery

institute: Abbvie

summary: Dual bromodomain BET inhibitors (DbBi) that bind with similar affinities to the first and second bromodomains across BRD2, BRD3, BRD4 and BRDt only displayed modest activity as monotherapy in clinical trials.  Thrombocytopenia, closely followed by symptoms characteristic of GI toxicity, have presented as dose limiting adverse events that may prevented escalation to higher dose levels for more robust efficacy. ABBV-744 is a highly selective inhibitor for the second bromodomain (BD2) of the four BET family proteins.  In contrast to the broad antiproliferative activities observed with DbBi, ABBV-744 displayed significant antiproliferative activities largely but not exclusively in cancer cell lines derived from AML and androgen receptor (AR) positive prostate cancer.  Studies in AML xenograft models demonstrated anti-tumor efficacy for ABBV-744 that was comparable to the pan-BET inhibitor ABBV-075 but with improved tolerability.  Enhanced anti-tumor efficacy was also observed with the combination of ABBV-744 and the Bcl-2 inhibitor, venetoclax (ABT-199) compared to monotherapies of either agent alone. These results collectively support the clinical evaluation of ABBV-744 in AML (Clinical Trials.gov identifier: NCT03360006).

overall_design: mRNA profiles of AML and NSCLC cell lines treated with ABBV-075, ABBV-744 or DMSO control, for 24 hours, using Illumina HiSeq3000.

first: Lu

last: Zhang

first: Tianyu

last: Cai

first: Xiaoyu

last: Lin


title: PAX5 promotes progression of SCLC

city: Tianjin

first: Zhe

last: LIU

address: 22 Qixiangtai Road

department: Department of Immunology

institute: TIanjin Medical University

summary: RNAseq of SCLC cell line H1155 with PAX5.knocked out. The goals of this study are to identify the function of  PAX5 in SCLC.

overall_design: Examination of 6 samples of H1155 cells including 3 vector lines and 3 PAX5 KO lines

first: Xiaobo

last: Li

first: Junrong

last: Liu


title: MYB is an essential regulator of primitive human hematopoiesis in human pluripotent stem cell differentiation cultures.

city: Guangzhou

first: ZAHIR

last: SHAH

state: Guangdong

address: 190 Kaiyuan avenue, Haungpu district, Guangzhou, China

department: Stem Cells and Regenerative Medicines

institute: GIBH,CAS, China

summary: MYB is well recognized to be a key regulator of definitive hematopoiesis that plays an important role in the maintenance and multilineage differentiation of hematopoietic stem cells (HSCs). In the vertebrate developmental context, MYB is widely regarded dispensable for primitive hematopoiesis but critically required for the development of definitive hematopoiesis. To explore the role of MYB in human hematopoietic development we have inactivated the gene by bi-allelic TALEN-supported gene targeting in several lines of human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs), and subjected these cells to hematopoietic differentiation in well-defined cell culture conditions. Venus gene reporter was inserted into the knock-in allele to monitor MYB expression during the course of the hESC/iPSC differentiation. The gene reporter system showed that MYB is specifically expressed during hematopoietic commitment in the earliest primitive blood cells. Moreover, the level of MYB expression was highest at the commitment stage of differentiation and significantly decreased at the maturations stage. We found that MYB was not required for initial hematopoietic commitment of nascent mesoderm and emergence of primitive, yolk sac-type human hematopoietic progenitors. However, inactivation of MYB severely abrogated proliferation of the primitive erythroid and mixed erythroid-macrophage-megakaryocyte progenitors. In addition, MYB-negative hESC/iPSC lines demonstrated major defects in myeloid cell development and completely failed to generate mature granulocytes. Transposon-mediated rescue of MYB expression in MYB-null cells efficiently restored both the primitive hematopoietic progenitors and immature myeloid cells. Our data indicate that in contrast to its previously attributed exclusive role in definitive hematopoiesis, MYB is indispensable for primitive human hematopoiesis.

overall_design: We inactivated the human MYB gene by biallelic integration of reporter donor cassette through TALENs-supported genetic engineering. The modified lines including MYB+/+, MYB+/- and MYB-/- were differentiated into hematopoietic cells in our new established serum-free, cytokine-free culture system with minimal BMP4 exposure for mesoderm induction. The cells were harvested at different time points for cell-sorting based on the expression of MYB-YFP and CD34 cell surface marker on day 6 and day 12. Subsequently the total mRNA was extracted using trizole reagent and subject to RNA-sequencing. In total 31 samples, 2 or 3 replicate samples per group being biological repeats, were analyzed.

first: Zahir

last: Shah

first: Igor

last: Samokhvalov


title: Integrated study of the circRNA, lncRNA, mRNA and miRNA networks in testicular heat exposure

status: Public on Jan 29 2021

city: Bengbu

first: Meng

last: Liang

state: Anhui

address: Donghai road 2600

institute: bengbu Medical College

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

overall_design: Refer to individual Series


title: Analysis of FOXO3 human targets in Huntington's disease neural stem cells: FOXO3 knock-down [RNA-seq2]

city: Paris

first: Christian

last: Neri

address: 9 quai St Bernard

department: CNRS UMR 8256, Inserm ERL U1164

country: France

institute: Sorbonne Université, CNRS, INSERM

summary: We report the identification of human genes that are differentially expressed upon growth factor deprivation of Huntington's disease neural stem cells, in a FOXO3-knockdown-dependent manner. To this end, we generated RNA-seq data in human Huntington's disease (HD) and CAG-corrected (C116) neural stem cells.

overall_design: mRNA profiles of control C116 and HD NSCs treated with FOXO3 siRNAs or scramble RNAs were generated by deep sequencing, in triplicate using Illumina NextSeq 500.

first: Francesca

last: Farina

first: Satish

last: Nair


title: Sequencing of RNA Isolated Through RNA Immunoprecipitation (RIP) of Murine Cortical Tissue Using STAU2 Antibody

city: Rensselaer

first: Sally

last: Temple

state: NY

address: One Discovery Drive

institute: Neural Stem Cell Institute

summary: We report here the sequencing and analysis of RNA isolated through RNA immunoprecipitation (RIP) of embryonic mouse cortical tissue. STAU2 antibodies were used to perform these RIPs at four different ages, and the RNA was compared against matching input samples. This allowed characterization of putative STAU2 binding sites in different RNA classes over the course of development, important as STAU2 is a known double-stranded RNA binding protein with a role in asymmetric division of neural progenitor cells.

overall_design: Examination of STAU2-bound RNA at four discrete time points during murine cortical development. Three STAU2 RIP samples (biological replicates) and three input samples (biological replicates) were analyzed at each time point.

first: Patrick

last: Gordon

first: Frank

last: Doyle

first: Scott

last: Tenenbaum


title: Integrated study of the circRNA, lncRNA and mRNA networks in testicular heat exposure

summary: The World Health Organization has recognized testicular function with temperature dependence. Testicular heat exposure caused by occupational factors, lifestyle and clinical disease, etc., can lead to different degrees of reproductive obstacles. The aim of this study is to reveal the transcriptional regulatory network and their potential crucial roles in testicular heat exposure. After passing quality control, the high throughput sequencing data of mouse testicular tissue for scrotum heat exposure and control group were carried out various analyses including differentially expressed transcriptome exploration, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and network regulation.  Differential transcriptome expression analysis revealed that 172 circRNA (91 upregulation and 81 downregulation), 465 lncRNA (96 upregulation and 369 downregulation) and 2721 mRNA (2003 upregulation and 718 downregulation) were identified as significant differential expression in the mouse testicular tissue of heat exposure compared with control group using the cut-off of log2fold change >= 0.585, p value <= 0.05 and q value <= 1.00. Through GO term analysis, differentially expressed lncRNA and mRNA may play important functions in negative regulation of cellular process [GO:0048523], meiotic cell cycle [GO:0051321], cytoplasm [GO:0005737], membrane raft [GO:0045121], amide binding [GO:0033218], extracellular matrix  binding [GO: 0050840]. KEGG pathway analysis of differentially expressed lncRNA and mRNA can be classified into MAPK signaling [mmu04010], purine metabolism [mmu00230], homologous recombination [mmu03440], RNA transport [mmu03013], nod-like receptor signaling pathway [mmu04621]. This research provides high throughput sequencing data of transcriptome in testicular heat exposure model and lays the foundation for further study on the circRNA and lncRNA in male reproductive diseases related to elevated testicular temperature.

overall_design: Mice were first anesthetized by 5% chloral hydrate with 0.01 ml/g, and then the scrotum were placed in water bath for 25 minutes at 33 °C in the control group or for 25 minutes at 43 °C in the high temperature group. The mice were sacrificed after 7 days, testes (3 testes of 33 °C treament and 3 testes of 43 °C treament) were separated from mouse body and used for experiments of histological detection and RNA isolation.

first: Ke

last: Hu


title: Functional and structural basis of extreme conservation in vertebrate 5’ untranslated regions [dmsmap1d]

first: Gun Woo

last: Byeon

overall_design: Multiplexed DMS mutational profiling

first: Gun

first: Elif

last: Sarinay Cenik

first: Lihua

last: Jiang

first: Hua

last: Tang

first: Rhiju

last: Das

first: Maria

last: Barna


title: Integrated study of the miRNA networks in testicular heat exposure

summary: The World Health Organization has recognized testicular function with temperature dependence. Testicular heat exposure caused by occupational factors, lifestyle and clinical disease, etc., can lead to different degrees of reproductive obstacles. The aim of this study is to reveal the transcriptional regulatory network and their potential crucial roles in testicular heat exposure. After passing quality control, the high throughput sequencing data of mouse testicular tissue for scrotum heat exposure and control group were carried out various analyses including differentially expressed transcriptome exploration, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and network regulation.  Differential transcriptome expression analysis revealed that 279 miRNAs (138 upregulation and 141 downregulation) were identified as significant differential expression in the mouse testicular tissue of heat exposure compared with control group using the cut-off of log2fold change >= 0.585, p value <= 0.05 and q value <= 1.00. This research provides high throughput sequencing data of transcriptome in testicular heat exposure model and lays the foundation for further study on the miRNA in male reproductive diseases related to elevated testicular temperature.


title: ZCCHC8 is required for the degradation of pervasive transcripts originating from multiple genomic regulatory features

first: Kenneth

last: Yamada

address: BG 30 RM 408 30 CONVENT DR

institute: NIDCR

summary: The vast majority of mammalian genomes are transcribed as non-coding RNA in what is referred to as “pervasive transcription.”  Recent studies have uncovered various families of non-coding RNA transcribed upstream of transcription start sites.  In particular, highly unstable promoter upstream transcripts known as PROMPTs have been shown to be targeted for exosomal degradation by the nuclear exosome targeting complex (NEXT) consisting of the RNA helicase MTR4, the zinc-knuckle scaffold ZCCHC8, and the RNA binding protein RBM7.  Here, we report that in addition to its known RNA substrates, ZCCHC8 is required for the targeted degradation of pervasive transcripts produced at CTCF binding sites, open chromatin regions, promoters, promoter flanking regions, and transcription factor binding sites.  Additionally, we report that a significant number of RIKEN cDNAs and predicted genes display the hallmarks of PROMPTs and are also substrates for ZCCHC8 and/or NEXT complex regulation suggesting these are unlikely to be functional genes.  Our results suggest that ZCCHC8 and/or the NEXT complex may play a larger role in the global regulation of pervasive transcription than previously reported.

overall_design: Examination of RNA-seq differential expression of genomic regulatory features in mouse salivary gland cells SIMS wild-type, Btbd7 KO (negative control), and Zcchc8 KO cells

first: Joshua

last: Collins


title: Differential Gene Expression in Adgrl3 KO Mice

city: Würzburg

first: Richa

last: Bharti

institute: University of Wuerzburg

summary: We report the differential expression of genes in Adgrl3 -/- mice in comparison to Adgrl3 +/+ mice. Three ADHD-relevant brain regions; hippocampus, pre-frontal cortex and striatum are included alongside a whole-brain analysis

overall_design: Examination of 3 independent brain regions in 2 genotypes. Combined analysis between genotypes across brain regions

first: Niall

last: Mortimer

first: Olga

last: Rivero

first: Klaus

middle: P

last: Lesch


title: RNAseq analysis of BXD mouse strains infected with PR8M virus

city: Münster

last: Schughart

address: Von-Esmarch-Str 56

department: Virology

institute: University Münster

summary:
Gene expression changes in the lung was studied by RNAseq
Results: Strong differences in the host response between strains

overall_design: Lungs were collected from mice, RNA was isolated and sequenced.


title: MIPP-Seq: Ultra-sensitive rapid detection and validation of low-frequency mosaic mutations

city: Boston

first: Ryan

middle: N

last: Doan

state: MA

address: 3 Blackfan Circle, CLS 15040

institute: Boston Children's Hospital

type: Genome variation profiling by high throughput sequencing

summary: MIPP-Seq provides an ultra-sensitive, low-cost approach for detecting and validating known and novel mutations in a highly scalable system with broad utility spanning both research and clinical diagnostic testing applications. The scalability of MIPP-Seq allows for multiplexing mutations and samples, which dramatically reduce costs of variant validation when compared to methods like ddPCR. By leveraging the power of individual analyses of multiple unique and independent reactions, MIPP-Seq can validate and precisely quantitate extremely low AAFs across multiple tissues and mutational categories including both indels and SNVs. Furthermore, using Illumina sequencing technology, MIPP-seq provides a robust method for accurate detection of novel mutations at an extremely low AAF.

overall_design: These data contain 9 raq fastq files used for the validation of the sensitivity of MIPP-seq to assess SNVs and Indels identified in a dilution series and from human brain tissue. The raw data include up to 3 unique primer amplicons for individual mutations identified in either a control DNA for the dilution series or a panel of Autism  and control brain tissues specimens. Each raw data file contains up to 96 different mutations, each barcoded using the primer sequence. Please see the MIPP-seq methods publication for further interpretations of the data. All autism data was analyzed and merged into a single set of analyzed files, located in the ASD.tar.gz


title: Analysis of FOXO3 human targets in Huntington's disease neural stem cells: FOXO3 nuclear induction [RNA-Seq]

first: Christian

last: Neri

summary: We report the identification of F0X03 targets in human Huntington's disease neural stem cells. To this end, we generated RNA-seq data upon FOXO3 nuclear induction in human Huntington's disease (HD) and CAG-corrected (C116) neural stem cells.

overall_design: RNA-seq profiles of control (C116) and Huntington's disease (72Q/19Q) neural stem cells treated with Ryk siRNA or scramble RNA were generated by deep sequencing, performed in duplicate using Illumina HiSeq 2500.

first: Jessica

last: Voisin


title: Analysis of FOXO3 human targets in Huntington's disease neural stem cells: FOXO3 nuclear induction [ChIP-Seq]

summary: We report the identification of F0X03 targets in human Huntington's disease neural stem cells. To this end, we generated FOXO3 ChIP-seq data upon FOXO3 nuclear induction in human Huntington's disease (HD) and CAG-corrected (C116) neural stem cells.

overall_design: ChiP-seq profiles of control (C116) and Huntington's disease (72Q/19Q) neural stem cells treated with Ryk siRNA or scrambled RNA were generated by deep sequencing, performed in duplicate using Illumina HiSeq 2500.

first: Satish

last: Nair


title: Analysis of FOXO3 human targets in Huntington's disease neural stem cells


title: Single-cell RNA-seq of air-liquid interface bronchioalveolar cells

city: Utrecht

first: Mauro

last: Muraro

state: Utrecht

address: Uppsalalaan, 8

country: Netherlands

institute: Single Cell Discoveries

summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), may result in acute respiratory distress syndrome (ARDS), multi-organ failure and death. The alveolar epithelium is a major target of the virus, but representative models to study virus host interactions in more detail are currently lacking. Here, we describe a human 2D air-liquid interface culture system which was characterized by confocal-, electron-microscopy and single cell mRNA expression analysis. In this model, alveolar cells, but also basal cells and rare neuroendocrine cells, are grown from 3D self-renewing lung bud tip organoids. These cultures were readily infected by SARS-CoV-2 with mainly surfactant protein C-positive ATII-like cells being targeted. Consequently, significant viral titers were detected and mRNA expression analysis revealed induction of type I/III interferon response program.  Treatment of these cultures with a low dose of interferon lambda dramatically reduced viral replication. Hence, these cultures represent an experimental model for SARS-CoV-2 infection and can be applied for drug screens.

overall_design: We have setup a bronchioalveolar model for studying COVID-19. scRNAseq was performed to characterize the model on air-liquid interface bronchioalveolar cells not infected with SARS-CoV-2.

first: Mart

last: Lamers

first: Jelte

last: van der Vaart

first: Hans

last: Clevers

first: Bart

last: Haagmans


title: Transcriptome Profile of Quantum Dots on Saccharomyces cerevisiae

city: Springfield

first: Kyoungtae

last: Kim

state: Missouri

address: 901 S National Ave

institute: MISSOURI STATE UNIVERSITY

summary: Transcriptome Profile of CdSe/ZnS and InP/ZnS Quantum Dots on Saccharomyces cerevisiae

overall_design:
Exposure of InP/ZnS quantum dots at 100 µg/mL on Saccaromyces cerevisiae (O.D. of 0.3-0.6) for six hours.
Exposure of CdSe/ZnS quantum dots at 10 µg/mL on Saccaromyces cerevisiae (O.D. of 0.3-0.6) for six hours.

first: Cullen

last: Horstmann

first: Chelsea

last: Campbell


title: Single cell gene expression profiling of the response of the dorsal motor nucleus of the vagus neurons to remote ischemic preconditioning [DMV_RIPC_RT-PCR]

city: Albuquerque

first: Rajanikanth

last: Vadigepalli

state: PA

address: 1 University of New Mexico

institute: University of New Mexico

summary: We developed a mesoscale single cell transcriptomics data from hundreds of  the dorsal motor nucleus of the vagus (DMV) neurons under homeostasis and following physiological perturbations. Our results revealed that homeostatic DMV neuronal states can be organized into distinguishable input-output signal processing units. Remote ischemic preconditioning induced a distinctive shift in the neuronal states towards diminishing the role of inhibitory inputs.

overall_design: Male sprague dawley rats were subjected to remote ischemia preconditioning (rIPC) through ligation of bilateral femoral arteries or sham operation incluing ketamine/xylazine anesthesia and surgical exposure without ligation. n=2-3 biological replicates. All samples were collected 2.5 hours after referfusion.

first: Jonathan

last: Gorky

first: James

last: Schwaber


title: The Bromodomain Containing 8 (BRD8) Transcriptional Network in Human Lung Epithelial Cells

city: Cleveland

first: Ann

last: Harris

state: Ohio

address: 2109 Adelbert Rd Building

department: Genetics and Genome Sciences

institute: Case Western Reserve University


title: Single cell gene expression profiling of the response of the dorsal motor nucleus of the vagus neurons to cardiac ischemia [DMV_Cardiac-Ischemia_RT-PCR]

summary: We developed a mesoscale single cell transcriptomics data from hundreds of  the dorsal motor nucleus of the vagus (DMV) neurons under homeostasis and following physiological perturbations. Our results revealed that homeostatic DMV neuronal states can be organized into distinguishable input-output signal processing units. Chronic cardiac ischemic injury resulted in a dramatic shift in DMV neuronal states suggestive of enhanced neurosecretory function.

overall_design: Male sprague dawley rats were subjected to ligation of the left anterior decending artery after exteriorizing the heart through a small left thoracotomy. Sham surgery included ketamine/xylazine anesthesia and surgical exposure without ligation. n=3-4 biological replicates. All samples were collected after either 1 week or 3 weeks post surgery.


title: The Bromodomain Containing 8 (BRD8) Transcriptional Network in Human Lung Epithelial Cells [RNA-Seq]

summary: Mechanisms regulating gene expression in the airway epithelium underlie its response to the environment.  A network of transcription factors (TFs) and architectural proteins, modulate chromatin accessibility and recruit activating or repressive signals. Bromodomain-containing proteins function as TFs or by engaging methyltransferase or acetyltransferase activity to induce chromatin modifications.  Here we investigate the role of Bromodomain Containing 8 (BRD8) in coordinating lung epithelial function. Sites of BRD8 occupancy genome-wide were mapped in human lung epithelial cell lines (Calu-3 and 16HBE14o-). CCCTC-Binding Factor (CTCF) was identified as a predicted co-factor of BRD8, based upon motif over-representation under BRD8 ChIP-seq peaks. Following siRNA-mediated depletion of BRD8, differentially expressed genes with peaks of BRD8 occupancy within 20 kb were subject to gene ontology process enrichment analysis. BRD8 targets are enriched for genes involved in the innate immune response and depletion of BRD8 increased the secretion of the antimicrobial peptide beta-defensin 1 and multiple chemokines.

overall_design: 6 RNA-seq (single end) datasets, 3 replicates between 2 treatment groups

last: Browne

first: Monali

last: Mazumdar

first: Alekh

last: Paranjapye

first: Jenny

last: Kerschner

first: Shih-Hsing

last: Leir


title: microRNA expression profiling of the response of the dorsal motor nucleus of the vagus to physiological perturbations and cardiac injury

summary: We developed microRNA expression profiling data from the dorsal motor nucleus of the vagus (DMV) neurons under homeostasis and following physiological perturbations of remote ischemic preconditioning and cardiac ischemia. Male Sprague-Dawley rats were subjected to remote ischemia preconditioning (rIPC), ligation of the left anterior descending artery (LAD), or rIPC with LAD following two hours later (rIPC 2h/LAD). All samples were collected 24 hours after LAD.

overall_design: Male sprague dawley rats were subjected to remote ischemia preconditioning (rIPC), ligation of the left anterior descending artery (LAD), or rIPC with LAD following two hours later (rIPC 2h/LAD). n=2 3 biological replicates. All samples were collected 24 hours after LAD.

first: Jon

first: Alison

last: Moss

first: Marina

last: Balycheva


title: The Bromodomain Containing 8 (BRD8) Transcriptional Network in Human Lung Epithelial Cells [ChIP-seq]

overall_design: 3 IDR ChIPseq datasets generated from 2 replicates each

last: NandyMazumdar


title: Expression profiling of the response of the dorsal motor nucleus

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

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

overall_design: Refer to individual Series


title: VELCRO-IP RNA-seq reveals ribosome expansion segment function in translation genome-wide

city: Stanford

first: Gun Woo

last: Byeon

address: 279 Campus Dr., Beckman Center B309

institute: Stanford University

summary: Roles for ribosomal RNA (rRNA) in gene regulation remain largely unexplored. With hundreds of rDNA units positioned across multiple loci, it is not possible to genetically modify rRNA in mammalian cells, hindering understanding of ribosome function. It remains elusive whether expansion segments (ESs), tentacle-like rRNA extensions that vary in sequence and size across eukaryotic evolution, may have functional roles in translation control. Here, we develop VELCRO-IP RNA-seq: a versatile methodology to generate species-adapted ESs and to map specific mRNA regions across the transcriptome that preferentially associate with ESs. By applying VELCRO-IP RNA-seq to a mammalian ES, ES9S, a large array of transcripts was identified that are selectively recruited to ribosomes via an ES. We further characterize a set of 5’ UTRs that facilitate cap-independent translation through ES9S-mediated ribosome binding. Thus, we present a technology for studying the enigmatic ESs of the ribosome, revealing their function in gene-specific translation.

overall_design: VELCRO-IP (variable expansion segment-ligand chimeric ribosome-IP) for human ribosome ES9S binding mRNAs

first: Kathrin

last: Leppek

first: Gun

first: Kotaro

last: Fujii

first: Maria

last: Barna


title: Potassium tellurite exerts its toxicity on ribosome in Escherichia coli

city: Beijing

first: Bin

last: Liu

state: Beijing

address: Hai Dian

department: School of Life Sciences

institute: Tsinghua University

summary:
Purpose: We use the ribosome profiling protocol to understand why EF4 confers resistance to tellurite and how tellurite affects ribosome.
Methods: We used ribosome profiling and transcriptomic data to analyze mainly by plastid software. The ribosome were purified by sucrose gradient separation.
Results: Using polysome profile and sequencing data, we found that tellurite disables the ribosome subunits to form a functional 70S ribosome and reduces the ribosome density after tellurite exposure. We also found that tellurite influences the ribosome reaching to stop codon. Tellurite shortened the ribosome protected fragment, this process was mediated by EF4. EF4 mediated more gene expression including these known tellurite resistance genes to confer tellurite resistance. Tellurite also induced many differential gene expression.
Conclusions: Tellurite exerts its toxicity on ribosome by disabling 70S ribosome formation, reaching to stop codon, and inducing differential gene expression.

overall_design: Ribosome footprints and mRNAs from BW25113 (WT) and JW2553 (ΔEF4) strains that were treated with potassium tellurite and sequenced, in two replicates, using Illumina HiSeq 2500

first: Chunlai

last: Chen


title: Rejuvenation of Human Stem Cells from Aged Dental Pulp by High Concentration of Serum Culture ex vivo

status: Public on Jan 28 2021

city: Seoul

first: Joung-Ho

last: Moon

address: Daehak-ro

department: Department of Conservative Dentistry and Dental Research Institute, School of Dentistry

institute: Seoul National University

summary: Adult stem cells maintain tissue integrity by continuous cellular turnover or serving progenitor cells. Human dental pulp stem cells (hDPSCs) are adult stem cells that can readily be isolated from extracted teeth, then expanded or stored for tissue repair and regeneration. However, stem cells undergo an aging process characterized by a decline in functional abilities, leading eventually to reduced organ function and delays in tissue repair. Like other stem cells, hDPSCs age and go through cellular senescence but little information is available on the mechanisms of aging or the details of the aged hDPSC phenotype. In this study, we investigated the aging phenotypes of human dental pulp and hDPSCs and attempted to rejuvenate them. In this study, hDPSCs were isolated from 23 third molars and primary cultured. Then, Flow cytometey, growth curve, dubling time, colony-forming-unit assay, cell viability after cryopreservation and in serum-free media culture, differntiation capacity for odonto-, adipo- and chondrogenesis, and RNA sequencing were analyzed. As results, the aged tooth maintained its weight of dental pulp however, the frequency of CD90+CD73+ mesenchymal stem cells inside pulp significantly decreased with donor aging. Moreover, each aged hDPSCs showed lower proliferative abilities, poorer survival rates, decreased tri-differentiation potential, and decline in metabolic activities than young hDPSCs. We also found those aged phenotypes could be recovered by cultivating aged hDPSCs in high concentration of fetal bovine serum (FBS) ex vivo and furthermore, the declined metabolic activities were restored by the culture. Here, we suggest a novel method of intervention for rejuvenating hDPSCs and these results have applications in both regenerative medicine and stem cell biology.

overall_design: mRNA expression profiles of the  'hDPSCs'   by Illumina NovaSeq 6000 Sequencing System. Three experimental groups, each group containg two cell-lines, were analysed. Group1, hDPSCs obtained from the 20s and cultured with 15% serum; Group2, hDPSCs obtained from the 40s and cultured with 15% serum; Group3, hDPSCs obtained from the 40s and cultured with 60% serum.

first: Joo-Young

last: Park

first: Sun-Young

last: Kim


title: Small RNA Sequencing facilitates quantitative analysis of miRNA expression in feces from mice during DSS-induced colitis and the recovery phase

city: changsha

first: xihong

last: zhou

address: No 644. Yuanda 2nd Road

institute: the Chinese Academy of Sciences

summary: Mice were exposed to 2.5% DSS (MW 36,000–50,000, MP Biomedicals) prepared in autoclaved drinking water for five days, after which they were provided DSS-free drinking water for 13 days. On day 12, 16.7% of mice (20 of 120) whose body weight returned to the same level as on day 1 (the change of body weight was less than 0.5 g) and exhibited an DAI of 0 or 1.00, were used as “well-recovered” mice. To identify which fecal miRNAs were affected during DSS-induced colitis and the recovery phase, we performed small RNA sequencing in feces obtained from well-recovered mice on days 0, 5, and 12 of the treatment regimen.

overall_design: Fecal miRNA profiles of mice before inflammation (n=4), acute inflammatory phase (n=3), and the recovery phase (n=4) were generated by Small RNA Sequencing

first: Xihong

last: Zhou

first: Liuqin

last: He


title: Effect of maternal dioxin exposure on pituitary mRNAs in fetal rats at gestational day 18

city: Hadano

first: Tomoki

last: Takeda

address: Hirasawa 2445

institute: Japan Bioassay Research center

summary: We found that oral administration of TCDD (1 µg/kg) to pregnant rats on gestational day 15 suppressed pituitary syntheisis of growth hormone during the last fetal stage. We performed a DNA microarray analysis to identify the genes linked to the attenuated expression of GH, using the male and female fetal pituitary at GD18 when the reduced expression of GH started to occur because of TCDD.

overall_design: Total RNAs were extracted from the pituitaries of the control and TCDD-exposed fetal rats  at gestational day 18 (both males and females, each N=3), and their cDNAs were applied to the analysis using 44K 60-mer oligomicroarray (Whole Rat Genome Microarray 4x44K v3; Agilent Technologies)

first: Yukiko

last: Hattori


title: Impaired bile secretion promotes hepatobiliary injury in Sickle Cell Disease.

city: Pittsburgh

first: Shuchang

address: 203 Lothrop Street

institute: University of Pittsburgh

summary: Sickle cell disease leads to impaired bile secretion and loss of bile transport

overall_design: Liver pathophysiology

first: Tirthadipa

last: Pradhan-Sundd

first: Satdarshan

last: Monga

first: Silvia


title: Genome-wide RNA-sequencing of E. coli strain 55989 from in vitro and in vivo samples

first: Marta

last: Lourenço

state: Please Select

address: 25-28 Rue du Dr Roux

institute: Institut Pasteur

summary: RNA-seq comparative analysis of an enteroaggregative Escherichia coli human isolate grown in vitro and in vivo (colon samples from monocolonized mice) revealed candidates genes that are either overexpressed or underexpressed. Comparisons included exponential growth vs stationary growth; exponential vs colon and stationary vs colon.

overall_design: Comparison of E.coli 55989 strain mRNA profiles in vitro and in vivo

first: Laurent

last: Debarbieux


title: Bulk RNA sequencing of CD8 T cell from smokers and nonsmokers

city: Research Triangle Park

first: Douglas

middle: A.

last: Bell

address: PO Box 12233

department: Immunity Inflammation and Disease Lab

institute: National Institute of Environmental Health Sciences

summary: Smoking associated gene expression changes from CD8 T cells

overall_design: Antibody-purified human CD8 T cell fractions isolated from peripheral blood from smoking and nonsmoking adults were extracted and libraries were prepared using the TruSeq Stranded Total RNA Library Prep Gold (Illumina).

first: Michelle

middle: R

last: Campbell


title: Single-cell RNA sequencing of peripheral blood immune cells from smokers and nonsmokers

summary: Smoking associated transcriptome changes from peripheral blood cells

overall_design: Peripheral blood cells from smoking and nonsmoking adults were extracted and libraries were prepared using Chromium™ Single Cell 3' Library & Gel Bead Kit v2 (10X Genomics) according to the manufacturer’s guidelines.

first: Suzanne

last: Martos


title: Response of human macrophages to gamma radiation is mediated via expression of endogenous retroviruses

city: Bethesda

first: Kory

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

summary: Ionizing radiation (IR) induces recruitment of monocytes into the exposed area where they are differentiated into macrophages, which elicit an inflammatory response to IR, but can also facilitate vascular growth and tumor progression by producing anti-inflammatory factors. Using primary human monocyte-derived macrophages (MDM) and the THP1 monocytic cell line, we demonstrated that therapeutically relevant gamma radiation doses triggered monocyte differentiation into macrophages with increased expression of both pro- and anti-inflammatory markers, induction of type I interferons (IFN-I), activation of their receptor IFNAR1, and expression of IFN-stimulated genes. We found that these changes correlate with significantly upregulated expression of 622 retroelements from various groups, particularly of several clades of human endogenous retroviruses (HERVs). Elevated transcription was detected in both sense and antisense directions in the HERV subgroups tested, including the most genetically homogeneous clade HERVK HML-2. This resulted in formation of long dsRNA bound to the dsRNA sensors MDA5 and TLR3 and triggering signaling pathways resulted in increased expression of IFN-I and inflammation related genes that enhanced the cumulative inflammatory effect of radiation-induced senescence. HML-2 knockdown was accompanied with reduced expression and secretion of IFNα, pro-inflammatory (IL-1β, IL-6, CCL2, CCL3, CCL8, and CCL20) and anti-inflammatory (IL10) modulators in irradiated monocytes and MDMs.  We conclude that radiation stress-induced HERV expression enhances the IFN-I and cytokine response and results in increased levels of pro-inflammatory modulators along with expression of anti-inflammatory factors associated with the macrophage tumorigenic phenotype.

overall_design: Paired-end stranded RNA-Seq was performed on 14 human samples for a target depth of >=40M read pairs per sample. Of these samples, four represented primary human monocyte-derived macrophages under no ionizing radiation exposure (MDM 0Gy), four represented primary human monocyte-derived macrophages under ionizing radiation exposure (MDM 5Gy), three represented a THP1 monocytic cell line under no ionizing radiation exposure (THP1 0Gy), and three represented a THP1 monocytic cell line under ionizing radiation exposure (THP1 5Gy).

first: Natallia

last: Mikhalkevich

first: Ina

last: O’Carroll

first: Rok

last: Tkavc

first: Kateryna

last: Lund

first: Gauthaman

last: Sukumar

first: Clifton

last: Dalgard

first: Wenxue

last: Li

first: Tongguang

last: Wang

first: Avindra

last: Nath

first: Sergey

last: Iordanskiy


title: RNAseq of primary colorectal cancer cell lines.

city: Palermo

first: Simone

last: Di Franco

address: Via del Vespro, 131

department: Surgical Oncological and Oral Sciences

country: Italy

institute: University of Palermo

summary: The aim of this study is to define a transcriptomic profile (RNA-seq)  from a large cohort of primary colorectal cancer cell lines.

overall_design: Examination of the transcriptome of primary colorectal cancer cell lines characterized by different mutational background, chemioresistance and expression of CD44v6.

first: Giorgio

last: Stassi


title: A genome-wide CRISPR screen identifies HuR as a regulator of apoptosis induced by dsRNA and viral infection

city: 广州

first: HUIXIN

last: GAO

address: 中山二路74号

institute: 中山大学

summary: Cell death is an important host defense in response to viral infections. In this study,we performed an unbiased whole-genome CRISPR/Cas9 screen in A549 lung   adenocarcinoma cells to identify potential regulators involved in cell death triggered dsRNA, a common byproduct of viral replication. Of several top candidate genes, we identified the RNA binding protein ELAV like protein 1 (ELAVL1) (ELAVL1, also called HuR) that encodes Hu antigen R (HuR). Depletion of HuR by gene editing led to less cell death induced by dsRNA. We further demonstrated that HuR regulated apoptosis, and the RNA recognition motif (RRM) 3 of HuR was essential for its proapoptotic function. HuR bound mRNA of anti-apoptotic gene BCL2. HuR depletion had no influence on BCL2 mRNA levels, but instead downregulated the BCL2 translation. Polysome fractionation studies showed that HuR retarded the BCL2 mRNA in the non-translating pool of polysomes. Moreover, protection from dsRNA-induced apoptosis by HuR depletion required the presence of BCL2, indicating that the proapoptotic function of HuR is executed by suppressing BCL2. Consistently, HuR regulated apoptosis induced by infection of encephalomyocarditis or Semliki Forest virus, two unrelated positive strand RNA viruses. Collectively, our work identified a suite of proteins that regulate dsRNA-induced cell death, and elucidated the mechanism by which HuR acts as a pro-apoptotic factor.

overall_design: mRNA profiles of control and HuR-KO cells

first: Huixin

last: Gao


title: Manipulation of noncanonical Ire1-dependent MAPK signaling by a Vibrio agonist-antagonist effector pair

city: Dallas

first: Nicole

middle: Janell

last: De Nisco

state: Texas

address: 6000 Harry Hines Blvd, NA5.146, NA5.146

department: Molecular Biology

institute: University of Texas Southwestern Medical Center

summary: Abstract: Many bacterial pathogens employ effector delivery systems to disrupt vital cellular processes in the host. The type III secretion system 1 of the marine pathogen, Vibrio parahaemolyticus, utilizes the sequential action of four effectors to induce a rapid, pro-inflammatory cell death uniquely characterized by a pro-survival host transcriptional response. Herein we show that this pro-survival response is due to the action of the channel-forming effector VopQ that disrupts autophagic flux through two activities: lysosomal deacidification and inhibition of lysosome-autophagosome fusion. Using a point mutation to separate these two functions, we demonstrate that VopQ acts as an agonist of host ERK1/2 MAPK signaling as a result of its fusion-blocking activity. The pulse of ERK1/2 phosphorylation is restricted to early infection by the timed inhibition of Rho GTPase signaling by the antagonist effector VopS. Inhibition of autophagosome-lysosome fusion and activation of MAPK kinase signaling can be linked to the UPR. VopQ not only activates the IRE1 branch of the UPR, but VopQ’s activation of ERK1/2 MAPK signaling is dependent on IRE1. Since VopS can dampen VopQ-induced IRE1-dependent ERK1/2 activation, we suggest that IRE1 must activate ERK1/2 signaling at or above the level of Rho GTPases. This work elucidates new connections between host autophagy, MAPK signaling and the UPR that bacterial pathogens have evolved to manipulate the host. Methods: We employed genome-wide transcriptional profiling methods (RNA-seq) to measure changes in gene expression in response to infection with V. para T3SS1+, T3SS1+ ΔvopQ, or T3SS1+ ΔvopS. Time points were collected 90 minutes post-infection. In total, libraries from 12 samples (triplicates of uninfected, T3SS1+, T3SS1+ ΔvopQ, and T3SS1+ ΔvopS) were sequenced and mapped to the human genome. EdgeR was used for differential expression analysis using statistical cutoffs of of false discovery rate (FDR) ≤0.01, log2counts-per-million (log2CPM) ≥0 and fold change (FC) cutoffs of -1.5≥ FC ≥1.5

overall_design: Overall 12 samples were analyzed. Each of the 4 conditions was performed in triplicate. There are two sets of reference groups. Group one is uninfected cells and  Group 2 is  V. para strain T3SS1+-infected cells, because we were trying to understand the individual effects of the effectors vopQ and vopS on host gene expression.

first: Mohammed

last: Kanchwala

first: Chao

last: Xing

first: Kim

last: Orth


title: Smoking effect on DNA methylation in human blood CD8T cells

first: Xuting

address: 111 TW Alexander Dr

institute: NIEHS/NIH

type: Methylation profiling by genome tiling array

summary: To better characterize smoking–associated methylation changes in human blood CD8T cells, we used Illumina HumanMethylation450 and HumanMethylationEPIC BeadChips to assess DNA samples from smokers (SM, n=61) and never smokers (NS, n=71).

overall_design:
As part of the Epigenetic Biomarkers of Tobacco Smoke Exposure project, a group of healthy volunteers (61 smokers and 71 nonsmokers) was recruited at the NIEHS Clinical Research Unit (protocol 10-E-0063) between March 2013 and January 2018 from the Raleigh, Durham and Chapel Hill, NC area. All nonsmokers were self-reported as not having smoked >100 cigarettes in their lifetime. Smokers reported their average daily cigarette consumption for the past 3 months [Su D et al. 2016].
For each individual, CD8 T cells were isolated from whole blood using anti-CD8+ antibody-coated magnetic beads.  Nucleated DNA from CD8T cells was collected after sucrose-induced osmotic lysis of cells followed by phenol-chloroform extraction and DNA was stored in Tris-EDTA buffer at -20°C. The HumanMethylation450  and HumanMethylationEPIC BeadChips (Illumina) were used to measure methylation by the NCI Center for Genome Research. Specifically, 500 ng of DNA was bisulfite converted using the EZ-DNA Methylation kit (Zymo Research), hybridized to HumanMethylation450 BeadChip arrays and then scanned with an iScan microarray scanner (Illumina) following the manufacturer’s protocols. The raw IDAT files of 450K and EPIC methylation arrays were read into R with the minfi package [Aryee MJ et al. 2014] separately; the combineArrays function in minfi was utilized to combine the two arrays’ data together based on their common CpG sites. Then, the data was preprocessed with background and dye bias correction using the preprocessNoob method [Fortin JP et al. 2017] and Methylation β value for each CpG site in each sample was output for further analyses.

first: Douglas

last: Bell

first: Michelle

last: Campbell

first: Gary

last: Pittman


title: INTACT vs. FANS for cell-type-specific nuclei isolation: A comprehensive qualitative and quantitative comparison

city: Mainz

first: Susanne

last: Gerber

address: Staudinger Weg 9

department: Institute for Human Genetics

institute: University Medicine Mainz

summary: In this study we used transgenic mouse model to comapre two isolation techniques INTACT and FANS for the isolation of activated neuronal nuclei. Comparison is perfomed on multiple levels like isolation efficiency, membrane integrity, transcriptional and epigenetic state using RNA-seq and ATAC-seq

overall_design: Comparison of two isolation techniques i.e INTACT and FANS for nuclei isolation.

first: Monika

last: Chanu Chongtham

first: Tamer

last: Butto

first: Kanak

last: Mungikar

first: Jennifer

last: Winter


title: The novel-cell free bioactive formulation (BIOF2) modulates specific osteoarthritis’ detrimental and protective genes: A microarray analysis

status: Public on Jan 27 2021

city: Mexico city

first: Ariana

last: Cabrera-Licona

state: Mexico city

address: Patricio Sanz 1582

department: Research

country: Mexico

institute: Esteripharma

summary: A novel-cell free bioactive formulation (BIOF2), US Patent No. 9669074B2, for arthrosic chondrocytes has been recently developed and proved as effective for treating severe knee osteoarthritis, we evaluated transcriptome changes in BIOF2-treated synovial fluid cells, isolated from patients with severe knee osteoarthritis to establish BIOF2 mechanism of action.

overall_design: A transcriptomic analysis of a pool of 3 cells samples from the synovial fluid of severe osteoarthritic knees exposed to BIOF2 for 48 hours was carried out compared to samples without treatment.

first: Juan

last: Paz-García

first: Iván

last: Delgado-Enciso

first: José

last: Valtierra-Álvarez

first: Carlos

middle: E

last: Barajas-Saucedo

first: Héctor

last: Galván-Salazar

first: Brenda

last: Paz-Michel


title: Cis-regulatory variation affects gene expression dynamics

city: Rochester

first: Justin

last: Fay

address: 319 Hutchison Hall, University of Rochester

department: Biology

institute: University of Rochester

summary: This study examined allele-specific expression dynamics in yeast. Gene expression was measured by an RNA-seq time-course over the diauxic shift for three strains of Saccharomcyes cerevisiae and two inter-specific hybrids of S. cerevisiae with S. paradoxus and S. uvarum.

sample_organism: Saccharomyces cerevisiae x Saccharomyces uvarum

sample_organism: Saccharomyces cerevisiae x Saccharomyces paradoxus

overall_design: Profiles of mRNA during the diauxic shift in intra-specific and inter-specific yeast hybrids

first: Ching-hua

last: Shih


title: RNA-seq of human multiple myeloma cell lines and cell lines with long-term exposure to lenalidomide

city: Chuo-ku

first: Yusuke

last: Yamamoto

state: Tokyo

address: 5-1-1, Tsukiji, Chuo-ku

institute: National cancer center research institute

summary: Multiple myeloma (MM) is a hematopoietic malignancy whose prognosis has been improved by immunomodulatory drugs (IMiDs); however, long-term exposure of these drugs caused drug resistance in MM patients. Here we applied RNA sequencing to analyze the novel mechanisms of the acquiring lenalidomide resistance in MM cell lines. Firstly, lenalidomide resistant cell lines were established by long-term exposure of lenalidomide nearly 1 year. Comparative analysis between resistant and sensitive cell lines revealed that the resistant cells secreted a greater number of exosomes and enhanced cell adhesion ability.  By whole transcriptome analysis, snare interaction pathway, which was associated with exosome secretion, was enriched in lenalidomide resistant cell lines. Finally, we identified SORT1 and LAMP2, which increased exosome secretion and cell adhesion ability in lenalidomide resistant cells. Notably, silencing of SORT1 or LAMP2 ameliorated the lenalidomide sensitivity in the resistant cells. In conclusion, our results showed that exosome secretion via SORT1 or LAMP2 could induce cell adhesion, leading to the acquisition of lenalidomide resistance in MM.

overall_design: Lenalidomide resistant cell lines were established by long-term exposure of lenalidomide nearly 1 year. Lenalidomide resistant cell lines had an ability to attach their culture dishes, and their morphology were changed round to spindle shape. Total RNA was extracted from parental cells (KMS21, KMS27, KMS34) and lenalidomide resistant cell lines (KMS21R, KMS27R, KMS34R). RNA-seq was performed to characterize these cells in detail.

first: Tomofumi

first: Yutaka

last: Hattori

first: Takahiro

last: Ochiya


title: Gene expression Profiles following mild and severe muslce contusion in rats

city: Jinzhong

first: Jun-hong

last: Sun

state: Shanxi Province

address: 98 University Street, Yuci District, Jinzhong

department: School of Forensic Medicine

institute: Shanxi Medical University

summary:
We used microarray to investigate gene expression profiles of mildly and severely contused muscle and aimed to provide more information about the molecular mechanisms underlying the repair process. Moreover, we have an attempt to identify useful markers with time-dependent expression for wound age estimation.
Animal models of muscle contusion (mild and severe) were developed to investigate the cellular response to mechanical muscle damage

overall_design: A total of 33 rats were divided randomly into control (n = 3), mild contusion (n = 15), and severe contusion (n = 15) groups; the contusion groups were further divided into five subgroups (1, 3, 24, 48, and 168 h post-injury; n = 3 per subgroup). Total RNA was isolated from muscle tissue for analysis by microarray using the Affymetrix rat Gene 2.0 ST chip.

first: Ru-feng

last: Bai


title: Genomic adaptation and mutational patterns in a HaCaT subline resistant to alkylating agents and ionizing radiation [aCGH]

city: Munich

first: Hanns Leonhard

last: Kaatsch

address: Neuherbergstraße 11

institute: Bundeswehr Institute of Radiobiology

summary: In this study, we compared the genomic landscape of resistant cell line HaCaT/SM to its progenitor HaCaT in order to gain insights into genetic changes associated with continuous alkylation and oxidative stress. We established chromosome numbers by cytogenetics, analyzed DNA copy number changes by means of array CGH, employed the genome-wide chromosome conformation capture technique Hi-C to detect chromosomal translocations and defined mutational signatures based on whole genome sequencing data. We observed the SM-associated elimination of the initially prevailing hypotetraploid cell population in favor of a hyperdiploid one, which contrasts with previous observations that link polyploidization to increased tolerance and adaptability towards genotoxic stress. Furthermore, we observed an accumulation of chromosomal translocations, frequently flanked by DNA copy number changes, which indicates a high rate of DNA double strand break misrepair. HaCaT/SM-specific single nucleotide variants showed enrichment of C>A and T>A transversions and a lower rate of deaminated cytosines in the CpG dinucleotide context. Given the frequent use of HaCaT in toxicology this study provides a valuable data source with respect to the original genotype of HaCaT and the mutational signatures associated with chronic alkylation and oxidative stress.

overall_design: Analysis of DNA copy number changes by means of array CGH in the sulfur mustard-resistant cell line HaCaT.

first: Reinhard

last: Ullmann

first: Hanns


title: Increased environment-related metabolism and genetic expression in the in vitro matured mouse oocytes by transcriptome analysis

city: nanjing

first: Zhang

last: haolin

address: xiaolingwei street

institute: Zhang haolin

summary: Infertility is a world-wide problem for the human at reproductive age, and oocyte in vitro maturation (IVM) is generally applied to acquire the embryo in assisted reproductive technology (ART) for this issue. However, it is still unclear for the differences of RNA expression profile in the oocytes between in vivo (IVO) and IVM culture environment. In this study, we compared the global RNA transcription pattern of oocytes from in vitro and in vivo maturation in mouse. Our results showed that 1864 genes differentially expressed between the IVO and IVM oocytes. Among these 1638 genes were up-regulated and 226 genes were down-regulated, and these changes were mainly divided into environmental adaption, metabolism and genetic expression. Our detailed analysis showed that the expression of genes which belong to metabolism-related processes such as energy metabolism, nucleotide metabolism and carbohydrate metabolism was changed; and these genes were also belonged to organismal systems including environmental adaptation and circulatory system; moreover, we also found that the relative gene expression of genetic expression processes, such as protein synthesis, modification, and DNA replication and repair were also altered. In conclusion, our data suggest that in vitro maturation of mouse oocyte resulted in metabolism and genetic expression changes by environmental changes compared with in vivo matured oocytes.

overall_design: Transcriptomic analysis of oocytes at M II stage was carried out using a protocol for RNA-Seq. The constructed library was sequenced with Geekgene and Gene Denovo platform.

first: Shaochen

first: Haolin

last: Zhang


title: Genomic adaptation and mutational patterns in a HaCaT subline resistant to alkylating agents and ionizing radiation [Hi-C]

overall_design:
Analysis of chromosome numbers by cytogenetic, DNA copy number changes by means of array CGH, chromosomal translocations by Hi-C and mutational signatures by means of whole genome sequencing in the sulfur mustard-resistant cell line HaCaT.
*** Submitter declares raw data are unavailable due to privacy issues.


title: Genomic adaptation and mutational patterns in a HaCaT subline resistant to alkylating agents and ionizing radiation [WGS]

overall_design:
Analysis of chromosome numbers by cytogenetics, DNA copy number changes by means of array CGH, chromosomal translocations by Hi-C and mutational signatures by means of whole genome sequencing in the sulfur mustard-resistant cell line HaCaT.
*** Submitter declares raw data are unavailable due to privacy issues.


title: Genomic adaptation and mutational patterns in a HaCaT subline resistant to alkylating agents and ionizing radiation

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

overall_design: Refer to individual Series


title: Loss of G-Protein Pathway Suppressor 2 promotes tumor growth through activation of AKT signaling

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: G Protein Suppressor 2 (GPS2) is a multifunctional protein that exerts important roles in inflammation and metabolism in adipose, liver and immune cells. GPS2 has recently been identified as a significantly mutated gene in breast cancer and other malignancies and proposed to work as a putative tumor suppressor. However, molecular mechanisms by which GPS2 prevents cancer development and/or progression are largely unknown. Here, we have profiled the phenotypic changes induced by GPS2 depletion in MDA-MB-231 triple negative breast cancer cells and investigated the underlying molecular mechanisms. We found that GPS2-deleted MDA-MB-231 cells exhibited increased proliferative, migratory, and invasive properties in vitro, and conferred greater tumor burden in vivo in an orthotopic xenograft mouse model.  Transcriptomic, proteomic and phospho-proteomic profiling of GPS2-deleted MBA-MB-231 revealed a network of altered signals that relate to cell growth and PI3K/AKT signaling. Overlay of GPS2-regulated gene expression with MDA-MB-231 cells modified to express constitutively active AKT showed significant overlap, suggesting that sustained AKT activation is associated with loss of GPS2. Accordingly, we demonstrate that the pro-oncogenic phenotypes associated with GPS2 deletion   are rescued by pharmacological inhibition of AKT with MK2206. Collectively, these observations confirm a tumor suppressor role for GPS2 and reveal that loss of GPS2 promotes breast cancer cell proliferation and tumor growth through uncontrolled activation of AKT signaling. Moreover, our study points to GPS2 as a potential biomarker for a subclass of breast cancers that would be responsive to PI3K-class inhibitor drugs.

overall_design: Transcriptomic profiling to examine effect of GPS2 depletion on the PI3K/AKT pathway using the MDA-MB231 cell line as a model. We carried out knockout and over-expression experiments using both wild type (WT) MB231 and the following modified MB231 cell lines: MB231-GPS2KO1, -KO2 (two independent pools with two different sets of sgRNAs targeting GPS2, made using CRISPR-Cas9 genome editing), MB231-myrAKT (MB231 cell line with myristoylated AKT, constitutively active AKT), MB231-GPS2KO1/2+MK (MB231-GPS2-KO cell lines treated with 10uM MK2206 (allosteric AKT inhibitor) for 4h prior to sample collection). We had 6 different conditions (WT, KO1 +/-MK, KO2 +/-MK, myr-akt) run in triplicate for a total of 18 samples run as 1 pool. This pool was run as two 75PE Next-Seq runs.

first: Stefano

last: Monti

first: Valentina

last: Perissi


title: RNA sequencing of AMD3100-treated E14 embryonic submandibular glands (eSMGs)

city: Seoul

first: Kyungpyo

last: Park

address: Jongno-Gu Daehak-Ro 101

institute: Seoul National University

summary: In order to elucidate the relationship between CXC chemokine receptor 4 (CXCR4) and embryonic organogenesis, we performed 3' mRNA-seq on control and AMD3100-treated eSMGs.

overall_design: mRNA profiles of control and AMD3100-treated E14 eSMGs

first: Junchul

last: Kim

first: Sang-Woo

last: Lee


title: Investigation of the functional contribution of Riplet in effector CD8 T cells

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary: To understand the function of Riplet in effector CD8 T cells, we have employed whole genome microarray expression profiling of effector CD8 T cells from wild-type (WT) and Riplet knockout (KO) mice. Naive CD8 T cells isolated from splenocytes in WT and Riplet KO mice were stimulated with anti-CD3 and anti-CD28 Abs and after resting culture, restimulated with anti-CD3 Ab in vitro and mRNA was isolated.

overall_design: Effector CD8 T cells from WT and Riplet KO mice were stimulated with anti-CD3 Ab in vitro for 4 hours.

first: Asuka

last: Iwamoto

first: Hiroyuki

last: Oshiumi


title: Identification of potential key genes and pathways associated with the Pashmina fiber initiation using RNA-Seq and integrated bioinformatics analysis

city: Gandarbal

first: Basharat

middle: Ahmad

last: Bhat

state: Kashmir

address: Shuhama

department: Animal Biotechnology

institute: Sher-e-Kashmir University of Agricultural Sciences and Technology

summary: In the present study transcriptomic profiling of skin biopsies containing secondary hair follicles were utilized to identify key genes and signaling pathways involved in hair follicle transition from no-growth phase (telogen) to growth phase (anagen).

overall_design: Ten unrelated Pashmina goats of the same age (24 months) and sex (males) were repeatedly sampled during anagen (October active growth phase) and telogen (March – resting phase, before combing). The skin samples containing Pashmina follicles were collected from the flanking region of each goat. A total of 19 (10 anagen and 9 telogen) samples were obtained for RNA-sequencing as one of the samples from telogen did not qualify the minimum quality criteria for RNA-sequencing.

first: Nazir

last: Ganai


title: Effects of glyphosate residues and different concentrate feed proportions in dairy cow rations on hepatic gene expression, liver histopathology and biochemical blood parameters

city: Braunschweig

first: Fabian

last: Billenkamp

address: Bundesallee 37

institute: Friedrich-Loeffler-Institute

summary: Glyphosate (GLY) is one of the most used active substances in broad-band herbicides worldwide. Although farm animals might be orally exposed to this herbicide via GLY contaminated feedstuffs, not much is known about possible hepatotoxic effects of GLY. As hepatic xenobiotic and nutrient metabolism are closely interlinked, the toxic effects of GLY residues might be influenced by nutrient supply to the liver. Therefore, a feeding trial with lactating dairy cows was conducted to investigate effects of GLY contaminated feedstuffs and different concentrate feed proportions (CFP) in the diets as a tool for varying nutrient supply to the liver. Therefore, 61 German Holstein cows (207 ± 49 days in milk; mean ± standard deviation) were either fed a GLY contaminated total mixed ration (TMR, GLY, average mean GLY intake 122.7 µg/kg bodyweight/day) or control TMR (CON, average mean GLY intake 1.2 µg/kg bodyweight/day) for 16 weeks. Additionally, both groups were further split into subgroups fed a lower (LC, 30% on dry matter basis) or a higher (HC, 60% on dry matter basis) CFP. Blood parameters aspartate aminotransferase, γ-glutamyltransferase, glutamate dehydrogenase, cholesterol, triglyceride, total protein, calcium, phosphorus, acetic acid and urea as well as histopathological evaluation were not influenced by GLY, whereas all mentioned parameters were at least affected by time, CFP or by an interactive manner between time and CFP. Total bilirubin blood concentration was significantly influenced by an interaction between GLY and CFP with temporarily elevated concentrations in GLYHC, whereas the reasons and biological relevance remain unclear. Gene expression analysis indicated 167 CFP-responsive genes, while seven genes showed altered expression in GLY groups compared to CON groups. Since expression changes of GLY-responsive genes were low and liver-related blood parameters changed either not at all or only slightly, the tested GLY formulation was considered to have no toxic effects on the liver of dairy cows.

overall_design: Liver transcriptome analysis of 31 cows fed with either glyphosate-contaminated or control ration as well as high or low concentrate feed proportions in their diets

first: Ann-Katrin

last: Heymann

first: Karina

last: Schnabel

first: Susanne

last: Bühler

first: Jana

last: Frahm

last: Kersten

first: Liane

last: Hüther

first: Ulrich

last: Meyer

first: Dirk

last: von Soosten

first: Nares

last: Trakooljul

first: Jens

last: Teifke

first: Sven

last: Dänicke


title: Gene expression profiling of mouse MPN cells with or without STK11 knockout

city: Memphis

first: Lance

last: Palmer

state: TN

address: 262 Danny Thomas Place

department: Computational Biology

institute: St. Jude Children's Research Hospital

summary: We performed RNA-sequencing of mouse cells derived from colony forming assays (CFA) to evaluate the transcriptome of MPN cells with deletion of the tumor suppressor STK11/LKB1 and relative controls. The CFA are from mouse primary floxed STK11 hematopoietic stem and progenitor cells (HSPCs) transduced with retroviruses encoding the MPN mutation MPLW515L and CRE recombinase to delete STK11.

overall_design: RNA sequencing differential expression analysis of hematopoietic cells from colony formation assays in triplicate: WT cells at plating 1, MPLW515L overxpressing cells at plating 1, MPLW515L STK11 -/- cells at plating 1,3,6

first: Christian

last: Marinaccio

first: John

middle: D

last: Crispino


title: Longitudinal analysis of T-cell receptor repertoires reveals persistence of antigen-driven CD4+ and CD8+ T-cell clusters in Systemic Sclerosis patients

city: Utrecht

first: Aridaman

last: Pandit

address: Heidelberglaan 100

institute: University Medical Center Utrecht

summary: The T-cell receptor (TCR) is a highly polymorphic surface receptor that allows T-cells to recognize antigenic peptides presented on the major histocompatibility complex (MHC). Changes in the TCR repertoire have been observed in several autoimmune conditions, and these changes are suggested to predispose autoimmunity  . Multiple lines of evidence have implied an important role for T-cells in the pathogenesis of Systemic Sclerosis (SSc), a complex autoimmune disease. One of the major questions regarding the roles of T-cells is whether expansion and activation of T-cells observed in the diseases pathogenesis is (auto)antigen driven. To investigate the temporal TCR repertoire dynamics in SSc, we performed high-throughput sequencing of CD4+ and CD8+ TCRβ chains on longitudinal samples obtained from four SSc patients collected over a minimum of two years. Repertoire overlap analysis revealed that samples taken from the same individual over time shared a high number of TCRβ sequences, indicating a clear temporal persistence of the TCRβ repertoire in CD4+ as well as CD8+ T-cells. Moreover, the TCRβs that were found with a high frequency at one time point were also found with a high frequency at the other time points (even after almost four years), showing that frequencies of dominant TCRβs are largely consistent over time. We also show that TCRβ generation probability and observed TCR frequency are not related in SSc samples, showing that clonal expansion and persistence of TCRβs is caused by antigenic selection rather than convergent recombination. Moreover, we demonstrate that TCRβ diversity is lower in CD4+ and CD8+ T-cells from SSc patients compared to healthy memory T-cells, as SSc TCRβ repertoires are largely dominated by clonally expanded persistent TCRβ sequences. Lastly, using “Grouping of Lymphocyte Interactions by Paratope Hotspots” (GLIPH2), we identify clusters of TCRβ sequences with homologous sequences that potentially recognize the same antigens and contain TCRβs that are persist in SSc patients. In conclusion, our results show that that CD4+ and CD8+ T-cells are highly persistent in SSc patients over time, and this persistence is likely a result from antigenic selection. Moreover, persistent TCRs form high similarity clusters with other (non-)persistent sequences, that potentially recognize the same epitopes. These data provide evidence for an (auto-)antigen driven expansion of CD4/CD8+ T-cells in Ssc.

overall_design: TCRβ profiles for 24 human samples were generated by deep sequencing on the Illumina MiSeq system. These samples were from 4 systemic sclerosis patients, including both CD4+ T-cells and CD8+ T-cells. From all patients, samples were collected at baseline, (T0), at least one year after inclusion (T1, ranging from 12-19 months) and at least two years after inclusion (T2, ranging from 24-46 months).

first: Nila

middle: H

last: Servaas

first: Fatiha

last: Zaaraoui-Boutahar

first: Catherina

middle: G

last: Wichers

first: Andrea

last: Ottria

first: Elena

last: Chouri

first: Alsya

last: Affandi

first: Sandra

last: Silva-Cardoso

first: Maarten

last: van der Kroef

first: Tiago

last: Carvalheiro

first: Peter

middle: C

last: de Greef

first: F

last: van Wijk

first: Rob

last: de Boer

first: Timothy

last: Radstake

first: Arno

last: Andeweg


title: Metabolic survival adaptations of Plasmodium falciparum exposed to sub-lethal doses of fosmidomycin

city: Frederick

first: Shivendra

last: Tewari

address: 2405 Whittier Drive, Suite 200

institute: Biotechnology HPC Software Applications Institute

summary: The malaria parasite Plasmodium falciparum contains the apicoplast organelle that synthesize isoprenoids, which are metabolites necessary for post-translational modification of Plasmodium proteins. We used fosmidomycin, an antibiotic that inhibits isoprenoid biosynthesis, to identify mechanisms that underlie the development of the parasite’s adaptation to the drug at sub-lethal concentrations. We first determined a concentration of fosmidomycin that reduced parasite growth by ~50% over one intraerythrocytic developmental cycle (IDC). At this dose, we maintained synchronous parasite cultures for one full IDC, and collected metabolomic and transcriptomic data at multiple time points to capture global and stage-specific alterations. We integrated the data with a genome-scale metabolic model of P. falciparum to characterize the metabolic adaptations of the parasite in response to fosmidomycin treatment. Our simulations showed that, in treated parasites, the synthesis of purine-based nucleotides increased, whereas the synthesis of phosphatidylcholine during the trophozoite and schizont stages decreased. Specifically, the increased polyamine synthesis led to increased nucleotide synthesis, while the reduced methyl-group cycling led to reduced phospholipid synthesis and methyltransferase activities. These results indicate that fosmidomycin-treated parasites compensate for the loss of prenylation modifications by directly altering processes that affect nucleotide synthesis and ribosomal biogenesis to control the rate of RNA translation during the IDC. This also suggests that combination therapies with antibiotics that target the compensatory response of the parasite, such as nucleotide synthesis or ribosomal biogenesis, may be more effective than treating the parasite with fosmidomycin alone.

overall_design: PfNF54 parasites were cultured for 48 hours in the presence of sub-lethal dose of fosmidomycin with samples taken every eight hours for transcriptomics and processed in quadruplicate, except for Time 0 Rep 3.

first: Krithika

last: Rajaram

first: Russell

last: Swift

first: Amanda

last: Dziedzic

first: Anne

last: Jedlicka

first: Jaques

last: Reifman

first: Sean

middle: T

last: Prigge

first: Anders

last: Wallqvist


title: Parallel in vivo analysis of large-effect autism genes implicates cortical neurogenesis and estrogen in risk and resilience

city: San Francisco

first: Arthur

middle: Jeremy

last: Willsey

state: CA

address: 675 Nelson Rising Lane, Mail Code 0518

department: Psychiatry

institute: UCSF

summary: Gene Ontology analyses of autism spectrum disorders (ASD) risk genes have repeatedly highlighted synaptic function and transcriptional regulation as key points of convergence. However, these analyses rely on incomplete knowledge of gene function across brain development. Here we leverage Xenopus tropicalis to study in vivo ten genes with the strongest statistical evidence for association with ASD. All genes are expressed in developing telencephalon at time points mapping to human mid-prenatal development, and mutations lead to an increase in the ratio of neural progenitor cells to maturing neurons, supporting previous in silico systems biological findings implicating cortical neurons in ASD vulnerability, but expanding the range of convergent functions to include neurogenesis. Systematic chemical screening identifies that estrogen, via Sonic hedgehog signaling, rescues this convergent phenotype in Xenopus and human models of brain development, suggesting a resilience factor that may mitigate a range of ASD genetic risks.

sample_organism:
Xenopus tropicalis
Homo sapiens

platform_organism:
Xenopus tropicalis
Homo sapiens


title: Parallel in vivo analysis of large-effect autism genes implicates cortical neurogenesis and estrogen in risk and resilience [human]

overall_design: iPSC cells at Day 0 and Day 6 of neuronal differentation with either an ESR2 targetting guide or non-targetting guide used as a control.

first: Helen

first: A

middle: J


title: Parallel in vivo analysis of large-effect autism genes implicates cortical neurogenesis and estrogen in risk and resilience [Xenopus]

overall_design: 3 pooled stage 46 brains in triplicate. DMSO-treated samples are the controls.


title: Proteomics analysis of a human brain sample from a mucolipidosis type IV patient reveals pathophysiological pathways

city: Rehovot

first: Anthony

last: Futerman

address: Herzl

country: Israel

institute: Weizmann Institute of Science

summary: We obtained accesses to brain tissue and cerebrospinal fluid (CSF) from the only available post- mortem mucolipidosis type IV (MLIV) patient which became available only recently. We performed mass spectrometry (MS)- based proteomics. Our data demonstrate that pathological players detected in Mcoln1-/- mice are also relevant in the human disease. Moreover, we suggest some previously un-known pathological players. We complement this study by using Mcoln1-/- mice, and were able to confirm that many pathological pathways are evident early in disease development, emphasizing the need for early therapeutic intervention.

overall_design: We performed mass spectrometry (MS)- based proteomics on MLIV and control samples. Moerover, we performed RNAseq on Mcon1 mice, a model for MLIV.

first: Ayelet

last: Vardi


title: Dual inhibition of EZH2 and G9a suppresses multiple myeloma cell proliferation by regulating interferon signal and IRF4-MYC axis

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

institute: Sapporo Medical University

summary: Epigenetic mechanisms including histone modifications play key roles in the pathogenesis of multiple myeloma (MM). We have previously shown that a histone H3 lysine 27 (H3K27) methyltransferase EZH2 and a H3K9 methyltransferase G9a are potential therapeutic targets in MM. Recent studies suggested that EZH2 and G9a cooperate to regulate gene expression. We thus aimed to evaluate the anti-tumor effect by dual targeting of EZH2 and G9a in MM. A combination of an EZH2 inhibitor and a G9a inhibitor strongly suppressed myeloma cell proliferation through inducing cell cycle arrest and apoptosis in vitro. Dual inhibition of EZH2 and G9a also repressed xenograft formation by myeloma cells in vivo. Higher expression levels of EZH2 and EHMT2, which encodes G9a, are significantly associated with poorer prognosis in MM patients, respectively. Microarray analysis revealed that EZH2/G9a inhibition significantly upregulated interferon (IFN)-stimulated genes and suppressed IRF4-MYC axis genes in myeloma cells. Notably, we found increased expression and reduced H3K27/H3K9 methylation levels of endogenous retrovirus (ERV) genes in myeloma cells with the dual inhibition, suggesting that activation of the ERV genes may cause the IFN response. These results suggest that dual targeting of EZH2 and G9a may be a novel therapeutic strategy in MM.

overall_design: RPMI-8226 and MM.1S cells treated with GSK126 (1 μM), UNC0638 (1 μM) or their combination (1 μM each) for 6 days.


title: Astrocytic ApoE reprograms neuronal cholesterol metabolism and histone acetylation mediated memory [ChIP-seq]

city: Hefei

first: Qiang

last: Liu

state: Anhui

address: 443 Huangshan Road

institute: University of Science and Technology of China

summary: We report chromatin profiling of H3K27ac in hippocampus neuronal cells

overall_design: Examination of H3K27ac histone modifications in hippocampus neuronal cells

first: Juan

last: Zhang

first: Xiaohui

last: Li


title: miRNA expression in Th17 cells after AhR activation

city: Ribeirão Preto

first: Paula

middle: Barbim

last: Donate

address: Bandeirantes avenue, 3900

country: Brazil

institute: University of São Paulo

summary: Th17 cells play a major role in the pathogenesis of Rheumatoid Arthritis, and it is well known the involvement of the Aryl Hydrocarbon Receptor (AhR) during the differentiation and activation of these cells. Due to its function as a transcription factor, we tested wether AhR would mediate part of its function in Th17 cells through the transcription of microRNAs (miRNAs). Therefore, we first perform a microarray experiment to identify the miRNAs induced after AhR activation in Th17 cells. Under a supervised hierarchical clustering, we identify 224 miRNAs differentially expressed (fold-change ³ 2.0 and FDR < 5%). Among them, 22 miRNAs were up regulated exclusively in Th17 cells in the presence of FICZ.

overall_design: Naïve T cells were differentiated in the presence of IL-6, TGF-b and IL-1. After 3 days, IL-17 producer cells were isolated and re-stimulated with IL-6, TGF-b, IL-1, and IL-23 in the presence or absence of FICZ for 24h. Th0 conditions used as a control, and isolated CD4+ T cells were re-stimulated with IL-2, in the presence or absence of FICZ during the same time.


title: Single-cell analysis reveals the landscape of tumor heterogeneity and identifies MLXIPL as a potential biomarker in tumor evolution trajectory of hepatocellular carcinoma

city: Shanghai

first: Sibo

last: Zhu

state: China

address: songhulu 2005

institute: Fudan University

summary: Hepatocellular carcinoma (HCC) is a globally prevailing cancer with a low five-year survival rate. Little is known about its intricate gene expression profile and tumor evolutionary traits. Single-cell RNA sequencing (scRNA-seq) is an indispensable tool to explore the genetic characteristics at the single-cell level. In this study, we profiled gene expression of single cells from human HCC tumor and para-tumor tissues using Smart-seq 2 sequencing method. Based on DEGs, we identified heterogeneous subclones in HCC tissues, including 4 HCC and 2 hepatocyte subclones. Then, we carried out hub-gene co-network and functional annotations analysis to further explain tumor heterogeneity. Next, we conducted the evolution trajectory by pseudo-time analysis and its regulated transcriptional factors (TF) gene network. In the following research, we found that MLXIPL, as a TF, was commonly upregulated in HCC tissues and cells at both the mRNA and protein levels, promoting cell proliferation and inhibiting its apoptosis. Mechanistically, MLXIPL activation is crucial for accelerating HCC cell glycolysis. Taken together, our work identified the heterogeneity of HCC cell subclones, and MLXIPL might be a promising therapeutic target of HCC.

overall_design: Examination of human HCC tumor and para-tumor tissues using Smart-seq 2 sequencing method

first: Xiao

last: Dong

first: Fan

last: Wang

first: Chuan

first: Jing

last: Ling

first: Xuebing

last: Jia

first: Feifei

last: Shen

first: Ning

last: Yang

first: Lin

last: Zhong

first: Qi


title: Multi-omic analysis unveils biological pathways in peripheral immune system associated to minimal hepatic encephalopathy appearance in cirrhotic patients

city: El Palmar

first: Teresa

last: Rubio

state: Murcia

address: Av. Buenavista, 32

department: Plataforma de Bioinformática

country: Spain

institute: IMIB

summary: Patients with liver cirrhosis may develop minimal hepatic encephalopathy (MHE) which affects their quality of life and life span. It has been proposed that a shift in peripheral inflammation triggers the appearance of MHE. However, the mechanisms involved in this immune system shift remain unknown. In this work we studied the broad molecular changes involved in the induction of MHE with the goal of identifying (1) altered genes and pathways in peripheral blood cells associated to the appearance of MHE, (2) serum metabolites and cytokines with modified levels in MHE patients and (3) MHE-regulated immune response processes related to changes in specific serum molecules. We adopted a multi-omic approach to profile the transcriptome, metabolome and a panel of cytokines of blood samples taken from cirrhotic patients with or without MHE.

overall_design: Gene expression was measured in whole blood cells of cirrhotic patients with and without minimal hepatic encephalopathy.

first: Vicente

last: Felipo

first: Sonia

last: Tarazona

first: Roberta

last: Pastorelli

first: Desamparados

last: Escudero-Garcia

first: Joan

last: Tosca

first: Amparos

last: Urios

first: Ana

last: Conesa

first: Carmina

last: Montoliu