title: Vitamin D3 Metabolites Demonstrate Prognostic Value in EGFR-Mutant Lung Adenocarcinoma and Can be Deployed to Oppose Acquired Therapeutic Resistance

status: Public on Mar 12 2020

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

summary: EGFR tyrosine kinase inhibitors (EGFR TKIs) are the standard of care treatment for patients with EGFR-mutant lung adenocarcinoma (LUAD). Although initially effective, EGFR TKIs are not curative. Disease inevitably relapses due to acquired drug resistance. Here, we tested the ability of 1,25(OH)2D3 to promote epithelial differentiation and restore EGFR TKI sensitivity in models of EGFR TKI resistance that were associated with epithelial–mesenchymal transition (EMT).

overall_design: RNA was isolated from 3 separate passages of H1975 and H1975–OR (osimertinib resistant) cells treated with either vehicle control, 500nM osimertinib, 100 nM 1,25(OH)2D3, or combination of the above agents for 96 h with treatments administered at t0, 48, and 92 h.

first: Tatiana

last: Shaurova

first: Grace

middle: K

last: Dy

first: Sebastiano

last: Battaglia

first: Alan

last: Hutson

first: Letian

last: Zhang

first: Yunkai

first: Christine

last: Lovly

first: Mukund

last: Seshadri

first: David

last: Goodrich

first: Candace

last: Johnson

first: Pamela

last: Hershberger


title: Transcriptome profiling of neonatal rat ventricular cardiomyocytes overexpressing NFYa or NFE2L1

status: Public on Mar 18 2020

city: New York

first: Zhaoning

last: Wang

state: New York

address: 701 West 168th Street Hammer 14 - 1410

department: Genetics and Development

country: USA

institute: Columbia University

type: Expression profiling by high throughput sequencing

summary: The adult mammalian heart is incapable of regeneration following injury. In contrast, the neonatal mouse heart has a transient ability to regenerate, however the molecular mechanism that mediates this regenerative response is not fully understood. Here, by single-nucleus RNA sequencing we map the transcriptome landscape of cardiomyocytes in neonatal mouse hearts at healthy, regenerative, and remodeling conditions. We show that an immature cardiomyocyte population enters cell-cycle in response to injury. Absence of this cardiomyocyte population overtime is associated with the loss of the ability of the heart to regenerate. We show a defined injury response in these cardiomyocytes, including activation of transcription factors NFYa and NFE2L1, which play proliferative and protective roles, respectively. We further show that overexpression of these two factors in vivo promotes heart regeneration. Thus, these findings refined our understanding of cellular basis of neonatal heart regeneration and reveal dynamic transcriptome landscape of cardiomyocytes in response to injury.

overall_design: NFYa or NFE2L1 was overexpressed in cultured neonatal rat ventricular cardiomyocytes (NRVMs) by adenoviral delivery. GFP was overexpressed as a negative control. RNA was isolated from NRVMs overexpressing GFP, NFYa, or NFE2L1 in triplicate for mRNA-Seq.

first: Miao

last: Cui

first: Eric

middle: N

last: Olson


title: The Sox2 transcription factor binds RNA

status: Public on Mar 16 2020

city: Boulder

first: Desmond

middle: J

last: Hamilton

state: CO

address: 3415 Colorado Ave

department: Biochemistry

institute: CU Boulder

summary: A subset of transcription factors is proposed to form functional interactions with RNA to facilitate proper regulation of gene expression. Sox2, a critical transcription factor for maintenance of pluripotency and neurogenesis, is found associated with several lncRNAs, although it is unknown whether these interactions are direct or via other proteins. We demonstrate that human Sox2 interacts directly with one of these lncRNAs with high affinity through its HMG DNA-binding domain. Furthermore, rather than interacting with a single high affinity site, Sox2 binds regions of dsRNA in a non-sequence specific fashion. RNA binding is competitive with dsDNA, yet interaction with RNA is primarily electrostatically driven using a partially overlapping set of amino acids as that used for DNA binding. Finally, we use two distinct crosslinking techniques, formaldehyde and UV, with RNA immunoprecipitation (respectively, “fRIP” and “UVRIP”) of Sox2 in mouse embryonic stem cells to identify >1000 potential Sox2-RNA interacting partners with ~75% overlap between the two techniques. Together, these data reveal that Sox2 productively binds dsRNA with affinities rivaling ChIP-validated promoter DNA sites, suggesting that the transcriptome plays a significant role in regulation of gene expression by Sox2.

overall_design: The four biological replicates for both fRIP and UVRIP, a total of eight, were generated to evaluate fold change of IP relative to input.

first: Taeyoung

last: Hwang

first: Zachariah

middle: E

last: Holmes

first: John

middle: L

last: Rinn

first: Deborah

middle: S

last: Wuttke

first: Robert

middle: T

last: Batey


title: Apoptotic cells actively release metabolite messanger with anti-inflammatory properties

status: Public on Mar 19 2020

first: Justin

middle: Shaun Arnold

last: Perry

address: 408 East 69th Street, 408-15

department: Immunology Program

institute: Sloan Kettering Institute for Cancer Research

summary: Apoptosis accounts for ~ 90% of homeostatic cell turnover in the body1. While caspase-dependent apoptosis is known to influence immune tolerance, induction of cell proliferation, and tissue regeneration2-4,  how these apoptotic cells contribute to such diverse effects is less understood. Soluble factors released from apoptotic cells could be a means of ‘talking’ to healthy cells in the tissue neighborhood. While a few phagocyte-attracting ‘find-me’ signals released from apoptotic cells are known5, the larger ‘metabolite secretome’ from apoptotic cells is not yet defined. Here, via unbiased profiling of the apoptotic cell secretome, we identified 123 metabolites that are specifically released during apoptosis, while cells still retain membrane integrity. Release of ~25 of these metabolites is dependent on Pannexin 1 (Panx1) channels, which are opened by caspase-dependent cleavage during apoptosis. Interestingly, one of the Panx1-dependent metabolites from apoptotic cells is spermidine, a polyamine whose release could be, in part, due to the continued metabolic activity of dying cells. RNAseq analysis of healthy cells exposed to the apoptotic secretome revealed Panx1-dependent gene programs, including genes linked to suppression of inflammation, cell proliferation, and wound healing. Analysis of the apoptotic secretome across cell types and different apoptotic stimuli, identified a core “set” of 8 Panx1-dependent metabolites. Strikingly, a selected cocktail of these metabolites demonstrated significant immunosuppressive effects by potently reducing disease severity in an inflammatory arthritis model and a lung graft rejection model. Collectively, these data advance the concept that apoptotic cells are not ‘inert’ corpses waiting for removal by phagocytes, but rather they actively communicate with the tissue environment through their metabolite secretome, with implications in tissue inflammation.

overall_design: The experiment consist of three conditions: Phagocytes (LR73 cells) treated for four hours with supernatants taken from either live Jurkats , apoptotic Jurkats, or apoptotic Jurkats expressing a dominant-negative form of the Panx1 channel (caspase site mutation that does not allow cleavage by executioner caspase).  All conditions consisted of four biological replicates.

first: Christopher

middle: B

last: Medina

first: Sanja

last: Arandjelovic

first: Yizhan

last: Guo

first: Parul

middle: M

last: Mehrotra

first: Brady

last: Barron

first: Scott

last: Walk

first: Alexander

last: SKrupnick

first: Ulrike

last: Lorenz

first: Kodi

last: Ravichandran


title: Genomic signature of the standardized uptake value in 18F-fluorodeoxyglucose positron emission tomography in breast cancer

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

summary: The standardized uptake value (SUV), an indicator of the glucose uptake degree in 18F-fluorodeoxyglucose positron emission tomography (FDG-PET), has been used as a prognostic factor in malignant tumors. We aimed to identify a signature reflecting prognostic SUV characteristics in breast cancer (BRC). Transcriptome profiling was performed to identify a signature associated with the SUV in BRC patients who underwent preoperative FDG-PET. We defined a signature consisting of 723 genes significantly correlated with the SUV (|r| > .35; P < .001). The patient subgroups classified by the signature were significantly similar to those classified by the SUV (odds ratio, 8.02; 95% CI, 2.45 to 29.3; P < 0.001). The SUV signature showed independent clinical utility for predicting BRC prognosis (hazard ratio, 1.25; 95% CI, 1.11 to 1.42; P < 0.001). Integrative analysis demonstrated a significance of the signature in predicting the response to immunotherapy and revealed that a signaling axis defined by TP53-FOXM1 and its downstream effectors in glycolysis-gluconeogenesis, including LDHA, might be important mediators in the FDG-PET process. Our results reveal characteristics of glucose uptake captured by FDG-PET, supporting an understanding of glucose metabolism as well as poor prognosis in BRC patients with a high SUV.

overall_design: We prospectively collected tumor tissues from specimens of surgically resected breast cancer at the Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea, between July 1997 and December 2007. A total of 301 patients with invasive BRC were enrolled for gene expression profiling. Among them, the standardized uptake values for 66 patients with breast cancer who underwent by 18F-fluorodeoxyglucose positron emission tomography scan were available.

first: Sun

middle: H

last: Leem

first: In

last: Chu

first: Joon

last: Jeong

first: Sung

middle: G

last: Ahn

first: Seon


title: High Throughput pMHC-I Tetramer Library Production Using Chaperone Mediated Peptide Exchange

first: Peter

last: Smibert

address: 101 Avenue of the Americas

institute: New York Genome Center

summary: Peptide exchange technologies are essential for the generation of pMHC-multimer libraries for probing diverse, polyclonal TCR repertoires in various settings. Here we report, using the molecular chaperone TAPBPR, a robust method for the capture of stable, empty MHC-I molecules, which can be readily tetramerized and loaded with peptides of choice in a high-throughput manner. Alternatively, catalytic amounts of TAPBPR can be used to exchange ‘goldilocks’ peptides with high-affinity peptides of interest in an overnight reaction. Using the same system, we describe high-throughput assays to validate binding of multiple candidate peptides on the empty MHCI groove. Combined with tetramer-barcoding via a multi-modal cellular indexing technology, ECCITE-seq, our approach allows a combined analysis of TCR repertoires and other T-cell transcription profiles together with their cognate pMHC-I specificities in a single experiment.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: spleen, jurkat, and neuroblastoma samples

first: Stephanie

last: Hao


title: Transcriptomic and metabolomic analysis provides insights into anthocyanin and procyanidin accumulation in pear

city: Tai’an

first: Feng

last: Shouqian

state: Shandong

address: 61 Daizong Avenue

department: College of Horticulture Sciences

country: China

institute: Shandong Agricultural University

summary:
Background: Pear is one of the most important fruit crops worldwide. Anthocyanins and procyanidins (PAs) are important secondary metabolites that affect the appearance and nutritive quality of pear. However, few studies have focused on the molecular mechanism underlying anthocyanin and PA accumulation in pear.
Results: We conducted metabolome and transcriptome analyses to identify candidate genes involved in anthocyanin and PA accumulation in young fruits of the pear cultivar ‘Clapp Favorite’ (CF) and its red mutation cultivar ‘Red Clapp Favorite’ (RCF). Gene–metabolite correlation analyses revealed a ‘core set’ of 20 genes that were strongly correlated with 10 anthocyanin and seven PA metabolites. Of these, PcGSTF12 was confirmed to be involved in anthocyanin and PA accumulation by complementation of the tt19-7 Arabidopsis mutant. Interestingly, PcGSTF12 was found to be responsible for the accumulation of procyanidin A3, but not petunidin 3, 5-diglucoside, opposite to the function of AtGSTs in Arabidopsis. Transformation with PcGSTF12 greatly promoted or repressed genes involved in anthocyanin and PA biosynthesis, regulation, and transport. Electrophoretic mobility shift and luciferase reporter assays confirmed positive regulation of PcGSTF12 by PcMYB114.
Conclusion: These findings identify a core set of genes for anthocyanin and PA accumulation in pear. Of these, PcGSTF12 was confirmed to be involved in anthocyanin and PA accumulation. Our results also identified an important anthocyanin and PA regulation node comprising two core genes, PcGSTF12 and PcMYB114. These results provide novel insights into anthocyanin and PA accumulation in pear and represent a valuable data set to guide future functional studies and pear breeding.

overall_design: mRNA expression profile of young fruits of the pear cultivar ‘Clapp Favorite’ (CF) and its red mutation cultivar ‘Red Clapp Favorite’ (RCF) in different times.


title: Arabidopsis retrotransposon virus-like-particles and their regulation by epigenetically activated small RNA

status: Public on Mar 13 2020

city: Cold Spring Harbor

first: Robert

middle: A

last: Martienssen

address: 1 Bungtown Rd

department: Delbruck Bldg.

institute: Cold Spring Harbor Laboratory

type: Non-coding RNA profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report polysomal RNA sequencing data (RNAseq), small RNAseq, and virus-like-particle (VLP) DNA sequencing (DNAseq) and ChIPseq data. Arabidopsis ddm1 mutants produce LTR retrotransposon transcripts that are processed into 21-22 nt easiRNAs by RNA-Dependent RNA polymerase 6 (RDR6). To test if 21-22 nt easiRNAs regulate transcription, translation and reverse transcription of LTR retrotransposons, we compared ddm1 and ddm1rdr6 in polysomal RNAseq, VLP DNAseq and ChIPseq data. We found a handful of ATHILA elements were differentially regulated in ddm1rdr6 for polysomal RNAseq, VLP DNAseq, and ChIPseq datasets. Using short read and long read technologies, we also profiled functional LTR retrotransposons that made full-length DNA by reverse transcription inside VLPs. Small RNAseq data were obtained in pollen and inflorescence tissues in wild-type and ddm1.

overall_design: Polysomal RNAseq from total extract and microsome fraction with each 3 biological replicates of ddm1 and ddm1rdr6; Small RNAseq data from pollen and inflorescence tissues of wild-type and ddm1 with one replicate; VLP DNAseq using short read with 2-3 biological replicates and long read technologies with one replicate from wild-type, ddm1 and ddm1rdr6. ChIPseq was performed with 2 biological replicates from wild-type, rdr6, ddm1, and ddm1rdr6.

first: Seung

middle: C

last: Lee

first: Evan

last: Ernst

first: Filipe

last: Borges

first: Benjamine

last: Berube


title: Remodeling of active endothelial enhancers is associated with aberrant gene-regulatory networks in pulmonary arterial hypertension [ChIP-seq]

city: Heidelberg

first: Judith

last: Zaugg

state: Heidelberg

address: Meyerhofstraße 1

country: Germany

institute: European Molecular Biology Laboratory (EMBL)

summary: Pulmonary Arterial Hypertension (PAH) is a cardiovascular disease characterized by progressively increasing blood pressure as a result of obliteration and loss of pulmonary arteries. We have extracted pulmonary arterial endothelial cells from lungs of a cohort of PAH patients (n=10) and controls (n=9), cultured the cells for 3-5 passages, and performed chromatin (H3K27ac, H3K4me1, and H3K4me3 ChIP-Seq), expression (RNA-Seq) and chromatin interaction profiling (ChIA-PET). We observed a large-scale remodelling of the active chromatin landscape at enhancers while promoters and gene expression remained unchanged.

overall_design: Profiling of chromatin states in pulmonary arterial endothelial cells of PAH-patients and donors.

first: Armando

last: Reyes-Palomares

first: Michael

last: Snyder

first: Marlene

last: Rabinovitch


title: Remodeling of active endothelial enhancers is associated with aberrant gene-regulatory networks in pulmonary arterial hypertension [RNA-seq]

overall_design: Transcriptome profiling of pulmonary arterial endothelial cells of PAH-patients and donors.


title: The STRIPAK complex regulates response to chemotherapy through p21 and p27

status: Public on Mar 17 2020

city: Lund

first: Chris

middle: Denis

last: Madsen

address: Scheelevägen 2

department: Laboratory Medicine

country: Sweden

institute: Lund University

summary: We report that loss of a component of the STRIPAK complex in MDA-MB-231 cells known as STRIP1 causes cell cycle arrest and decreased proliferation due to increased expression of cyclin dependent kinase inhibitors, p21 and p27. This change in p21 and p27 expression results in a subset of cells forgoing therapy-induced senescence and becoming proliferative.

overall_design: Examination of the varying RNA levels in control MDA-MB-231 cells versus STRIP1-depleted cells

middle: D

first: Carmen

last: Rodriguez Cupello


title: Remodeling of active endothelial enhancers is associated with aberrant gene-regulatory networks in pulmonary arterial hypertension

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

overall_design: Refer to individual Series


title: Gene expression data from splenocytes of 3 week-old offspring after maternal exposure to benzyl butyl phthalate (BBP)

status: Public on Mar 11 2020

city: Leipzig

first: Tobias

last: Polte

address: Permoserstrasse 15

institute: Helmholtz Centre for Environmental Research GmbH - UFZ

summary: The prenatal and early postnatal period is highly sensitive to environmental exposures that may interfere with the developmental programming of the immune system leading to an altered disease risk in later life. To clarify the role of early influences in activation or exacerbation of autoimmune diseases like rheumatoid arthritis (RA) we investigated the effect of maternal exposure during the prenatal and weaning period of DBA/1 mice to the plasticizer benzyl butyl phthalate (BBP) on the development of RA in the offspring. Using a mild collagen-induced arthritis (CIA) model, maternal BBP-exposure increased both the prevalence and the severity of RA in the progeny compared to un-exposed dams. Additionally, maternal BBP exposure led to elevated serum IgG1 and IgG2a level in the offspring and increased the IFN-? and IL-17 release from collagen-re-stimulated spleen cells. Transcriptome analysis of splenoytes isolated from 3-week-old pups before RA-induction revealed considerable changes in gene expression in the offspring from BBP-exposed dams. Among them were regulator of G-protein signaling 1 (rgs1), interleukin-7 receptor (il-7r) and CXC chemokine 4 (cxcr4), all genes that have previously been described as associated with RA pathology. In summary, our results demonstrate that perinatal exposure to BBP increases the susceptibility of the offspring to RA, probably via a phthalate-induced disturbed regulation of RA-relevant genes or signalling pathways.

overall_design: Perinatal phthalate exposure increases the susceptibility to rheumatoid arthritis in mice. After perinatal exposure of mothers, splenocytes of 3-week old offsprings were pooled and analyzed.


title: Transcrpition landscapes of CD4 T cell exhaustion in response to transplant antigen

city: Houston

first: Yulin

last: Dai

state: TX

address: 7000 fannin, suite 600

department: School of Biomedical Informatics

institute: University of Texas health science center at Houston

summary: We report the gene profiles of exhaustion-like and effector-like CD4 T cells in response to transplant antigen. To obain the transcprition landscapes of exhuasted and effector CD4 T cells , we generated RNA-seq of TCR transgeneic TEa cells in response to abundant IE-α antigen (exhuast) or to Balb/c skin grafts (effector). We find that TEa cells upregulated the expression level of key exhaustion genes, including Pdcd1, Tox, lag3, Cd38, Cd200, as well as downregulated the expression levels of effector genes Ifng, Gzmb, Prf1, Tbx21, Il2ra, Fasl and Klrg1. This study provides a better understanding of CD4 T cell exhaustion in response to alloantigen.

overall_design: Gene profiles of TEa cells in response to abundant or moderate IE-α antigen were generated.

first: Dawei

last: Zou

first: Wenhao

last: Chen


title: Bmal1 -/- RNA-seq in mouse embryonic stem cells

city: Granada

first: Jordi

last: Martorell-Marugan

address: Avenida de la Ilustración 114

department: Bioinformatics Unit

country: Spain

institute: GENyO

summary: RNA seq experiment comparing mRNA expression in Bmal1 -/- and parental wild-type mESCs

overall_design: Biological replicates of mutant and wild-type cells

first: Amador

last: Gallardo

last: Martorell-Marugán

first: Pedro

last: Carmona-Sáez

first: David

last: Landeira


title: Remodeling of active endothelial enhancers is associated with aberrant gene-regulatory networks in pulmonary arterial hypertension [ChIA-PET]

overall_design: chromatin interaction profiling (ChIA-PET)

first: Fabian

last: Grubert


title: Comparing 2-dimensional vs. 3-dimensional human prostate cancer transcriptomes uncovers growth-specific gene signatures

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: Prostate cancer research has relied heavily on patient-derived cell lines, which may be used for in vitro (2-dimensional) studies or cultivated as 3-dimensional xenografts in mice. These approaches are likely to have differential impacts on cell differentiation, with implications for research outcomes. Therefore, defining and comparing the transcriptional signatures associated with 2-dimensional and 3-dimensional approaches is essential to adequately plan experiments and interpret research data. In this study, LNCaP, VCaP, and 22Rv1 human prostate cancer cells were either cultivated in monolayers or as xenografts in NOD Scid mice, and their gene transcription profiles were studied and compared using microarray and RT-PCR techniques. This comparison identified gene sets featuring similar expression patterns in all three cancer cell lines and unique transcriptional signatures associated with 3-dimensional versus 2-dimensional growth. Pathway over-representation analysis revealed an enrichment of pathways related to cell-cell interactions, differentiation and the extracellular matrix. Immunohistochemical analyses confirmed that gene up-regulation in xenografts occurred in implanted cancer cells and not mouse stromal cells. Cultivating cells in vitro in the presence of mouse - rather than bovine - serum failed to elicit the gene transcription profile observed in xenografts, further supporting the hypothesis that this profile reflects 3-dimensional growth and enhanced microenvironmental interactions, rather than exposure to mouse-related factors. Overall, these findings define the expression profiles observed in prostate cancer cells cultivated in monolayers and in xenografts, highlighting differentially regulated pathways in each setting and providing essential information for performing and interpreting research in this field.

overall_design: Custom Agilent 44K whole human genome expression oligonucleotide microarrays were used to profile human prostate tumor cells grown in vitro (2-dimensional) and as 3-dimensional xenografts. RNA was amplified prior to hybridization against a common reference pool of prostate tumor cell lines.

first: Lauren

last: Brady

first: Rui

last: Gil da Costa

first: Clinton

last: Matson

last: Risk

first: Roger

first: Peter

last: Nelson


title: A single cell atlas of tumor resistance to PD-1 blockade and radiotherapy: Bulk Tumor RNA Sequencing

status: Public on Mar 10 2020

city: Durham

last: Kirsch

state: NC

address: PO Box 96100

institute: Duke University

summary: Abstract: Transplanted tumors in syngeneic mice treated with immune checkpoint blockade and radiotherapy demonstrate synergy and an abscopal effect. Indeed, tumors generated from sarcoma cell lines transplanted into syngeneic mice are cured by PD-1 blockade and radiotherapy, but autochthonous, primary sarcomas from the same high mutational load model are resistant to the identical treatment. Here, we generated a single cell atlas of tumor-infiltrating immune cells from allograft and primary tumors, which demonstrates marked differences in their immune landscapes before and after radiation and immunotherapy. Allograft tumors are enriched for effector CD8+ T cells that mediate response to combination therapy, but the immune response to primary sarcomas shows tumor-specific tolerance. Genetic barcoding of primary tumors reveals a cellular response to combination therapy, but resistance of specific clones. Together, this comprehensive comparison of the primary and allograft tumor microenvironments identifies immune tolerance and clonal resistance to immunotherapy and radiotherapy specific to primary tumors.

overall_design: Primary and allograft sarcomas were harvested 3 days after treatment with either 0 or 20 Gy radiation and anti-PD-1 or isotype control treatment.

first: Amy

last: Wisdom

first: Yvonne

last: Mowery

first: Dadong

last: Zhang

first: Xiaodi

last: Qin

first: Kouros

last: Owzar


title: Multiple links between 5-methylcytosine content of mRNA and translation

status: Public on Mar 09 2020

city: Canberra

first: Thomas

last: Preiss

state: Acton

address: 31 Garran Road

department: Genome Science

country: Australia

institute: Australian National University, John Curtin School of Medical Research

type: Methylation profiling by high throughput sequencing

summary: 5-methylcytosine (m5C) is a prevalent base modification in tRNA and rRNA but it also occurs more broadly in the transcriptome, including in mRNA. In pursuit of potential links of m5C with mRNA translation, we performed polysome profiling of human HeLa cell lysates and subjected RNA from resultant fractions to efficient bisulfite conversion followed by RNA sequencing (bsRNA-seq). Bioinformatic filters for rigorous site calling were devised to reduce technical noise. We obtained ~1,000 candidate m5C sites in the wider transcriptome, most of which were found in exonic regions of mRNA. Multiple novel sites were validated by amplicon-specific bsRNA-seq in independent samples of either human HeLa, LNCap and PrEC cells. Furthermore, RNAi-mediated depletion of either the NSUN2 or TRDMT1 m5C:RNA methyltransferases showed a clear dependence on NSUN2 for the majority of tested sites in mRNA and noncoding RNA. Candidate m5C sites in mRNAs are enriched in 5’UTRs and near start codons, and commonly embedded in a local context reminiscent of the NSUN2-dependent m5C sites found in the variable loop of tRNA. Analysing mRNA sites across the polysome profile revealed that non-conversion levels, at bulk and for many individual sites, were inversely correlated with ribosome association. Altogether, these findings emphasise the major role of NSUN2 in making this mark transcriptome-wide and further substantiate a functional interdependence of cytosine methylation level with mRNA translation

overall_design: Bisulfite RNA sequencing of HeLa cell polysome profiling-derived samples representing different translational states; in biological triplicates.

first: Ulrike

last: Schumann

first: He-Na

first: Tennille

last: Sibbritt

first: Attila

last: Horvath

first: Anyu

last: Pan

first: Simon

last: Gross

first: Susan

last: Clark

first: Li

last: Yang


title: Transcriptomic changes during senescence of leaves and fine roots of Populus trichocarpa

status: Public on Mar 07 2020

city: Poznan

first: Katarzyna

last: Marzec-Schmidt

address: Umultowska 89

department: General Botany

country: Poland

institute: Adam Mickiewicz University

summary: We studied the changes that occur in gene transcription during seasonal senescence in Populus trichocarpa pioneer leaves and fine roots. Plant senescence is a strictly regulated physiological process that allows relocating of valuable nutrients from senescent tissues before death. It might be induced by internal or external factors and among them, phytohormones play an undoubtedly significant role. Senescence was extensively studied in leaves, but the aging of other ephemeral organs, located underground, and its drivers are still poorly understood. We focused on collective results to fill in the knowledge gap about senescence of fine, absorptive roots and leaves in order to check if there are universal mechanisms involved during plant organ senescence. Transcriptional profiling was conducted with the use of microarrays to identify genes involved in developmental PCD. Samples were collected three times during a growth season. The first collection was considered as a control and was collected in early summer (July 7–15) when leaves and the root system were fully developed and functional. The second group of leaf and root samples were harvested in early autumn (October 1–7) when chlorophyll levels in leaves had decreased by approximately 40% and when fine roots had changed in color from white to brown. The third group of samples were harvested in the middle of autumn (November 2–9) when chlorophyll levels in leaves decreased by approximately 65% and fine roots were dark brown or black color. Our results reveal the important role of phytohormones in regulating the senescence of both studied organs. The transcriptomic analyses showed significant changes in gene expression that are associated with phytohormones, especially with ABA and jasmonates. We conclude that phytohormonal regulation of senescence in roots and leaves is organ-specific. In roots, phytohormones are involved indirectly in regulation of senescence by increasing tolerance for cold or resistance for pathogens, whereas such correlation was not observed in leaves.

overall_design: All experiments were performed on seed-grown Populus trichocarpa (Torr. & Gray) growing in rhizotrons filled with natural soil with shoots extending from the top into the air. Waterlogging was avoided by installing a drainage hole in the bottom of each rhizotron that permitted soil aeration and drainage of excess water. Samples were collected three times during a growth season. The first collection was considered as a control and was collected in early summer (July 7–15) when leaves (LC) and the root (RC) system were fully developed and functional. The second group of leaf (LS1) and root (RS1) samples were harvested in early autumn (October 1–7) when chlorophyll levels in leaves had decreased by approximately 40% and when fine roots had changed in color from white to brown. The third group of samples were harvested in the middle of autumn (November 2–9) when chlorophyll levels in leaves (LS2) decreased by approximately 65% and fine roots (RS2) were dark brown or black color. Total RNA was extracted from three biological replicates of each stage of senescence of fine roots and leaves using an RNeasy Plant Mini kit (Qiagen, USA). RNA quantity and quality were assessed using a NanoDrop1000 (Thermo Fisher Scientific Inc., USA). cRNA synthesis and microarray hybridization to an Affymetrix GeneChip Poplar Genome Array (A-AFFY-131) were performed according to the provided Affymetrix protocol.

first: Agnieszka

last: Bagniewska-Zadworna


title: Integrative proteomics reveals increased non-degradative ubiquitylation during CD4+ T cell activation

city: Philadelphia

first: Joseph

last: Dybas

state: PA

address: 3501 Civic Center Blvd

department: Department of Biomedical and Health Informatics

institute: Children's Hospital of Philadelphia

summary: In spite of gathering evidence that ubiquitylation can direct non-degradative outcomes, most investigations of ubiquitylation in T cells remain focused on degradation. Here we integrated proteomic and transcriptomic datasets to establish a framework for predicting degradative or non-degradative outcomes of ubiquitylation in primary CD4+ T cells. Di-glycine remnant proteomics revealed ubiquitylated proteins, while whole cell proteomic and transcriptomic data were used to predict whether ubiquitylated proteins showed evidence of degradation. Applying this analysis to ubiquitylated proteins with functions in TCR signaling led us to the prediction that early T cell activation promotes increased non-degradative ubiquitylation. Supporting this, we observed an increase in non-proteasome targeted K29, K33 and K63 polyubiquitin chains during T cell activation, while K48 chains appeared unchanged. This study reveals over 1,200 proteins that are ubiquitylated in primary CD4+ T cells and supports the relevance of non-proteasomally targeted ubiquitin chains in T cell signaling.

overall_design: The study consists of six RNAseq samples in total; three biological replicates of unstimulated mouse CD4+ T cells and three biological replicates of mouse CD4+ T cells stimulated for 4hr with anti-CD3/CD28 to induce T cell receptor signaling.

first: Claire

last: O'Leary

first: Paula

last: Oliver


title: Global DNA hypomethylation in ovarian cancer (Affymetrix_expression_data)

status: Public on Mar 06 2020

city: Omaha

first: Adam

middle: R

last: Karpf

state: NE

address: S 42nd &, Emile St

institute: UNMC

summary: Comparison of DNA methylome, mRNA transcriptome, and copy number variation in tumors with global loss of DNA methylation to tumors with normal global methylation.

overall_design: Human tissue samples were obtained from patients undergoing surgical resection at Roswell Park Comprehensive Cancer Center, using Institutional Review Board Protocol I-215512.  Normal controls were obtained from patients without malignancy, and tumor samples contained >90% neoplastic cells.  IOSE-121 and OVCAR3 cells at ~50% confluence were treated with decitabine or PBS vehicle control.  Affymetrix HG 1.0ST arrays and Total RNA-sequencing were used to analyze gene expression. Total RNA sequencing used the Illumina TruSeq Stranded Total RNA kit and an Illumina HiSeq 2000 Genome Analyzer.  Illumina Infinium 450K BeadChips and Agilent SureSelect Methylome sequencing were used to analyze DNA methylation.  High-throughput sequencing of library tags was performed using an Illumina HiSeq 2000 Genome Analyzer.  Genomic copy number analysis was performed using Affymetrix Cytoscan HD microarrays.

first: Mustafa

last: Albahrani


title: Global DNA hypomethylation in ovarian cancer (CNV_data)


title: Global DNA hypomethylation in ovarian cancer (Methylseq_data)


title: Chromatin states and transcriptome of CD8+ T cells over the course of differentiation

city: PARIS

first: Mengliang

last: YE

address: 26 Rue d'ULM

country: France

institute: Institut Curie

summary: The goal of this study is to analyze the contribution of transposable elements (TEs) tocis-regulation in CD8+ T cells. Using a combination of NGS techniques we show that specific subfamilies of TEs are enriched, and distributed in a lineage-specific fashion in core and boundary domains of CD8+T cell enhancers.This study represents the first detailed analysis of the topology and the enhancer domain-associated putative functions of distinct TE types.

overall_design: ATAC-Seq and ChIP-Seq for H3K4me3 (in replicates), and total RNA-seq (in replicates or triplicates) performed in CD8+ T cells, naive (D0) and activated in vitro during one day (D1) and three days (D3).

first: Elina

last: Zueva

first: Christel

last: Goudot

first: Sebastian

last: Amigorena


title: Global DNA hypomethylation in ovarian cancer (450K_data)

type: Methylation profiling by genome tiling array


title: Global DNA hypomethylation in ovarian cancer


title: Fluidigm real-time PCR analysis of mouse tissue

status: Public on Mar 05 2020

city: Melboune

first: Saeedeh

last: Darzi

state: VIC

address: 27-31 Wright Street, Clayton

institute: Hudson Institute of Medical Research

summary:
Purpose: Transvaginal meshes for the treatment of Pelvic Organ Prolapse (POP) have been associated with severe adverse events and have been banned for clinical use in many countries. We recently reported the design of degradable poly (L-lactic acid)-co-poly (e-caprolactone) nanofibrous mesh (P nanomesh) bioengineered with endometrial mesenchymal stem/stromal cells (eMSC) for POP repair. We showed that such bioengineered meshes had high tissue integration as well as immunomodulatory effects in vivo. This study aimed to determine the key molecular players enabling eMSC- based foreign body response modulation.
Methods: SUSD2+ eMSC were purified from single cell suspensions obtained from endometrial biopsies from cycling women by magnetic bead sorting. Electrospun P nanomeshes with and without eMSC were implanted in a NSG mouse skin wound repair model for 1 and 6 weeks. Quantitative PCR was used to assess the expression of extracellular matrix (ECM), cell adhesion, angiogenesis and inflammation genes as log2 fold changes compared to sham controls. Histology and immunostaining was used to visualize the ECM, blood vessels and multinucleated foreign body giant cells around implants.
Results: Bioengineered P nanomesh/ eMSC constructs explanted after 6 weeks showed significant increase in 35 genes associated with ECM, ECM regulation, cell adhesion angiogenesis and immune response in comparison to P nanomesh alone. In the absence of eMSC, acute inflammatory genes were significantly elevated at 1 week. However, in presence of eMSC, there was an increased expression of anti-inflammatory genes including Mrc1 and Arg1 by 6 weeks. There was formation of multinucleated foreign body giant cells around both implants at 6 weeks that expressed CD206, a M2 macrophage marker.
Conclusion: This study reveals that eMSC modulate the foreign body response to degradable P nanomeshes in vivo by altering the expression profile of mouse genes. eMSC reduce acute inflammatory and increase ECM synthesis, angiogenesis and anti-inflammatory gene expression at 6 weeks while forming newly synthesized collagen within the nanomeshes and neo-vasculature in close proximity. From a tissue engineering perspective, this is a hallmark of a highly successful implant, suggesting significant potential as alternative surgical constructs for the treatment of POP.

overall_design: Electrospun PLACL nanomeshes with and without eMSC were implanted in a NSG mouse skin wound repair model for 1 and 6 weeks. Quantitative PCR was used to assess the expression of extracellular matrix (ECM), cell adhesion, angiogenesis and inflammation genes as log2 fold changes compared to sham controls.


title: Roles of different regions in dairy nitrogen conversion: transcriptome based insights on utilization of low quality forage resources

city: Hangzhou

first: Diming

last: Wang

address: 866 yuhangtang RD

institute: Zhejiang University

summary: Total RNA from duodenum, jejunum, liver and mammary gland tissues of cows fed alfalfa hay (AL),Rice straw (RS) or Corn stover (CS) diet were sequenced using Illumina HiSeq 2000 system. For comparative analysis, differentially expressed genes were identified with edgeR and SAS software.

overall_design: We performed a correlation and differential analysis of transcriptomes of duodenum, jejunum,liver and mammary tissues collected from cows fed AL, RS or CS diets, to study molecular mechanisms of forage source changing N conversion rate in terms of amino acids and energy metabolism.

first: G

last: Leluo

first: D


title: Kentucky assay

city: Lexington

first: Timothy

last: McClintock

state: Kentucky

address: 508 Medical Science Buildi

department: Physiology

institute: University of kentucky


title: Next generation sequencing facilitates quantitative analysis of retinal transcriptomes under normal light and high-intensity light condition

status: Public on Mar 03 2020

city: Wenzhou city

first: Huirong

last: Li

state: Zhejiang province

address: NO.268, Xueyuan road, Lucheng district

department: School of Ophthalmology and Optometry and Eye Hospital

institute: Wenzhou medical university

summary: Photoreceptor cell degeneration is a major cause of blindness and a considerable health burden during aging but effective therapeutic or preventive strategies have not so far become commercially available. Here we show in mouse models that signaling through the tyrosine kinase receptor KIT protects photoreceptor cells against both light-induced and inherited retinal degeneration. Upon light damage, photoreceptor cells upregulate Kit ligand (KITL) and activate KIT signaling, which in turn induces nuclear accumulation of the transcription factor NRF2 and stimulates the expression of the antioxidant gene Hmox1. Conversely, a viable Kit mutation promotes light-induced photoreceptor damage, which is reversed by experimental expression of Hmox1. Furthermore, overexpression of KITL from a viral AAV8 vector prevents photoreceptor cell death and partially restores retinal function after light damage or in genetic models of human retinitis pigmentosa. Hence, application of KITL may provide a novel therapeutic avenue for prevention or treatment of retinal degeneration

overall_design: Retinal mRNA profiles of 2-month old BALB/c mice exposed to normal light or high-intensity light were generated by deep sequencing, in quintupled, using Illumina Novaseq

first: Ling

last: Hou


title: Autophosphorylation at serine 166 regulates RIPK1-mediated cell death and inflammation

status: Public on Mar 04 2020

city: Cologne

first: Manolis

last: Pasparakis

state: NRW

address: Joseph Stelzmann Strasse, 26

department: Institute for Genetics

institute: University of Cologne

summary:
NEMO-IEC KO mice spontaneously develop chronic colitis characterized by inflammatory gene expression. We characterized the role of RIPK1 auto-phosphorylation in the upregulation of inlflammatory genes in these mice.
We used microarray to study the effect of a RIPK1S166A mutation on the gene expression profile in NEMO IEC-KO mice and detect effects on specific inflammatory genes.

overall_design: Colon samples were collected from 11week old mice for RNA extraction and subsequent microarray analysis.


city: Cambridge

first: Frederic

last: Sorgeloos

address: Addenbrookes Hospital, Hills Road

department: Pathology

country: United Kingdom

institute: University of Cambridge

summary: Transcriptional profiling of human intestinal organoids following human norovirus infection.

overall_design: Two different human intestinal organoids were generated and infected with GII.4 human norovirus for 48h. Controls included mock-infected and UV-inactivated GII.4 HuNoV.

first: Myra

last: Hosmillo

first: Yasmin

last: Goodfellow

first: Alessandra

last: Merenda

first: Bon-Kyoung

last: Koo

first: Komal

last: Nayak

first: Matthias

last: Zilbauer

first: Ian


title: Pro-BMP9 and pro-BMP10 signalling in pulmonary arterial endothelial cells

first: Wei

address: Hills Road

department: Medicine

summary: This study was designed to compare the global gene expression change induced by the circulating, prodomain bound forms of BMP9 and BMP10 (pro-BMP9 and pro-BMP10) in human pulmonary arterial endothelial cells (PAECs). This is different from many previous studies which used the growth factor domain of BMP9 and/or BMP10.

overall_design: Four independent PAEC lines were purchased from Lonza. Each line was grown up and seeded separately for the treatment. BMP samples were made up on the day of the treatment, and cells were treated at 0.3 ng/ml of final growth factor domain concentration. Treatment was carried out for 1.5 hours at 37 C to detect the genes directly regulated by pro-BMP9 and pro-BMP10.

first: Richard

last: Salmon

first: Nicholas

middle: W

last: Morrell


title: Human cytomegalovirus long noncoding RNA4.9 regulates viral DNA replication

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

summary: Viruses are known for their extremely compact genomes composed almost entirely of protein-coding genes. Nonetheless, four long noncoding RNAs (lncRNAs) are encoded by human cytomegalovirus (HCMV).  Although these RNAs accumulate to high levels during lytic infection, their functions remain largely unknown. Here, we show that HCMV-encoded lncRNA4.9 localizes to the viral nuclear replication compartment, and that its depletion restricts viral DNA replication and viral growth. RNA4.9 is transcribed from the HCMV origin of replication (oriLyt) and forms an RNA-DNA hybrid (R-loop) through its G+C-rich 5’ end, and this may be important for the initiation of viral DNA replication. Furthermore, interference with RNA4.9 expression drastically reduces the levels of the viral single-stranded DNA-binding protein (ssDBP), and overexpression of ssDBP alleviates the inhibition of viral DNA replication and growth caused by RNA4.9 depletion. We also identified a similar, oriLyt-embedded, G+C-rich lncRNA in murine cytomegalovirus (MCMV). Knockdown of this lncRNA interferes with MCMV ssDBP expression and viral DNA replication. These results indicate that HCMV RNA4.9 plays an important role in regulating viral DNA replication by coupling oriLyt activity to ssDBP levels, and that this novel activity may be conserved in other betaherpesviruses.

sample_organism:
Homo sapiens
Mus musculus
Human betaherpesvirus 5
Murid betaherpesvirus 1

overall_design: RNA-sequencing of ribosome protected footprints (FP) of HCMV infected fibroblasts (HFF) that expressed CAS9 and either a control sgRNA (sgUS2) or a sgRNA against the viral lincRNA RNA4.9 (sgRNA4.9) and RNA-seq of according samples; each in replicates.   mRNA-seq of HCMV infected fibroblasts (HFF) that expressed CAS9 and either a control sgRNA (sgUS2)or a sgRNA against the viral lincRNA RNA4.9 (sgRNA4.9) at 24 and 48 hpi; each in replicates.  Infections were performed in presence of the viral DNA replication inhibitor phosphonoformic acid (PFA).  mRNA-seq of fibroblasts (MEF) infected with murid herpesvirus 1.

first: Julie

last: Tai-Schmiedel

first: Aharon

last: Nachshon


title: RNA-seq data of TAGAP WT or KO BMDMs treated with Curdlan

status: Public on Mar 02 2020

city: Wuhan

first: Chenhui

last: Wang

state: Hubei

address: 1037 Luoyu Rd

institute: Huazhong University of Science and Technology

summary: Bone marrow derived macrophages (BMDMs) were isolated form WT or TAGAP-KO mice, followed by stimulation with Curdlan (10ug/ml) for 0 or 3 hours, and samples were collected and sent to BGI for RNA SEQ analysis.

overall_design: BMDMs were isolated from WT or TAGAP-KO mice  (3 replicates for each group), and cells were left untreated or treated with Curdlan (10ug/ml) for 3 hours. Cells were harvested and send to BGI company for RNA SEQ analysis.

first: Jianwen

last: Chen

first: Ruirui

last: He


title: Map of nucleosome positions on the HIV DNA

city: Montpellier

first: Monsef

last: Benkirane

address: 141 rue de la cardonille

institute: CNRS

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

overall_design: Refer to individual Series


title: MNase-seq analyses for primary CD4 T cells infected with HIV (NL4-3 WT or IND116A)

summary: We used the technology of MNase-seq and capture-based target enrichment to analyze nucleosome positioning on the HIV DNA.

overall_design: Chromatin extracted from cells infected with HIV were treated with MNase.

first: Shinichi

last: Machida

first: David

last: Depierre

first: Olivier

last: Cuvier

first: Motoki

last: Takaku


title: MNase-seq analyses for Jurkat cells infected with HIV (NL4-3 WT or IND116A)


title: RXRs are required for neonatal expansion of the serosal macrophage pool and contribute to ovarian cancer progression

city: Madrid

first: Mercedes

last: Ricote

address: Darwin 3

institute: CNB-CSIC

summary: Distinct macrophage populations throughout the body display highly heterogeneous transcriptional and epigenetic programs. However, the regulation of chromatin accessibility of tissue-resident macrophages is poorly understood. In this study, we generated a data set for genome-wide transposase-accessible chromatin analysis (ATAC-seq) of large peritoneal macrophages in animals with myeloid-specific double deletion of the nuclear receptors RXRa and RXRb.

overall_design: The chromatin accessibility profiles of sorted large peritoneal macrophages (LPMs) from 9-week-old wild type (WT) and RXRa/RXRb-deficient (KO) mice were generated by deep sequencing in duplicate using 2×50 HiSeq 3000 (Illumina) and with an average of 25 million paired-end reads per sample.


title: Expression data from mice normal MΦs and multiple myeloma tumor-associated macrophages (TAMs)

status: Public on Mar 01 2020

city: Houston

first: Pan

last: Su

address: 6550 FANNIN STREET

institute: Houston Methodist Research Institute

summary:
TAMs play an important role in MM drug resistance and progression. To determine the mechanisms about how tumor microenvironment regulate the generation of TAMs from normal MΦs in vitro and in vivo. We generated TAMs in vitro by tumor cells-MΦs coculture from CD36 WT and KO mice bone marrow cells. Total RNAs of 2 x 106 MΦs and TAMs were extracted by RNeasy Mini Kit (Qiagen). 5-10 µg RNA samples were sent to Gene Expression and Genotyping Facility at Case Western Reserve University (Cleveland, OH) for RNA-seq followed by data analysis.
We use microarray data to determine differential expression of genes in between normal MΦs and TAMs.

overall_design: Examination of gene-profiling data in normal control MΦs and TAMs.


title: Magnaporthe oryzae Auxiliary Activity Protein MoAa91 Functions as Chitin-Binding Protein To Induce Appressorium Formation on Artificial Inductive Surfaces and Suppress Plant Immunity

city: Nanjing

first: Ying

last: Li

department: College of Plant protection

institute: Nanjing Agricultural University

summary: Here, we performed comparative transcriptomic studies of ΔMorgs mutant and wild-type strains and found that M. oryzae Aa91 (MoAa91), a homolog of the auxiliary activity family 9 protein (Aa9), was required for surface recognition of M. oryzae. We found that MoAA91 was regulated by the MoMsn2 transcription factor and that its disruption resulted in defects in both appressorium formation on the artificial inductive surface and full virulence of the pathogen. We further showed that MoAa91 was secreted into the apoplast space and was capable of competing with the immune receptor chitin elicitor-binding protein precursor (CEBiP) for chitin binding, thereby suppressing chitin-induced plant immune responses. In summary, we have found that MoAa91 is a novel signaling molecule regulated by RGS and RGS-like proteins and that MoAa91 not only governs appressorium development and virulence but also functions as an effector to suppress host immunity.

overall_design: Examination of 4 Dmorgs mutants against wild type Guy11 at 4 time points.

first: Xinyu

last: Liu

first: Zhengguang

last: Zhang


title: Smooth muscle cell reprogramming in aortic aneurysms

city: New Haven

first: Michael

last: Simons

state: CT

address: 3oo George St, Suite 773

department: Department: Internal Medicine Cardiology

institute: Yale University

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Inference of single-cell phylogenies from lineage tracing data using Cassiopeia

city: San Francisco

first: Matthew

middle: Gregory

last: Jones

state: CA

institute: UCSF

summary: The pairing of CRISPR/Cas9-based gene editing with massively parallel single-cell readouts now enables large-scale lineage tracing. However, the rapid growth in complexity of data from these assays has outpaced our ability to accurately infer phylogenetic relationships. First, we introduce Cassiopeia - a suite of scalable maximum parsimony approaches for tree reconstruction. Second, we provide a simulation framework for evaluating algorithms and exploring lineage tracer design principles. Finally, we generate the most complex experimental lineage tracing dataset to date, 34,557 human cells continuously traced over 15 generations, and use it for benchmarking phylogenetic inference approaches. We show that Cassiopeia outperforms traditional methods by several metrics and under a wide variety of parameter regimes, and provide insight into the principles for the design of improved Cas9-enabled recorders. Together these should broadly enable large-scale mammalian lineage tracing efforts.Cassiopeia and its benchmarking resources are publicly available at https://www.github.com/YosefLab/Cassiopeia.

overall_design: scRNA-seq of 4 samples from an in vitro CRISPR/Cas9-based lineage experiment, resulting in 34,557 A549 cells across 11 clones. Please note that scRNAseq was performed solely to acquire the resulting lineage information, stored as insertions or delection (indels) on transcribed molecules, and that no other transcriptional data was used in this study. Included in this repository are: (1) Fastq reads for each of the four samples (each corresponding to a plate in the original experiment); (2) possorted_genome_bam's produced from cell ranger (3) a processed "alleleTable" describing the lineage information for all the cells, across the 11 clones; and (4) reconstructed trees for each clone, in newick format.

first: Alex

last: Khodaverdian

first: Jeffrey

last: Quinn

first: Michelle

last: Chan

last: Hussmann

first: Robert

first: Chenling

last: Xu

first: Jonathan

last: Weissman

first: Nir

last: Yosef


title: Human iPSC-derived neurons and cerebral organoids establish differential effects of germline NF1 gene mutations

city: St Louis

first: David

last: Gutmann

state: MO

address: 660 S Euclid Ave

department: Neurology

institute: Washington University in St Louis

summary: Neurofibromatosis type 1 (NF1) is a common neurodevelopmental disorder caused by a spectrum of distinct germline NF1 gene mutations, traditionally viewed as equivalent loss-of-function alleles. To specifically address the issue of mutational equivalency in a disease with considerable clinical heterogeneity, we engineered seven isogenic human induced pluripotent stem cell lines, each with a different NF1 patient NF1 mutation, to identify potential NF1 mutation-specific effects on human central nervous system cells and tissues. While all mutations increased proliferation and RAS activity in two-dimensional (2D) neural progenitor cells (NPCs) and astrocytes, we observed striking NF1 mutation-specific effects on 2D NPC dopamine levels and NPC proliferation, apoptosis, and neuronal differentiation in developing cerebral organoids. Together, these findings demonstrate NF1 mutational specificity at the cellular and tissue levels, suggesting that the germline NF1 gene mutation is one factor that underlies clinical variability.

overall_design:
Analyze differential clustering of gene expression between patient-derived and isogenic NPCs harboring two separate NF1 mutations (1185+1G>A; 6513T>A) or no NF1 mutation (control; CTL)
nf1 = NF1 mutation 1185+1G>A
nf8 = NF1 mutation 6513T>A

first: Corina

last: Anastasaki

last: Wegscheid

first: Kelly

last: Hartigan

first: Jason

last: Papke

first: Nathan

last: Kopp

first: Jiayang

last: Chen

first: Joseph

last: Dougherty

first: Olivia

last: Cobb


title: Smooth muscle cell reprogramming in aortic aneurysms [RNA-Seq]

first: Michael

last: Simons

summary: Smooth muscle cell TGFβ signaling is one of the primary drivers of smooth muscle cell maturation.  Inhibition of smooth muscle cell TGFβ signaling in hyperlipidemic mice induces vessel wall inflammation and vessel wall dilation/dissection and leads aortic aneurysm. We performed bulk RNAseq method to examine smooth muscle cell gene expression profile using fresh human tissues from normal aortic media smooth muscle cells and aneurysm aortic media smooth muscle cells.

overall_design: Examination of human aortic media smooth muscle cell gene expression in normal and aneurysm

first: Pei-Yu


title: Smooth muscle cell reprogramming in aortic aneurysms [scRNA-Seq]

summary: Smooth muscle cell TGFβ signaling is one of the primary drivers of smooth muscle cell maturation.  Inhibition of smooth muscle cell TGFβ signaling in hyperlipidemic mice induces vessel wall inflammation and vessel wall dilation/dissection and leads aortic aneurysm. We performed scRNAseq method to examine smooth muscle cell gene expression profile using Apoe and SMC specific TGFbR2 KO in Apoe background mice.

overall_design: Using scRNAseq to compare the gene expression profiles of smooth muscle cells beteewn ApoE mice and SMC specific TGFbR2 KO Apoe mice fed with high fat diet


title: Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection [VIII]

city: Shanghai

first: Xiao

last: Ge

address: No. 800 Dongchuan Road

institute: Shanghai JiaoTong University

summary: By CRISPR DNA-fragment editing, in conjunction with chromosome conformation capture, we find that CBSs, if located between enhancers and promoters in the clustered Pcdh and b-globin clusters, function as an enhancer-blocking insulator by forming distinct directional chromatin loops, regardless whether enhancers contain CBS or not. Moreover, computational simulation in silico and genetic deletions in vivo revealed balanced promoter usage in cell populations and stochastic monoallelic expression in single cells by large arrays of tandem variable CBSs. Finally, gene expression levels are negatively correlated with CBS insulators located between enhancers and promoters on a genome-wide scale. Thus, single CBS insulators ensure proper enhancer insulation and promoter activation while tandem-arrayed CBS insulators determine balanced promoter choice. This finding has interesting implications on the role of topological insulators in 3D genome folding and developmental gene regulation.

overall_design: To investigate the impacts of insertion or deletion of CTCF sites on 3D chromatin conformation and gene expression, chromasome conformation capture and RNA-seq experiments were performed on DNA-fragment editting cell lines and transgenic mice.

first: Zhilian

last: Jia

first: Yonghu

last: Wu

first: Qiang


title: Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection [VII]

overall_design: To investigate the impacts of insertion or deletion of CTCF sites on 3D chromatin conformation and gene expression, chromasome conformation capture, ChIP-seq, and RNA-seq experiments were performed on DNA-fragment editting cell lines and transgenic mice.


title: Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection [VI]


title: Transcriptome analysis reveals candidate genes related to anthocyanin biosynthesis in different carrot genotypes and tissues

city: Frederiksberg C

first: Søren

middle: K.

last: Rasmussen

state: Region Hovedstaden

address: Thorvaldsensvej 40

department: Department of Plant and Environmentalt Sciences

country: Denmark

institute: University of Copenhagen

summary: Taproots of different carrot genotypes were used to identify the candidate genes related to anthocyanin synthesis with particular focus on R2R3MYB, bHLH transcription factors, and glutathione S-transferase gene (GST). The RNA-sequencing analysis (RNA-Seq) showed that DcMYB6 and DcMYB7 had genotypic dependent expressed and they are likely involved in the regulation of anthocyanin biosynthesis. They were specifically upregulated in solid black taproots, including both black phloem and xylem. DcbHLH3 (LOC108204485) was upregulated in all black samples compared with the orange ones. We also found that GST1 (LOC108205254) might be an important anthocyanin transporter, and its upregulated expression resulted in the increasing of vacuolar anthocyanin accumulation in black samples.

overall_design: 120-day-old carrot taproots of three cultivars (‘H13.360IND’, ‘Purple 68’, and ‘Purple Haze’) were used. For H31.360IND, the whole slice was used; for ‘Purple 68’ and ‘Purple Haze’ the carrot discs were dissected into the xylem and phloem tissue samples. Following this,  RNA-Seq libraries were constructed and labeled as follows: CT (whole slice of H13.360IND), E (xylem of ‘Purple 68’), F (phloem of ‘Purple 68’), G (xylem of ‘Purple Haze’) and H (phloem of ‘Purple Haze’). Two biological replicates were used for each sample using Illumina® (NEB, USA).

middle: K

first: Geng

last: Meng


title: Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection [III]

summary: CTCF is a key insulator-binding protein and mammalian genomes contain numerous CTCF-binding sites (CBSs), many of which are organized in tandem arrays. Here we provide direct evidence that CBSs, if located between enhancers and promoters in the clustered Pcdh and b-globin clusters, function as an enhancer-blocking insulator by forming distinct directional chromatin loops, regardless whether enhancers contain CBS or not. Moreover, computational simulation and experimental capture revealed balanced promoter usage in vivo in cell populations and stochastic monoallelic expression in single cells by large arrays of tandem variable CBSs. Finally, gene expression levels are negatively correlated with CBS insulators located between enhancers and promoters on a genome-wide scale. Thus, single CBS insulators ensure proper enhancer insulation and promoter activation while tandem-arrayed CBS insulators determine balanced promoter choice. This finding has interesting implications on the role of topological insulators in 3D genome folding and developmental gene regulation.

overall_design: QHR-4C profiles of P0 old wild type (WT) and 8 mouse line mice were seperately generated by deep sequencing using Illumina HiSeq X-ten


title: Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection [I]

overall_design:
Single-cell mRNA profiles of P0 cortex from wild type (WT) and b-e deletion mice were separately generated by deep sequencing using Illumina HiSeq X-ten.

b-e deletion range: chr18:38011471-38040871(mm9).

43 single-cell mRNA profiles of HEC-1-B wild type (WT) cells were separately generated by deep sequencing using Illumina HiSeq X-ten.


title: Sexual and asexual inheritance of epigenetic marks in Apple [array]

city: BEAUCOUZE

first: Adrien

last: PERRIN

address: 42 Rue Georges Morel

institute: INRA - IRHS

summary: In order to compare sexual and asexual multiplication in Malus domestica we performed mircoarray to study change in gene expression level in our sample.

overall_design: With this microarray we compare Tree versus Seed gene expression (sexual transmission) and Tree versus Graft gene expression (asexual transmission). We study two biological replicate per comparison

first: Perrin

last: Adrien

first: Celton

last: Jean-Marc

first: Bucher

last: Etienne


title: The translational landscape of ground state pluripotency

city: Nijmegen

first: Hendrik

last: Stunnenberg

address: Geert Grooteplein 30

country: Netherlands

institute: Radboud University


title: Sexual and asexual inheritance of epigenetic marks in Apple


title: RNA: The translational landscape of ground state pluripotency

summary: Translational control plays a central role in regulation of gene expression and can lead to significant divergence between mRNA- and protein-abundance. Here we used genome-wide approaches combined with time-course analysis to measure the mRNA-abundance, mRNA-translation rate and protein expression during the transition of naïve-to-primed mouse embryonic stem cells (ESCs). We find that the ground state ESCs cultured with GSK3-, MEK-inhibitors and LIF (2iL) display higher ribosome density on a selective set of mRNAs. This set of mRNAs undergo  strong translational buffering to maintain stable protein expression levels in 2iL-ESCs. Importantly, we show that the global alteration of cellular proteome during the transition of naïve to primed pluripotency is largely accompanied by transcriptional rewiring. Thus, we provide a comprehensive and detailed overview of the global changes in gene expression in different states of ESCs and dissect the relative contributions of RNA-transcription, translation and regulation of protein stability in controlling protein abundance.

overall_design: Analysis of genome wide mRNA translation by ribosome profiling and mRNA expression by RNA-seq. 9-conditions were used that include: 2iL, 2iLday1, 2iLday3, 2iLday7, SL, SLday1, SLday3, SLday7, EpiLSCs. Biological duplicates were used per condition; they are indicated as Rep1 and Rep2. In total 18 samples for RNA-seq and 18-samples for Ribosome profiling were generated.


title: Rbm24 functions as a critical translational regulator to pretect crystallin proteins accumulation for lens transparency. RNA-seq data of 33 hpf rbm24a-/- and wildtype zebrafish embryo

status: Public on Feb 29 2020

city: Jinan

first: Ming

last: Shao

state: Shandong

address: 27# Shan Da Nan Lu Road

department: School of Lifesciences

institute: Shandong University

summary: This experiment is aimed to compare the transcriptomes of rbm24a mutant and wildtype at 33 hpf. As Rbm24a is an RNA binding protein, this comparation is suitable to obtain information on differential gene expression and alternative splicing. We found that the expression of most of the crystallin genes and many other lens specific genes are down regulated in rbm24a mutant, without changes in splicing patterns.

overall_design: It contains two groups: wildtype and rbm24a-/-. Wildtype was used as control, and each group has three replicates

first: De-li

last: Shi


title: RFP: The translational landscape of ground state pluripotency


title: G47∆-mIL12 treatment leads to maturation of dendritic cells and T cell activation in vivo

status: Public on Feb 28 2020

city: Abilene

first: Dipongkor

last: Saha

state: Texas

address: 1718 Pine Street

institute: Texas Tech University Health Sciences Center

summary: G47∆-mIL12  teatment of orthotpic mammary tumors leads to increased mRNA levels of genes assocaited with DC maturation, DC-specific co-stimulatory signaling, CD8+ T cell activation and genes involved in antigen processing and presentations, compared to PBS treatment group.

overall_design: G47∆-mIL12  teatment


title: T cell-derived miR-214 mediates perivascular fibrosis in hypertension

city: Glasgow

first: Ryszard

last: Nosalski

address: 126 University Ave

department: 1Institute of Cardiovascular and Medical Sciences

institute: University of Glasgow

summary: Despite increasing understanding of the prognostic importance of vascular stiffening linked to perivascular fibrosis in hypertension, the molecular and cellular regulation of this process is poorly understood. We aimed to study the functional role of microRNA-214 (miR-214) in the induction of perivascular fibrosis and endothelial dysfunction driving vascular stiffening. Out of 381 miRs screened in the perivascular tissues (PVAT) in response to angiotensin II (Ang II)-mediated hypertension, miR-214 showed the highest induction (8-fold, p<0.01). MiR-214 induction was pronounced in perivascular and circulating T cells, but not in PVAT adipocytes. Global deletion of miR-214-/- prevented Ang II-induced periaortic fibrosis Col1a1, Col3a1, Col5a1 and Tgfb1 expression, hydroxyproline accumulation and vascular stiffening, without difference in blood pressure. Mechanistic studies revealed that miR-214-/- mice were protected against endothelial dysfunction, oxidative stress and increased Nox2, all of which were induced by Ang II in WT mice. Ang II-induced recruitment of T cells into PVAT was abolished in miR-214-/- mice. Adoptive transfer of miR-214-/- T cells into RAG1-/- mice resulted in reduced perivascular fibrosis compared to the effect of WT T cells. Ang II induced hypertension caused significant change in the expression of 1380 T cell genes in WT, but only 51 in miR-214-/-. T cell activation, proliferation and chemotaxis pathways were differentially affected. miR-214-/- prevented Ang II-induction of pro-fibrotic T cell cytokines (IL-17, TNF, IL-9 and IFN) and chemokine receptors (CCR1, CCR2, CCR4, CCR5, CCR6 and CXCR3). This manifested in reduced in vitro and in vivo T cell chemotaxis resulting in attenuation of profibrotic perivascular inflammation. Translationally, we show that miR-214 is increased in plasma of hypertensive patients and is directly correlated to pulse wave velocity as a measure of vascular stiffness.

overall_design: RNA-Seq analysis of isolated splenic T cells from sham and angiotensin II infused WT and miR-214 KO mice  (n=3 in each group)

first: Mateusz

last: Siedlinski

first: Laura

last: Denby

first: Eilidh

last: McGinnigle

first: Michal

last: Nowak

first: Aurelie

middle: N

last: Cat

last: Medina-Ruiz

first: Marco

last: Cantini

first: Dominik

last: Skiba

first: Grzegorz

last: Wilk

last: Osmenda

first: Julie

last: Rodor

first: Manuel

last: Salmeron-Sanchez

first: Gerard

last: Graham

first: Pasquale

last: Maffia

first: Delyth

first: Andrew

last: Baker

first: Tomasz

middle: J

last: Guzik


title: Genetic interaction mapping and exon-resolution functional genomics with a hybrid Cas9-Cas12a platform

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

summary: Systematic mapping of genetic interactions and interrogation of the functions of sizeable genomic segments in mammalian cells represent important goals of biomedical research. To advance these goals, we present a CRISPR-based screening system for combinatorial genetic manipulation that employs co-expression of Cas9 and Cas12a nucleases and machine learning-optimized libraries of hybrid Cas9-Cas12a guide RNAs. This system, named CHyMErA (Cas Hybrid for Multiplexed Editing and Screening Applications), outperforms genetic screens using Cas9 or Cas12a editing alone. Application of CHyMErA to the ablation of mammalian paralog gene pairs reveals extensive genetic interactions and uncovers phenotypes normally masked by functional redundancy. Application of CHyMErA in a chemo-genetic interaction screen identifies genes that impact cell growth in response to mTOR pathway inhibition. Moreover, by systematically targeting thousands of alternative splicing events, CHyMErA identifies exons underlying human cell line fitness. CHyMErA thus represents an effective screening approach for genetic interaction mapping and the functional analysis of sizeable genomic regions, such as alternative exons.

overall_design: RNA-Seq of HAP1N2A cells upon RNAi-mediated knockdown RBM26, RBM27, bothf11, or control non-targeting knockdown, in two replicates.

first: Thomas

last: Gonatopoulos-Pournatzis

first: Michael

last: Aregger

first: Kevin

last: Brown

first: Shaghayegh

last: Farhangmehr

first: Henry

last: Ward

last: Ha

first: Alexander

last: Weiss

first: Maximilian

last: Billmann

first: Tanja

last: Durbic

first: Chad

middle: L

last: Myers

first: Benjamin

last: Blencowe

first: Jason

last: Moffat


title: Rbm24 functions as a critical translational regulator to pretect crystallin proteins accumulation for lens transparency. RNA-seq data of 33 hpf rbm24a-/- and wildtype embryo, head explant

first: Ming

last: Shao

overall_design: It contains two groups: wildtype and rbm24a-/-. Wildtype was used as control

first: De-li

last: Shi


title: Regulation of enhancer transcription by Spt5 directly couples enhancer activation with enhancer function

status: Public on Feb 27 2020

city: Vienna

first: Tobias

last: Neumann

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

summary: Transcription is a ubiquitous feature of active enhancers, yet the regulatory role of enhancer transcription or transcripts remains debated. Here, we depleted the RNA polymerase II pausing and elongation factor Spt5 in activated mouse B cells and found that approximately 50% of enhancer-gene pairs showed correlated changes in transcription, consistent with a potential functional requirement for enhancer transcription. In particular, Spt5 depletion led to loss of super-enhancer-promoter physical interaction and gene expression at the immunoglobulin heavy chain locus (Igh), abrogating antibody class switch recombination. This defect correlated strictly with loss of enhancer transcription and did not affect enhancer activation, as inferred from histone H3K27 acetylation, chromatin accessibility and occupancy of Mediator and cohesin. Strikingly, CRISPRa-mediated rescue of enhancer transcription in Spt5-depleted cells restored Igh gene expression. Thus, Spt5-mediated enhancer transcription serves as a direct and causal link between Igh super-enhancer activation and its physical interaction with target promoters.

overall_design: For all experiments, we ablated the Supt5h gene in vitro by adding 4-hydroxy tamoxifen (4-HT) to primary Supt5hFl/- Rosa26ERT2-cre/+ mouse primary mature B cells for 32 hours. As controls, we used Rosa26ERT2-cre/+ primary B cells treated with 4-HT for 32 hours (referred to as wild-type, WT).

first: Johanna

last: Fitz

first: Monika

last: Steininger

first: Eva-Maria

last: Wiedemann

first: Adriana

last: Cantoran-Garcia

last: Athanasiadis

first: Ursula

last: Schoeberl

first: Rushad

last: Pavri


title: Chromatin architecture reorganization in somatic cell nuclear transfer embryos

first: Qianshu

last: Zhu

state: Shanghai

address: Siping Road

department: School of Life Science and Technology

institute: Tongji University

summary: The oocyte cytoplasm can reprogram somatic cell nucleus into a totipotent state but with low efficiency. The spatiotemporal chromatin organization of somatic cell nuclear transfer (SCNT) embryos remains elusive. Here, we examined higher-order chromatin structures of mouse SCNT embryos using an optimized low-input Hi-C approach. We found that the donor cell chromatin transformed to metaphase state rapidly after injection along with the dissolution of typical 3D chromatin structures. Intriguingly, the donor cell genome underwent a transition from mitotic metaphase-like state to meiosis metaphase II-like state within one hour after activation. Subsequently, weak chromatin compartments and topologically associating domains (TADs) emerged at 6 hours after activation. Then TADs were gradually removed until the 2-cell stage and then progressively reestablished. We found that relative few distal (> 2 Mb) interactions were present in 2-cell stage SCNT embryos. Also, obvious differences in compartment and TAD organization between fertilization-derived and SCNT embryos were observed in early stages (2-8 cell stages). Many interactions between super-enhancers and promoters were not successfully established in SCNT embryos, and these interactions were further shown important for zygotic genome activation (ZGA). Moreover, we demonstrate that the aberrant chromatin architecture reorganization in SCNT embryos may be due to the persistent H3K9me3 and can be partially rescued by the Kdm4d overexpression. This study therefore provides novel insight into chromatin architecture reorganization during SCNT embryo development.

overall_design: 1. Examination of chromatin architecture organization in 13 SCNT embryo development time point including cumulus cell (CC), 0.5-hpi, 1-hpi, 1-hpa, 6-hpa, 12-hpa, early-2-cell, late-2-cell, 4-cell, 8-cell, morula, inner cell mass (ICM) and trophectodern (TE). 2. Examination of chromatin architecture organization in early-2-cell embryos of overexpression Kdm4d and TSA treatment. 3. Eamination of chromatin architecture organization in mouse R1 ESCs. 4. Eamination of histone 3 lysine 9 tri-methylation in CC. 5. RNA-seq data for ICM and TE.

first: Mo

last: Chen

first: Chong

last: Li


title: Shifts in pigeon limb identity reveal conserved genetic networks

city: SLC

first: Elena

last: Boer

state: UT

department: School of Biological Sciences

institute: University of Utah

summary: In feather-footed pigeons, mutant alleles of PITX1 and TBX5 drive the partial redeployment of an evolutionarily conserved forelimb genetic program in the hindlimb.

sample_organism:
Columba livia
Gallus gallus

platform_organism:
Columba livia
Gallus gallus

overall_design: mRNA profiles were generated in quadruplicate by deep sequencing of forelimb and hindlimb buds from scale-footed pigeons, feather-footed pigeons, and scale-footed chicken embryos at Hamburger-Hamilton (HH) stages HH21, HH25, and HH29.

middle: F

first: Hannah

last: Van Hollebeke

first: Michael

last: Shapiro


title: Gene expression analysis of chicken dendritic cells (DCs) in response to H9N2 avian influenza virus infection

status: Public on Feb 26 2020

city: nanjing

first: liu

last: qingtao

state: jiangsu

address: zhongling road NO. 50

department: Institute of veterinary medicine

institute: jiangsu academy of agricultural sciences

summary: We analyze the differentially expressed genes (DEGs) at the transcriptome level in chicken DCs infected with H9N2 influenza virus compared to mock infection by high-throughput RNA-sequencing technology, and found that H9N2 influenza virus infection induced a strong innate immune response in chicken DCs, but impaired the antigen-processing and –presenting capacity of this cell,

overall_design: Gene expression profiles of chicken DCs infected without or with H9N2 influenza virus were generated by deep sequencing, in triplicate, using Illumina HiSeq X

first: Qingtao

last: Liu

first: Yin

first: Jing

last: Yang


title: TNF-signaling modulates neutrophil-mediated immunity at the feto-maternal interface  during LPS-induced intrauterine inflammation

city: Los Angeles

first: Suhas

last: Kallapur

address: 10833 Le Conte Avenue

institute: UCLA

summary: We demonstrate that anti-TNF antibody (Adalimumab) inhibited ~80% of highly LPS-induced genes that sub-serve inflammatory signaling and innate immunity in chorio-decidua neutrophils.

overall_design: RNAseq of purified blood maternal neutrophils vs. FACS-sorted chorio-decidua neutrophils in a Rhesus model of intrauterine infection/inflammation

first: Pietro

last: Presicce

first: Monica

last: Cappelletti

first: Paranthaman

last: Senthamaraikannan

first: Faiyang

last: Ma

first: Marco

last: Morselli

first: Courtney

last: Jackson

first: Shibabrata

last: Mukherjee

first: Lisa

last: Miller

first: Matteo

last: Pellegrini

first: Alan

last: Jobe

first: Claire

last: Chougnet


title: Transcriptional profiling of stem cell-derived polarized hepatocytes

status: Public on Feb 25 2020

city: Heidelberg

first: Viet Loan

last: Dao Thi

address: Im Neuenheimer Feld 344

department: University Hospital Heidelberg

institute: Center for Integrative Infectious Disease Research (CIID)

summary: Human stem cell-derived hepatocyte-like cells (HLCs) offer an attractive platform to study liver disease and to test drugs. However, despite their advantages over other hepatocyte culture systems, HLCs lack several in vivo characteristics including cell polarity, which is critical for proper hepatocyte biology. We report a stem cell-based differentiation protocol that uses transwell filters to generate columnar polarized HLCs with clearly defined basolateral and apical membranes separated by tight junctions. Unlike conventional HLCs, polarized HLCs secrete cargo directionally, similar to hepatocytes in vivo. This novel system provides a powerful tool to study hepatocyte biology, disease mechanisms, genetic variation, and drug metabolism in a more physiologically relevant setting.

overall_design: Expression profiling by RNA-seq of polarized versus non-polarized stem cell-derived hepatocyte-like cells (HLCs).

first: Luis

last: Vale-Silva

first: Viet


title: Cerebrospinal fluid microRNA profile in leptomeningeal metastasis patients [pre- vs post-treatment]

city: Changchun

first: Guozi

state: Jilin

address: No.71 Xinmin Street

department: Radiation-Oncology

institute: The First Hospital of Jilin University

summary: This study aimed to identify specific CSF miRNAs for diagnosing and monitoring leptomeningeal metastasis with lung adenocarcinoma. In discovery phase, we performed miRNA microarray analysis in matched CSF samples from leptomeningeal metastasis patients at diagnosis and after initial leptomeningeal metastasis-directed therapy.

overall_design: Matched CSF samples from 6 leptomeningeal metastasis patients at diagnosis and after initial therapy were collected for miRNA microarray analysis.

first: Zhenyu

last: Pan


title: Reduced extracellular matrix survival and altered metabolic activity in iPSC-derived RPE cells from AMD patients

city: New Haven

first: Hui

middle: Cong

last: Cai

address: 300 George St, Suite 8100

institute: Yale University

summary:
Comparing iPS derived RPE cells from human AMD and non-AMD donors
It has been a challenge to model retinal disorders such as geographic atrophy (GA) in in vivo animals, primarily because several factors, including genetics and aging itself, contribute to disease phenotype of age-related macular degeneration (AMD). We generated retinal pigment epithelial (RPE) cells from patients with advanced AMD and assessed their ability to model disease. We observed alterations in the transcriptome of AMD patients compared to non-diseased controls. RPE cells from AMD patients displayed decreases in mitochondrial function (basal respiration and adenosine triphosphate (ATP) production) compared with non-diseased controls. Using a system of mimicing AMD diseased ECM, we showed RPE cells derived from patients with AMD have a reduced ability to survive and proliferate on nitrite-modified extracellular matrix (ECM) when compared to non-diseased controls. These results demonstrate changes in the cell biology and phenotype of RPE cells from patients with advanced AMD, providing a platform for disease modeling to understand AMD pathophysiology.

overall_design: RPE cells were differentiated from iPScs of patients with four (4) advanced AMD and age matched three (3) non-AMD donors.

first: Jie

last: Gong

first: Lucian

last: Del Priore

first: Mark

last: Fields


title: Cerebrospinal fluid microRNA profile in leptomeningeal metastasis patients [LM vs non-LM]

last: Yang

summary: This study aimed to identify specific CSF miRNAs for diagnosing and monitoring leptomeningeal metastasis with lung adenocarcinoma. In discovery phase, we performed miRNA microarray analysis in CSF samples from leptomeningeal metastasis patients and non-leptomeningeal metastasis controls.

overall_design: Ten CSF samples from leptomeningeal metastasis patients with lung adenocarcinoma and ten CSF samples from non-leptomeningeal metastasis controls (five CSF samples from brain metastasis patients with lung adenocarcinoma and five non-cancer patients) were collected for miRNA microarray analysis


title: RNA-Seq analysis to compare immature myeloid cells from PARP1CKO and PARP2CKO mice with their corresponding littermate controls

status: Public on Feb 24 2020

city: Dallas

first: Yihong

last: Wan

state: TX

address: 6001 Forest Park Rd.

department: Pharmacology

institute: UT Southwestern Medical Center

summary: We compared expression profiles of immature myeloid cells from PARP1CKO and PARP2CKO mice with their corresponding littermate controls by Next-generation sequencing (NGS). The results showed that genes regulated by PARP1 and PARP2 were largely distinct with only a small subset overlapping. PARP1 regulated genes are related to secretion, whereas PARP2 regulated genes are related to response to external stimulus and leukocyte migration. PARP2 deficiency down-regulated the expression of immune cytokines such as CCL3, CCL4, CCL6 and CCL9. In contrast, these genes were unaffected by PARP1 deficiency. This study has uncovered important functional and mechanistic distinctions between PARP1 and PARP2. The findings has also revealed specific roles of PARP2 in immature myeloid cells in regulating chemokine expression and immune response.

overall_design: Examiniation of mRNA profiles of immature myeloid cells from mice with PARP1 WT or lysozyme-Cre mediated PARP1 conditional knockout, or mice with PARP2 WT or lysozyme-Cre mediated PARP2 conditional knockout, by deep sequencing, in biological duplicate, using Illumina HiSeq 2500

first: Hao

last: Zuo


title: Single Cell and Bulk RNA Sequencing Analysis on the Effects of Cytoskeletal Modulation on Stem Cell Derived Pancreatic Progenitors

city: St. Louis

first: Jeffrey

middle: Robert

last: Millman

address: 660 South Euclid

institute: Washington University in St. Louis

summary: We revealed that the cytoskeletal state of pancreatic progenitors can influence differentiation into multiple endodermal cell lineages. Specifically, pancreatic progenitors treated with cytoskeletal-modulating compounds show gene signatures not only of endocrine cells but also of exocrine, liver, stomach, intestine, and esophagus. We used bulk and single cell RNA sequencing to study these effects of cytoskeletal compounds on pancreatic progenitor cell fate.

overall_design:
Single cell RNA sequencing of pancreatic progenitor cells left untreated or treated with either Latrunculin A or Nocodazle during all of stage 4 of differentiation. Bulk RNA sequencing of stage 6 SC-beta cells at the end of differentiation that were treated with Latrunculin A during either all of stage 4 or on the first day of stage 5 only.

"Biott" refers to cells that have been grown in a bioreactor as described in Velazco-Cruz et al., Stem cell reports 12.2 (2019): 351-365.

"Plated_control" refers to cells that have been grown in a 6 well tissue culture plastic plate. These cells did not receive any cytoskeletal compound treatments and are therefore considered as a control. The other conditions were grown in the plated format as well.

first: Punn

last: Augsornworawat

first: Nathaniel

last: Hogrebe


title: Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection [V]

city: Shanghai

first: Xiao

last: Ge

address: No. 800 Dongchuan Road

institute: Shanghai JiaoTong University

summary: CTCF is a key insulator-binding protein and mammalian genomes contain numerous CTCF-binding sites (CBSs), many of which are organized in tandem arrays. Here we provide direct evidence that CBSs, if located between enhancers and promoters in the clustered Pcdh and b-globin clusters, function as an enhancer-blocking insulator by forming distinct directional chromatin loops, regardless whether enhancers contain CBS or not. Moreover, computational simulation and experimental capture revealed balanced promoter usage in vivo in cell populations and stochastic monoallelic expression in single cells by large arrays of tandem variable CBSs. Finally, gene expression levels are negatively correlated with CBS insulators located between enhancers and promoters on a genome-wide scale. Thus, single CBS insulators ensure proper enhancer insulation and promoter activation while tandem-arrayed CBS insulators determine balanced promoter choice. This finding has interesting implications on the role of topological insulators in 3D genome folding and developmental gene regulation.

overall_design: ChIP profiles of P0 mouse cortex and HEC-1-B cell were seperately generated by deep sequencing using Illumina HiSeq X-ten

first: Zhilian

last: Jia

first: Yonghu

last: Wu

first: Qiang


title: TNIK signaling imprints CD8+ T memory formation early after priming

city: Bern

first: Ramin

last: Radpour

address: Murtenstrasse 35

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

summary:
Purpose: The goal of this study is to compare NGS-derived transcriptome profiling (RNA-seq) of naïve/ effector (D6)/ memory (D80) p14 T cell [wild-type (WT) and Tnik-/- (KO)] isolated form spleen of naïve or adoptively transferred and LCMV-WE immunized mice.
Methods: Transcriptomic profiles of splenic naïve wild-type (WT) and Tnik-/- (KO) p14 T cells (8-week-old mice) or splenic effector (D6) and memory (D80) p14 T cells (post adoptive transfer and LCMV-WE immunization) were assessed in duplicates or triplicate by deep sequencing, using Illumina HiSeq 2500. qRT–PCR validation was performed using TaqMan and SYBR Green assays.
Results: We mapped about 30 million sequence reads per sample to the mouse genome (GRCm38 - mm10) and identified expressed transcripts in splenic WT and Tnik−/− p14 T cells. RNA-seq data confirmed stable expression of known housekeeping genes. Differentially expressed genes between the WT and Tnik−/− p14 T cells from naïve, D6 or D80 were identified with a fold change ≥1.5 and p-value <0.05. Hierarchical clustering and gene ontology analysis of differentially expressed genes uncovered genes that may contribute to regulation of stemness, transcriptional regulation, cell cycle regulation, survival and function of T cells.
Conclusions: Our study represents the first detailed transcriptome analysis of WT versus Tnik-/- p14 T cells in the context of acute viral infection, with biologic replicates, generated by RNA-seq technology. Our results show that TNIK regulates T cell fate. Evaluation of mRNA content in effector (D6) and memory (D80) p14 T cells revealed that TNIK-deficiency during T cell activation enhances proliferation, terminal differentiation and glycolysis of effector T cells, while compromising steady-state metabolic activity of memory T cells. We conclude that TNIK imprints memory formation early after CD8+ T cell priming.

overall_design: mRNA of naïve and adoptively transferred D6 or D80 wild-type (WT) and knock-out (KO) p14 Tcells isolated from spleen of naïve and LCMV-WE immunized mice, using Illumina HiSeq 2500.

first: Carla

last: Jaeger-Ruckstuhl

first: Carsten

last: Riether

first: Adrian

last: Ochsenbein


title: Dissecting the transcriptional regulation during the transition from proliferation to terminal differentiation during fly spermatogenesis

city: Stanford

first: Margaret

last: Fuller

state: California

address: 279 Campus Drive, Beckman Center B301

department: Developmental Biology

institute: Stanford University

summary: To investigate how the cell-type-specific gene expression program for spermatocyte differentiation turns on in male flies, we used RNA-seq to map transcript levels, CAGE to map transcription start sites (TSS), and ATAC-seq to map chromatin accessibility as proliferating spermatogonia transition to differentiating spermatocytes. Combining these data, we showed that the promoters that turn on when germ cells become spermatocytes lack most of the canonical core promoter motifs. Instead these promoters require tMAC function to become open and accessible, and are enriched for the tMAC ChIP motif and putative Achi/Vis binding motif. Within the local open region that tMAC creates, a good match to the Inr at +1 and ACA and CNAAATT motifs at specific positions downstream correlates with efficiency of individual TSS usage. Our results reveal a robust cell-type-specific and gene-selective developmental transcription program orchestrated by promoter-proximal elements and protein complexes that interact with them.

overall_design: Each sequencing assay included spermagonia-enriched and spermatocyte-enriched samples, with 2 or 3 replicates for each condition

first: Dan

last: Lu

first: Ho-Su

last: Sin

middle: T


title: Imipridone anticancer compounds ectopically activate the ClpP protease and represent a new scaffold for antibiotic development

status: Public on Feb 23 2020

first: Micheal

last: Tyers

address: 555 University Avenue

institute: The Hospital for Sick Children

summary: Systematic genetic interaction profiles can reveal the mechanism-of-action of bioactive compounds. The imipridone ONC201, which is currently in cancer clinical trials, has been ascribed a variety of different targets. To investigate the genetic dependencies of imipridone action, we screened a genome-wide CRISPR knockout library in the presence of either ONC201 or its more potent analog ONC212. Loss of the mitochondrial matrix protease CLPP or the mitochondrial intermediate peptidase MIPEP conferred strong resistance to both compounds. Biochemical and surrogate genetic assays showed that impridones directly activate CLPP and that MIPEP is necessary for proteolytic maturation of CLPP into a catalytically competent form. Quantitative proteomic analysis of cells treated with ONC212 revealed degradation of many mitochondrial as well as non-mitochondrial proteins. Prompted by the conservation of ClpP from bacteria to humans, we found that the imipridones also activate ClpP from Escherichia coli, B. subtilis and Staphylococcus aureus in biochemical and genetic assays. ONC212 and acyldepsipeptide (ADEP)-4, a known activator of bacterial ClpP, caused similar proteome-wide degradation profiles in S. aureus. ONC212 suppressed the proliferation of a number of Gram-positive (S. aureus, B. subtilis, Enterococcus faecium) and Gram-negative species (E. coli, Neisseria gonorrhoeae). Moreover, ONC212 enhanced the ability of rifampin to eradicate antibiotic-tolerant S. aureus persister cells. These results reveal the genetic dependencies of imipridone action in human cells and identify the imipridone scaffold as a new entry point for antibiotic development.

overall_design: Nalm-6 cells infected with the EKO sgRNA library (Bertomeu et al. 2017, PMID:29038160), after 7 days of Cas9 induction with doxycycline, were exposed to either 150nM ONC212, 10uM ONC201/TIC10 or media only for 8 days. sgRNA abundance was then assessed by high-throughput sequencing. Cells exposed to media only for two days served as controls.

first: Samuel

last: Jacques

first: Almer

middle: M

last: van der Sloot

first: Caroline

last: Huard

first: Jasmin

last: Coulombe-Huntington

first: Sarah

last: Tsao

first: Sylvain

last: Tollis

first: Thierry

last: Bertomeu

first: Elizabeth

last: Culp

first: Daniel

last: Pallant

first: Michael

last: Cook

first: Eric

last: Bonneil

first: Pierre

last: Thibault

first: Gerard

last: Wright


title: Micro-RNA Expression Patterns Predict Metastatic Spread in Solid Pseudopapillary Neoplasms of the Pancreas

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

institute: Tel Aviv University

summary: Solid pseudopapillary neoplasm (SPN) of pancreas is a rare pancreatic neoplasm with a low metastatic potential. Up to 10% of patients with localized disease at presentation will develop systemic metastases, usually in the peritoneum or the liver. Due to the rarity of SPNs and the overall excellent prognosis, reliable prognostic factors to predict malignant biological behavior remain undetermined. Therefore, we aimed to define clinical, histological, and microRNA patterns that are associated with metastatic disease. We conducted a retrospective single center study on all patients operated for SPN of pancreas between 1995 and 2018. Clinical and pathological data were collected, and expression patterns of 2578 human microRNAs were analyzed using microRNA array (Affimetrix 4.1) in normal pancreases (NPs), localized tumors (LTs), and metastatic tumors (MTs). The diagnosis of SPN was confirmed in 35 patients who included 28 females and 3 males, with a mean age of 33.8 ± 13.9 years. The only clinical factor associated with metastases was tumor size (mean tumor size 5.20 ± 3.78 in LT versus 8.13± 1.03 in MT, p < 0.012). Microscopic features of malignancy were not associated with metastases, nor were immunohistochemical stains, including the proliferative index KI67. Higher expressions of miR-184, miR-10a, and miR-887, and lower expressions of miR-375, miR-217, and miR-200c were observed in metastatic tissues on microarray, and validated by real-time polymerase chain reaction. Hierarchal clustering demonstrated that the microRNA expression pattern of MTs was significantly different from that of LTs. The only clinical factor associated with metastases of SPN of pancreas was tumor size. Histological features and immunohistological staining were not predictive of metastases. A panel of six microRNAs was differentially expressed in MTs, and these findings could potentially be used to predict tumor behavior. Validation of these results is needed in larger series.

overall_design: Characteristics of metastatic and localized solid pseudopapillary neoplasms of the pancreas

first: Shmuel

last: Cohen

first: Michail

last: Papoulas

first: Nadine

last: Graubardt

first: Esther

last: Ovdat

first: Shelly

last: Loewenstein

first: Juliane

last: Kania-Almog

first: Eli

last: Brazowski

first: Emanuela

last: Cagnano

first: Ido

last: Nachmany

first: Guy

last: Lahat

first: Joseph

last: Klausner

first: Nir

last: Lubezky