title: Notch3 signaling promotes tumor cell adhesion and progression in a murine epithelial ovarian cancer model

city: New York

first: Elham

last: Azizi

state: NY

institute: Memorial Sloan Kettering Cancer Center

summary: High grade serous ovarian cancer (HGSC) is the most common and deadly type of ovarian cancer, largely due to difficulties in early diagnosis and rapid metastasis throughout the peritoneal cavity. Previous studies have shown that expression of Notch3 correlates with worse prognosis and increased tumorigenic cell behaviors in HGSC. We investigated the mechanistic role of Notch3 in a model of metastatic ovarian cancer using the murine ovarian surface epithelial cell line, ID8 IP2. Notch3 was activated in ID8 IP2 cells via expression of the Notch3 intracellular domain (Notch3IC). Notch3IC ID8 IP2 cells injected intraperitoneally caused accelerated ascites and reduced survival compared to control ID8 IP2, particularly in early stages of disease. We interrogated downstream targets of Notch3IC in ID8 IP2 cells by RNA sequencing and found significant induction of genes that encode adhesion and extracellular matrix proteins. Notch3IC ID8 IP2 showed increased expression of ITGA1 mRNA and cell-surface protein. Notch3IC-mediated increase of ITGA1 was also seen in two human ovarian cancer cells. Notch3IC ID8 IP2 cells showed increased adhesion to collagens I and IV in vitro. We propose that Notch3 activation in ovarian cancer cells causes increased adherence to collagen-rich peritoneal surfaces. Thus, the correlation between increased Notch3 signaling and poor prognosis may be influenced by increased dissemination and metastasis of HGSC via increased attachment to the peritoneum.   Implications: Expression of Notch3 accelerates the progression of ovarian cancer by increasing the adherence of disseminating cells to new metastatic sites.

overall_design: RNA was extracted from Notch3IC and Control Sets #1-#4 with a RNeasy Mini Kit (QIAGEN, 74104) and the RNase-Free DNase Set (QIAGEN, 79254). Library preparation and sequencing was performed by the JP Sulzberger Columbia Genome Center using Illumina TruSeq RNA Prep Kit with poly-A pulldown followed by sequencing ~30 million 100-base pair single-end reads on an Illumina HiSeq 2000 or 2500 instrument.

first: Jessica

last: Price

first: Jenny

last: Parvani

first: Priyanka

last: Shukla

first: Seoyeon

last: Kim

first: L

last: Naiche

first: Jill

last: Slack-Davis

first: Dana

last: Pe’er

first: Jan

last: Kitajewski


title: Expression profiles of circRNAs in visceral adipose tissue from obese and non-obese individuals

status: Public on May 19 2020

city: Chengdu

first: Hongtao

last: Liu

state: Sichuan

address: No.82, qinglong street, qingyang district, chengdu

department: General surgery

country: China

institute: Chengdu third people's hospital

summary: A growing body of evidence has suggested that circular RNAs (circRNAs) are crucial for the regulation of gene expression. circRNA dysregulation has been implicated in several diseases. However, the expression and function of circRNAs in obesity remain unknown. In this study, we investigated global changes in the expression patterns of circRNAs in adipose tissues

overall_design: Visceral adipose tissue (VAT) that were obtained during bariatric surgery (Obese) or laparoscopic hernia repair (Lean) were donated by patients after obtaining informed consent. Three cases with BMI>30 kg/m2 and three controls with BMI<25 kg/m2 were selected and processed extracting total RNA, processing on microarrays

first: Tongtong

last: Zhang

first: Yanjun

last: Yu

first: Huawu

last: Yang

first: Yuanchuan

first: Yu

first: Mao

last: Rui

first: Pengsen

last: Guo

first: Dafang

last: Zhan


title: BREM-SC: A Bayesian Random Effects Mixture Model for Joint Clustering Single Cell Multi-omics Data

status: Public on May 18 2020

city: Pittsburgh

first: Xinjun

last: Wang

state: PA

address: 4401 Penn Ave., Rangos Research Building

country: USA

institute: Children’s Hospital of Pittsburgh of UPMC

type: Expression profiling by high throughput sequencing

summary: Droplet-based single cell transcriptome sequencing (scRNA-seq) technology is able to measure the gene expression from tens of thousands of single cells simultaneously. More recently, coupled with the cutting-edge Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq), the droplet-based system has allowed for immunophenotyping of single cells based on cell surface expression of specific proteins together with simultaneous transcriptome profiling in the same cell. In this study, we developed BREM-SC, a novel Bayesian Random Effects Mixture model that jointly clusters paired single cell transcriptomic and proteomic data, which will greatly facilitate researchers to jointly study transcriptome and surface proteins at the single cell level to make new biological discoveries.

overall_design: Peripheral blood mononuclear cells were profiled by RNA-seq, CITE-seq using a panel of 10 antibodies.

first: Wei

last: Chen


title: Removal of H2Aub1 by ubiquitin-specific proteases 12 and 13 is required for stable Polycomb-mediated gene repression in Arabidopsis

city: Uppsala

first: Claudia

last: Köhler

address: Almas Allé 5

department: Plant Biology

country: Sweden

institute: SLU

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Background: Stable gene repression is essential for normal growth and development. Polycomb Repressive Complexes 1 and 2 (PRC1 & PRC2) are involved in this process by establishing monoubiquitinated histone 2A (H2Aub1) and subsequent trimethylation of lysine 27 of histone 3 (H3K27me3). Previous work proposed that H2Aub1 removal by the ubiquitin-specific proteases 12 and 13 (UBP12 & UBP13) is part of the repressive PRC1&2 system, but its functional role remains elusive.

Results: We show that UBP12 and UBP13 work together with PRC1, PRC2, and EMF1 to repress genes involved in stimulus response. We found that H2Aub1 is associated with responsiveness, and that it’s only indirectly repressive via PRC2 recruitment. Our analyses also revealed that PR2 targets that do not require PRC1 are pre-repressed. Lastly, we have found that removal of H2Aub1 by UBP12/13 prevents loss of H3K27me3, consistent with our finding that the H3K27me3 demethylase REF6 is enriched at H2Aub1 marked genes.

Conclusions: Our data allow us to propose a model in which deposition of H2Aub1 permits recruitment of PRC2 and provides a state that allows for a rapid switch between gene activation and repression. Removal of H2Aub1 by UBP12/13 is required to achieve stable repression.

overall_design: RNAseq of single and double mutants for the UBP12/13 genes, plus wild-type control, three biological replicates of each genotype. Three ChIP-seq experiments on the double mutant and wild-type; the first including H2Aub1, H2A.Z, H3, and input. The second including H3K27me3, and H3. The third including REF6 (GFP), and input. Two biological replicates were included for each genotype * IP combination.

first: Lejon

last: Kralemann

first: Shujing

first: Minerva

middle: S

last: Trejo-Arellano

first: Rafael

last: Muñoz-Viana

first: Lars

last: Hennig


title: Endothelial cells control muscle regeneration through angiocrine lactate

city: schwerzenbach

first: jing

last: zhang

state: Schwerzenbach

address: schorenstrasse 16

department: Department Health Sciences and Technology

country: Switzerland

institute: DHEST

summary: We studied metabolic angiocrine mechanisms by which endothelial cell_ECs_ can contribute to muscle regeneration from ischemia by using endothelial specific pfkfb3 knockout mice_pfkfb3DEC_ after hind-limb ischemia_HLI_. During muscle regeneration,  monocytes are recruited to the injured area and rapidly become macrophages which initially exhibit a more pro-inflammatory M1-like phenotype but soon thereafter functionally repolarize towards an M2-like phenotype to actively support muscle regeneration. Interestingly, macrophages derived from pfkfb3DEC failed to polarized to M2-like macrophages after HLI. Reduced macrophage polarization impairs angiogenesis and muscle regeneration. The RNAseq data are pfkfb3DEC and pfkfb3WT muscle derived macrophages 3 days after HLI.

overall_design: pfkfb3EC and pfkfb3WT muscle derived macrophages 3 days after HLI.

first: Jing

first: Jonathan

last: Muri

first: Gillian

last: Fitzgerald

first: Tatiane

last: Gorski

first: Roberto

last: Gianni-Barrera

first: Evi

last: Masschelein

first: Gommaar

last: D'Hulst

first: Paola

last: Gilardoni

first: Guillermo

last: Turiel

first: Zheng

last: Fan

first: TongTong

first: Mélanie

last: Planque

first: Peter

last: Carmeliet

first: Luc

last: Pellerin

first: Christian

last: Wolfrum

first: Sarah-Maria

last: Fendt

first: Andrea

last: Banfi

last: Stockmann

first: Inés

last: Soro-Arnaiz

first: Manfred

last: Kopf

first: Katrien

last: De Bock


title: A single-cell atlas of the peripheral immune response to severe COVID-19

city: Stanford

first: Aaron

middle: James

last: Wilk

state: California

address: 300 Pasteur Dr Bldg S131, Grant

institute: Stanford University

summary:
There is an urgent need to better understand the pathophysiology of Coronavirus disease 2019 (COVID-19), the global pandemic caused by SARS-CoV-2 which has infected more than 3 million people worldwide. Approximately 20% of patients with COVID-19 develop severe disease and 5% require intensive care. Severe disease has been associated with changes in peripheral immune activity, including increased levels of pro-inflammatory cytokines that may be produced by a subset of inflammatory monocytes, lymphopenia, and T cell exhaustion. To elucidate pathways in peripheral immune cells that might lead to immunopathology or protective immunity in severe COVID-19, we applied single-cell RNA sequencing (scRNA-seq) to profile peripheral blood mononuclear cells (PBMCs) from 7 patients hospitalized for COVID-19 and 6 healthy controls. We identify reconfiguration of peripheral immune cell phenotype in COVID-19, including a heterogeneous interferon-stimulated gene (ISG) signature, HLA class II downregulation, and a developing neutrophil population that appears closely related to plasmablasts appearing in patients with acute respiratory failure requiring mechanical ventilation. Importantly, we found that peripheral monocytes and lymphocytes do not express substantial amounts of pro-inflammatory cytokines. Collectively, we provide a cell atlas of the peripheral immune response to severe COVID-19.

Sample IDs used in the manuscript were shortened for clarity. They relate to the titles of deposited files as follows:
covid_555_1: C1 A
covid_555_2: C1 B
covid_556: C2
covid_557: C3
covid_558: C4
covid_559: C5
covid_561: C7
HIP002: H1
HIP015: H2
HIP023: H3
HIP043: H4
HIP044: H5
HIP045: H6

overall_design: Single-cell RNA sequencing of peripheral blood mononuclear cells (PBMCs) from 8 samples from COVID-19 patients and 6 healthy controls.

middle: J

first: Catherine

middle: A

last: Blish


title: High-throughput sequencing of circRNAs in ovarian cancer SKOV3 cell line

status: Public on May 21 2020

city: Changsha

first: Guanming

last: Deng

state: Hunan

address: 283 Tongzipo Road, Yuelu District

department: Gynecologic Oncology

institute: Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University

type: Non-coding RNA profiling by high throughput sequencing

summary: Circular RNAs(circRNAs) are conservative and stable and have been extensively studied in cancer in recent years. Expression profile of circRNA is largely unknown in ovarian cancer. This study explored circRNAs in the ovarian cancer cell line SKOV3.

overall_design: We injected untreated SKOV3 ovarian cancer cells into nude mice peritoneal cavity to mimic the circRNAs formation and degradation during tumor cell growth. Tumor tissues with good growth were obtained from nude mice, and high-throughput sequencing was performed to obtain circRNAs stably expressed in all samples.

first: Jie

last: Tang

first: Le

last: Chen


title: Impact of high salinity and the compatible solute glycine betaine on global gene expression of Bacillus subtilis

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

country: Germany

institute: University Medicine Greifswald

summary: In order to reveal so far unknown facets of the adaptation of B. subtilis to growth under high-salinity conditions, a whole-transcriptome analysis of B. subtilis BSB (168 Trp+) was performed using strand-specific tiling arrays (tiling step of 22 nucleotides). In addition, the effects of glycine betaine (GB) were analyzed under high salinity and standard growth conditions in a chemically defined medium. Important novel findings were a sustained low-level induction of the SigB-dependent general stress response and strong repression of biofilm matrix genes under high-salinity conditions. GB influences gene expression not only under high-salinity, but also under standard growth conditions without additional salt.

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design:
Cells were grown aerobically at 37 °C in Spizizen's minimal medium either supplemented with 1 mM glycine betaine, 1.2 M NaCl or 1.2 M NaCl and 1 mM glycine betaine. Cells were harvested in the exponential growth phase at an optical density of 1.0.
Microarray hybridizations were performed with RNA from three biological replicates. The individual samples were labeled with Cy3.

first: Hermann

last: Rath

first: Leif

last: Steil

first: Uwe

last: Völker


title: RNA-seq of S. meliloti strain ectopically overexpressing trpL and RIP-seq with 3xFLAG-tagged peptide peTrpL from S. meliloti

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: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Analysis of RNA coimmunoprecipitated with 3xFLAG-tagged peptide peTrpL from Sinorhizobium meliloti

summary: We show that specific RNAs are coimmunoprecipitated in a tetracycline-dependent manner with the Flag-tagged peptide peTrpL of S. meliloti

overall_design:
RNA coimmunoprezipitated with  the Flag-tagged peptide was compared to the RNA of the mock CoIP with a strain with similarly induced, non-tagged peptide. Three biological experiments were performed. The RNA samples were subjected to RNAseq analysis (Illumina)
contributor: vertis Biotechnologie AG (Munich, Germany)

first: Hendrik

last: Melior

first: Elena

last: Evguenieva-Hackenberg

middle: U


title: Transcriptome analysis of Sinorhizobium meliloti strain ectopically overexpressing trpL

summary: We show that the RNA leves of many genes in the S. meliloti overexpressing strain (OE) 2011 (pRK-RcsR1) are more similar to the levels of in  wild type (WT) strain 2011 than in the empty vector control (EVC) strain 2011(pRK4352). Since the plasmid-containing strains were grown in the presence of 10 µg/ml tetracycline (Tc), while the WT was grown without Tc, the results suggest that the intrecellular Tc concentration in the OE strain are lower than in the EVC. This is explained by an increased efflux pump activity in the OE strain.

overall_design:
Total RNA of the three strains was subjected to RNAseq analysis (Illumina)
contributor: vertis Biotechnologie AG (Munich, Germany)


title: Arabidopsis NRP switches off the PP6 phosphatase FyPP3 to repress auxin-mediated growth in response to abscisic acid

status: Public on May 16 2020

city: Shanghai

first: Liming

last: Luo

address: 800 Dongchuan RD. Minhang District

department: School of Life Sciences and Biotechnology

institute: Shanghai Jiao Tong University

summary: How environmentally challenged plants can switch from growth to stress adaptation is an important question in plant physiology. To identify the key regulatory proteins and to characterize the underlying signaling pathways are essential in answering this question. Here we show that the abiotic stress hormone Abscisic acid (ABA) induces the expression of the Asparagine rich proteins (NRP), DCD1 and DCD2, to repress the auxin-induced growth by promoting vacuolar degradation of PIN2, the auxin efflux carrier. ABA-induced degradation of PIN2 is inhibited in the dcd1 dcd2 double mutant, and inhibition of FyPP3, the catalytic subunit of the PP6 protein phosphatase, can restore the PIN recycling and growth phenotype in the double mutant. Transcriptome analyses on WT, dcd1 dcd2, the FyPP3 Dominant Negative line (FyPP3-DN), and dcd1 dcd2/FyPP3-DN supported the essential function of the NRP-FyPP3 module in the growth- to stress-response switch.

overall_design: Arabidoposis thaliana mRNA extracted from 7-day old wild type (WT), nrp1 nrp2, FyPP3DN and nrp1 nrp2 / FyPP3DN seedling (6 days for growing and 1day treated with 5 μM ABA or not), deep sequencing, in triplicate, using Illumina HiSeq 2500 system

first: Yanying

last: Wu

first: Xinqi

last: Liu

first: Qingqiu

last: Gong


title: Distinctions between sex and time in patterns of DNA methylation across puberty

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

type: Methylation profiling by genome tiling array

summary: Background: There are significant sex differences in human physiology and disease; the genomic sources of these differences, however, are not well understood. During puberty, a drastic neuroendocrine shift signals physical changes resulting in robust sex differences in human physiology. Here, we explore how shifting patterns of DNA methylation may inform these pathways of biological plasticity during the pubertal transition.   Methods: In this study we analyzed DNA methylation (DNAm) in saliva at two time points across the pubertal transition within the same individuals. We targeted two domains of DNAm patterns that may inform processes of sexual differentiation 1) sex related sites, which demonstrated differences between males from females and 2) time related sites in which DNAm shifted significantly between timepoints. We further explored the correlated network structure sex and time related DNAm networks and linked these patterns to pubertal stage, assays of salivary testosterone, a reliable diagnostic of free, unbound hormone that is available to act on target tissues, and overlap with androgen response elements.  Results: Sites that differed by biological sex were largely independent of sites that underwent change across puberty. Time-related DNAm sites, but not sex-related sites, formed correlated networks that were associated with pubertal stage. Both time and sex DNAm networks reflected salivary testosterone levels that were enriched for androgen response elements, with sex-related DNAm networks being informative of testosterone levels above and beyond biological sex later in the pubertal transition.   Conclusions: These results inform our understanding of the distinction between sex- and time-related differences in DNAm during the critical period of puberty and highlight a novel linkage between correlated patterns of sex-related DNAm and levels of salivary testosterone.

overall_design: 240 samples from 118 individuals (2 time points each); replicates indicated by extensions:"_Rep" or "_B"; second time point indicated by "_T2"

first: Sarah

middle: R

last: Moore


title: ARS2/MAGL signaling in glioblastoma stem cells promotes self-renewal and M2-like polarization of tumor-associated macrophages I

city: Seoul

first: Young Taek

last: Oh

address: 50 Irwon-dong, Gangnam-gu

country: South Korea

institute: Samsung Medical Center

summary: The interplay between glioblastoma stem cells (GSCs) and tumor-associated macrophages (TAMs) promotes progression of glioblastoma multiforme (GBM). However, the detailed molecular mechanisms underlying the relationship between these two cell types remain unclear. Here, we demonstrate that ARS2 (arsenite-resistance protein 2), a zinc finger protein that is essential for early mammalian development, plays critical roles in GSC maintenance and M2-like TAM polarization. ARS2 directly activates its novel transcriptional target MGLL, encoding monoacylglycerol lipase (MAGL), to regulate the self-renewal and tumorigenicity of GSCs through production of prostaglandin E2 (PGE2), which stimulates β-catenin activation of GSC and M2-like TAM polarization. Specific knockdown of ARS2 or MAGL significantly suppressed self-renewal and tumor growth, and increased survival in a mouse intracranial xenograft model of GSCs. We identify M2-like signature downregulated by which MAGL-specific inhibitor, JZL184, increased survival rate significantly in the mouse xenograft model by blocking PGE2 production. The M2-like signature is enriched in mesenchymal subtype and predicted poor survival in GBM patients. Taken together, our results suggest that blocking the interplay between GSCs and TAMs by targeting ARS2/MAGL signaling offers a potentially novel therapeutic option for GBM patients.

overall_design: shARS


title: ARS2/MAGL signaling in glioblastoma stem cells promotes self-renewal and M2-like polarization of tumor-associated macrophages II

summary:
The interplay between glioblastoma stem cells (GSCs) and tumor-associated macrophages (TAMs) promotes progression of glioblastoma multiforme (GBM). However, the detailed molecular mechanisms underlying the relationship between these two cell types remain unclear. Here, we demonstrate that ARS2 (arsenite-resistance protein 2), a zinc finger protein that is essential for early mammalian development, plays critical roles in GSC maintenance and M2-like TAM polarization. ARS2 directly activates its novel transcriptional target MGLL, encoding monoacylglycerol lipase (MAGL), to regulate the self-renewal and tumorigenicity of GSCs through production of prostaglandin E2 (PGE2), which stimulates β-catenin activation of GSC and M2-like TAM polarization. Specific knockdown of ARS2 or MAGL significantly suppressed self-renewal and tumor growth, and increased survival in a mouse intracranial xenograft model of GSCs. We identify M2-like signature downregulated by which MAGL-specific inhibitor, JZL184, increased survival rate significantly in the mouse xenograft model by blocking PGE2 production. The M2-like signature is enriched in mesenchymal subtype and predicted poor survival in GBM patients. Taken together, our results suggest that blocking the interplay between GSCs and TAMs by targeting ARS2/MAGL signaling offers a potentially novel therapeutic option for GBM patients.
Methods: X01 subcutatneous model treated vehicle or JZL184
Results: abstract copy and paste
Conclusion: abstract copy and paste

first: Jong

middle: B

last: Park

first: Jinlong

last: Yin

first: Sung

last: Kim

first: Young

middle: T


title: Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation

first: Howard

middle: Y.

last: Chang

state: CALIFORNIA

address: 269 Campus Drive, CCSR 2130

institute: Stanford


title: Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation [ChIP-Seq]

summary: We show that Spen, an Xist binding repressor protein essential for XCI, binds to ancient retroviral RNA transcribed genome-wide, performing a surveillance role to recruit chromatin silencing machinery to these parasitic loci. Spen inactivation leads to de-repression of endogenous retroviral (ERV) elements in embryonic stem cells, with gain of chromatin accessibility, active histone modifications, and ERV RNA transcription.  Spen binds directly to ERV RNAs that are highly similar to the A-repeat of Xist, a region critical for Xist-mediated gene silencing. ERV RNA and Xist A-repeat bind the RRM3 domain of Spen in a competitive manner and insertion of an ERV into an A-repeat deficient Xist rescues binding of Xist RNA to Spen.

overall_design: ChIP-seq was performed in WT and Spen KO mESCs . Libraries(2 replicates per line) were sequenced on an Illumina HiSeq 4000 or Nextseq (2x75bp)

first: Ava

last: Carter

first: Jin

last: Xu

middle: Y


title: DSCAM-AS1-driven proliferation of breast cancer cells involves regulation of alternative exon splicing and 3’-end usage

status: Public on May 15 2020

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

summary:
Background: DSCAM-AS1 is a cancer-related long noncoding RNA with higher expression levels in Luminal A, B and HER2-positive Breast Cancer (BC), where its expression is strongly dependent on Estrogen Receptor Alpha (ERα).
Method: To decipher its function, DSCAM-AS1 expression was measured by qRT-PCR in tissue samples from 93 BC patients in addition to a meta-analysis of 30 gene expression datasets, together with the evaluation of its association with clinical data. By computational analyses of our RNA-Seq in MCF-7 cells, we investigated the DSCAM-AS1 knock-down effects at both gene and isoform levels
Results: We confirmed DSCAM-AS1 overexpression in high grade Luminal A, B and HER2+ BCs and found a significant correlation with disease relapse. 908 genes were regulated by DSCAM-AS1-silencing, primarily involved in cell cycle and inflammatory response. Noteworthy, the analysis of alternative splicing and isoform regulation revealed 2,085 splicing events regulated by DSCAM-AS1, enriched in differential polyadenylation sites and 3’UTR shortening events. Finally, the DSCAM-AS1-interacting splicing factor hnRNPL was predicted as the most enriched RBP for exon skipping and 3’UTR events.
Conclusion: The relevance of DSCAM-AS1 overexpression in BC is confirmed by clinical data and further enhanced by its possible involvement in the regulation of RNA processing, which is emerging as one of the most important dysfunctions in cancer.

overall_design: Total RNA-Seq profile of MCF-7 cells treated with DSCAM-AS1 LNA or control

first: Jamal

last: Elhasnaoui

first: Valentina

last: Miano

last: Doria

first: Antonette

middle: E

last: Leon

first: Aline

last: Fabricio

first: Laura

last: Annaratone

first: Isabella

last: Castella

first: Anna

last: Sapina

first: Michele

last: De Bortoli


title: BAM15 RNAseq

status: Public on May 14 2020

city: Baton Rouge

first: John

middle: P

last: Kirwan

state: LA

address: 6400 Perkins Road

institute: Pennington Biomedical Research Center

summary: C2C12 myotubes were treated with 20uM BAM15 or DMSO overnight and harvested for RNA.

overall_design: n=6 treated with BAM15 and n=6 treated with DMSO vehicle

first: W

last: King

first: Christopher

middle: L

last: Axelrod

first: J

first: Susan

last: Newman

first: Richard

last: Carmouche

first: Jasleen

last: Kaur

first: Sara

last: Webb

first: G

last: Davuluri


title: Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation [RNA-Seq]

first: Howard

last: Chang

overall_design: RNA-seq was performed in WT and Spen KO mESCs . Libraries(2 replicates per line) were sequenced on an Illumina Nextseq(2x75bp)

first: Ava

last: Carter

first: Jin

last: Xu


title: Single-cell transcriptome reveals the novel role of T-bet in suppressing the immature NK gene signature  the immature NK gene signature

status: Public on May 13 2020

city: Milwaukee

first: Subramaniam

last: Malarkannan

state: WI

address: 8727 W Watertown Plank Rd

institute: Versiti Blood Research Institute

summary: Using scRNAseq, we identified five distinct NK cell clusters and define their relative developmental maturity in the murine bone marrow of WT mice. Transcriptome-based machine-learning classifiers revealed that half of the mTORC2-deficient NK cells belongs to the least mature NK cluster. Mechanistically, loss of mTORC2 results in an increased expression of signature genes representing immature NK cells. We further characterized the T-bet-deficient NK cells and found an augmented immature transcriptomic signature. Moreover, deletion of Foxo1 restores the expression of T-bet and corrects the abnormal expression of immature NK genes in Rictor-deficient NK cells.

overall_design: Single-cell RNA-sequencing analysis of NK cells from bone marrow of WT, Rictor cKO, Rptor cKO, and Tbet KO mice

first: Chao

last: Yang

first: Jason

last: Siebert

first: Robert

last: Burns

first: Yongwei

last: Zheng

first: Ao

last: Mei

first: Benedetta

last: Bonacci

first: Demin

last: Wang

first: Raul

last: Urrutia

first: Matthew

last: Riese

first: Sridhar

last: Rao

first: Karen-Sue

last: Carlson

first: Monica

last: Thakar


title: DNA Double-Strand Breaks Induce H2Ax Phosphorylation Domains in a Contact-Dependent Manner

city: Columbus

first: Patrick

middle: Leonard

last: Collins

state: OH

address: 770 BRT,  460 W 12th Ave

department: Microbial Infection and Immunity

institute: Ohio State University

summary: Efficient repair of DNA double-strand breaks (DSBs) requires a coordinated DNA Damage Response (DDR), which includes phosphorylation of histone H2Ax, forming γH2Ax. This histone modification spreads beyond the DSB into neighboring chromatin, generating a DDR platform that protects against end disassociation and degradation, minimizing chromosomal rearrangements. However, mechanisms that determine the breadth and intensity of γH2Ax domains remain unclear. Here, we show that chromosomal contacts of a DSB site are the primary determinants for γH2Ax landscapes. DSBs that disrupt a topological border permit extension of γH2Ax domains into both adjacent compartments. In contrast, DSBs near a border produce highly asymmetric DDR platforms, with γH2Ax nearly absent from one broken end. Collectively, our findings lend insights into a basic DNA repair mechanism and how the precise location of a DSB may influence genome integrity.

overall_design:
Examination of 2 different chromatin modification in 3 cell types
Examination of chromatin topology by Hi-C in 3 different types and 3 different conditions

first: Katharina

last: Hayer

first: Eugene

last: Oltz


title: Differential gene expression in WT v. MZoep-/- zebrafish gastrulae

city: Saint Louis

first: Bo

last: Zhang

state: Missouri

address: 4515 McKinley Research Bldg 03212

department: Developmental Biology

institute: Washington University School of Medicine

summary: We report RNA-sequencing data from zebrafish embryos lacking both maternal and zygotic expression of oep (which encodes Tdgf1) (MZoep-/-) at 90% epiboly stage. Transcripts were compared to stage-matched wild-type (WT) embryos to identify differentially expressed genes.

overall_design: Sequencing of ribo-depleted RNA from MZoep mutant and control WT embryos with 3 biological replicates per genotype.

first: Margot

last: Williams


title: Functional characterization of the novel GWAS-identified GP2 coding variant

city: Nagoya

first: Masahiro

last: Nakatochi

state: Aichi

address: 1-1-20 Daiko-Minami, Higashi-ku

country: Japan

institute: Nagoya University

summary: In a meta-analysis of three GWASs in the Japanese population, we identified a novel locus at 16p12.3 significantly associated with pancreatic cancer susceptibility. A series of experiments were performed to explore the functional impact of the nonsynonymous lead SNP rs78193826 of the GP2 gene at 16p12.3 on global gene expression. Based on CRISPR-Cas9-induced mutation, RNA-seq, and GSEA analyses, we demonstrated that the functional relevance of rs78193826 may involve modulation of KRAS activity.

overall_design: GP2-expressing pancreatic cancer cell line PaTu 8988s was used for functional characterizations of the lead SNP rs78193826. The genome-edited PaTu 8988s cell line (GP2_V282M) was generated through mutation induced by CRISPR-Cas9-mediated homologous recombination. Control cell line (GP2_WT) was obtained from clones without induced mutation by the same plasmid transfection. RNA-seq was performed using two biological replicates in each of GP2_V282M and GP2_WT groups. Differentially expressed genes between the two groups were identified using GFOLD. The GSEA was performed using the MSigDB v6.2 collections - H and C6.

first: Yasuyuki

last: Hosono

first: Issei

last: Imoto

first: Yingsong

last: Lin

first: Shogo

last: Kikuchi

first: Keitaro

last: Matsuo


title: Dietary lipids accumulate in macrophages and stromal cells and change the microarchitecture of the mesenteric lymph node

city: Hannover

first: Oliver

last: Dittrich-Breiholz

address: Carl-Neuberg-Str. 1

department: Research Core Unit Genomics

institute: Medical School Hannover


title: Basal transcriptome profiles of breast cancer PDXs.

city: Barcelona

first: Miguel Angel

last: Pujana

address: Gran Via 199

country: Spain

institute: Institut Catala d'Oncologia IDIBELL

summary: Basal transcriptome profiling of breast cancer patient-derived xenografts (PDXs) as a resource to identify predictive biomarkers of target therapeutic approaches.

overall_design: RNA sequencing of bulk PDX tissue.

first: Violeta

last: Serra

first: Miquel


title: Transcriptional signature of MAITs in LTBI (memory CD8 T cells and subsets of TRAV1-2+CD161+ MAITs)

city: San Diego

first: Mikhail

last: Pomaznoy

state: CA

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

summary: We applied a cell population transcriptomics strategy to sorted human memory CD8 T cells to define novel immune signatures of latent tuberculosis infection (LTBI) and understand the phenotype of tuberculosis (TB)-specific T cells. We found a 41-gene signature that could discriminate between memory CD8 T cells from healthy LTBI subjects and noninfected controls. The gene signature was dominated by genes known to be associated with mucosal associated invariant T cells (MAITs) and reflected the lower frequency of MAITs observed in individuals with LTBI. There was no evidence for a conventional CD8 T cell specific signature between the two cohorts. We therefore investigated the MAITs in more detail in these cohorts. Phenotyping based on Vα7.2 and CD161 expression and MR1 tetramers revealed 2 distinct populations of CD8+Vα7.2+CD161+ T cells: MR1 tetramer+ and MR1 tetramer−, both of which had a distinct gene expression profile compared to CD8 memory T cells. Transcriptomic analysis of LTBI vs. noninfected individuals did not reveal significant differences for MR1 tetramer+ cells. However, gene expression of MR1 tetramer− cells showed a very different profile with large inter-individual diversity and a TB-specific signature. This was further strengthened by a more diverse TCR-α and -β repertoire of MR1 tetramer− cells as compared to MR1 tetramer+. Thus, cell population transcriptomics revealed a dominant MAIT signature in CD8 memory T cells that upon detailed investigation provided novel insights into the phenotype of different MAIT populations implicated in tuberculosis.

overall_design: RNAseq of sorted memory CD8 T cells and subsets of TRAV1-2+CD161+ MAITs from cryopreserved PBMC of 10 individuals with latent TB infection and 7 uninfected controls.

first: Rebecca

last: Kuan

first: Mikaela

last: Lindvall

first: Julie

last: Burel

first: Grégory

last: Seumois

first: Pandurangan

last: Vijayanand

first: David

middle: M

last: Lewinsohn

first: Randy

last: Taplitz

first: Robert

middle: H

last: Gilman

first: Mayuko

last: Saito

first: Alessandro

last: Sette

first: Bjoern

last: Peters

first: Cecilia

last: Lindestam Arlehamn


title: NTRK2 splice variant, TrkB.T1, is the predominant isoform in gliomas and enhances gliomagenesis via PI3K signaling

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

summary: Independent scientific achievements have led to the discovery of aberrant splicing patterns in oncogenesis while more recent advances have uncovered novel gene fusions involving NTRK2 in gliomas. The exploration of NTRK2 splice variants in normal and neoplastic brain provides an intersection of these two rapidly evolving fields – alternative splicing and NTRK2 involvement in brain tumors. Tropomyosin receptor B (TrkB), encoded by the NTRK2 gene, is known for critical roles in neuronal survival, differentiation, molecular properties associated with memory, and exhibits intricate splicing patterns. Here we show a novel role for a TrkB splice variant, TrkB.T1, in human glioma via NTRK2 transcript analyses and immunostaining using a novel antibody. TrkB.T1 enhances PDGF-driven gliomas in vivo, augments PDGF-induced Akt signaling in vitro, while next generation sequencing broadly implicates TrkB.T1 in the PI3K/Akt signaling cascade in a ligand independent fashion. NTRK2 appears to be a specific example that highlights the importance of expanding upon whole gene and gene fusion analyses to explore splice variants in basic and translational neuro-oncology research

overall_design: For infection of NSC-U5 cells, 1e5 cells/well were seeded into 6-well plates. Lentivirus was used unconcentrated and cells were infected at a MOI<1 24 hours after seeding. 72 hours after seeding, selection was begun for cells successfully expressing the constructs using 2 μg/mL puromycin (for 3 days). Cells were expanded after selection to create a stable line and collected for RNAseq three weeks post infection.

first: Siobhan

middle: S

last: Pattwell

first: Patrick

last: Cimino

first: Tatsuya

last: Ozawa

first: Frank

last: Szulzewsky

first: Pia

last: Hoellerbauer

first: Benjamin

middle: G

last: Hoffstrom

first: Norman

last: Boiani

first: Hamid

last: Bolouri

first: Colin

last: Correnti

first: John

last: Silber

last: Paddison

first: Eric

middle: C

last: Holland


title: Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation [ATAC-Seq]

city: Stanford

first: Howard

last: Chang

overall_design: ATAC-seq was performed in mESCs . Libraries (2 replicates per line) were sequenced on an Illumina Nextseq (2x75bp).

first: Ava

last: Carter

first: Jin

last: Xu


title: miR-26a regulate the extracellular vesicle secretion from prostate cancer cells via targeting PFDN4, CHORDC1 and SHC4

status: Public on May 12 2020

city: Chuo-ku

first: Yusuke

last: Yamamoto

state: Tokyo

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

institute: National cancer center research institute

summary: Extracellular vesicles (EVs) are known to be involved in inter-cellular communication during cancer progression,  however, the biogenesis of EVs in cancer cells is not completely unveiled. It has been shown that microRNAs (miRNAs) regulated variety of physiological and pathological phenomena, thus, miRNAs could regulate the EV secretion. Here, we have performed high throughput miRNA-based screening to identify the regulators of EV secretion using ExoScreen assay. By this miRNA-based screening, we identified miR-26a, which was reported as tumor suppressive miRNA, was found to be an miRNA involved in EV secretion from prostate cancer (PCa) cells. To study the effect of miR-26a on gene expression in EV secretion, transcriptome analysis for miR-26a overexpressing PCa cell lines was performed.

overall_design: Transfections of 10 nM miR-26a mimics or negative control miRNA (miRNA mimic Negative Control #1, Ambion) were accomplished with the DharmaFECT Transfection Reagent 1 according to the manufacturer’s protocol.  After 24 hours, the conditioned medium was changed to Advanced RPMI medium containing an antibiotic-antimyotic and 2mM L-glutamine. Forty-eight hours after the medium change, total RNAs were extracted from them. We used Agilent microarray chip (SurePrint G3 Human GE v3).

first: Fumihiko

last: Urabe

first: Nobuyoshi

last: Kosaka

first: Yurika

last: Sawa

first: Tomofumi

first: Kagenori

last: Ito

first: Takahiro

last: Ochiya


title: Impact of sevoflurane priming on B16F10 transcriptome after in vivo growth

city: Heidelberg

first: Dominik

last: Schaack

address: Im Neuenheimer Feld 420

institute: Heidelberg University Hospital

summary: Murine skin melanoma cell line B16-F10 (ATCC no. CRL-6475) was obtained from the national standard repository (LGC Standards, Wesel, Germany). Priming of B16-F10 cells with sevoflurane was accomplished within a closed hypoxia chamber located in an 37ºC heating cabinet. Cell flasks were put into the chamber and the chamber was flushed with 2% sevoflurane (Baxter, Unterschleissheim, Germany) in normal air with 21% O2 for 30min, followed by an incubation for additional 2h. Subsequently, cells were prepared and injected into adult male C57BL/6 mice within 2h. Processing of the cells before injection was as described above. After a maximum of 4 weeks after injection, animals were euthanized and the tumor was resected for further analysis.

overall_design: Examination of sevoflurane treatment in comparison to control.

first: Isabella

last: Sztwiertnia

first: Florian

last: Uhle


title: Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation [irCLIP-seq]

overall_design: irCLIP-seq was performed in WT and SpenKO mESCs in vivo and vitro conditions . At least two Libraries(2 replicates per line) were sequenced on an Illumina Illumina Nextseq


title: RNA-seq analysis of Prss14 target genes in mouse thymoma cells

first: Youngkyung

last: Cho

department: Biological Science

institute: Seoul National University

summary: Prss14/ST14 is a type II transmembrane serine protease which is reported to be overexpressed in many epithelial cancers and plays critical roles in cancer initiation, progression, and metastasis. Prss14/ST14 undergoes ectodomain shedding in response to various stimulus including serum, TGF-β, and PMA. The fate of the residual membrane anchored N-terminal fragment (NTF) remains unknown. We show that the membrane-bound remnant, which is resulted from PMA-induced ectodomain shedding mediated by tumor necrosis factor-a converting enzyme (TACE) is subjected to regulated intramembrane proteolysis (RIP). The signal peptide peptidase-like 2b (SPPL2b) is identified as the enzyme carrying out this RIP. After RIP, we demonstrate that the generated soluble Prss14/ST14 intracellular domain (EICD) translocates to the nucleus. The ability of cell invasion and migration is abolished in SPPL2b-knockdown cells and these are recovered by transfection of exogenous EICD (N55). Furthermore, EICD is able to activate transcription and this observation prompts us to investigate target genes of EICD using RNA-seq. Analysis of RNA-seq results using samples from multiple conditions and network analysis reveal the EICD target genes that are associated with migration, invasion, and EMT. Furthermore, N55-overexpressing cell lines show scattered phenotype and increased EMT markers expression. ER-negative breast cancer patients with high expression of FOS or MMP13, the target genes, and Prss14/ST14 show poor survival outcomes, suggesting these genes can be used for prognosis markers of ER negative breast cancer. In this study, we propose a new mechanism to facilitate the cancer cell migration, invasion, and EMT by transcriptional regulation of EICD generated by SPPL2b.

overall_design: We performed RNA-seq of mouse thymoma cell lines, 427.1.86 cells from 6 conditions to identify the target genes of EICD using Illumina HiSeq 2500. We tested the effect of EICD on transcriptional regulation in cells with increased EICD by PMA-induced shedding and transfection of exogenous EICD and with decreased EICD by knockdown of SPPL2b.

first: Sang

last: Kim

first: Chungho

first: Eun

first: Jang

last: Lee

first: Dongeun

last: Park

first: Youngcheol

first: Moon

last: Kiim


title: Transcriptional signatures of participant-derived neural progenitor cells and neurons implicate altered Wnt signaling in Phelan McDermid syndrome and autism

city: New York

first: Michael

last: Breen

state: NY

address: 1468 Madison Ave

department: Depts. of Psychiatry, Genetics and Genomic Sciences

institute: Ichan School of Medicine at Mount Sinai

summary: We developed human induced pluripotent stem cell (hiPSC)-based models of PMS by reprogramming peripheral blood samples from individuals with PMS (n=7) and their unaffected siblings (n=6).

overall_design: For each participant, up to three hiPSC clones were generated and differentiated into induced neural progenitor cells (hiPSC-NPCs; n=39) and induced forebrain neurons (hiPSC-neurons; n=41). Genome-wide RNA-sequencing was applied to explore transcriptional differences between PMS probands and unaffected siblings.

first: Joseph

middle: D

last: Buxbaum


title: Differentiation of syncytialized trophoblasts elicits widespread 3’UTR shortening that accompanies increased cellular function in protein secretion

city: Philadelphia

first: Bin

last: Tian

state: PA

address: 3601 Spruce Street

department: Program in Gene Expression and Regulation; Center for Systems and Computational Biology

institute: Wistar Institute

summary: Most eukaryotic genes express alternative polyadenylation (APA) isoforms with different 3’UTR sizes. The APA profile varies across tissue types and under different growth and differentiation conditions. Here we report that, unlike many other cell differentiation lineages, differentiation of syncytiotrophoblasts (SCTs) elicits widespread 3’UTR shortening, as shown in multiple in vitro trophoblast differentiation models as well as in single placental cells at different stages of pregnancy. We show that the 3’UTR shortening is unrelated to cell proliferation, a feature previously associated with 3’UTR size control, but rather accompanies increased cell function in protein secretion. In addition, 3’UTR shortening correlates with increased transcript abundance and is coupled with enhanced intronic APA site usage, suggesting activation of 3’ end processing in SCT differentiation. Together, our data indicate that SCTs utilize APA to express transcripts with short 3’UTRs, which may enhance hormone production and secretion, contributing to their functions in pregnancy.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 2 3'READS libraries for analysis of APA isoforms in TB differentiation of H9 cells; 6 3'READS libraries for analysis of APA isoforms in TB differentiation of mESC cells by inducing HrasQ61L with doxycycline; 4 3'READS libraries for analysis of APA isoform stability in BeWo trophoblast cell line

first: Larry

last: Cheng

first: Dinghai

last: Zheng

first: Koichi

last: Ogami

first: Percy

last: Yeung

first: Mainul

last: Hoque

first: Chi-Wei

last: Lu

first: James

last: Manley


title: Heterogeneity of Brain Metastasis-associated Microglia and Macrophages

city: Freiburg

last: Schulz

address: Breisacher Straße 64

department: Institute for Neuropathology

institute: University Hospital Freiburg

summary: Brain metastasis (BrM) represents a challenging clinical issue. The most common treatment options are surgery and irradiation. Little is known about the complex cellular and molecular microenvironment of BrM, thus lacking molecular targets to combat this dismal disease. It is known that macrophages from the periphery (monocyte-derived macrophages, MDM) and microglia, the brain-resident macrophages, comprise the most abundant stromal cell types in BrM. However, it is not known if both cell types represent a homogeneous cell population with redundant functions or if there are differences due to their ontologic origin. Besides breast cancer and melanoma, the highest incidence of BrM can be found in lung cancer. To gain deeper insight into the myeloid immune landscape and the heterogeneity of BrM-associated immune cells, we here provide single cell RNA Seq data of microglia and MDMs which were associated with a lung cancer (LuCa) BrM, as well as with an irradiated LuCa BrM. Cells were FACS purified into 384 well plates, snap frozen on dry ice and single cell RNA-Seq performed. Together, our data hint towards cell type-specific heterogeneity both, before and upon application of irradiation.

overall_design: Single cell RNA-Seq of FACS-purified microglia and macrophages out of lung cancer brain metastasis

first: L

last: Sevenich

first: M


title: Cellular and molecular changes of brain metastases-associated myeloid cells during disease progression and therapeutic response

summary: Brain metastasis (BrM) represents a challenging clinical issue. The most common treatment options are surgery and irradiation. Little is known about the complex cellular and molecular microenvironment of BrM, thus lacking molecular targets to combat this dismal disease. It is known that macrophages from the periphery (monocyte-derived macrophages, MDM) and microglia, the brain-resident macrophages, comprise the most abundant stromal cell types in BrM. However, it is not known if both cell types represent a homogeneous cell population with redundant functions or if there are differences due to their ontologic origin. Besides breast cancer and melanoma, the highest incidence of BrM can be found in lung cancer. To gain deeper insight into the myeloid immune landscape, we here provide a resource for the transcriptional landscape of distinct myeloid immune cells associated with lung-to-brain metastasis. Microglia, MDMs, inflammatory monocytes, and granulocytes were FACS-purified from lung-to-brain metastasis at distinct stages following tumor onset and during BrM progression. To evaluate molecular changes due to application of standard therapy, these 4 cell types were also purified at distinct time points upon whole brain radiotherapy of tumor-bearing mice. Additionally, microglia of irradiated mice without BrM were analyzed. Together, our RNA Seq data provide a framework for the identification of molecular targets of the myeloid immune cell landscape in lung cancer BrMs.

overall_design: RNA-Seq of FACS purified myeloid cells out of lung-to-brain metastasis (infl. Monocytes, granulocytes, monocyte-derived macrophages, microglia) and their normal cellular counterparts (healthy microglia and peripheral blood monocytes)

first: B

last: Michels

first: K

last: Niesel

first: S

last: Stein

first: H

last: Farin

first: F

last: Rödel


title: The myeloid immune cell landscape in lung-to-brain metastases

first: Michael

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

overall_design: Refer to individual Series


title: Transcriptional signature of MAITs in LTBI (CD8+ or CD8-)

first: Mikhail

last: Pomaznoy

overall_design: RNAseq of sorted cell populations MR1 tetramer+ CD8+ or CD8- MAITs from cryopreserved PBMC of 5 Mtb infected individuals.

first: Rebecca

last: Kuan

first: Mikaela

last: Lindvall

first: Julie

last: Burel

first: Grégory

last: Seumois

first: Pandurangan

last: Vijayanand

first: David

last: Lewinsohn

first: Randy

last: Taplitz

first: Robert

last: Gilman

first: Mayuko

last: Saito

first: Alessandro

last: Sette

first: Bjoern

last: Peters

first: Cecilia

last: Lindestam Arlehamn


title: Comparative transcriptome analysis between inbred and hybrids reveals molecular insights into yield heterosis of upland cotton

status: Public on May 08 2020

city: Anyang

first: Jianyong

last: Wu

address: Huanghe Dadao 38#

institute: Institute of Cotton Research, CAAS

summary: Through genome-wide comparative transcriptome analysis of 63 samples, the current study identified nine key genes and pathways associated with biological process of yield heterosis in upland cotton. Our results and data resources provide novel insights and will be useful for dissecting the molecular mechanism of yield heterosis in cotton.

overall_design: Three tissues examined across seven cotton varieties, in triplicate

first: Chaozhu

last: Xing


title: Transcriptional signature of MAITs in LTBI

overall_design: RNAseq of sorted memory CD8 T cells from cryopreserved PBMC of 31 individuals with latent TB infection and 29 uninfected controls.


title: Genome-wide identification of distinct target loci for de novo DNA methylation by DNMT3A and DNMT3B during mammalian development

city: Tokyo

first: Yasuhiro

last: Yamada

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

department: Department of Molecular Pathology

institute: University of Tokyo

type: Methylation profiling by high throughput sequencing

summary: DNA methylation plays essential roles in mammalian development. During post-implantation development, de novo establishment of DNA methylation is accomplished by DNA methyltransferases, in particular DNMT3A and DNMT3B. At present, the distinct functions of these two enzymes remain largely elusive. To comprehensively identify the target sites for de novo DNA methylation by the DNMT3 enzymes, we took advantage of female mouse ES cells established in the presence of MEK and Gsk3 inhibitors, which lack most DNA methylation (2i/L ES cells), in combination with genetic ablation of Dnmt3a or Dnmt3b. We analyzed de novo DNA methylation in mouse embryonic fibroblasts (2i-MEFs) derived from Dnmt3 knockout (KO) 2i/L ES cells. Both Dnmt3a and Dnmt3b KO 2i-MEFs exhibited a modest but global reduction in CpG methylation, which was particularly notable on the X chromosome in Dnmt3b KO cells. Although most genes were methylated similarly in both knockouts, we identified 355 and 333 uniquely unmethylated genes in Dnmt3a and Dnmt3b KO 2i-MEFs, respectively. Notably, Dnmt3a was exclusively required for de novo methylation at both TSS regions and gene bodies of Polycomb group (PcG) target developmental genes. Consistent with this, tissue-specific DNA methylation at PcG target developmental genes was substantially reduced in Dnmt3a KO embryos. Finally, we found that human patients with DNMT3A mutant acute myeloid leukemia (AML) or harboring DNMT3B mutation associated with immunodeficiency, centromere, and facial anomalies (ICF) syndrome exhibited reduced CpG methylation at regions that were hypomethylated in Dnmt3a or Dnmt3b KO 2i-MEFs, respectively. Collectively, our findings in DNA-hypomethylated 2i/L ES cells revealed a set of unique de novo DNA methylation target sites for both DNMT3 enzymes during mammalian development that overlap with hypomethylated sites in human patients.

overall_design: Analyzing DNA methylation profiles and transcriptional profiles by WGBS, Methylseq and RNA-seq in WT, Dnmt3a KO, Dnmt3b KO MEFs and Dnmt3a KO brain, limb, heart, lung, liver to unveil Dnmt3 function in mammalian development.

first: Masaki

last: Yagi

first: Mio

last: Kabata

first: Takuya

last: Yamamoto


title: Genes regulated by COUP-TFII inhibitor

city: houston

first: Ming-Jer

last: Tsai

state: Texas

address: One Baylor Plaza

institute: baylor college of medicine

summary: The orphan nuclear receptor COUP-TFII is expressed at a low level in adult tissues, but its expression is increased and shown to promote progression of multiple diseases including prostate cancer, heart failure and muscular dystrophy. Suppression of COUP-TFII slows disease progression, making it an intriguing therapeutic target. Here, we identified a potent and specific COUP-TFII inhibitor through high-throughput screening. The inhibitor specifically suppressed COUP-TFII activity to regulate its target genes.

overall_design: mRNA profiles of LNCaP cells treated with COUP-TFII inhibitor for 18 hours or transfected with siCOUP-TFII for 72 hours. RNA-sequencing and analysis was performed by EA | Q² Solutions, Morrisville, NC 27560.

first: Leiming

last: Wang


title: 10x 3’ scRNA-seq analysis on Jurkat cells post TCR acivation in CRISPR/Cas9 screening

status: Public on May 11 2020

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

department: School of Life Sciences

institute: Westlake university

summary: By performing 10x 3’ scRNA-seq on Jurkat cells post TCR acivation in CRISPR/Cas9 screening, we want to investigate the compatibility of the A/G mixed capture sequence on multiple single cell RNA-seq platforms. By mimicking the adenylated endogenous mRNA, gRNA transcripts could be directly captured by poly(dT) primer during the reverse transcription, and serve as perturbation index in high identification rate.

overall_design: In this study, we provided a framework of direct ‘genotyping’ for single cell CRISPR screen, by incorporating a capture sequence into the gRNA scaffold. With that, genotype, transcriptome and phenotype can be analyzed simultaneously. We used an A/G mixed capture sequence to mimic the poly(A) tail of pol II transcripts and facilitate the direct annealing of gRNA with poly(dT) RT primer that is widely used in versatile scRNA-seq platforms.

first: Qingkai

last: Song

first: Ke

last: Ni

first: Min

last: Liu


title: Effect of CD5-2 on endothelial cells with or without VE-cadherin expression

status: Public on May 07 2020

city: Camperdown

first: Jennifer

last: Gamble

state: New South Wales

address: Building 93, Royal Prince Alfred Hospital

department: Vascular Biology

country: Australia

institute: CENTENARY INSTITUTE

summary:
Purpose: The goals of this study are to confirm whether CD5-2 works through VE-cadherin
Methods: mRNA profiles of HUVEC and VE-cadherin-/- EC  treated with either control or CD5-2 were generated by deep sequencing using Illumina Hiseq4000 platform and 150 bp paired-end reads were generated. Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indices of the reference genome were built using Bowtie (v2.2.3) and paired-end clean reads were aligned to the reference genome using TopHat (v2.0.12). Differentially expressed genes were then determined using DESeq R package (v1.12.0). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR). Genes with an adjusted P-value<0.05 and FDR<0.005 were assigned as differentially expressed.
Results: 585 differentially expressed genes (DEGs) in CD5-2 treated ECs compared with control treated ECs (P < 0.05; false discovery rate [FDR] ≤ 0.005). In stark contrast to that seen in normal ECs, in VE-cadherin-/- ECs, no gene was significantly differently expressed between control and CD5-2 treated group when using the same cut-off criteria,
Conclusions: Our study suggests VE-cadherin is essential for the CD5-2 mediated gene changes

overall_design: mRNA profiles of HUVEC and VE-cadherin-/- EC  treated with either control or CD5-2 were generated by deep sequencing, a pool of 3-5 biological replicates, using Illumina Hiseq4000 platform

first: Jia

last: Li


title: Next Generation Sequencing Analysis of Transcriptomes of the HEK293T-Cas9 cells transfected with plasmid containing programmed scaffold RNA

summary: By performing RNA sequencing (RNA-seq) analysis on the HEK293T-Cas9 cells which transfected with plasmid containing programmed scaffold RNA for non-targeting or for targeting Hemoglobin subunit gamma-1 (HBG1) we want to investigate whether the scaffold RNA and the endogenous mRNA could be captured in regular reverse transcription reaction. RNA-seq analysis showed that we can capture the scaffold RNA together with the endogenous mRNA  precisely.

overall_design:
Our framework offered strategies that can be conveniently applied to study the genotype and mRNA profiles after CRISPR-mediated genome perturbation with single-cell transcriptional  readout
We incorporated a poly(A)-like capture sequence (8A8G) into the gRNA scaffold, thus the gRNA transcript and endogenous mRNA can be recognized by oligo(dT) in the reverse transcription and characterized using various RNA-seq or single-cell RNA-seq platforms. HNT-8A8G: CRISPR activation targeting a non-target control with the 8A8G scaffold; HBG1-8A8G: CRISPR activation targeting HBG1 with the 8A8G scaffold; HBG1-WT: CRISPR activation targeting HBG1 but with WT-SAM scaffold.


title: Interaction of YAP1 with the Myb-MuvB (MMB) complex sustain proliferation in the postnatal heart

city: Wuerzburg

first: Stefan

last: Gaubatz

address: Am Hubland

department: Biochemistry and Cell Biology

institute: University of Wuerzburg

summary: YAP, a major downstream effector of the Hippo signaling pathway, is an important regulator of cell proliferation. Previous studies have shown that YAP cooperates with the two transcription factors E2F and MYC to mediate G1 to S transition by regulating early cell cycle gene expression. On the other hand, the ability of YAP to regulate G2/M gene expression is dependent on the Myb-MuvB (MMB) complex, consisting of the evolutionary MuvB core complex of five proteins and the facultative subunit B-MYB, a transcription factor. We now carried out interaction studies and found that YAP directly binds to the B-MYB subunit of MMB. Disruption of the YAP/B-MYB interaction by overexpression of the YAP binding domain of B-MYB results in errors in cell division. We also show that YAP and MMB interact in vivo in the developing heart. Genome wide expression and binding studies revealed that YAP and MMB regulate an overlapping set of cell cycle genes in cardiomyocytes. Cardiac specific deletion of the LIN9 subunit of MMB prevents the upregulation of cell cycle genes and the increased proliferation of cardiomyocytes lacking the hippo-signaling component SAV1. Similarly, we find that proliferation of postnatal cardiomyocytes induced by constitutive active YAP depends on MMB. Our findings provide new insights in the mechanisms of cell cycle regulation by the Hippo pathway in cardiomyocytes and suggests that YAP and MMB interact to induce genes critical for cell cycle regulation.

overall_design: RNAseq analysis in the murine heart after Lin9 and Sav1 knockout. DNA binding of LIN9 was analyzed in E16 and P10 hearts using ChIPseq.

first: Marco

last: Gründl

first: Susanne

last: Walz

first: Laura

last: Hauf

first: Melissa

last: Schwab

first: Kerstin

last: Werner

first: Carsten

last: Ade

last: Spahr


title: Intragenic recruitment of NF-kB drives splicing modifications upon activation by the oncogene Tax of HTLV-1

city: lyon

first: franck

last: mortreux

address: 46 allee d'Italie

country: France

institute: oncovirology and Biotherapies, UMR5239, LBMC

summary: Chronic NF-kB activation in inflammation and cancer has long been linked to persistent activation of NF-kB–responsive gene promoters. However, NF-kB factors also massively bind to gene bodies. Here, we demonstrate that recruitment of the NF-kB factor RELA to intragenic regions regulates alternative splicing upon NF-kB activation by the viral oncogene Tax of HTLV-1. Integrative analyses of RNA splicing and chromatin occupancy, combined with chromatin tethering assays, demonstrate that DNA-bound RELA interacts with and recruits the splicing regulator DDX17, in an NF-kB activation–dependent manner. This leads to alternative splicing of target exons due to the RNA helicase activity of DDX17. Similar results were obtained upon Tax-independent NF-kB activation, indicating that Tax likely exacerbates a physiological process where RELA provides splice target specificity. Collectively, our results demonstrate a physical and direct involvement of NF-kB in alternative splicing regulation, which significantly revisits our knowledge of HTLV-1 pathogenesis and other NF-kB–related diseases.

overall_design: HEK 293T-LTR-GFP cells (Delebecque et al., 2002) containing an integrated GFP reporter gene under the control of the TAX-responsive HTLV-1 LTR were transiently transfected with siRNAs against DDX5 and DDX17 (GGCUAGAUGUGGAAGAUGUdTdT)  (or siRNA control siGL2 (CGUACGCGGAAUACUUCGAdTdT)) and/or expression vectors pSG5M-TAX or pSG5M empty. PolyA transcripts were extracted at 48h post-transfection and RNA-seq analyses were performed as previously described (Lambert et al., 2018). RNA-seq libraries were generated at the Aros Applied Biotechnology (Aarhus, Denmark) using Stranded mRNA Sample Prep kit (Illumina) and sequenced using the illumina HiSeq 2500 technology. RNA-seq data were analyzed using FaRLine with the FasterDB database (Benoit-Pilven et al., 2018; Mallinjoud et al., 2014).

first: Franck

last: Mortreux


title: Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

city: Perth

first: Alistair

middle: R. R.

last: Forrest

address: 6 Verdun Street, Nedlands

institute: Harry Perkins Institute of Medical Research, the University of Western Australia

summary:
Background: Single-cell RNA sequencing has been widely adopted to estimate the cellular composition of heterogeneous tissues and obtain transcriptional profiles of individual cells. Multiple approaches for optimal sample dissociation and storage of single cells have been proposed as have single-nuclei profiling methods. What has been lacking is a systematic comparison of their relative biases and benefits.
Results: Here, we compare gene expression and cellular composition of single cell suspensions prepared from adult mouse kidney using two tissue dissociation protocols. For each sample we also compare fresh cells to cryopreserved and methanol-fixed cells. Lastly, we compare this single-cell data to that generated using three single-nucleus RNA sequencing workflows. Our data confirms prior reports that digestion on ice avoids the stress response observed with 37°C dissociation. It also reveals cell types more abundant either in the cold or warm dissociations that may represent populations that require gentler or harsher conditions to be released intact. For cell storage, cryopreservation of dissociated cells results in a major loss of epithelial cell types; in contrast, methanol fixation maintains the cellular composition but suffers from ambient RNA leakage. Finally, cell type composition differences are observed between single-cell and single-nucleus RNA sequencing libraries. In particular, we note an under-representation of T, B and NK lymphocytes in the single-nucleus libraries.
Conclusions: Systematic comparison of recovered cell types and their transcriptional profiles across the workflows has highlighted protocol-specific biases and thus enables researchers starting single cell experiments to make an informed choice.

overall_design: 27 single-cell, 12 single-nuclei and 15 bulk RNA sequencing experiments using healthy adult mouse kidneys, three biological replicates are included per condition.

first: Elena

last: Denisenko

first: Belinda

last: Guo

first: Matthew

last: Jones

first: Rui

last: Hou

first: Leanne

last: de Kock

first: Timo

last: Lassmann

first: Daniel

last: Poppe

first: Olivier

last: Clement

first: Rebecca

middle: K

last: Simmons

first: Ryan

last: Lister


title: Benchmarking dataset for measurement and removal of index hopping artifacts in multiplexed droplet-based single-cell RNA-seq data

status: Public on May 09 2020

city: Montreal

first: Hamed

last: Najafabadi

state: QC

address: 740 Dr. Penfield Avenue, Room 7202

department: Human Genetics

institute: McGill University

summary: Sample index hopping refers to the incorrect sample assignment of a demultiplexed sequencing read in a library pool. To enable benchmarking of methods for measurement of index hopping rate and removal of its artifacts in single-cell RNA-seq data, we developed a validation dataset consisting of a multiplexed library of two samples, in which the true sample of origin of most reads are known. The reads with known sample of origin provide the ground truth for measuring the performance of index hopping correcting methods.

overall_design: Two 10X Genomics scRNA-seq sample libraries were sequenced in two conditions. In the first condition, the samples were multiplexed on the same lane. In the second condition, two sample libraries were sequenced on two separate lanes of HiSeq 4000 (this non-multiplexed condition provides the ground truth for the true sample of origin of each read, based on the cell-UMI-gene information encoded in each read).

first: Rick

last: Farouni

first: Haig

last: Djambazian

first: Lorenzo

last: Ferri

first: Jiannis

last: Ragoussis


title: Elizabethkingia anophelis response to iron stress: physiologic, genomic, and transcriptomic analyses

status: Public on May 06 2020

city: East Lansing

first: Shicheng

last: Chen

state: MI

address: 567 Wilson Rd

department: Microbiology and Molecular Genetics

institute: Michigan State University

summary: Elizabethkingia anophelis bacteria encounter fluxes of iron in the midgut of mosquitoes, where they live as symbionts. They also establish bacteremia with severe clinical manifestations in humans, and live in water service lines in hospitals.  In this study, we investigated the global gene expression responses of E. anophelis to iron fluxes in the midgut of female Anopheles stephensi mosquitoes fed sucrose or blood, and in iron-poor or iron-rich culture conditions. Of 3,686 transcripts revealed by RNAseq technology, 218 were upregulated while 112 were down-regulated under iron-poor conditions. Most of these differentially expressed genes were enriched in functional groups assigned within “biological process,” “cell component” and “molecular function” categories. E. anophelis possessed 4 iron/heme acquisition systems. Hemolysin gene expression was significantly repressed when cells were grown under iron-rich or high temperature (37℃) conditions. Furthermore, hemolysin gene expression was down-regulated after a blood meal, indicating that E. anophelis cells responded to excess iron and its associated physiological stress by limiting iron loading. By contrast, genes encoding respiratory chain proteins were up-regulated under iron-rich conditions, allowing these iron-containing proteins to chelate intracellular free iron. In vivo studies showed that growth of E. anophelis cells increased 3-fold in blood-fed mosquitoes over those in sucrose-fed ones. Deletion of aerobactin synthesis genes led to impaired cell growth in both iron-rich and iron-poor media. Mutants showed more susceptibility to H2O2 toxicity and less biofilm formation than did wild-type cells. Mosquitoes with E. anophelis experimentally colonized in their guts produced more eggs than did those treated with erythromycin or left unmanipulated, as controls. Results reveal that E. anophelis bacteria respond to varying iron concentration in the mosquito gut, harvest iron while fending off iron-associated stress, contribute to lysis of red blood cells, and positively influence mosquito host fecundity.

overall_design: Three biological replicates per group (with or without iron supplemented into the media) were analyzed for differential expression.

first: Benjamin

last: Johnson

first: Ting

last: Yu

first: Brooke

middle: N

last: Nelson

first: Edward

last: Walker


title: CRISPRi-mediated functional analysis of lung disease-associated loci at non-coding regions [RNA-seq]

status: Public on May 05 2020

city: Cincinnati

first: Minzhe

last: Guo

address: 3333 BURNET AVENUE

department: Pulmonary Biology

institute: Cincinnati Children's Hospital Medical Center

summary: RNA-seq was performed to identify genes affected by CRISPRi (dCas9-KRAB) with sgRNA (sgTGFB1_B9D2) targeting a region that contains rs1800469 in an unbiased genome-wide fashion using H441 lung papillary adenocarcinoma cells.

overall_design: Expression of genes in H441 cells stably expressing dCas9-KRAB with the sgRNA was compared with those stably expressing dCas9-KRAB without the sgRNA.

first: Yutaka

last: Maeda


title: CRISPRi-mediated functional analysis of lung disease-associated loci at non-coding regions


title: CRISPRi-mediated functional analysis of lung disease-associated loci at non-coding regions [ChIP-seq]

summary: ChIP-seq was performed to identify dCas9-KRAB binding sites in the presence of sgRNA (sgTGFB1_B9D2) targeting a region with rs1800469 between TGFB1 and B9D2 in H441 lung papillary adenocarcinoma cells.

overall_design: Locations of dCas9-KRAB and its associated repressive histone mark H3K9me3 were investigated in two lines of H441 cells expressing dCas9-KRAB with or without the sgRNA.


title: Epigenetic deregulation of lamina-associated domains in Hutchinson-Gilford Progeria Syndrome (RNA-Seq)

first: Guenter

last: Raddatz

address: Im Neuenheimer Feld 580

institute: German Center for Cancer Research

summary: Hutchinson-Gilford Progeria Syndrome (HGPS) is a progeroid disease characterized by the early onset of some classically age-related phenotypes including arthritis, loss of body fat and hair and atherosclerosis. Cells from affected individuals express a mutant version of the nuclear envelope protein Lamin A (termed Progerin) and have previously been shown to exhibit prominent chromatin changes. Here, we identify epigenetic deregulation of lamina-associated domains (LADs) as a central feature in the molecular pathology of HGPS. Using ATAC-see/-seq and Infinium MethylationEPIC BeadChip-mediated DNA methylation profiling, we demonstrate that dermal fibroblasts from HGPS patients exhibit both chromatin accessibility and DNA methylation changes that are enriched in LADs. Importantly, we further show that these epigenetic alterations are associated with HGPS-specific gene expression changes. Together, our results establish a central involvement of LADs in the epigenetic deregulation of HGPS and provide novel insight into the molecular changes associated with the disease.

overall_design: Whole transcriptome analysis of H. sapiens using fibroblasts from six HGPS patients and three controls.

first: F

last: Lyko

first: M

last: Rodriguez Paredes


title: Gene expression in response to knockdown of GLI1.

city: Rochester

first: Stephanie

middle: Lynn

last: Safgren

state: Minnesota

address: 200 1st Street SW, Gonda 19 366C

department: Oncology Research

institute: Mayo Clinic

summary: GLI1 is a transcription factor correlated to decreased survival in several cancers. We have identified SMARCA2 as a co-regulator that enhances GLI1-mediated transcriptional activity and functions through the C-terminal transcriptional activation domain of GLI1. Central domains including the ATPase motif of SMARCA2 physically interact with GLI1.  Evaluation of DNA density indicates GLI1, like SMARCA2, can increase the DNA accessibility with a preference for sites distal to gene transcription start sites and outside the promoter regions (i.e. enhancers).  The putative enhancers where accessibility is decreased by the knock down of GLI1 and SMARCA2 are located cis to genes, such as HHIP, that are regulated by GLI1 and implicated in cancer functions.  At the putative enhancer for HHIP, the localization of SMARCA2 is at least partially dependent on GLI1’s presence.  Understanding this transcriptional regulation by GLI1 and SMARCA2 through altering chromatin accessibility at enhances can provide additional therapeutic targets for cancers dependent on GLI1.

overall_design: Gene expression was measured in RMS13 cells following the siRNA knockdown of GLI1.

first: Alexandre

last: Gaspar-Maia

first: Martin

last: Fernandez-Zapico


title: Loss of microRNA-21 in K-Ras-driven mouse models of pancreatic cancer

city: Grand Rapids

first: Ian

last: Beddows

address: 333 Bostwick Ave NE

institute: Van Andel Institute

summary: The microenvironment of pancreatic cancer adenocarcinoma (PDAC) is highly desmoplastic with distinct tumor-restraining and tumor-promoting fibroblast subpopulations. Re-education rather than indiscriminate elimination of these fibroblasts has emerged as a new strategy for combination therapy. Here, we studied the effects of global loss of pro-fibrotic non-coding regulatory microRNA-21 (miR-21) in K-Ras-driven p53-deleted genetically engineered mouse models of PDAC. Strikingly, loss of miR-21 accelerated tumor initiation via mucinous cystic neoplastic lesions and progression to locally advanced invasive carcinoma from which animals precipitously succumbed at an early age. The absence of tumor-restraining myofibroblasts and a massive infiltrate of immune cells were salient phenotypic features of global miR-21 loss. Stromal miR-21 activity was required for induction of tumor-restraining myofibroblasts in in-vivo isograft transplantation experiments. Low miR-21 expression negatively correlated with a fibroblast gene expression signature and positively with an immune cell gene expression signature in TCGA PDAC data set (n = 156) mirroring findings in the mouse models.  Our results exposed an overall tumor suppressive function of miR-21 in in-vivo PDAC models. These results have important clinical implications for anti-miR-21-based inhibitory therapeutic approaches under consideration for PDAC and other cancer types. Mechanistic dissection of the cell-intrinsic role of miR-21 in cancer-associated fibroblasts and other cell types will be needed to inform best strategies for pharmacological modulation of miR-21 activity in order to remodel the tumor microenvironment and enhance treatment response in PDAC.

overall_design: Twenty two samples derived from Bl6 mouse tumor (n=12) and a pancreatic cell line (n=10). For both tumor and cell line, there are WT and miR21-KO samples.

middle: F

last: Sempere

first: Josh

last: Schipper


title: Transcriptome profiling of porcine testis reveals genes related to sperm hyperactive motility

city: Hamar

first: Maren

last: van Son

address: Storhamargata 44

country: Norway

institute: Norsvin

summary: The aim of this study was to use RNA sequencing to investigate gene expression differences in testis tissue from Landrace and Duroc boars with high and low levels of sperm hyperactive motility. Twelve gene ontology terms were enriched in the day 0 contrast in Landrace and the most significant term was “extracellular exosome”. For the 96 hours storage contrast in Landrace, seven gene ontology terms were enriched and the most significant one was “extracellular space”.

overall_design: Boars with divergent phenotypes were selected based on their sperm hyperactivity values at the day of ejaculation (day 0) and after 96 hours liquid storage at 18ºC (difference in value between day 0 and 4).

first: Nina

last: Tremoen

first: Ann

last: Gaustad

first: Dag

middle: I

last: Våge

first: Teklu

middle: T

last: Zeremichael

first: Frøydis

last: Myromslien

first: Eli

last: Grindflek


title: The transcriptional profile of neutrophils in different organs during pancreatic cancer

city: Portland

first: Kevin

last: Burfeind

state: OR

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health & Science University

summary: It was previously demonstrated that myeloid cells assume a distinct transcriptional profile when infiltrating the brain during chronic inflammation. We demonstrated that neutrophils infiltrate the brain during pancreatic cancer. To determine if the transcriptional profile of brain-infiltrating neutrophils is distinct from those infiltrating other organs, we compared the gene signatures of brain-infiltrating neutrophils, circulating neutrophils, liver-infiltrating neutrophils, and tumor-infiltrating neutrophils to that of circulating neutrophils from healthy mice.

overall_design: Brain-infiltrating neutrophils (n=4), Liver-infiltrating neutrophils (n=4), Tumor-infiltrating neutrophils (n=4), Circulating neutrophils (from tumor-bearing mice) (n=4), Circulating neutrophils (from sham mice) (n=4)

first: Sophia

last: Jeng


title: Epigenetic deregulation of lamina-associated domains in Hutchinson-Gilford Progeria Syndrome (ATAC-Seq)

city: Heidelberg

first: Guenter

last: Raddatz

overall_design: Open chromatin analysis of H. sapiens using fibroblasts from six HGPS patients and two controls.

last: Lyko


title: Epigenetic deregulation of lamina-associated domains in Hutchinson-Gilford Progeria Syndrome

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

overall_design: Refer to individual Series


title: Asian Zika virus isolate significantly changes the transcriptional profile and alternative RNA splicing events in a neuroblastoma cell line

status: Public on May 04 2020

city: Albany

first: Cara

last: Pager

address: 1400 Washington Ave.

institute: University At Albany

summary: Total RNA was isolated for preparation of RNAseq libraries and sequenced on the Illumina NextSeq500 platform.

overall_design: Three libraries were concurrently prepared from four independent experiments of mock-, ZIKV- (MR766 and PRVABC59) and DENV2-infected SH-SY5Y cells.

first: Gaston

last: Bonenfant

first: Ryan

last: Meng

first: Carl

last: Shotwell

first: Pheonah

last: Badu

first: Anne

last: Payne

first: Alexander

last: Ciota

first: Morgan

last: Sammons

first: Andrew

middle: J

last: Berglund


title: Estrogen receptor beta excerts tumorsuppressive effects in prostate cancer through repression of androgen receptor activity

city: Houston

first: Anders

middle: Mikael

last: Strom

address: 3517 Cullen Blvd Bldg 545 room 3018

department: Biology & Biochemistry

institute: University od Hpuston

summary: We found that ERbeta activated by ligand eithe E2 or LY3201 repressed AR activity and affected downstream genes regulated by AR

overall_design: To investigate the mechanisms of action of ERβ and its potential cross-talk with AR, we used RNA-seq to study the effects of estradiol or the synthetic ligand, LY3201, in AR-positive LNCaP PCa cells which had been engineered to express ERβ.

first: Surendra

last: Chaurasiya

first: Scott

last: Widmann

first: Cindy

last: Botero

first: Chin-Yo

last: Lin

first: Jan-Åke

last: Gustafsson


title: microRNA form extracellular vesicles-enriched preparations of the free-livingnematode Caenorhabditis elegans (strain N2, Bristol) cultured in vitro

city: Sainte-Anne-de-Bellevue

first: Lucienne

last: Tritten

address: 21111 Lakeshore Road

department: Institute of Parasitology

summary: Total RNA secreted or excreted by C. elegans incubated for 5h or 24h in M9 culture media and isolated. Extracellular vesicles were isolated by differential ultracentrifugation, and subjected to miRNA sequencing.

overall_design: Synchronized young adults (hermaphrodites) were incubated in liquid culture media for either 5 h or 24 h

first: Julien

last: Soichot

first: Thomas

last: Duguet


title: Discovery and Characterization of a Potent and Selective Pin1 Inhibitor Targeted to an Active Cysteine Site

city: Boston

first: Zainab

middle: Murtaza

last: Doctor

state: MA

address: 360 Longwood Ave, LC-2106

institute: Dana Farber Cancer Institute

summary: We report the development of rationally designed peptide inhibitors that covalently target Cys113, a highly conserved cysteine located in the Pin1 active site. The inhibitors were iteratively optimized for potency, selectivity, and cell permeability to give BJP-06-005-3, a versatile tool compound with which to probe Pin1 biology and interrogate its role in cancer, with the negative control compound BJP-06-115-3 (BJP-R). RNA-sequencing was performed to characterize the transcriptome-wide effects of 4h compound treatment.

overall_design: Profiling of the effects of the covalent Pin1 inhibitor BJP-06-005-3 and the negative control BJP-06-115-3 (BJP-R) with the control DMSO for 4h in PATU-8988T cells.

first: Benika

last: Pinch


title: Transcriptomic prediction of pig Leg1s functions in HepG2 cells

status: Public on May 01 2020

city: Hangzhou

first: Yanna

last: Dang

email: yannadang@126.com, yannadang@zju.edu.cn

address: 866 Yuhangtang Rd

department: College of Animal Sciences

institute: Zhejiang University

summary: The newly identified liver-enriched gene 1 (Leg1) encodes a protein with characteristic Domain of Unknown Function 781 (DUF781/LEG1) domain constituting a protein family with only one member. Functional study in zebrafish suggested that Leg1 genes were involved in the liver development, while the platypus MLP homolog that was enriched in mammary gland and milk acts as an anti-bacterial substance. However, no functional study on eutherian Leg1s has been published at present. Thus, we first report here a functional prediction research in a cellular model. As previously reported, eutherian Leg1s could be classified into three paralogous groups. Pig has all three Leg1 genes, while human and mouse only have retained Leg1a. Hence, pig is an ideal model to study the gene function. RNA-seq was then performed by overexpression of pig Leg1s and platypus MLP in the HepG2 cells. Enrichment analysis showed that pLeg1a and pLeg1b might be of little function in the liver cell; however, pLeg1c was probably involved in the ER stress response and protein folding. Additionally, gene set enrichment analysis revealed that platypus MLP has anti-bacterial activity confirming the functional study in the platypus. Therefore, our study, from the transcriptomic perspective of view, concluded that the mammalian Leg1s have different functions in the liver cells due to subfunctionalization of the paralogous genes.

overall_design: Two batches of experiments were conducted in series. In the first batch, the HepG2 cells were transfected with pLeg1a, pLeg1b expression plasmids and an empty vector as control; the second batch involved the experiment using pLeg1c plasmid and the empty vector.

first: Jin

last: He

first: Zhe

last: Zhang


title: Transient and lineage-restricted requirement of Ebf3 for sternum ossification

city: Kyoto city

first: Mao

last: Kuriki

address: 53 Shogoin Kawahara-cho, Sakyo-ku

department: Regenerative immunity

institute: Institute for Frontier Life and Medical Sciences, Kyoto University

summary: Osteoblasts arise from bone-surrounding connective tissue  containing tenocytes and fibroblasts. Lineages of these cell  populations and mechanisms of their differentiation are not well  understood. Screening enhancer-trap lines of zebrafish allowed us to  identify Ebf3 as a transcription factor marking tenocytes and  connective tissue cells in skeletal muscle of embryos. Knockout of  Ebf3 in mice had no effect on chondrogenesis but led to sternum  ossification defects as a result of defective generation of Runx2+  pre-osteoblasts. Conditional and temporal Ebf3 knockout mice  revealed requirements of Ebf3 in the lateral plate mesenchyme  cells (LPMs), especially in tendon/muscle connective tissue cells,  and a stage-specific Ebf3 requirement at embryonic day 9.5-10.5.  Upregulated expression of connective tissue markers, such as Egr1/2  and Osr1, increased number of Islet1+ mesenchyme cells, and  downregulation of gene expression of the Runx2 regulator Shox2 in  Ebf3-deleted thoracic LPMs suggest crucial roles of Ebf3 in the onset  of lateral plate mesoderm differentiation towards osteoblasts forming  sternum tissues.

overall_design: Thoracic LPM mRNA profiles of E10.5 Hetero (Prx1-Cre Ebf3 flox/+)  and Homo KO (Prx1-Cre Ebf3 flox/flox) mice were generated by RNA sequencing, in triplicate, using Illumina NextSeq500.

first: Fuminori

last: Sato

first: Msafuni

last: Muratani


title: Gene expression changes in rat liver induced by 6 PA

city: Berlin

first: Stefanie

last: Hessel-Pras

address: Max-Dohrn-Str. 8-10

department: Food Safety

institute: German Federal Institute for Risk Assessment

summary:
Pyrrolizidine alkaloids (PA) are secondary plant metabolites that occur as food and feed contaminants. Acute and subacute PA poisoning can lead to severe liver damage in humans and animals. Chronic exposure to low levels of PA can induce liver cirrhosis and liver cancer. However, it is not well understood which transcriptional changes are induced by PA and whether all hepatotoxic PA, regardless of their structure, induce similar responses. Therefore, a 28-day subacute rat feeding study was performed with six structurally different PA heliotrine, echimidine, lasiocarpine, senecionine, senkirkine, and platyphylline, administered at not acutely toxic doses from 0.1 to 3.3 mg/kg body weight. This dose range is relevant for humans, since consumption of contaminated tea may result in doses of ~8 µg/kg in adults and cases of PA ingestion by contaminated food was reported for infants with doses up to 3 mg/kg. ALT and AST were not increased in all treatment groups. Whole genome microarray analyses revealed pronounced effects on gene expression in the high-dose treatment groups resulting in a set of 36 commonly regulated genes. However, platyphylline, the only 1,2-saturated and therefore presumably non-hepatotoxic PA, did not induce significant expression changes. Biological functions identified to be affected by high dose treatments (3.3 mg/kg body weight) comprise cell cycle regulation associated with DNA damage response. These functions were found to be affected by all analyzed 1,2-unsaturated PA.
Transcriptomic analysis with six structurally different PA heliotrine, echimidine, lasiocarpine, senecionine, senkirkine, and platyphylline after subacute treatment of rats

overall_design: 110 array samples (each condition: livers of 5 animals): 4 doses of 5 PA (echimidine, heliotrine, lasiocarpine, senecionine, senkirkine)+ 5 CTR+1 dose of non-toxic PA platyphylline

first: Johanna

last: Ebmeyer


title: Transcriptome profiling of organoids and tissues derived from murine oviductal and ovary surface epithelium (OSE) to study high-grade serous ovarian cancer (HG-SOC)

city: Utrecht

first: Kadi

last: Lõhmussaar

state: -- Select State/Province --

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary:
Purpose: Transcriptome profiling of organoids/tissues derived from murine oviduct and OSE was performed to study and compare the gene expression profiles in the both suspected origins of HG-SOC. CRISPR-Cas9 modified oviductal organoids (TBP clones, which were mutated in Trp53, Brca1 and Pten), the tumors derived upon xenotransplantation of the TBP-clones and subsequent tumor-derived organoids were additionally profiled to show the transcriptional change upon aquiring mutations and tumor development.
Methods: Both oviductal and OSE organoids as well as oviductal TBP-clones and tumor-derived organoids were grown in Wnt-conditioned media prior harvesting for RNA extraction. Additionally, RNA was extracted from healthy oviductal and OSE tissues and Ovi-TBP-clone-derived tumor tissues. RNA was converted to cDNA and libraries were prepared using the CelSeq2 method and sequenced. Samples were sequenced on Illumina NextSeq500 by using 75-bp paired-end sequencing. Paired-end reads from Illumina sequencing were aligned to the mouse genome (GRCm38 assembly)  by BWA. DESeq2 (v1.18.0) package was used for read normalization and differential expression analysis. Gene set enrichment analysis (GSEA) was performed using gene lists for motile cilium assembly against normalized RNA-seq reads of healthy oviductal an OSE organoids using GSEA software v3.0 beta2. GSEA was additionally used to detect enrichment of signature gene sets of different HG-SOC subtypes in the TBP-clone-derived murine tumors
Results: Transcriptome analysis of oviductal and OSE organoids/tissues revealed tissue-specific gene expression pattern in the organoid systems. In contrast to OSE counterparts, oviductal organoids showed enrichment in motile cilium assembly genes, reflecting the presence of ciliated cells in this model.
Results: Oviductal TBP-clones gave rise to different tumor phenotypes with distinct gene expression profiles. Analysis of the transcriptomes of these tumors divided the TBP-clone-derived tumors into two distinct HG-SOC molecular subtypes (differentiated- or immunoreactive-like subtypes), confirming the potential of organoids in modeling HG-SOC.
Results: The tumor-derived organoids retained the distinct phenotypes observed in the originating Ovi-TBP-clone derived tumors. Subset of tumors showed epithelial and others mesenchymal features that were maintained in the respective organoid cultures also in the gene expression level.
Conclusions: RNA sequencing showed tissue specific differences in murine oviductal and OSE organoids, and revealed HG-SOC-like features of oviductal mutants.

overall_design: mRNA profiles of murine oviductal and OSE organoids were generated by Deep Sequencing (Illumina NextSeq500 by using 75-bp paired-end sequencing). Transcriptome profiles were generated from 3 biologically independent replicates for wildtype organoids, tissue and oviductal TBP-clones. As an exception, one independent wildtype OSE organoid line was excluded from the analysis due to the evident contamination. Additionally, mRNA profiles were generated from 6 independent Ovi-TBP-clone-derived tumors and from 4 independent tumor-derived organoids lines.

first: Hans

last: Clevers


title: Transcriptomics of  xylem from a Populus deltoides population

city: Gainesville

first: Matias

last: Kirst

state: FL

address: Newin-Ziegler, Room 320

institute: University of Florida

summary:
We sequenced the xylem transcriptome from a population of unrelated individuals of P. deltoides to uncover a master regulator of lignin biosynthesis.

Grant ID: IOS-1444543
Grant Title: Genome and transcriptome based prediction, and regulator inference, o molecular and whole-plant phenotypes.
Funding source: NSF Plant Genome Research Program.

overall_design: Experiment was set with three biological replicates, using a row-column design.

first: Kelly

last: Balmant


title: Genome-wide maps of Meis1 and Hoxb13 chromatin binding in murine heart

city: Dallas

first: Hesham

last: Sadek

state: TX

address: 5323 Harry Hines Blvd

department: Internal Medicine: Cardiology

institute: UT Southwestern Medical Center

summary: A major factor in the progression to heart failure in humans is the inability of the adult heart to repair itself after injury. As a result, strategies to induce heart regeneration have received significant interest. We reported that transcription factors Meis1 and Hoxb13 contributes to postnatal cardiomyocyte cell cycle exit, and inhibiting these genes expression promote adult cardiomyocyte regeneration. In order to indentify the downstream targets of these transcription factors we generated ChIP-seq of mouse heart for Meis1 and Hoxb13. The results demonstrate that Meis1 and Hoxb13 act cooperatively to regulate cardiomyocyte maturation and proliferation and provide insights into the link between hyperplastic and hypertrophic growth of cardiomyocytes.

overall_design: Examination of Meis1 and Hoxb13 binding site in the murine heart

middle: A


title: Gene expression patterns from hcfc1a Co60 brain homogenates.

city: El Paso

first: Anita

middle: Maria

last: Quintana

address: 500 West University Avenue

department: Biological Sciences

institute: University of Texas at El Paso

summary: We report that mutation of hcfc1a results in abnormal expression of novel downstream target genes.

overall_design: Examination of downstream targets of hcfc1a.

first: Victoria

last: Castro


title: The transcriptional repressor Blimp-1/Prdm1 controls the maternal decidual response during pregnancy [RNA-seq]

city: Oxford

first: Arne

middle: Wyndham

last: Mould

state: Oxfordshire

address: Warneford Hospital

department: Psychiatry

country: United Kingdom

institute: Oxford University

summary: Transcriptional profiling of E5.5 and E6.5 wild type and Blimp1 mutant decidua was performed using RNA-seq to identify maternal Blimp1 functions during pregnancy .

overall_design: To induce Prdm1 gene deletion in the uterus, Prdm1 BEH/+;PRCre/+ studs (Vincent et al., 2005, Soyal et al., 2005) were crossed with female Prdm1CA/CA mice (Shapiro-Shelef et al., 2003) to generate Prdm1 BEH/CA ;PRCre females, hereinafter referred to as Blimp1 mutant. Female littermates (6–10 weeks of age) were used as the wild type. Whole decidua from E5.5 and E6.5 Blimp1 mutant and wild type mice were analysed by RNA-Seq.

first: Mubeen

last: Goolam

first: Maria-Eleni

last: Xypolita

first: Elizabeth

last: Bikoff

last: Robertson


title: The transcriptional repressor Blimp-1/Prdm1 controls the maternal decidual response during pregnancy [ChIP-seq]

summary: To identify candidate Blimp1 target genes in maternal decidua we performed GFP antibody ChIP-seq analysis of E6.5 decidua from homozygous female EGFP-BLIMP1 mice that express an endogenous N-terminal EGFP-tagged Blimp1 protein (Mitani et al., 2017).

overall_design: GFP-ChIP-seq profiles of triplicate homozygous EGFP-Blimp1 and WT decidual samples generated by deep sequencing using Illumina HiSeq4000.


title: Gene expression changes in skeletal muscle following aerobic exercise training

city: Orlando

first: Rick

last: Vega

address: 303 E. Princeton

institute: AdventHealth

summary: Microarray analysis was performed with RNA isolated from vastus lateralis muscle biopsies of lean/overweight subjects following 18 days of aerobic exercise training. Samples from lean active individuals were also included. Exercise training led to robust changes in trained muscle. The lean active group profile was distinct from the pre-exercise samples. These results help define the molecular changes associated with aerobic training and contrast with an active phenotype.

overall_design: Microarray analysis was performed on RNA isolated from vastus lateralis biopies from 6 individual lean/overweight subjects before and after 18 days of aerobic training. Six lean, active individuals were also included.

middle: B

first: Gongxin

last: Yu

first: Stephanie

last: Parsons

first: Bram

last: Browers

first: Natalie

last: Stephens

first: Fanchao

last: Yi

first: Steven

middle: R

last: Smith

first: Lauren

middle: M

last: Sparks


title: RNAseq analyses of BvgA in Bordetella pertussis

city: Lille

first: loic

last: coutte

address: 1 rue du Pr Calmette, U1019 INSERM

department: microbiology

institute: INSERM

summary: We examined the global transcription of B. pertussis in different strains and culture conditions

overall_design: NextSeq 500 sequencing of RNAseq samples obtained in different Bordetella pertussis strains and culture conditions

first: Loic

last: Coutte


title: Novel analogs of the Quassinoid family inhibitor for treatment of hematologic malignancies

city: Shenzhen

first: Yonggang

last: Pei

state: GD

address: 1088 Xueyuan Avenue

department: School of Public Health and Emergency Management

institute: Southern University of Science and Technology

summary: Our study is to reveal the molecular mechanism associated with Brusatol-mediated inhibition. RNA-Seq experiment was performed with Brusatol-treated EBV-transformed LCLs to investigate its ability to regulate the cellular transcription program.

overall_design: Examine mRNA profiles of untreated and Brusatol-treated LCL cells

first: Hem

middle: C

last: Jha

first: Erle

middle: S