title: Gene expression analysis of U937 cells during the differentiation by phorbol 12-myristate 13-acetate (PMA)

status: Public on Nov 30 2020

city: Itabashi-ku

first: Kensuke

last: Ohse

address: Sakaecho

country: Japan

institute: Tokyo Metropolitan Institute of Gerontology

type: Expression profiling by high throughput sequencing

summary: U937 cells, human lyphoma cell line, differentiate to the macrophage-like cells by the phorbol 12-myristate 13-acetate (PMA). We investigated the regulation mechanisms of gene expression during the U937 differentiation by RNA-seq.

overall_design: We cultured the U937 cells with or without 10 nM PMA. Total RNA was extracted from cells and polyA(+) RNA was concentrated by oligo-dT conjugated dynabeads. RNA-seq were performed by Ion Proton Platform.


title: A unique population of regulatory T cells in heart potentiates cardiac protection from myocardial infarction

city: Wuhan

first: Muyang

last: Gu

address: 1277 Jiefang Road, Jianghan District

country: China

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

summary:
Purpose: The aims of the study were to identify that transctiptome of heart Tregs was different from lymphoid organ Tregs.
Methods: Tregs and conventional T cells (Tconvs) from injured hearts and paired lymphoid organs of the Foxp3-GFP transgenic mice were double-sorted by magnetic-activated cell sorting (MACS) and fluorescence activated cell sorting (FACS) to generate RNA-sequence 7 days after myocaridal infarction (MI).
Results: Transcriptional profiling revealed that  the transcriptome of heart Tregs has unique characteristics when compared to lymphoid Tregs.

overall_design: mRNA profiles of injured heart Tregs and Tconvs, spleen Tregs and Tconvs, non-draining lymph node (NDLN) Tregs and Tconvs, and mediastinal lymph node (MLN) Tregs isolated from 8-week-old Foxp3-GFP mice 7 days post-MI.

first: Ni

last: Xia

first: Yuzhi

last: Lu

first: Nana

last: Li

first: Meilin

last: Liu

first: Xiang

last: Cheng


title: RNA sequencing of rodent myocardial tissue when subjected to mitral regurgitation (MR) for different time-points, compared to normal Sham tissue.

city: Atlanta

first: Muralidhar

last: Padala

state: GA

address: 380B Northyards Blvd NW

country: USA

institute: Emory University

summary:
Purpose: The goal of this study is to compare mRNA related cellular pathways associated with mitral regurgitation compared to Sham
Methods: RNA was extracted from myocardial tissue at 2, 10, 20, 40 weeks after MR surgery (n=5 samples/time-point) and was subjected to unbiased RNA sequencing.
Conclusions: RNA sequencing revealed an early activation of multiple cellular pathways.

overall_design: Rats were subjected to MR surgery (left thoracotomy and perforation of the mitral leaflet to create MR) or Sham surgery (mitral leaflet was not perforated) and followed until 2, 10, 20, or 40 weeks

first: Corporan

last: Daniella

first: Padala

last: Muralidhar

first: Kumar

last: Sandeep


title: Blood Serum Stimulates p38-Mediated Proliferation and Changes in Global Gene Expression of Adult Human Cardiac Stem Cells

city: Bielefeld

first: Christian

last: Kaltschmidt

address: Universitätstraße 25

department: Department of Cell Biology

country: Germany

institute: University of Bielefeld

summary: Global transcriptome analysis of blood serum-treated adult human cardiac stem cells shows p38-MAPK mediated changes of proliferation and survival compared with untreated cells

overall_design: RNAseq Data of adult human cardiac stem cells treated with young or old male blood serum with 3 biological replicates each and 1 control of untreated cells

first: Anna

last: Höving

first: Kazuko

middle: E

last: Schmidt

first: Madlen

last: Merten

first: Jassin

last: Hamidi

first: Ann-Katrin

last: Rott

first: Isabel

last: Faust

first: Johannes

last: Greiner

first: Jan

last: Gummert

first: Barbara

first: Cornelius

last: Knabbe


title: Transcriptomic analysis of tudor[1] mutant Drosophila brain and ovaries

status: Public on Nov 27 2020

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: In Drosophila, Tudor protein and its germline partners, Piwi proteins, are expressed in the brain. However, the potential significance of Tudor in neurobiology has not been explored. Here, we test a hypothesis that Tudor is an essential regulator of post-transcriptional gene expression in the brain where it controls levels of certain RNAs required for brain functions. Specifically, transcriptome of tudor mutant brains is compared with that of wild-type brains using next-generation sequencing (RNA-Seq). The hypothesis that Tudor regulates the same genes in both brain and germline is tested by comparing the transcriptomes from tudor mutant brains and ovaries. This research aims at providing innovative outcomes which may reveal exciting commonalities between the germline and brain and may contribute to our understanding of neurodegenerative disorders and the mechanisms of learning and memory.

overall_design: A total of twelve brain samples (3 biological replicates for Tudor (tud) mutant and 3 biological replicates for wild-type control, isolated separately from males and females) and 6 ovarian samples (3 biological replicates for tud mutant and 3 biological replicates for wild-type control) were sequenced for gene expression. Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) were prepared without poly(A) selection.

first: Samuel

middle: J

last: Tindell

middle: C

first: Alexey

middle: L

last: Arkov


title: Differential effect of repeated lipopolysaccharide treatment and aging on hippocampal function and biomarkers of hippocampal senescence

city: Gainesville

first: Tom

last: Foster

state: FL

address: 1149 Newell Drive

institute: University of Florida

summary: Aging is associated with low-grade chronic systemic inflammation. Elevated peripheral serum cytokines and chemokines contribute to age-related diseases and correlate with cognitive decline. This study compared the effects of repeated lipopolysaccharide (LPS) treatment in young rats to age-related changes in hippocampal-dependent cognition, synaptic transmission, and transcription. Young (5-7 months) Fischer 344 X Brown Norway hybrid rats were injected intraperitoneally once a week for 6-7 weeks with either LPS (1 mg/kg) or vehicle. Older (14-16 months) rats received a similar injection schedule of vehicle. Older-vehicle animals and young-LPS rats exhibited impaired retention of spatial memory. Examination of the transcriptome of the CA1 and the dentate gyrus indicated that older-vehicle and young-LPS animals exhibited an increase in immune response genes. In contrast to aging, young-LPS animals exhibited an increased expression of genes related to the synapse. Even though young-LPS animals increased the expression of synaptic genes, LPS treatment reduced hippocampal CA3-CA1 total synaptic response and N-methyl-D-aspartate receptor (NMDAR)-mediated component of the synaptic response. Interestingly, the decrease in NMDAR function was not redox-sensitive. This study demonstrates that repeated exposure to LPS has long-term effects on hippocampal synaptic transmission and memory; however, young animals exhibited transcriptional recovery after LPS treatment. Recovery likely results from the acute nature of repeated LPS injections, relative to chronic systemic inflammation observed during aging.

overall_design: RNA-sequencing was performed on the hippocampal subregions CA1 and DG from young-vehicle (n=8), young-LPS (n=8), and old-vehicle (n=6) animals. Three different comparisons were made treatment (young-LPS v young-vehicle), age (aged-vehicle v young-vehicle), and young-LPS v aged-vehicle. The final comparison was performed to determine the similarities/differences between the effect of peripheral inflammation and age on the hippocampal transcriptome.

first: Jolie

last: Barter

first: Ashok

last: Kumar

first: Asha

last: Rani

first: Luis

middle: M

last: Colon-Perez

first: Marcelo

last: Febo

first: Thomas


title: piRNA analysis of tudor[1] mutant Drosophila brain and ovaries

type: Non-coding RNA profiling by high throughput sequencing

summary: 23-29 nt Piwi-interacting RNAs (piRNAs) are crucial components of the ribonucleoprotein complexes which silence the most abundant class of mobile genetic elements in human genome, retrotransposons, in germline (germ) cells. In these cells, antisense piRNAs serve as RNA guides for Piwi proteins, base pairing with transposon RNAs which are subsequently cleaved by Piwi proteins. Germ cells belong to special class of stem cells which ultimately give rise to eggs and sperm and therefore, to next generations. Therefore, piRNAs protect next-generation genomes from devastating mutations caused by transposon insertions. Although, role of piRNAs in germ cells has been studied, functions of piRNAs and their associated proteins in somatic cells are not well understood. Importantly, Piwi proteins are expressed in the fruit fly Drosophila brain and are required for the silencing of transposable elements there, clearly indicating that Piwi-associated piRNAs are involved in this process in the brain. Furthermore, piRNAs have been implicated in the memory formation mechanisms in Aplysia brain. In addition to Piwi proteins, their associated partner, molecular scaffold Tudor protein, participates in piRNA biogenesis in germ cells and it is absolutely required for germline development. However, although tudor gene is expressed in the fly brain, its role in the central nervous system is not understood. In this study, we look at the role of Tudor as an essential player in piRNA biogenesis in Drosophila brain.

overall_design: A total of five brain samples (2 biological replicates for tudor (tud) mutant and 3 biological replicates for wild-type control) and 6 ovarian samples (3 biological replicates for tud mutant and 3 biological replicates for wild-type control) were sequenced for small RNAs, including miRNAs and piRNAs.


title: RNA sequencing of rodent myocardial tissue when subjected to a myocardial infarction (MI) or an MI and a surgical device (TRD) for 12 weeks.

first: Muralidhar

last: Padala

summary:
Purpose: The goal of this study is to compare mRNA related cellular pathways associated with a myocardial infarction (MI) with a surgical device to prevent cardiac remodeling compared to an MI only
Conclusions: RNA sequencing revealed an activation of multiple cellular pathways with the device group.

overall_design: Methods: RNA was extracted from myocardial tissue at 12 weeks after surgery in both the MI and TRD group (n=6/group) and was subjected to unbiased RNA sequencing.

first: Daniella

last: Corporan

first: Daisuke

last: Onohara


title: Multi-locus imprinting disturbances in a family harboring a ZFP57 truncation

city: L'Hospitalet de Llobregat, Barcelona

first: Jose Ramon

last: Hernandez

address: Av. Gran Via de l'Hospitalet 199-203

department: Cancer Epigenetics and Biology Program (PEBC)

country: Spain

institute: Institut d'Investigació Biomèdica de Bellvitge (IDIBELL)

type: Methylation profiling by genome tiling array

summary: We previously reported a child with transient neonatal diabetes mellitus (TNDM), who upon molecular diagnosis was homozygous for a one base-pair deletion in ZFP57, inheriting the mutations from both heterozygous parents. Methylation profiling at diagnosis revealed severe hypomethylation at PLAGL1 and mosaic loss-of-methylation (LOM) at GRB10, NAP1L5 and GNAS-XL DMRs.  Some years after the first child, a second sibling was born with a comparable clinical presentation. Upon molecular investigation this child was shown to have the same homozygous deletion. Using  Illumina Infinium BeadChip arrays, we confirmed similar hypomethylated signatures at ubiquitous imprinted DMRs. To further characterize the stability of the imprinting defects and understand the role of this mutation in tissue-specific mosaicism, we hybridised buccal-derived DNA and a second leukocyte sample from first child to the HumanMethylationEPIC arrays. When comparing the two blood-derived samples, we observed that the hypomethylation signature is stable over time with the PLAGL1 DMR being the most severely affected, consistent with this being the disease-causing locus. Furthermore, when comparing the leukocyte and buccal samples, the same imprinted DMRs were affected to a similar extent.

overall_design: Bisulphite converted DNA from blood (two samples at different times), saliva (one sample) and lymphoblasts (one sample) of an individual carrying a homozygotic ZFP57 mutation, a blood sample from his brother (carrying also the same homozygotic mutation) and another blood sample from their mother (heterozygotic carrier of the mutation) were hybridized to the Illumina Infinium HumanMethylationEPIC and HumanMethylation450 BeadChips.

first: Jose

middle: R

first: David

last: Monk


title: Small RNA sequencing of Nippostrongylus infected with lentivirus for specific gene knockdown

status: Public on Nov 28 2020

city: London

first: Peter

last: Sarkies

address: Du Cane Road

department: MRC Clinical Sciences Centre

country: United Kingdom

institute: Imperial College London

summary: Gene silencing in parasitic nematodes was achieved by infecting Nippostrongylus with lentivirus designed to produce small RNAs to silence specific genes.  Small RNA sequencing was used to investigate production of small silencing RNAs in infected nematodes

overall_design: Small RNA sequencing was used to determine whether small RNAs mapping to knockdown targets were formed

first: Jana

last: Hagen

first: Murray

last: Selkirk


title: Characterization of lung tissue-resident helper T cells

city: Rochester

first: Yougnmin

last: Son

address: 200 1st Stabile 8-21

institute: Mayo Clinic

summary: To identify the characters of tissue resident CD4 T cells following influenza virus infection, we sorted lung CD45iv-CD4+CD44hi T cells from influenza PR8 infected mice (28 d.p.i.). Then the cells were performed single cell RNA sequencing. At the result, we found clera 5 differnt clusters and each cluster represent different helper T cell types including TH1, TH17 and Treg. One cluster exhibited both tissue residency and TFH cell features. So, we identify the characters of this hybrid lung CD4 T cells.

overall_design: Examined with lung-resident CD4+ T cells sorted from influenza PR8-infected mice (28 days post infection)

first: Jie

last: Sun

first: Youngmin


title: Transcriptional profiling for lung tissue-resident helper T cell and spleen follicular T cells

summary: We reported hybrid CD4+ T cell population following influenza viru infection. The hybrid CD4+ T cells exhibit both tissue residency and follicular helper T cell features. To further charaterization, we sorted lung tissue-resident helper T (TRH or TTH) cells (CD45iv-CD4+CD44+GITR-PD1hiFR4hi), non-TRH (CD45iv-CD4+CD44+GITR-PD1lowFR4low), spleen follicalar helper T (TFH) cells (CD4+CD44+GITR-PD1hiCXCR5hi) and non-TFH cells (CD4+CD44+GITR-PD1lowCXCR5low). Then the cells were applied for RNA sequencing. At the resut, we showed tissue-residency related genes are highly enriched in lung TRH but not spleen TFH cells. And The lung TRH cells express higher levels of TFH-related genes than lung-non TRH cells. Therefore, we suggest TRH cells play a role as tissue-resident helper T cells.

overall_design: Examined with 2 repeated each cell population (lung TRH (or TTH), lung non-TRH (or TTH), spleen TFH and spleen non-TFH)


title: Single-cell RNA profiling of human bone marrow Natural Killer cells from healthy donors and from acute myeloid leukemia patients

city: Marseille

first: Bertrand

last: Escaliere

address: 163 avenue de Luminy

country: France

institute: CIML

summary: We report here the identification, by single-cell RNA sequencing (scRNAseq), of three subpopulations of NK cells in human bone marrow. Pseudotime analysis identified a subset of resident CD56bright NK cells, NK0 cells, as the precursor of both circulating CD56dim NK1-like NK cells and CD56bright NK2-like in the human bone marrow and spleen at steady state. Transcriptomic profiles of bone marrow NK cells from patients with acute myeloid leukemia (AML) showed a stress-induced repression of NK cell effector functions, highlighting the profound impact of the disease on NK cell heterogeneity. Bone marrow NK cells from AML patients exhibited reduced levels of CD160 but the CD160high group had a significantly higher survival rate.

first: Adeline

last: Crinier

first: Pierre-Yves

last: Dumas

first: Christelle

last: Piperoglou

first: Laurine

last: Gil

first: Arnaud

last: Villacreces

first: Frederic

last: Vely

first: Zoran

last: Ivanovic

first: Pierre

last: Milpied

first: Emilie

last: Narni-Mancinelli

first: Eric

last: Vivier


title: A unique population of regulatory T cells in heart potentiates cardiac protection from myocardial ischemia/reperfusion injury

first: Muyang

last: Gu

summary:
Purpose: The aims of the study were to identify that transctiptome of heart Tregs was different from lymphoid organ Tregs after I/R injury.
Methods: Tregs from injured hearts and paired lymphoid organs of the Foxp3-GFP transgenic mice were double-sorted by magnetic-activated cell sorting (MACS) and fluorescence activated cell sorting (FACS) to generate RNA-sequence 3 days after myocardial ischemia/reperfusion injury (I/R injury).
Results: Transcriptional profiling revealed that  the transcriptome of heart Tregs has unique characteristics when compared to lymphoid Tregs.

overall_design: mRNA profiles of injured heart Tregs, spleen Tregs and mediastinal lymph node (MLN) Tregs isolated from 8-week-old Foxp3-GFP mice 3 days after I/R injury.

first: Ni

last: Xia

first: Yuzhi

last: Lu

first: Nana

last: Li

first: Meilin

last: Liu

first: Xiang

last: Cheng


title: Illumina 3'UTR biased-sequencing of total homogenate from mPFC and CeA of mice following  chronic intermittent ethanol exposure and microglia depletion

city: Austin

first: Anna

last: Warden

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

summary:
Purpose: Alcohol dependence results in microglia proliferation in brain and changes in microglia morphology and function. However, it remains unknown if microglia initiate or simply amplify the neuroadaptations that lead to alcohol dependence.  Here we determined microglia function in chronic intermittent ethanol exposure behaviors using a colony stimulating factor 1 receptor inhibitor (PLX5622) and 3’UTR biased-sequencing. Therefore, the purpose of this study was to provide insight into how microglia may regulate neuroadaptations due to alcohol dependence.
Methods: We performed 3’UTR biased transcriptome sequencing (3’Tag-seq) on total homogenate isolated from the prefrontal cortex (PFC)  and central nucleus of the amygdala (CeA) of C57BL6/J mice following microglia depletion and chronic intermittent ethanol exposure.
Results: Differential expression analysis and WGCNA network analysis revealed that microglia depletion prevents both immune and synaptic gene expression changes that are linked with the formation of alcohol dependence.  This suggested that microglia are key regulators of the transition from alcohol misuse to alcohol dependence.
Conclusion: Taken together our behavioral and transcriptional data indicate that microglia are the primary effector cell responsible for regulation of alcohol dependence.  In addition, our data represents a novel resource for groups interested in transcriptional effects of microglia depletion after alcohol dependence.

middle: S

first: R

middle: D

last: Mayfield

first: Marisa

last: Roberto

middle: A

last: Harris


title: HIF1α/RelB cross-talk and miR-138-5p modulate APOBEC3B-mediated HBV cccDNA decay

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

institute: LMU University Hospital

summary:
Purpose: We aim to identify changes in the miRNA-ome upon lymphotoxin beta receptor activation
Methods: miRNAs were analyzed by sequencing after 2 and 4 days of treatment
Results: We could identify different clusters with distinct time-dependent expression after treatment
Conclusion: The miRNA-ome is responding on lymphotoxin beta receptor activation

overall_design: Small RNAseq analysis of human liber cells after treatment with BS1 and controls after 2 and 4 days.

first: Tobias

last: Riedl

first: Mathias

last: Heikenwälder


title: STAT1 Dissociates Adipose Tissue Inflammation from Insulin Sensitivity in Obesity

city: Houston

first: Sean

last: Hartig

address: One Baylor Plaza, BCM130

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary:
Purpose: To determine how STAT1 activity in white adipocytes affects insulin sensitivity.
Methods: Adipocyte specific (ADIPOQ-Cre) STAT1 fl/fl mice (STAT1 fKO) and littermate controls (STAT1 fl/fl) were placed on 60% HFD for 18 weeks, followed by metabolic phenoptying and tissue harvest for RNA-seq
Results: STAT1 expression in WAT inversely correlated with fasting plasma glucose in both obese mice and humans. Metabolomic and gene expression profiling established STAT1 deletion in adipocytes (STAT1 fKO) enhanced mitochondrial function and accelerated TCA cycle flux coupled with subcutaneous WAT hyperplasia. STAT1 fKO reduced WAT inflammation, but insulin resistance persisted in obese mice. Rather, elimination of type I cytokine interferon gamma (IFNg) activity enhanced insulin sensitivity in diet-induced obesity.
Conclusions: Our findings reveal a permissive mechanism that bridges WAT inflammation to whole-body insulin sensitivity.

overall_design: 5 biological replicates per group

first: Aaron

last: Cox

first: Natasha

last: Chernis

first: David

last: Bader

first: Pradip

middle: K

last: Saha

first: Peter

last: Masschelin

first: Jessica

middle: B

last: Felix

first: Zeqin

last: Lian

first: Vasanta

last: Putluri

first: Kimal

last: Rajapakshe

first: Kango

middle: H

last: Kim

first: Dennis

middle: T

last: Villareal

first: Reina

last: Armamento-Villareal

first: Huaizhu

last: Wu

first: Cristian

last: Coarfa

first: Nagireddy


title: SARS-CoV-2 stock sequencing for infection of nonhuman primates

first: Thomas

last: Vanderford

address: 954 Gatewood Rd.

department: Yerkes National Primate Research Center

summary: SARS-CoV-2 USA/WA1 strain stock was sequenced to determine whether the furin cleavage site was intact.

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: SARS-CoV-2 WA1 viral stock


title: Quantitative glycoproteomics reveals cellular substrate selectivity of the endoplasmic reticulum protein quality control sensors UGGT1 and UGGT2

city: Amherst

first: Daniel

last: Hebert

state: MA

address: 240 Thatcher Road LSL

institute: University of Massachusetts

summary: The protein quality control sensors UDP-glucose: glycoprotein glucosyltransferase (UGGT) 1 and 2 are proposed to act as gatekeepers of the early secretory pathway. They initiate rebinding to the carbohydrate-dependent chaperones calnexin and calreticulin that associate with proteins possessing monoglucosylated glycans. The UGGTs control glycoprotein exit from the endoplasmic reticulum (ER) for trafficking to the Golgi or ER retention to provide additional folding opportunities. A quantitative glycoproteomics strategy was used to identify cellular glycoproteins modified by the UGGTs at endogenous levels and delineate the specificities of UGGT1 and UGGT2. UGGT substrates were comprised of seventy-one mainly large multidomain and heavily glycosylated proteins when compared to the general N-glycome. UGGT1 was the dominant glucosyltransferase with a preference towards large plasma membrane proteins whereas UGGT2 favored the modification of smaller, soluble lysosomal proteins. This study provides insight into the cellular secretory load that utilizes multiple rounds of carbohydrate-dependent chaperone intervention for proper maturation.

overall_design: 5 different cell lines are analyzed (ALG6-/-, ALG6/UGGT1-/-, ALG6/UGGT2-/-, ALG6/UGGT1/2-/-, WT. Each sample has 3 biological replicates. Each biological replicate has 4 technical replicates. WT is used as a reference set.

first: Benjamin

last: Adams

first: Nathan

middle: P

last: Canniff

first: Kevin

last: Guay

first: Ida

last: Larsen

middle: N


title: LncRNA Expression Profile of Human Thoracic Aortic Dissection by High-Throughput Sequencing

city: Guangzhou

first: jie

last: sun

state: Gongdong

address: 1838 North Guangzhou Avenue

department: Department of Cardiology

institute: Nanfang Hospital, Southern Medical University

summary: In this study, the long non-coding RNA (lncRNA) expression profile in human thoracic aortic dissection (TAD), a highly lethal cardiovascular disease, was investigated. Human TAD (n=3) and normal aortic tissues (NA) (n=3) were examined by high-throughput sequencing. Bioinformatics analyses were performed to predict the roles of aberrantly expressed lncRNAs. Quantitative real-time polymerase chain reaction (qRT-PCR) was applied to validate the results. A total of 269 lncRNAs (159 up-regulated and 110 down-regulated) and 2, 255 mRNAs (1 294 up-regulated and 961 down-regulated) were aberrantly expressed in human TAD (fold-change>1.5, P<0.05). QRT-PCR results of five dysregulated genes were consistent with HTS data. A lncRNA-mRNA coexpression analysis showed positive correlations between the up-regulated lncRNA (ENSG00000269936) and its adjacent up-regulated mRNA (MAP2K6, R=0.940, P<0.01), and between the down-regulated lncRNA_1421 and its down-regulated mRNAs (FBLN5, R=0.950, P<0.01; ACTA2, R=0.96, P<0.01; TIMP3, R=0.96, P<0.05). The lncRNA-miRNA-mRNA network indicated that the up-regulated lncRNA XIST and p21 had similar sequences targeted by has-miR-17-5p. The results of luciferase assay and fluorescence immuno-cytochemistry were consistent with that. And qRT-PCR results showed that lncRNA XIST and p21 were expressed at a higher level and has-miR-17-5p was expressed at a lower level in TAD than in NA. The predicted binding motifs of three up-regulated lncRNAs (ENSG00000248508, ENSG00000226530, and EG00000259719) were correlated with up-regulated RUNX1 (R=0.982, P<0.001; R=0.967, P<0.01; R=0.960, P<0.01, respectively). Our study revealed a set of dysregulated lncRNAs and predicted their multiple potential functions in human TAD. These findings suggest that lncRNAs are novel potential therapeutic targets for human TAD.

overall_design: Aortic specimens were collected from three type A TAD patients undergoing aortic replacement in the intimal tear position at the hospital. Normal thoracic aortas (NA) were obtained from three age- and gender-matched organ donors without aortic diseases.

first: Jie

last: Sun

first: Guojun

last: Chen

first: Yuanwen

last: Jing

first: Xiang

last: He

first: Jianting

last: Dong

first: Junmeng

last: Zheng

first: Meisheng

last: Zou

first: Hairui

last: Li

first: Shifei

last: Wang

first: Yili

first: Wangjun

last: Lia

first: Yulin

last: Liao

first: Li

last: Feng

first: Jianping

last: Bin


title: Manipulation of Mir140 3p and 5p expression

city: Boston

first: Tatsuya

last: Kobayashi

address: 50 Blossom st

department: Endocrine unit

institute: Massachusetts general hospital

summary: The goal of this study was to change the stoichiometry of Mir140-3p and Mir140-5p expression, thereby increasing the expression levels of Mir140-5p, and observe the biological effects on skeletal development. This was done by introducing two types of nucleotide changes into the seed regions of Mir140. The first was by changing the initial bases of Mir140-3p from 'TACCACAGGGTAGAACCACGGACAGGGTACTGGAGC' to 'CGCCACAGGGTAGAACCACGGACAGGGTACTGGAGC' lowering the expression levels of Mir140 3p and disrupting its function. The second change to alter Mir140 expression was by changing the Mir140-5p seed region from 'CAGTGGTTTTACCCTATGGAGG' to 'TAGTGGTTTTACCCTATGGAGG' increasing mi140-5p's ability to be bound by Argonaute.

overall_design:
Chondrocyte mRNA profiles of 10-day old wild type (WT) and Mir140 5p overexpressing mice produced by two different mutations were generated by deep sequencing, in duplicate, using DNBSEQ.

CG WT - wildtype for the CG mutants
CG CG - mutant mice with 3p seed region mutation
C>T CT - mice with a C>T base change
C>T WT - wildtype group for the C>T mutant mice

first: Melissa

last: Caffrey


title: Differentially expressed mRNAs with statistical significance in cisplatin treated wild-type PTECs infected with Ad-FXRα2 or Ad-VP16

city: Shanghai

first: sujuan

last: xu

address: No.180, Fenglin Road

institute: Zhongshan Hospital

summary: We report the application of RNA-sequence in Primary PTECs, by obtaining the sequence from cisplatin treated wild-type PTECs infected with Ad-FXRα2 or Ad-VP16

overall_design: Examination of Ad-FXRα2 or Ad-VP16  treatment in primary PTECs

first: Sujuan

first: Ping

last: Jia

first: Xiaoqiang

last: Ding


title: Methylation for adult blood and cord blood samples

first: Jose Ramon

last: Hernandez

summary: Good quality standard adult blood samples and cord blood samples hybridized to the Illumina Infinium HumanMethylation450 BeadChip and used as methylation controls.

overall_design: Bisulphite converted DNA from 3 adult human blood samples and 20 human cord blood samples were hybridised to the Illumina Infinium HumanMethylation450 BeadChip.

first: Jose

first: David

last: Monk


title: Functional Genomic Analyses of Hep-G2 Cell Line after FTO knockdown

city: Beijing

first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

summary: To explore the molecular mechanism underlying glucose regulation by hepatic FTO, we used the human hepatocyte Hep-G2 cell line as an experimental platform and analyzed transcriptome changes following FTO knock-down.

overall_design: Examination of two Hep-G2 cell lines: FTO is knocked down using shRNA and the control is the scramble.

first: Peng

last: Shiming

first: Ju

last: Dapeng

first: Huang

last: Niu

first: Zhang

last: Erquan

last: Huanwei

first: Cai

last: Tao


title: Co-dependency for MET and FGFR1 in basal triple negative breast cancers

city: Montreal

first: Alain

last: Pacis

state: QC

address: 740 Dr Penfield Ave

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

summary: Triple-negative breast cancer (TNBC) is a heterogeneous disease that lacks both effective patient stratification strategies and therapeutic targets. In the present study, we assay tumour-initiating cells (TICs) properties, using established Met-dependent transgenic mouse models of TNBC, breast cancer cell lines and, patient-derived xenografts, to directly investigate the role of Met in tumour initiation and identify FGFR1 signaling as a key convergent pathway with Met for the maintenance of TICs. To understand the events that occur in TICs upon inhibition of Met and FGFR1, we performed gene expression profiling by RNA-Sequencing of RNA prepared from tumoursphere from 3 independent MMTV-Metmt;Trp53fl/+;Cre derived spindloid tumour cell lines (A1005, A1129, A1471) following treatment with Met or FGFR inhibitor alone (Crizotinib or PD173074, respectively), or in combination for 24h.

overall_design: Differential gene expression profile following drugs treatment of tumoursphere from 3 independent MMTV-Metmt;Trp53fl/+;Cre derived spindloid tumour cell lines (A1005, A1129, A1471) following treatment with Met or FGFR inhibitor alone (Crizotinib or PD173074, respectively), or in combination for 24h, by RNA-Sequencing using a NextSeq500 sequencer (Illumina).

first: Vanessa

middle: Y

last: Sung

first: Stephanie

last: Duhamel

first: Morag

last: Park


title: Mechanisms Coordinating Ribosomal Protein Gene Transcription in Response to Stress

city: Geneva

first: Sevil

last: Zencir

address: 30, quai Ernest-Ansermet

department: Department of Molecular and Cellular Biology

country: Switzerland

institute: University of Geneva

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In this study, we elucidate the common logic of the RPGs regulatory network by evaluating both the architecture and activity of promoters under conditions of stress or modulation of TF levels, and we identified the proteins regulating the activity of promoters lacking Rap1 binding, thus demonstrating that RPG co-regulation requires the complementary action of two different mechanisms involving both Ifh1 and Sfp1.

overall_design: Transcriptional responses were measured by RNA Polymerase II binding upon depletion of transcription factors in budding yeast. Sfp1 and Ifh1 binding on RPG promoters was measured by ChEC-Seq.

first: Daniel

last: Dilg

first: Maria

last: Rueda

last: Shore

first: Benjamin

last: Albert


title: Low-input mRNA Sequencing Analysis of Epidermal Langerhans cells (LC) from Murine Imiquimod (IMQ)-Induced Psoriasis-Like Dermatitis

first: Xilin

last: Zhang

state: Shanghai

address: No. 1278#, Baode Rd, Jingan District

department: Dermatology

institute: Shanghai Skin Disease Hospital

summary:
Purpose: To compare epidermal LC transcriptomes of control group (wild-type IMQ-untreated C57/BL6 mice) and IMQ group (wild-type IMQ-treated C57/BL6 mice).
Results: KEGG pathway analysis implied that lesional LCs were highly enriched in several inflammatory signalling pathways, including cytokine-cytokine receptor interactions, Th1, Th2 and Th17 cell differentiation, tumor necrosis factor signalling and IL-17 signalling pathways, complement and coagulation cascades, and NOD-like receptor signalling and PI3K-Akt signalling pathways. Gene set enrichment analysis plots revealed enrichment of cytokine activity, chemoattractant activity, protein lipid complex binding, and low-density lipoprotein particle binding gene sets in LCs from IMQ+ mice compared with IMQ- mice.
Conclusions: These results confirmed a proinflammatory role for epidermal LCs in the pathogenesis of psoriasis.

overall_design: Epidermal LC Transcriptomes of IMQ-Induced Psoriasis-Like Dermatitis

first: Xiaorui

last: Li


title: piRNA and transcriptomic analysis of tudor[1] mutant Drosophila brain and ovaries

first: Eric

last: Rouchka

address: 522 East Gray Street

institute: University of Louisville

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

overall_design: Refer to individual Series


title: Derivation of formative-like pluripotent stem cells from mammalian embryos [ChIP-Seq]

city: shenzhen

first: CNSA

last: CNGB

address: BGI

institute: BGI

summary: Two phases of pluripotency, naïve and primed, have been captured in vitro and studied in details1. A third formative phase was recently proposed to exist between naïve and primed phases2. Formative pluripotency entails permissiveness for direct primordial germ cell (PGC) induction and competence for blastocyst chimeras, and is characterized by transcriptional and epigenetic features intermediate of naïve and primed pluripotency. To date, however, stable pluripotent stem cells (PSCs) harboring formative features haven’t been derived from early mammalian embryos. Here we develop a method which enabled the derivation and culture of stable formative-like embryonic stem cells (ESCs) from mouse blastocysts. Formative-like mouse ESCs share molecular features characteristic of early post-implantation epiblasts and are competent for PGC-like cell induction and blastocyst chimera formation. The same culture also supported the derivation of ESCs and transgene-free induced pluripotent stem cells (iPSCs) from horse blastocysts and fibroblasts, respectively. Horse ESCs/iPSCs transcriptionally resembled mouse formative cells, and could also be directly induced into PGC-like cells. Formative-like horse iPSCs could efficiently chimerize horse, mouse, goat, sheep and pig embryos. Stable formative-like PSCs will be invaluable for studying mammalian pluripotency, and our method may be broadly applicable for the derivation of PGC and chimera competent PSCs from other mammalian species.

sample_organism:
Mus musculus
Equus ferus

platform_organism:
Mus musculus
Equus ferus

overall_design: We collected Embryonic cells form mouse and horse.

first: Leqian

last: Yu

first: Yulei

last: Wei

first: Haixi

last: Sun

first: Ahmed

last: Mahdi

first: Masahiro

last: Sakurai

first: Carlos

last: Pinzon

first: Daiji

last: Okamura

first: Adrian

last: Mutto

first: Jie

first: Ying

last: Gu

first: Pablo

last: Ross

first: Jun

last: Wu


title: Derivation of formative-like pluripotent stem cells from mammalian embryos [RNA-Seq]

sample_organism:
Homo sapiens
Mus musculus
Equus ferus

platform_organism:
Homo sapiens
Mus musculus
Equus ferus


title: Deletion of the gene encoding the N-methyl-D Aspartate Receptor GluN1 subunit in Schwann cells causes ultrastructural changes in Remak bundles and hypersensitivity in pain processing

city: La Jolla

first: Wendy

middle: Marie

last: Campana

state: CA

address: 9500 Gilman Drive

department: Anesthesiology

institute: University of California San Diego

summary: Mouse  DRGs (n=3 per genotype)  were isolated from a novel mouse model with conditional deletion of Glun1 in Schwann cells (GluN1-)  and corresponding  littermate controls (Glun+).  P0Cre recombinase is the driver. Transcriptome profiling of DRGs revealed 138 differenially regulated genes in Glun1- mice.  On third of the regulated genes are known to be involved in pain processing.

overall_design: 6 samples total. Examined differential expression between wildtype DRG (n=3) versus NMDA-R knockout DRG (n=3).


title: miRNA-Seq analysis of the early phase of BoMac cell stimulation with a viral and a bacterial pathogen associated molecular patterns

city: Basseterre

first: Felix

last: Toka

address: West Farm

department: Biomedical Sciences

country: Dominica

institute: Ross University School of Veterinary Medicine

summary: Purpose: To examine differential expression of miRNA in bovine macrophages under the influence of Toll-like receptor agonists. Goal: to study and understand the miRNA regulation of early phase of transcriptomic changes induced by Toll-like receptor in bovine macrophage cell line.

overall_design: Examination of the effect of CpG and poly I:C on small RNA expression in BoMac cell line.

first: Kiera

last: Dunaway

first: Felicia

last: Smaltz

first: Lidia-Szulc

last: Dabrowska

first: Magdalena

last: Bossowska-Nowicka

first: Matylda

last: Mielcarska

first: Matthias

last: Schweizer


title: Plasma circRNA expression profile in systemic lupus erythematosus and its clinical significance

city: Heifei

first: Ming-Yue

last: Zhang

address: Anhui Medical University of meishan road 81

institute: Anhui Medical University

summary: Circular RNAs (circRNAs) are a novel class of non-coding RNA and stably conserved in mammalian cells. Although circRNAs have been widely reported in some diseases and tissues, the expression of circRNAs in systemic lupus erythematosus (SLE) have yet to be explored. To reveal the implications of circRNAs in SLE, we used Human circRNA Array v2.0 microarrays to measure the expression profiles of circRNAs in plasma of patients with SLE and healthy controls. A total of 4763 circRNAs were detected in plasma of SLE sample, and 112 circRNAs were identified to be differentially expressed in plasma of SLE patients as compared to healthy controls (fold change >1.5 and P < 0.05), including 53 up-regulated circRNAs and 59 down-regulated circRNAs. Hsa_circRNA_407176, hsa_circRNA_406567 and hsa_circRNA_001308 were established using Real-time quantitative PCR. These results showed abrrant expression profiles of circRNAs in T cells of SLE patients and revealed their potential role in SLE.

overall_design: In this study, we determined expression profile of circRNAs in plasma of four SLE patients (S19, S21, S22, S42) and four healthy controls (C1, C2, C4, C5) using Human circRNA Array v2.0 microarray (8×15K, Arraystar).

first: Dong-Qing

last: Ye


title: Derivation of formative-like pluripotent stem cells from mammalian embryos

first: CNSA

last: CNGB


title: PD-1 and TIGIT co-expression identifies a circulating CD8 T cell population predictive of response to anti-PD-1 therapy in melanoma and Merkel-cell carcinoma patients [TCR-seq]

city: SEATTLE

first: Sylvain

last: Simon

state: WA

address: 1100 Fairview Ave

department: Clinical Research

institute: Fred Hutchinson cancer research center

summary: Clinical benefit from PD-1 inhibitors relies on reinvigoration of endogenous anti-tumor immunity. Efforts to define cellular populations associated with PD-1 clinical efficacy have been largely restricted to analysis of tumor material and the description of subsets of relevant cellular-based biomarkers in the blood of PD-1 inhibitor treated cancer patients are yet to be characterized. Given the particular expression pattern of PD-1 and TIGIT inhibitory receptors on peripheral CD8 T-cell subsets and the reported importance of CD8 T cells co-expressing these two markers for anti-PD-1 efficacy, we sought to determine the distinct biological features of peripheral CD8 subsets delineated based on PD-1 and TIGIT expression. Our findings identify the  PD-1+TIGIT+ (DPOS) CD8+ T-cell population as a subset of highly activated and proliferating T cells, enriched in tumor-specific T-cell clones and overexpressing CXCR5, a key marker of the recently described CD8 cytotoxic follicular T cell (Tfc) population. Strikingly, the frequency of DPOS T cells after 1 month of anti-PD-1 therapy was associated with clinical response in three independent cohorts of cancer patients treated with PD-1 inhibitor. Additionally, transcriptomic profiling of this subset described common features with the PD-1high CXCL13+ lymphocyte subset previously demonstrated in tumor infiltrates to be predictive of PD-1 blockade efficacy. Furthermore, TCR repertoire analysis described a cluster of emerging T-cell clonotypes in the DPOS population as a key feature of PD-1 therapeutic efficacy.

overall_design: Four CD8 T cell populations flow sorted according to differential PD-1 and TIGIT expression patterns (PD-1negTIGITneg: thereafter called DNEG, PD-1posTIGITneg: thereafter called PD1, PD-1posTIGITpos thereafter called DPOS, PD-1negTIGITpos thereafter called TIGIT) before total RNA extraction at baseline and after 1 or 2 months of PD-1 therapy (TCRseq, 12 patients).

first: Valentin

last: Voillet

first: Nathalie

last: Labarriere


title: A T cell immune suppression signature distinguishes European American auto-antibody positive (ANA+) healthy individuals

city: Oklahoma City

first: Judith

middle: A.

last: James

state: Oklahoma

address: 825 NE 13th Street

department: Arthritis and Clinical Immunology

institute: Oklahoma Medical Research Foundation

summary: Anti-nuclear antibody (ANA) positivity is a principal feature of individuals with an autoimmune disease, yet up to one in five healthy individuals are ANA+ and most will never develop clinical autoimmunity. Here, we show that immune profiles in ANA+ healthy individuals are altered, and differ by race. A suppressive immune signature distinguished by reduced T cell numbers and altered gene expression of HLA class I, IFN-associated, and apoptosis pathways, characterized European American (EA) ANA+ healthy individuals. In contrast, African American (AA) ANA+ healthy individuals had more elements of activation with increased CD69 gene expression on T cells and heightened pro-inflammatory cytokines. Increases in STAT4, IFNGR2 and STAT1 T cell transcripts and decreases in TGFBR1 gene expression in monocytes correlated with T cell expansion and clinical SLE. Thus, a suppressive immune signature in EA ANA+ healthy individuals may avert clinical autoimmune disease, which is associated with activation of Type I and II IFN pathways and T cell expansion.

overall_design: PBMCs from 36 subjects (ANA-, ANA+ healthy or SLE patients) were stained with antibodies for CD3 (UCHT1), CD19 (SJ25-C1), HLA-DR (G46-6), CD14 (61D3), CD16 (3G8), CD56 (NCAM16.2), CD66b (G10F5) and CD66b-CD19-CD3+ T cells, CD66b-CD3-CD19+ B cells, CD66b-CD3-CD19-CD56-HLA-DR+CD14+CD16+/- monocytes were sorted using a FACS Aria III (BD Biosciences). RNA was isolated using TRIZOL reagent (Invitrogen/Thermo Fischer (Waltham, MA), purified with Direct-zol RNA microprep kit (Zymo Research, Irvine, CA), and quantitated using 2100 Bioanalyzer (Agilent, Santa Clara, CA). QuantSeq 3’ mRNA-sequencing library prep kit for Illumina (FWD) (Lexogen, Vienna, Austria) was used to create cDNA libraries, amplify and sequence 3 million reads/sample using NextSeq 550 (Illumina, San Diego, CA). Libraries were evaluated for poor sample quality using FASTQC (version 0.11.8), and adaptors and contaminating non-specific reads removed using BBTools (version38.56). Reads were aligned to the GENCODE release 28 transcriptome using STAR (version 2.5.3a). BAM files were then converted to a gene count matrix using StringTie (version 1.3.6). Examination of differentially expressed genes between African American and European American ANA-, ANA+ healthy, and SLE patients were completed between sorted T cells, B cells and monocytes using DESeq2 normalized files and visualizations created using DESeq2 vst transformed data.

first: Joel

last: Guthridge

first: Samantha

last: Slight-Webb

first: Miles

last: Smith

first: Susan

last: Macwana

first: Nicolas

last: Dominguez

first: Aleksandra

last: Bylinska


title: PD-1 and TIGIT co-expression identifies a circulating CD8 T cell population predictive of response to anti-PD-1 therapy in melanoma and Merkel-cell carcinoma patients


title: Genome-wide occupancy of linker histone variant H1T2 in round/elongating spermatids of rats

status: Public on Nov 26 2020

city: Bangalore

first: Manchanahalli

middle: Rangaswamy

last: Satyanarayana Rao

state: Karnataka

address: Jakkur, Bengaluru, Karnataka

department: Molecular Biology and Genetics Unit (MBGU)

country: India

institute: Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)

summary:
Background: H1T2 is a germ cell specific linker histone variant, identified as critical for spermiogenesis based on knockout studies, shows a specialized localization at the apical pole of the spermatids and maintains an inherent polarity within the spermatid nucleus. However, the exact genomic loci bound to H1T2 in spermatids is unknown.
Method: Genome-wide occupancy of the rat H1T2 protein was studied by ChIP-sequencing of pulldown DNA isolated from nuclei of 35-50 days old rat testis, using highly specific anti H1T2 antibody.
Conclusion: Present study revealed that H1T2 is preferentially associated with the intergenic loci(majorly LINE L1 elements).

overall_design: Nuclei of elongating/condensing spermatids cell types of the Rat (Rattus norvegicus) testicular cells were used for this purpose. Two runs were made with two different samples having two replicates each with a control for the ChIP used in each run. Illumina HiSeq X Ten sequencing platform was used with 150bp read length and paired end read type.

first: Vasantha

last: Shalini

first: Utsa

last: Bhaduri

first: Anusha

last: Rengarajan

first: Anjhana

last: Ravikkumar

first: M

last: Rao


title: Lung Megakaryocytes are Immune Modulatory Cells

city: St Louis

first: Farshid

last: Guilak

state: Missouri

address: Couch Building, 3rd Floor, #3213

department: Orthopaedics

institute: Washington University in St Louis

summary: Our data demonstrate that lung and bone marrow-derived megakaryocytes (Mks) have distinct immune phenotypes and functions; lung Mks secrete inflammatory cytokines and express molecules that are similar to many tissue resident leukocytes and antigen presenting cells (APCs), and lung Mks process live intact bacteria and present bacteria-derived antigen to CD4+ T cells both in vitro and in vivo.  Our in vivo data suggest that lung Mks have important roles in the early activation of T cell responses to a pulmonary pathogen challenge, identifying a novel immune regulatory role for lung Mks.

overall_design: Cells were isolated from either the lung or the bone marrow, and enriched for the megakaryocyte population. Single cell RNA-seq was subsequently performed on isolated cells.

first: Daphne

last: Pariser

first: Zachary

last: Hilt

first: Sara

last: Ture

last: Blick-Nitko

first: Mark

last: Looney

first: Simon

middle: J

last: Cleary

first: Estheany

last: Roman-Pagan

first: Jerry

last: Saunders

first: Steve

last: Georas

first: Janelle

last: Veazey

first: Ferralita

last: Madera

first: Laura

last: Santos

first: Alison

last: Arne

first: Nguyen

last: Huynh

middle: C

last: Livada

first: Selena

last: Guerrero-Martin

first: Claire

last: Lyons

first: Kelly

last: Metcalf-Pate

first: Kathleen

middle: E

last: McGrath

first: James

last: Palis

first: Craig

last: Morrell


title: RNA-Seq analysis used to explore the bone-froming mechanism of microbially catalyzed biomaterials

first: Mengmeng

last: Li

address: 1295 Dingxi Road

institute: Shanghai Institute of Ceramics, Chinese Academy of Sciences

summary: We developed a microbial catalytic concept and strategy to prepare calcium carbonate with micro/nanostructures on the surface of bioceramics to improve bone-forming bioactivity. It involves three processes: bacterial adhesion on biomaterials, production of carbonate assisted with bacteria, nucleation and growth of calcium carbonate nano-crystals on the surface of bioceramics. The microbially catalyzed biominerals exhibited relatively uniform micro/nanostructures on both 2D and 3D CaSiO3 bioceramics. The descriptive analysis of RNA-sequencing revealed that the topographic and chemical cues presented by microbially catalyzed micro/nanostructures could stimulate the biological processes including adhesion, proliferation and differentiation. The study offers a microbially catalytic concept and strategy of fabricating micro/nanostructured biomaterials for tissue regeneration.

overall_design: Examination of New Zealand White rabbit bone marrow mesenchymal stem cell (rBMSC) samples subjected to 3 different treatments, 3 replicates per sample.

first: Fei

last: Han

first: Hongshi

last: Ma

first: Dong

last: Zhai


title: PRMT1 inhibition induces differentiation of colon cancer cells

city: Rehovot

first: Dan

last: Ben-Avraham

address: Hertzel 234

department: Grand Israel National Center for Personalized Medicine

country: Israel

institute: Weizmann Institute of Science

summary: Colorectal cancer (CRC) is the third most commonly occurring cancer in men and the second most commonly occurring cancer in women with over 1.8 million new cases in 20181. Differentiation therapy has been recently revisited as a prospective approach in cancer therapy2 by targeting the aberrant growth, and repairing differentiation and cell death programs of cancer cells. Standard of care chemotherapy may kill cancer cells, but the aggressive cells can survive and resistance gradually develops. In contrast, differentiation therapy aims not to eradicate cancer bulk, but rather directs cancer cells towards inhibited proliferation and restoration of the apoptotic program, while maintaining a limited toxicity. Current data suggests that differentiation therapy can be an effective anti-cancer treatment approach, however discovery of the new differentiation inducing molecules with a higher therapeutic index is essential. We performed High Throughput Screening (HTS) for discovery of compounds, which induce differentiation of colon cancer cells, using a novel dual multiplex assay3. Here we show that MS023, arginine methyl transferase (PRMT) type 1 inhibitor, is a potent inducer of colon cancer cell differentiation with a large therapeutic window. Our findings have a great impact for future research and development of an effective, clinically applicable, differentiation based anti-CRC therapy.

overall_design: 5790 compounds from different chemical libraries were screened at 10µM concentration for their ability to induce ALP activity and delay growth of HT-29 cells. RNA sequencing of HT-29 that were treated with either MS023, entiostat or DMSO(control) was done in quadruplicates, using Illumina Hi-seq 2500.

first: Alexander

last: Plotnikov

first: Noga

last: Kozer

first: Galit

last: Cohen

first: Silvia

last: Carvalho

first: Shirly

last: Dubershtein

first: Ofir

last: Almog

first: Leonardo

last: Solmesky

first: Khriesto

last: Shurrush

first: Ilana

last: Babaev

first: Benjamin

last: Sima

first: Shlomit

last: Gilad

first: Meital

last: Kupervaser

first: Yishai

last: Levin

first: Michael

last: Gershovits

first: Haim

middle: M

last: Barr


title: Updated and validated global cis-regulatory element map which includes the M/m sex-determining region of Aedes aegypti

city: Milwaukee

first: Ronald

last: Nowling

state: WI

address: 1025 N Broadway

institute: Milwaukee School of Engineering

summary: Formaldehyde assisted isolation of regulatory element (FAIRE) enrichment was used to recover open chromatin from A. aegypti embryos.  Next-generation sequencing of FAIRE DNA was performed.  Computational detection and analysis of FAIRE-enriched DNA sequences followed.

overall_design: For each of three biological replicates, A. aegypti eggs were collected for two hours and aged until 49-51 hrs after egg laying, at which point they were used as starting material for preparation of FAIRE-enriched DNA.  The FAIRE DNA enrichment protocol involved formaldehyde crosslinking and shearing of chromatin, followed by phenol chloroform extraction to recover open promoter regions from the aqueous phase.  Next-generation Illumina sequencing followed by computational detection and analysis of FAIRE-enriched sequences followed.

first: Molly

last: Duman-Scheel


title: Minor intron retention drives clonal hematopoietic disorders and diverse cancer predisposition.

city: Seattle

first: Robert

middle: K.

last: Bradley

state: Washington

address: 1100 Fairview Ave N

department: Public Health Sciences/Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: Most metazoans contain two distinct pre-mRNA splicing machineries: the major spliceosome, which removes >99% of introns, and the minor spliceosome, which recognizes <1% of introns. Despite their rarity, minor introns are exquisitely conserved amongst species, suggesting important regulatory functions. However, physiologic roles for the minor spliceosome and the relevance of recurrent, leukemia-associated mutations affecting minor spliceosome components are not well understood. Here, we identify that mutational loss of the minor spliceosomal factor ZRSR2 enhances hematopoietic stem cell self-renewal via impaired minor intron splicing that converges on LZTR1, a regulator of Ras-related GTPases. LZTR1 minor intron retention is additionally observed in Noonan syndrome and diverse cancers. These data uncover minor intron recognition as a regulator of hematopoiesis and mechanistic links between ZRSR2 mutations, LZTR1, and leukemia.

overall_design: eCLIP of human K562 cell lines expressing either empty vector FLAG or ZRSR2 with an N-terminal FLAG tag.

first: Daichi

last: Inoue

first: Jacob

last: Polaski

first: Justin

last: Taylor

first: Omar

last: Abdel-Wahab


title: Inter-myeloid cell synaptic antigen dispersal drives diversified anti-tumor T cell priming

city: San Francisco

first: Matthew

last: Krummel

state: CALIFORNIA

address: 513 Parnassus Ave, UCSF, Dept. of pathology, HSW518

institute: UCSF

summary: Using a labelled tumor antigen we identify dendritic cell subsets containing tumor derived antigen in the tumor draining lymph nodes and used these to stimulate anti-tumor OTI CD8 T cells. These were subsequently interrogated by RNAseq to determine how diverse DC subsets drive distinct patterns of CD8 T cell differentiation

overall_design: OTI CD8 T cell RNAseq analysis on cells stimulated in vitro by different DC subsets

first: Edward

last: Roberts


title: Transcriptomic analysis of evolved strains.

city: shanghai

first: Ming

last: Zhao

address: 130 Meilong Road, Xuhui District

institute: East China University of Science and Technology

summary: We develop a CRISPR-Cas assisted random mutation (CARM) technology for whole genome mutagenesis. As a proof-of-principle, CARM was applied to evolve the capacity of Saccharomyces cerevisiae to produce β-carotene. Thees files are transcriptomic analysis of finally evolutionary strain  C7-143, processed evolutionary strain  C3-06 and C5-63, and the original strains C0 and BY47419.

first: Feng-Qing

last: Wang

first: Dong-Zhi

last: Wei


title: The identification of differentially expressed genes in granulosa cell specific Cbfb and Runx2 double knockout mice

city: Lexington

first: Misung

last: Jo

address: 800 Rose street

department: Ob/Gyn

institute: University of Kentucky

summary: The removal of RUNX1/2 and CBFb affects the expression of many genes involved in ovulation and CL formation in mice

overall_design: The ovaries of wild-type and mutant mice (granuosa cell specific Cbfb and Runx2 knockout) was used to perform RNA-seq analysis


title: PD-1 and TIGIT co-expression identifies a circulating CD8 T cell population predictive of response to anti-PD-1 therapy in melanoma and Merkel-cell carcinoma patients [RNA-seq]

first: Sylvain

last: Simon

overall_design: Four CD8 T cell populations flow sorted according to differential PD-1 and TIGIT expression patterns (PD-1negTIGITneg, PD-1posTIGITneg, PD-1posTIGITpos, PD-1negTIGITpos) before total RNA extraction at baseline and after 1 or 2 months of PD-1 therapy (GEX, 12 patients).

first: Valentin

last: Voillet

first: Nathalie

last: Labarriere


title: An RNA-recognition motif protein from Helicobacter pylori binds single-stranded RNAs and stabilizes a pathogenicity island-encoded small RNA (RIP-seq)

status: Public on Nov 25 2020

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

summary: In this study several putative targets of the RRM protein RbpH (HP0827/HPG27_786) were identified. RNA binding targets of RbpH in two strains of H. pylori (G27 and 26695) were identified using RIP-seq.

overall_design: Identification of RbpH binding sites in 2 strains of H. pylori using RIP-seq

first: Marcus

last: Resch

first: Mona

last: Alzheimer

first: Thorsten

last: Bischler

first: Sara

last: Eisenbart

first: Giacomo

last: Golfieri

first: Cynthia

last: Sharma


title: Epigenetic control of transposable elements in the mouse male germ line by Tex15

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

institute: University of Geneva

summary: The piRNA biogenesis was evaluated in the mouse testes lacking TEX15. Total small RNAs, MILI-, and MIWI2-associated small RNAs from control (Tex15+/-) and Tex15(-/-) knock-out testes were sequenced. Data analysis revealed that the abundance of miRNAs and piRNAs was comparable between control and Tex15 knock-out testes, suggesting that loss of TEX15 function does not impair piRNA biogenesis. However, the relative abundance of MILI- and MIWI2-bound sense piRNAs derived from transposable elements was increased.

overall_design: RNA sequencing was used to identify the effect of TEX15 absence on the global population of total small testicular RNAs and piRNAs associated with MILI and MIWI2.

first: F

last: Yang

first: Radha

middle: R

last: Pandey

first: David

last: Homolka

middle: S

first: Jeremy


title: Modulation of the complex regulatory network for methionine biosynthesis in fungi

city: London

first: Vanessa

last: Dumeaux

state: Ontario

address: Elgin Dr

department: Anatomy and Cell Biology

institute: Western University

summary: In this study, C. albicans regulates its methionine biosynthetic pathways using the transcription  factors Met4 and Cbf1. This circuitry appears more complex than that of  filamentous fungi, which use orthologs of the Met4 transcription factor, but lack versions of Cbf1, but is considerably less complex than that of S. cerevisiae, which 2 requires two transcription complexes, involving Cbf1 and Met31/32 as DNA binding modules, and Met4 and the Met4 ortholog Met28 as co-activators, to regulate Met biosynthesis. Although C. albicans contains Met31/32 and Met28 orthologs, they do not appear to be linked to regulation of the methionine circuit. Thus, the phylogenetic progression from filamentous fungi to S. cerevisiae is characterized by increasing complexity of the regulators, although the structural elements of the pathways are fundamentally the same.

overall_design: Liquid cultures of all strains were adjusted to OD600 at 0.8 in 10 mL liquid YPD medium and incubated at 30 degrees with shaking at 220 rpm. We conduted RNAseq profiling for 2 replicates.

first: Manjari

last: Shrivastava

first: Jinrong

last: Feng

first: Mark

last: Coles

first: Benjamin

last: Clark

first: Amjad

last: Islam

first: Malcolm

last: Whiteway


title: An RNA-recognition motif protein from Helicobacter pylori binds single-stranded RNAs and stabilizes a pathogenicity island-encoded small RNA

first: Konrad

last: Förstner

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

overall_design: Refer to individual Series


title: An RNA-recognition motif protein from Helicobacter pylori binds single-stranded RNAs and stabilizes a pathogenicity island-encoded small RNA (RNA-seq)

summary: In this study several putative targets of the RRM protein RbpH (HPG27_786) were identified. Potential targets of RbpH in H. pylori (G27) were identified using total RNA-seq.

overall_design: Identification of RNAs with expression levels affected by RbpH using total RNA-seq

first: Marcus

last: Resch

first: Mona

last: Alzheimer

first: Thorsten

middle: K


title: Epigenetic biomarkers for EZH2 inhibitor sensitivity in neuroblastoma [array]

city: Kitaadachi-gun

first: Hisanori

last: Takenobu

state: Saitama

address: 818, Komuro, Ina-machi

department: Research Institute for Clinical Oncology

institute: Saitama Cancer Center

summary: EZH2 is a H3K27 methylase and a target of cancer epigenetic treatments. We recently reported the oncogenic roles and NTRK1 (TRKA) epigenetic regulation by EZH2 in the MYCN-amplified aggressive neuroblastomas (NB) (L. Here, we investigated the effects and function of small molecule EZH2 inhibitor (EZH2i) on aggressive NB model cell lines. We examined the antitumor effects of EZH2i using WST assay and colony formation assay. By EZH2i treatments, suppression of proliferation, G0/G1 cell cycle arrest, and apoptosis were observed in sensitive NB cells dose-dependently, whereas they were not observed in resistant NB cells. Transcriptome analysis and GSEA indicated significant changes were observed in the gene set related to differentiation and cell cycle arrest in the sensitive cells. We selected genes induced at mRNA level by EZH2i only in the sensitive cells and confirmed tumor suppressor function in NB cells. Almost of the EZH2i-induced gene promoters were marked by H3K27me3 in the sensitive NB cell line. Interestingly, a part of the EZH2i-induced gene promoters have CpG islands and methylated in NB tumor samples registered in databases and the EZH2i-resistant NB cells. Further, combination of EPZ-6438 and 5-aza-deoxycitide, resulted in effective suppression of proliferation in the EPZ-6438-resistant 3 NB cell lines. Transcriptome/methylome analysis of the EPZ-6438 and 5-aza-deoxycitide-treated NB cells revealed the combinational epigenetic regulation of the tumor suppressors and oncogene expression. Finally, we found that methylome analysis of the promoter regions, e.g. VSTM2L, GPNMB, and TIMP3 CpG islands can be biomarkers of EPZ-6438-registancy in unfavorable NB patients. These responsible CpG island methylation appears to be biomarkers for the application of EZH2i/DNMTi combination therapy.

overall_design:
IMR32 cells were treated with 0.1% DMSO, 1 uM EPZ-6438, and/or 1 uM 5-Aza-dc for 5 days.
Bisulfite converted DNA from the 4 samples were hybridized to the Infinium Human MethylationEPIC BeadChip.

first: Yuki

last: Endo

first: Naoko

last: Hattori

first: Toshikazu

last: Ushijima

first: Takehiko

last: Kamijo


title: Young and aged Myeloid cell treatment with EP2 antagonist PF044

status: Public on Nov 24 2020

city: Stanford

first: Paras

middle: Singh

last: Minhas

state: California

address: 1201 Welch Road

department: Neurology & Neurological Sciences

institute: Stanford University

summary: Peritoneal macrophages from young (3-4mo.) and aged (20-22mo.) mice were isolated from mice treated with EP2 antagonist PF044 (2.5mg/kg/d) for 6 weeks.

overall_design: In the study presented here, n = 3 mice were treated per experimental group with PF044 (2.5mg/kg/d) for 6 weeks by oral gavage

first: Katrin

middle: I

last: Andreasson


title: Expression data from PTC cell lines transfected with FAM60A-shRNA

city: Yiwu

first: Qiang

last: Sun

state: Zhejiang

address: No. N1, Shangcheng Avenue

institute: Zhejiang University

summary:
The mRNA and protein levels of FAM60A were significantly upregulated in PTC cancer tissues compared with paired normal tissue. Knockdown of FAM60A1 in TPC-1 and K1 significantly supressed cell growth, colony formation ability, tumor invasion, and  phase transition of the cell cycle.
We used microarrays to investigate the gene expression alterations of PTC cells after FAM60A knockdown by shRNA.

overall_design: FAM60A-shRNA-expressing and control-shRNA-expressing lentivirus were constructed and infected into PTC cancer cells TPC-1. Then total RNA was prepared for RNA extraction and hybridization on Affymetrix microarrays. Three independent samples were collected for each group.

first: Mengzhe

last: Guo

first: Houfa

last: Geng


title: CLIC4 is essential for host competence for metastasis in murine models of breast cancer and a prognostic indicator for human breast cancer

city: Bethesda

first: Philip

last: Murphy

state: MD

address: 10 CENTER DR RM 11N111

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

summary: CLIC4 belongs to a family of highly conserved metamorphic proteins of the glutathione‐S‐transferase superfamily and dysregulation is implicated in pulmonary arterial hypertension, asthma, and ovarian cancer. We show that genetic ablation of host Clic4 eliminated the establishment of breast cancer lung metastases in two independent mouse models while Clic4 null tumor cells retained metastatic capability. TCGA and METABRIC data indicated that CLIC4 is elevated in human breast cancers from young women, those with poor prognosis and those with early stage metastatic disease. Experimentally, the essential Clic4 host contributions for metastatic competence depended on circulating levels of pro‐ metastatic mediators, neoangiogenesis, tumor cell attachment to lung tissue, myofibroblast differentiation, and leukocyte migration. CLIC4 was abundant in circulating extracellular vesicles (EVs) from tumor‐bearing wildtype mice but absent in EVs from tumor‐bearing Clic4 null hosts or wildtype hosts bearing Clic4 null‐tumors suggesting cross‐talk between host and tumor cells is required to deposit CLIC4 in EVs. These results illuminate CLIC4 as a critical host factor for metastatic competence, a potential prognostic marker for breast cancer patients and a target for anti‐metastatic therapy.

overall_design: Examination of Clic4 KO vs WT at day 0 and 14 days in mouse lung. At day 0, we have 5 WT mice and 6 KO mice. At day 14, we have 2 WT mice and 6 KO mice.

first: Vanesa

last: Sanchez

first: Alayna

last: Craig-Lucas

first: Wendy

last: Dubois

first: Justin

last: Lack

first: Howard

middle: H

last: Yang

first: Max

last: Lee

first: Ji

last: Luo

first: Kent

middle: W

last: Hunter

first: Stuart

last: Yuspa


title: TREM2 Alzheimer’s variant R47H causes similar transcriptional dysregulation to knockout, yet only subtle functional phenotypes in human iPSC-derived macrophages

city: Oxford

first: Devika

last: Agarwal

address: JR hospital, Headley way

department: The MRC Weatherall Institute of molecular medicine

institute: University of Oxford

summary: TREM2 is a microglial cell surface receptor, with risk mutations linked to Alzheimer’s disease (AD), including R47H. TREM2 signalling via SYK aids phagocytosis, chemotaxis, survival, and changes to microglial activation state. In AD mouse models, knockout (KO) of TREM2 impairs microglial clustering around amyloid, and prevents microglial activation.  The R47H mutation is proposed to reduce TREM2 ligand binding. We investigated cell phenotypes of the R47H mutant and TREM2 KO in a model of human microglia, and compared their transcriptional signatures, to determine the mechanism by which R47H TREM2 disrupts function.   We generated human microglia-like iPSC-macrophages (pMac) from isogenic induced pluripotent stem cell (iPSC) lines, with homozygous R47H mutation or TREM2 knockout (KO). We firstly validated the effect of the R47H mutant on TREM2 surface and subcellular localization in pMac. To assess microglial phenotypic function we measured phagocytosis of dead neurons, cell morphology, directed migration, survival, and LPS-induced inflammation. We performed bulk RNA-seq, comparing significant differentially-expressed genes (DEGs: p<0.05) between the R47H and KO versus WT, and bioinformatically predicted potential upstream regulators of TREM2-mediated gene expression. Altered gene expression in the R47H TREM2 pMac overlapped by 90% with the TREM2 KO, and was characterized by dysregulation of genes involved with immunity, proliferation, activation, chemotaxis and adhesion. Downregulated mediators of ECM adhesion included the vitronectin receptor αVβ3, and consequently R47H TREM2 pMac adhered weakly to vitronectin compared with WT pMac. To counteract these transcriptional defects, we investigated TGFβ1, as a candidate upstream regulator. TGFβ1 failed to rescue vitronectin adhesion of pMac, although improved αVβ3 expression. The R47H mutation is not sufficient to cause gross phenotypic defects of human pMac under standard culture conditions. However, overlapping transcriptional defects with TREM2 KO supports the hypothesised partial loss-of-function effects of the R47H mutation. Furthermore, transcriptomics can guide us to more subtle phenotypic defects in the R47H cells, such as reduced cell adhesion, and can be used to predict targets for therapeutic intervention.

overall_design: We generated human microglia-like iPSC-macrophages (pMac) from isogenic induced pluripotent stem cell (iPSC) lines, with homozygous TREM2 R47H mutation (R47H), TREM2 knockout (KO) or a wildtype condtion (WT).  Bulk RNA sequencing with full length transcripts and polyA library prepration was perfromed on a total of 9 samples with 3 replicates harvested at 7,8, and 9 differentiation weeks for each of the conditions.

first: Hazel

last: Hall-Roberts

first: Juliane

last: Obst

first: Thomas

middle: B

last: Smith

first: Jimena

last: Monzón-Sandoval

first: Elena

middle: D

last: Daniel

first: Caleb

last: Webber

first: William

last: James

first: Emma

last: Mead

first: John

last: Davis

first: Sally

middle: A

last: Cowley


title: CBX2/PRC1 regulates the chromatin targeting of the Histone H3.3 Chaperone DAXX (RNA-Seq)

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research (FMI)

summary: Transcriptome of HEK293 cells

overall_design: Total RNA expression analysis from HEK293 cells

first: Mathieu

last: Tardat

first: Helene

last: Royo

first: Zichuan

last: Liu


title: T cells and Dendritic cells from MC38 tumors treated with anti-PD-1 or anti-PD-1 plus D18

city: Beijing

first: Liangliang

last: Wang

address: #30 Shuangqing Road

institute: Tsinghua University

summary: We treated mice bearing MC38 tumors with anti-PD-1 antibody (twice each week) or D18 (once one week). CD4+ T cells, CD8+ T cells and DCs were respectively isolated from tumors by FACS and RNA-seq performed. The goals of this study are to identify the activated cellular pathways in different subtype cells with the combination treatment. Samples were sequenced on an Illumina Hiseq 4000 instrument. The sequence reads were aligned to mouse mm10 reference genome using STAR (2.4.0) and then assembled and quantified by HTSeq (0.6.1) with Gencode M8 as annotation. DESeq2 was used for differential gene expression analysis among subgroups. Hierarchical clustering and principal component analysis were plotted applying FactoMineR and gplots libraries in R. log2 [FPKM] was calculated for each gene. We found that Granzyme, IFNγ, TNF were up-regulated and the related interferon induction pathway was activated in CD8+ T cells; the Th1 pathway and interferon signaling pathway were activated in CD4+ T cells; the expression of interferon-related and antigen-presenting machinery-related genes were increased in DCs by the combination treatment.

overall_design: Examination of CD4+ T cells, CD8+ T cells and DCs isolated from MC38 tumors treated with anti-PD-1 or anti-PD-1 plus D18.  Both conditions were run in triplicate.

first: Xuebin

last: Liao


title: Gene and miRNA expression in radioiodine refractory and avid papillary thyroid carcinomas (gene expression dataset)

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

summary: We performed gene and miRNA expression profiling in a series of 39 papillary thyroid carcinomas (PTCs) and 13 matched non-neoplastic thyroids derived from PTC patients with metastatic disease and submitted to radioiodine (RAI) treatment.

overall_design: Gene and miRNA expression profiles were established by microarray analysis in a retrospective series of 52 snap-frozen thyroid samples including 35 tissues collected before RAI treatment (17 primary PTC tumors, 5 synchronous lymph node metastases (LNMs), and 13 matched non-neoplastic thyroids included as control) and 17 RAI-refractory LNMs collected as successive surgery following RAI treatment. Patients were stratified based on RAI uptake at the metastatic site and on RAI response in either avid or refractory, displaying disease remission or persistance, respectively, after RAI treatment. Gene profiles were established by Thermo Fisher Human Clariom S Assay, and the corresponding miRNA profiles were established by Agilent SurePrint Human miRNA microarrays. Tumor samples were also characterized for the most common driving mutations and gene fusions typical of PTC by a PTC-Mass Array platform (PTC-MA).

first: C

last: Colombo

first: L

last: Fugazzola

first: E

last: Minna

first: M

middle: G

last: Borrello

last: De Cecco


title: ITGA6+ human testicular cell populations acquire a mesenchymal rather than germ cell transcriptional signature during long-term culture

city: Amsterdam

first: Robin

last: Struijk

address: Meibergdreef 9

department: Center for Reproductive Medicine

country: Netherlands

institute: Amsterdam UMC location AMC

summary: Abstract: Autologous spermatogonial stem cell transplantation is an experimental technique aimed at restoring fertility in infertile men. Although effective in animal models, in vitro propagation of human spermatogonia prior to transplantation has proven to be difficult. A major limiting factor is endogenous somatic testicular cell overgrowth during long-term culture. This makes the culture both inefficient and necessitates highly specific cell sorting strategies in order to enrich cultured germ cell fractions prior to transplantation. Here, we employed RNAseq using differential gene expression and cell deconvolution analyses, to determine cell type composition in sorted integrin alpha-6 (ITGA6+) primary human testicular cells (n = 4 donors) cultured for up to two months. Our data and analyses reveal that long-term cultured ITGA6+ testicular cells are composed mainly of cells expressing markers of peritubular myoid cells, Leydig cell progenitors, fibroblasts and mesenchymal stromal cells and only a limited number of spermatogonial cells as compared to their uncultured counterparts. These findings provide valuable insights into the cell type composition of cultured human ITGA6+ testicular cells during in vitro propagation and may serve as a basis for optimizing future cell sorting strategies as well as optimizing the current human testicular cell culture system for clinical use.

overall_design: RNAseq analysis of ITGA6+ primary human testicular cells during in vitro culture. Cultures were initiated from 4 testicular tissue donors and analyzed at 6 time points in culture, totalling 24 samples.

first: Robert

first: Callista

middle: L

last: Mulder

first: Saskia

last: van Daalen

first: Cindy

last: de Winter-Korver

first: Aldo

last: Jongejan

first: Sjoerd

last: Repping

first: Ans

last: van Pelt


title: iCLIP analysis of RNA substrates of the archaeal exosome (iCLIP)

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

institute: Justus-Liebig University Gießen

summary: In this study, an exoribonuclease was analyzed by iCLIP. The data documents the role of the archaeal exosome as an exoribonuclease and RNA-tailing enzyme interacting with all RNA classes. Mapping of most reads to mRNAs underlines the role of exosome in mRNA turnover, which is important for adaptation of prokaryotic cells to changing environmental conditions. The clustering of crosslink sites near 5’-ends of genes suggests simultaneous binding of both RNA ends by the S. solfataricus exosome. This may serve to prevent translation of mRNAs designated to degradation in 3’-5’ direction.

overall_design: 3 samples, 2 replicates each, 1 control sample

first: Jochen

last: Bathke

first: Elena

last: Evguenieva-Hackenberg


title: EEF1D RNAi in Bovine mammary epithelial cell

first: Shan

last: Lin

address: No.2 Yuan Mingyuan West Road

institute: China Agricultural University

summary: To further investigate the transcriptome profiles of EEF1D knocked-down and control BMECs, total RNA from the knocked-down BMECs treated with EEF1D-1357 or EEF1D-1893 shRNA, and the BMECs treated without shRNA, was extracted and purified, reversely transcribed into cDNA, and synthesized into cRNAs labeled with Cy3 using a Quick Amp Labeling Kit (Agilent). Afterwards, the labeled cRNAs (1.65 μg) were hybridized to a piece of Agilent Bovine Gene Expression 4×44K Chip using a Gene Expression Hybridization Kit (Agilent).

overall_design: Three EEF1D knocked-down replicates for BMECs treated with EEF1D-1357 or EEF1D-1893 shRNA and two control replicates were obtained.

first: Dongxiao

last: Sun

first: Yan

last: Xie


title: Quercetin promotes in vitro maturation of oocytes from humans and aged mice

city: JINAN

first: Yongzhi

last: Cao

address: NO. 44 Wenhuaxi Road

institute: Shandong University

summary: The flavonol compound quercetin is considered to be an anti-aging agent due to its cytoprotective actions as an antioxidant. The RNA sequencing analysis of oocytes after in vitro maturation from aged mice identified many genes altered by quercetin treatment and suggested that such treatment has a pronounced impact on genetic programs associated with mitochondrial dysfunction.

overall_design: 15 MII stage oocytes after IVM from three mice were considered one group, and three replicates were assessed per group. Samples included groups collected with or without 10 μM quercetin treatment.

first: Yueran

last: Zhao

first: Changming

last: Zhang


title: Characterization of prostate cancer cell expression profile upon treatment with extracellular vesicles derived from senescent stromal cells in the tumor microenvironment

city: Shanghai

first: Yu

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

summary: Recent advances in next generation sequencing (NGS) has revolutionized system-based analysis of genome-wide expression, cellular pathways and responses. We performed this study to establish the transcriptomic profiling (RNA-seq) of human prostate cancer cells exposed to extracellular vesicles (EVs) released by stromal cells developing a typical senescence-associated secretory phenotype (SASP) in a genotoxic setting.

overall_design: Overall transcript profiles of prostate cancer cell lines including PC3 and DU145 were generated by deep sequencing, in triplicate, using Illumina NovaSeq 6000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays

first: Liu

last: Han


title: RNAseq for Nestin+ bone marrow stromal cells in normal and MLL-AF9 mice

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

institute: University of Cambridge

summary: Cumulative evidence points out to the importance of the bone microenvironment for leukaemic development. Our preliminary results show that bone marrow stem cells, identified by the expression of the intermediate filament protein nestin (Nestin+ cells), provide support and chemoresistance to leukaemic cells. The rationale for these experiments is that leukaemic/Nestin+ cells crosstalk might regulate Nestin+ cells genetic profile to become more supportive elements for leukaemia. Nestin expression level distinguish two different Nestin+ populations, which seem to possess distint characteristics. Therefore, we would like to separately study high-expressing (Nestin high) and low-expressing Nestin cells (Nestin low). From our in vitro results, Nestin+ cells seem to be providing detoxifying tools to leukaemic cells such as antioxidant aminoacids and enzymes. The aim of the project is to identify pathways and genes differentially regulated in Nestin+ high and/or low cells in a leukaemic background.

overall_design: The submitted samples have been taken by sorting Nestin+ high or low cells from normal or leukaemic mice. Some samples are from a single mouse whereas some others are pool of two mice (if number of cells was too little). The code for the samples is: N = normal mice L = leukaemic mice We have established four groups where we assume samples should be similar (just biological variability): (a) Nestin+ high cells from Normal mice (samples N1, N2, N3); (b) Nestin+ low cells from Normal mice (samples N4, N5, N6, N7, N8 and N9); (c) Nestin+ high cells from Leukaemic mice (samples L1, L2 and L3): (d) Nestin+ low cells from Leukaemic mice (samples L4, L5, L6 and L7)We would like to specially compare groups: (a)   versus (c); (b)  versus (d); (a)   versus (b); ((c)versus (d).

first: Dorian

last: Forte

first: María

last: García-Fernández

first: Abel

last: Sánchez-Aguilera

first: Vaia

last: Stavropoulou

first: Claire

last: Fielding

first: Daniel

last: Martín-Pérez

first: Juan

last: Antonio López

first: Ana

last: Costa

first: Laura

last: Tronci

first: Efterpi

last: Nikitopoulou

first: Michael

last: Barber

first: Paolo

last: Gallipolli

first: Ludovica

last: Marando

first: Carlos

last: López Fernández de Castillejo

first: Alexandar

last: Tzankov

first: Sabine

last: Dietmann

first: Michele

last: Cavo

first: Lucia

last: Catani

first: Antonio

last: Curti

first: Jesús

last: Vázquez

first: Christian

last: Frezza

first: Brian

middle: J

last: Huntly

first: Juerg

last: Schwaller

first: Simón

last: Méndez-Ferrer


title: Longevity strategies in response to light in the reef coral Stylophora pistillata

city: Nice

first: Melanie

last: Pousse

address: Faculty of Medicine - Pasteur tower - 28, av. Valombrose

department: Bioinformatics

institute: IRCAN

summary: Aging is a multifactorial process that results in progressive loss of regenerative capacity and tissue function while simultaneously favoring the development of a large array of age-related diseases. Evidence suggests that the accumulation of senescent cells in tissue promotes both normal and pathological aging. Oxic stress is a key driver of cellular senescence. Because symbiotic long-lived reef corals experience daily hyperoxic and hypoxic transitions, we hypothesized that these long-lived animals have developed specific longevity strategies in response to light. We analyzed transcriptome variation in the reef coral Stylophora pistillata during the day–night cycle and revealed a signature of the FoxO longevity pathway. We confirmed this pathway by immunofluorescence using antibodies against coral FoxO to demonstrate its nuclear translocation. Among genes that were specifically up- or downregulated on exposure to light, human orthologs of two “light-up” genes (HEY1 and LONF3) exhibited anti-senescence properties in primary human fibroblasts. Therefore, these genes are interesting candidates for counteracting skin aging. We propose a large screen for other light-up genes and an investigation of the biological response of reef corals to light (e.g., metabolic switching) to elucidate these processes and identify effective interventions for promoting healthy aging in humans.

overall_design: RNA-Seq of tissues of coral Stylophora pistillata was performed using SOLiD 3 sequencer in three biological replicates.

first: Alexandre

last: Ottaviani

first: Rita

last: Eid

first: Didier

last: Zoccola

first: Mélanie

first: Jean-Marc

last: Dubal

first: Edwige

last: Barajas

first: Karine

last: Jamet

first: Kevin

last: Lebrigand

first: Pascal

last: Lapebie

last: Baudoin

first: Marie-Josèphe

last: Giraud-Panis

first: Alice

last: Rouan

first: Gallic

last: Beauchef

first: Christelle

last: Guéré

first: Katell

last: Vié

last: Barbry

first: Sylvie

last: Tambutté

first: Eric

last: Gilson

first: Denis

last: Allemand


title: Metabolic dysfunction is integral to TGFb signaling and tissue fibrosis

city: Boston

first: Thomas

last: Gan

state: MA

address: 33 Ave Lous Pasteur

department: Genetics and Pharmacogenomics

institute: Merck

summary: Fibrosis, or the accumulation of extracellular matrix, causes loss of organ function and is a common feature of many chronic diseases. To interrogate core molecular pathways underlying fibrosis, we cross–examine human primary cells from various tissues treated with TGFβ, as well as rodent kidney and liver fibrosis models. Transcriptome analyses reveal that in addition to the known TGFβ signature, cluster of genes involved in fatty acid oxidation are significantly perturbed. Furthermore, defective mitochondrial oxidative phosphorylation and acylcarnitine accumulation are found in fibrotic tissues. Substantial down-regulation of the PGC1α gene is evident in both in vitro and in vivo fibrosis models, suggesting a common node of metabolic signature for all tissue fibrosis. In order to identify suppressors of fibrosis, we carry out a compound library phenotypic screen and identify AMPK and PPAR as highly enriched targets. We further show that pharmacological treatment of MK-8722 (AMPK activator) and MK-4074 (ACC inhibitor) reduce fibrosis in vivo. Altogether, our work demonstrate that metabolic defect is integral to TGFβ signaling and fibrosis, targeting which represents a promising therapeutic approach for multiple fibrotic diseases.

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design:
Total RNA from human cells treated with TGFb in vitro, and rodent models of fibrosis (UUO, CCL4, and BDL) was sequenced.

Rodent models of fibrosis:
UUO: unilateral ureteral obstruction
CCL4: carbon tetrachloride
BDL: bile duct ligation

last: Muise

first: Ji

last: Zhang


title: ATAC seq of Gnas mutant subcutaneous progenitor cells

status: Public on Nov 23 2020

first: Qian

last: Cong

address: 188 Longwood Ave

department: Harvard School of dental medicine

institute: Harvard University

summary: The Gnas mutant mice driver by AdCre injection showed heterotopic osssification. In order to understand the underlying mechanism, we performed ATAC seq experiments  from the control and Gnas mutant subcutaneous progenitor cells.

overall_design: Isolation subcutaneous progenitor cells from Gnas flox mice with AdCre/GFP infection, than cultured for 7 days with osteogenic medium

first: Yingzi

last: Yang

first: Yuchen

last: Liu


title: iCLIP analysis of RNA substrates of the archaeal exosome

first: Gabriele

last: Klug

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

overall_design: Refer to individual Series


title: RNA-sequencing analysis of the OsIMA overexpression and knockdown rice lines and Fe deficiency responsiveness of non-transformant (NT) rice

city: Nonoichi

first: Takanori

last: Kobayashi

state: Ishikawa

address: 1-308 Suematsu

department: Research Institute for Bioresources and Biotechnology

institute: Ishikawa Prefectural University


title: Expression data of BCPAP cells with EPB41L4A knockdown

city: Columbus

first: Albert

last: de la Chapelle

address: 460 W. 12th Avenue

institute: The Ohio State University Wexner Medical Center

summary: A recent genome-wide association study in thyroid cancer discovered 5q22 as one of five loci implicated in thyroid cancer predisposition. The tag single-nucleotide polymorphism, rs73227498, is located downstream of coding isoforms of EPB41L4A and has a significant association with the expression of EPB41L4A in thyroid tissue, according to the GTEx Portal. In order to reveal the regulatory gene network of EPB41L4A in thyroid cells, microarray analysis was performed in the BCPAP cell line treated with siRNA against EPB41L4A.

overall_design: BCPAP cells were seeded in 6-well-plate and grown to 75% confluence at the time of transfection. 40 uM siEPB41L4A or siNS were transfected into BCPAP cells using 7.5 ul Lipofectamine RNAiMAX (Thermo Fisher Scientific). After transfection for 72 hours, cells were harvested and total RNA was extracted by using RNeasy (Qiagen) then treated by DNase I (Ambion) to eliminate DNA contamination. Experiments described above were performed at four different time points in order to obtain four biological replicates for expression analysis.

first: Daniel

middle: F

last: Comiskey Jr


title: iCLIP analysis of RNA substrates of the archaeal exosome (RNA-Seq)

overall_design: 1 samples, 3 replicates

first: Jochen

last: Bathke

first: Elena

last: Evguenieva-Hackenberg


title: Identification of differentially expressed between MCF7 and TAMR after ATF2 silencing

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

institute: Cancer Research UK, Cambridge Institute

summary: The goal of this study was to identify genes that were differentially regulated by ATF2 in TAMR cells (tamoxifen-resistant MCF7 derivatives) when compared to the tamoxifen-sensitive MCF7.

overall_design: MCF7 and TAMR cells were treated with either vehicle control (siNT) or siATF2 (2 probes, si1 and si2).   Treatments were conducted in replicates of 4 for the initial experiment of MCF7 vs TAMR and  in replicates of 5 for the ATF2 silencing.


title: Deletion of brain-specific isoforms of adapter protein SH2B1 protects mice from obesity in a non-leptin-mediated manner

city: Ann Arbor

first: Christin

last: Carter-Su

address: 1137 E. Catherine St

institute: University of Michigan

summary: Deletion or mutation of SH2B1 (SH2-B, PSM) is associated with severe obesity and insulin resistance in mice and humans. SH2B1 is alternatively spliced into four known isoforms: a, b, g, and d. Contrasting the ubiquitous expression of SH2B1b and g, SH2B1a and d are expressed almost exclusively in brain. Here, we generated mice lacking the brain-specific SH2B1 isoforms (SH2B1adKO mice). SH2B1adKO mice are protected from weight gain on standard and high fat diets, a phenotype caused by hypophagia. SH2B1adKO mice exhibit improvements in glucose homeostasis, yet these are mostly adiposity-dependent. Surprisingly, SH2B1adKO mice demonstrate normal leptin sensitivity. RNA sequencing highlights potential mechanisms underlying the decreased appetite of SH2B1adKO mice including gene expression changes associated with neuronal synapses. These findings suggest that SH2B1a and/or d are key regulators of energy balance. Furthermore, they highlight the profound importance of alternative splicing regulation for body weight.

overall_design: Hypothalamus mRNA was sequenced from control (WT, n = 9) and mutant mice lacking alpha/delta isoforms of Sh2b1 (SH2B1adKO, n = 12) to identify genes differentially expressed in mutant animals.

first: Alan

last: Rupp


title: Sperm miRNAs - potential mediators of bull age and early embryo development

city: Québec

first: Marc-André

last: Sirard

state: Québec

address: 2325 Rue de l'Université

department: Département des sciences animales

institute: Université Laval

summary: To identify if the patterns of spermatic  small non-coding RNAs (sncRNAs) are affected by paternal age and/or impact early embryogenesis, we generated sncRNAs libraries of sperm collected from same bulls at 10, 12, and 16 months of age, using 16 months as control for differential expression and functional analysis. miRNAs present in measurable quantity in oocytes were excluded. Of the remaining miRNAs, ten sperm-borne miRNAs were significantly differentially expressed in younger bulls (four in the 10 vs 16 months contrast and six in the 12 vs 16 months contrast). Targets of miRNAs were identified and compared to the transcriptomic database of two-cell embryos, to genes related to two-cell competence, and to the transcriptomic database of blastocysts. Ingenuity pathway analysis of the targets of these miRNAs suggested potential influence on the developmental competence of two-cell embryos and on metabolism and protein synthesis in blastocysts. The results showed that miRNA patterns in sperm are affected by the age of the bull and may mediate the effects of paternal age on early embryonic development.

overall_design: sncRNAs profile of four bulls at 10, 12, and 16 months old were generated.

first: Chongyang

last: Wu

first: Patrick

last: Blondin

first: Christian

last: Vigneault

first: Rémi

last: Labrecque


title: Typical western diet exacerbates dystrophic neurite pathology in APP/PS1 and APP/PS1/Tau mouse models by reducing the clustering of microglia around β-amyloid plaques

city: Kuopio

first: Mikael

last: Marttinen

address: Yliopistonranta 1E

department: Biomedicine

country: Finland

institute: University of Eastern Finland

summary: Here, we studied the interaction between dietary (TWD) and genetic factors (APPswe/PS1dE9 and tau P301L mutations) and their effect on memory, brain pathology, global gene expression and on insulin-Akt-GSK3β pathway in brain of mice with four different AD-linked genetic backgrounds: wild-type (AwTw), APPswe/PS1dE9 (A+Tw), P301Ltau (AwT+), and triple transgenic (A+T+).

overall_design: The study comprised of 45 female mice, 12 wild-type (AwTw), 11 APP/PS1 transgenic (A+Tw), 12 tau P301L transgenic (AwT+) and 10 transgenic for both APP/PS1 and tau P301L (A+T+).

first: Mikko

last: Hiltunen


title: Electronic cigarette exposure disrupts blood-brain barrier integrity, promotes neuroinflammation, and leads to cognitive dysfunction

first: Xiang

last: Yu

state: Shanghai

address: 800 DongChuan

institute: Shanghai Jiao Tong University

summary: Electronic cigarette (EC) use has grown substantially since entry into the US market, particularly among adolescents and combustible tobacco users. Despite growing popularity and claims of harm reduction, the health effects of these products outside the lung is poorly understood. Several constituents of cigarette smoke (CS) with known neurovascular and inflammatory effects are present in EC liquids or formed during the generation of vapor. The present study characterizes the impact of EC exposure on neuroinflammation and blood-brain barrier (BBB) function, and provides comparison of outcomes with reference cigarette exposure normalized to comparable levels of nicotine delivery. Additionally, the contribution of nicotine to observed effects is elucidated through comparison with EC liquids which are verified to be nicotine-free. C57BL/6 mice are exposed to 2 hrs of daily EC vapor or CS, beginning at 8 wks of age. Changes in BBB gene expression are first characterized by whole exome sequencing of isolated brain microvessels following chronic (2 month) EC exposure.

overall_design: RNAseq of mouse with Electronic cigarette exposure and smoke as compared to room air

first: Nathan

last: Heldt

first: Alecia

last: Seliga

first: Malika

last: Winfield

first: Sachin

last: Gajghate

first: Nancy

last: Reichenbach

first: Slava

last: Rom

first: Brian

last: Gregory

first: Yuri

last: Persidsky