title: Fission yeast condensin contributes to interphase chromatin organization and prevents transcription-coupled DNA damage

city: Tokyo

first: Yasutaka

last: Kakui

address: 1-21-1 Nishiwaseda, Shinjuku-ku

institute: Waseda Institute for Advanced Study

summary:
Background: Structural maintenance of chromosomes (SMC) complexes are central organizers of chromatin architecture throughout the cell cycle. The SMC family member condensin is best known for establishing long-range chromatin interactions in mitosis. These compact chromatin and create mechanically stable chromosomes. How condensin contributes to chromatin organization in interphase is less well understood.
Results: Here, we use efficient conditional depletion of fission yeast condensin to determine its contribution to interphase chromatin organization. We deplete condensin in G2 arrested cells to preempt confounding effects from cell cycle progression without condensin. Genome-wide chromatin interaction mapping, using Hi-C, reveals condensin-mediated chromatin interactions in interphase that are qualitatively similar to those observed in mitosis, but quantitatively far less prevalent. Despite its low abundance, chromatin mobility tracking shows that condensin markedly confines interphase chromatin movements. Without condensin, chromatin behaves as an unconstrained Rouse polymer with excluded volume, while condensin constrains its mobility. Unexpectedly, we find that condensin is required during interphase to prevent ongoing transcription from eliciting a DNA damage response.
Conclusions: In addition to establishing mitotic chromosome architecture, condensin-mediated long-range chromatin interactions contribute to shaping chromatin organization in interphase. The resulting structure confines chromatin mobility and protects the genome from transcription-induced DNA damage. This adds to the important roles of condensin in maintaining chromosome stability.

overall_design: 2 biological replicates of Hi-C data of fission yeast G2-arrested cells in control condition or in condensin shut off condition.


title: Expression analysis of adult zebrafish enteric nervous system

status: Public on Sep 14 2020

city: London

first: Vassilis

last: Pachnis

state: London

address: 1 Midland Road

department: Development and Homeostasis of the Nervous System Laboratory

country: United Kingdom

institute: The Francis Crick Institute

type: Expression profiling by high throughput sequencing

summary: The enteric nervous system (ENS) encompasses the intrinsic neuroglia networks of the gastrointestinal (GI) tract that are essential for digestive function and gut homeostasis. To investigate the ENS of zebrafish, we carried out bulk RNA sequencing on nuclei purified by FACS (fluorescent-activated cell sorting) representing both the Cherry+ (ENS) and Cherry- (non-ENS) muscularis externa cell populations of Tg(sox10:Cre;Cherry) zebrafish gut.

overall_design: The smooth muscle layers and associated myenteric plexus were separated from the epithelial layers of the adult gut and subjected to Dounce homogenization. After filtering the homogenate to remove large debris, samples were centrifuged at 1000 x G for 10 min at 4°C to obtain a pellet containing muscularis externa nuclei. For flow cytometric analysis, doublet discrimination gating was applied to exclude aggregated nuclei, and intact nuclei were determined by subsequent gating on the area and height of DAPI intensity. Both Cherry+ (ENS) and Cherry- (non-ENS) nuclear populations were collected directly into 1.5mL tubes containing Trizol LS reagent. For each replicate, sorted cells from an average of 30 adult guts were pooled, containing approximately 30,000 Cherry+ or Cherry- nuclear populations.

first: Tiffany

last: Heanue

first: Stefan

last: Boeing


title: Aggressive PDACs show hypomethylation of repetitive elements and the execution of an intrinsic IFN program linked to a ductal cell-of-origin. [Activation of stellate cells by tumor conditioned medium]

status: Public on Oct 15 2020

city: Heidelberg

first: Elisa

last: Espinet

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center

summary: Pancreatic ductal adenocarcinoma (PDAC) is characterized by extensive desmoplasia, which challenges the molecular analyses of bulk tumor samples. Here we FACS-purified epithelial cells from human PDAC and normal pancreas and derived their genome-wide transcriptome and DNA methylome landscapes. Clustering based on DNA methylation revealed two distinct PDAC groups displaying different methylation patterns at regions encoding repeat elements. Methylationlow tumors are characterized by higher expression of endogenous retroviral (ERV) transcripts and dsRNA sensors which leads to a cell intrinsic activation of an interferon signature (IFNsign). This results in a pro-tumorigenic microenvironment and poor patient outcome. Methylationlow/IFNsignhigh and Methylationhigh/IFNsignlow PDAC cells preserve lineage traits, respective of normal ductal or acinar pancreatic cells. Moreover, ductal-derived KrasG12D/Trp53-/- mouse PDACs show higher expression of IFNsign compared to acinar-derived counterparts. Collectively, our data point to two different origins and etiologies of human PDACs, with the aggressive Methylationlow/IFNsignhigh subtype potentially targetable by agents blocking intrinsic IFN-signaling.

overall_design: Normal human pancreatic stellate cells were treated with conditioned medium from different primary PDAC cells for 12 hours. Cells were lysed and RNA was extracted.

first: Andreas

last: Trumpp


title: Molecular mechanisms of transcriptional regulation by the nuclear zinc-finger protein ZFAT in HEK293 cells

city: Setagaya

first: Kazuhiko

last: Nakabayashi

state: Tokyo

department: Department of Maternal-Fetal Biology

country: Japan

institute: National Research Institute for Child Health and Development

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ZFAT is a nuclear protein that harbors putative DNA-binding domains. Studies in mice have shown that ZFAT plays a critical role in survival and differentiation in T cells. However, molecular mechanisms whereby ZFAT regulates gene expression programs in human cells remain poorly unknown. We here identify the direct target genes of ZFAT in HEK293 human embryonic kidney cells  through combination of chromatin immunoprecipitation with sequencing and transcriptional profiling.

overall_design: ChIPseq data were obtained for a zinc-finger transcription factor ZFAT to elucidate the functions of ZFAT in HEK293 cells.

first: Shuhei

last: Ishikura

first: Toshiyuki

last: Tsunoda

first: Senji

last: Shirasawa


title: Transcriptome analysis of HT1080 cells expressing HA-hZFAT-EGFP and EGFP

summary: We report the effects of overexpression of ZFAT on mRNA profiles in HT1080 cells.

overall_design: Examination of mRNA profiles in HT1080 cells expressing HA-hZFAT-EGFP and EGFP.


title: mTORC1 and B cell survival signal regulate formation of memory precursors in the germinal center

status: Public on Sep 13 2020

city: Suita-shi

first: Takeshi

last: Inoue

state: Osaka

address: 3-1 Yamadaoka

institute: Osaka University

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

overall_design: Refer to individual Series


title: mTORC1 and B cell survival signal regulate formation of memory precursors in the germinal center [2]

summary: A still unanswered question is what drives the small fraction of activated germinal center (GC) B cells that survive to become long-lived quiescent memory B cells. We found here that a small population of light zone GC cells (CD38intBcl6hi/intEfnb1+) with lower mTORC1 activity favored the memory B cell fate. Constitutively high mTORC1 activity led to defects in formation of the CD38intBcl6hi/intEfnb1+ cells; conversely, decreasing mTORC1 activity resulted in relative enrichment of this memory-prone GC population over the recycling-prone one. Furthermore, the CD38intBcl6hi/intEfnb1+ cells had higher levels of Bcl2 and surface BCR, which in turn, contributed to their survival. Given the positive correlation between the strength of T cell help and mTORC1 activity, our data suggest a model in which weak help from T cells together with provision of an increased survival signal are key for GC B cells to assume a memory B cell fate.

overall_design: mRNA profiles of GC and memory precursor B cells were generated by deep sequencing in duplicate or triplicate, using Illumina HiSeq 1500.

first: Chie

last: Kawai

first: Osamu

last: Ohara

first: Tomohiro

last: Kurosaki


title: mTORC1 and B cell survival signal regulate formation of memory precursors in the germinal center [1]

overall_design: mRNA profiles of Blimp1 single deficient, and Bach2/Blimp1 double deficient DZ, LZ GC B cells were generated by deep sequencing in duplicate, using Illumina HiSeq 1500.


title: Abscission couples cell division to embryonic stem cell fate

city: Cambridge

first: Celine

last: Labouesse

address: Puddicombe Way

department: Cambridge Stem Cell Institute

institute: University of Cambridge

summary: This study was designed to investigate how the cell cycle phase impacts the kinetics of exit from pluripotency of mouse embryonic stem cells (mESC). mESC maintained in naïve medium conditions (2i) then sorted based on cell cycle phase before replating in self-renewing or differentiating media for 6hours, followed by single-cell RNA sequencing. Clustering of cells based on their expression of naive pluripotency genes indicate that cells that exit early in the cell cycle downregulate pluripotency genes faster than the bulk population. This study provides evidence that cell cycle phase is important in determining the timing of exit from pluripotency.

overall_design: mESC underwent sorting based on forward and side scatter to specifically extract small cells (exit of mitosis and G1). An ungated population was used as control. Cells were replated in 2i (naïve medium) or N2B27 (differentiating medium) for 6hr, followed by single-cell sorting into 96 well plates for single-cell RNAseq. 1 plate (96 cells) of 2i and of N2B27 were sequenced with, in each plate, 24 small cells and 24 of an ungated population.

first: Agathe

last: Chaigne

first: Céline

first: Kevin

middle: J

last: Chalut

first: Ewa

middle: K

last: Paluch


title: Expression data from SAN tissue of WT and HCN4FEA mice

status: Public on Sep 11 2020

city: Hannover

first: Christian

last: Wahl-Schott

address: Carl-Neuberg-Str. 1

department: Institute for Neurophysiology

institute: Hannover Medical School

summary:
HCN4 channels are the major HCN channel isoform expressed in the sinoatrial node (SAN) and play a key role in cardiac pacemaking. We have characterized the gene expression profile in the SAN of adult mice expressing cAMP-insensitive HCN4 channels (HCN4FEA mice) in comparison to WT mice.
In this dataset, we include the expression data obtained from dissected mouse SAN tissue of WT and HCN4FEA mice. These data are used to show that there are no relevant compensatory up- oder down-regulated genes in the SAN of HCN4FEA mice.

overall_design: 6 total samples were analyzed. The probe sets were used to calculate differentially expressed transcripts using Welch's t-test with a p-value cut-off of 0.05 and a Fold-change of 1.5.

first: Stefanie

last: Fenske


title: Identification of sensory receptors in murine liver

status: Public on Sep 12 2020

city: Washington

first: Blythe

middle: D

last: Shepard

state: DC

address: 3700 Reservoir Road NW

department: Human Science

country: USA

institute: Georgetown University

summary: Sensory receptors, including olfactory receptors, taste receptors, and opsins have recently been found in a variety of non-sensory tissues where they have distinct physiological functions.  As G protein-coupled receptors, these proteins can serve as important chemosensors by sensing and interpreting chemical cues in the environment.  We reasoned that the liver, the largest metabolic organ in the body, is primed to take advantage of some of these sensory receptors in order to sense and regulate blood content and metabolism.  In this study, we designed a custom TaqMan array to screen for all bitter, sweet, and umani taste receptors, the non-visual optins, and 44 olfactory receptors in the murine liver.

overall_design: 2 male livers (M3 and HF1) were used to screen for the sensory receptors.  These livers were obtained from 2 age-matched C57BL6 mice.  18s RNA served as the endogenous control and was used for normalization while Gapdh was used as another housekeeping gene.

first: Ryan

last: Kurtz


title: Dual RNA-seq analysis of pig alveolar macrophage infected with china-isolated TgHB1 compared to TgRH and TgMe49 toxoplasma gondii standard strain

city: Wuhan

first: Yanqin

last: Zhou

state: Hubei province

address: No.1, Shizishan Street, Hongshan District

country: China

institute: Huazhong agricultural university

summary: Toxoplasma gondii is an apicomplexan parasite infecting human and animals, causing huge health concerns and economic losses. However, it is unclear about the exact mechanism of T.gondii tachyzoite infected macrophage and macrophage resisted T.gondii, especially for local isolates such as TgHB1 isolated in China. Our study focused on the transcriptional difference of pig alveolar macrophages (3D4/21) infected with china isolated TgHB1 compared to TgRH and TgME49 toxoplasma gondii standard strains.

sample_organism:
Toxoplasma gondii
Sus scrofa

platform_organism:
Toxoplasma gondii
Sus scrofa

overall_design: The pig alveolar macrophage was infected with TgRH, TgMe49 and TgHB1 at 3 different time points (6h, 12h and 24h) with three biological replicates. The control group (TgRH, TgMe49, TgHB1 and pig alveolar macrophage) was also collected for RNA-seq. After removing low-quality reads, clean reads were aligned to the reference genome of pig Sscrofa10.2 (GCA_000003025.4) and TgME49 (ToxoDB-41) respectively. Differentially expressed genes were obtained through DEseq analysis with default parameter then analysed through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG).

first: Yongle

last: Song

first: Lindong

first: Xiaoting

last: Wan


title: Integration of Innate 1 Immune Signaling by Caspase-8-Mediated Cleavage of N4BP1

status: Public on Sep 10 2020

city: South San Francisco

first: Rohit

last: Reja

state: CA

address: 1 DNA Way

institute: Genentech


title: An Atlas of Immune Cell Exhaustion in HIV-Infected Individuals Revealed by Single-Cell Transcriptomics

city: SAN DIEGO

first: Shaobo

last: Wang

state: California

address: 9500 Gilman Dr., La Jolla, San Diego

institute: University of California San Diego

summary: We investigated the effects of HIV infection on immune cell exhaustion at the transcriptomic level by analyzing single-cell RNA sequencing of peripheral blood mononuclear cells from four healthy subjects (37,847 cells) and six HIV-infected donors (28,610 cells). We identified nine immune cell clusters and eight T cell subclusters according to their unique gene expression programs; three of these (exhausted CD4+ and CD8+ T cells and interferon-responsive CD8+ T cells) were detected only in samples from HIV-infected donors. An inhibitory receptor KLRG1 was identified in the exhausted T cell populations and further characterized in HIV infected individuals. We identified a HIV-1 specific exhausted CD8+ T cell population expressing KLRG1, TIGIT, and T-betdimEomeshi markers. Ex-vivo antibody blockade of KLRG1 restored the function of HIV-specific exhausted CD8+ T cells demonstrating the contribution of KLRG1+ population to T cell exhaustion and providing an immunotherapy target to treat HIV chronic infection. Analysis of gene signatures also revealed impairment of B cell and NK cell function in HIV-infected donors. These data provide a comprehensive analysis of gene signatures associated with immune cell exhaustion during HIV infection, which could be useful in understanding exhaustion mechanisms and developing new cure therapies.

overall_design: PBMCs from 6 HIV patients and 1 Healthy donor were subjected to scRNA seq.

first: Qiong

last: Zhang

first: Hui

last: Hui


title: Genome binding of SMARCA2 and SMARCA4 in lung cancer cells reconstituted with SMARCA4 WT with and without SMARCA2 depletion

first: Robert

last: Piskol

department: gRED Computational Sciences

institute: Genentech Inc.

summary: Using ChIP-seq, we identified the genome-wide occupancy of SMARCA2 and SMARCA4 in lung cancer cells (NCI-H1944) reconstituted with SMARCA4 WT. We also determined how SMARCA4 occupancy changed in NCI-H1944 after SMARCA2 depletion.

overall_design: NCI-H1944 cells stably expressing a doxycycline-inducible SMARCA2-targeting shRNA were lentivirally transduced with LACZ and SMARCA4 WT and selected with blasticidin for 5 d. Cells were treated with vehicle or 0.5 ug/mL doxycycline for 4 d to obtain significant SMARCA2 knockdown. Cells were fixed, quenched and washed for ChIP.

first: Tharu

last: Fernando


title: Integration of Innate 1 Immune Signaling by Caspase-8-Mediated Cleavage of N4BP1 (NGS3269 RNA-seq)

summary: Human mutations in the death receptor Fas or its ligand FasL cause autoimmune lymphoproliferative syndrome (ALPS), whereas mutations in caspase-8 or its adaptor FADD â which mediate cell death downstream of Fas/FasL â cause severe immunodeficiency in addition to ALPS. Mouse models have corroborated a role for FADD-caspase-8 in promoting inflammatory responses, but the mechanisms underlying immunodeficiency remain undefined. Here, we identify NEDD4-binding protein 1 (N4BP1) as a suppressor of cytokine production that is cleaved and inactivated by caspase-8. N4BP1 deletion in mice significantly increased production of select cytokines upon Toll-like receptor (TLR) 1/2, TLR7, or TLR9 stimulation, but not upon TLR3 or TLR4 engagement. N4BP1 did not suppress TLR3 or TLR4 responses in wild-type macrophages owing to TRIF- and caspase-8-dependent cleavage of N4BP1. Notably, impaired TLR3 and TLR4 cytokine responses of caspase-8-deficient macrophages were largely rescued by co-deletion of N4BP1. Thus, persistence of intact N4BP1 in caspase-8-deficient macrophages impairs their ability to mount robust cytokine responses. Tumor necrosis factor (TNF), like TLR3 or TLR4 agonists, also induced caspase-8-dependent cleavage of N4BP1, thereby licensing TRIF-independent TLRs to produce higher levels of inflammatory cytokines. Illustrating the importance of this function of TNF in vivo, TNF blockade increased the mortality of mice infected with Streptococcus Pneumoniae, but did not do so when infected mice lacked N4BP1. Collectively, our results identify N4BP1 as a potent suppressor of cytokine responses; reveal N4BP1 cleavage by Caspase-8 as a point of signal integration during inflammation; and offer an explanation for immunodeficiency caused by FADD-caspase-8 mutations.

overall_design: RNA was extracted from BMDMs for the following genotypes: Wild type, MLKL knockout, MLKL knockout+Casp8 knockout, MLKL knockout + N4bp1 knockout, and MLKL knockout+Casp8 knockout+N4bp1 knockout after 8 hrs post LPS treatment.

first: R

first: A

last: Gitlin


title: PWWP2A variant NuRD complex represses intragenic spurious transcription initiation

status: Public on Sep 15 2020

city: Oxford

first: Guifeng

last: Wei

address: South Parks Road

department: Department of Biochemistry

institute: University of Oxford

summary: H3 trimethylation at K36 deposited over the body of actively transcribed gene, is recognized by readers to modulate the epigenetic states, such as DNA methylation and histone deacetylation, to ensure the proper gene transcription. PWWP2A was identified as the reading component of variant NuRD complex to deacetylate gene bodies in mammalian cells. However, whether this deacetylation affects intragenic transcription is not investigated. Here, we performed CAGE-seq to profile transcription initiation in PWWP2A/B double knockout and fount that intragenic spurious transcription initiations at pre-existing low-level initiation from highly expressed genes were enhanced, accompanying with elevated acetylation level at H3K9 and H3K27, as well as nascent transcription. Additionally, the intragenic spurious transcriptions in PWWP2A/B loss are distinct with those in DNMT3B loss which is prone to produce de novo initiation and lack of PWWP2A/B-related chromatin changes. Collectively, PWWP2A/B-NuRD complex deacetylates active gene bodies to suppress intragenic spurious transcription in mammals.

overall_design: CAGE-seq in E14 and PWWP2A/B double knockouts

first: G

first: T

first: N

last: Brockdorff


title: Transcriptional profiling of mouse pancreatic tumor cells II

city: New York

first: Jinyang

last: Li

state: New York

address: 1230 York Ave

institute: The Rockefeller University

summary: RNA-seq analysis of sorted WT and Kdm3a-KO 6419c5 and 6694c2 mouse pancreatic tumor cells from subcutaneously implanted mouse pancreatic tumors

overall_design: Compare gene expression between WT and Kdm3a-KO tumor cells in two tumor cell lines (6419c5 and 6694c2) with two knockout tumor cell clones (KO1 and KO2).

first: Ben

last: Stanger


title: Transcriptional profiling of mouse pancreatic tumor cells III

summary: RNA-seq analysis of sorted 6419c5 mouse pancreatic tumor cells from subcutaneously implanted mouse pancreatic tumors with or without treatment of a combination immunotherapy

overall_design: Compare gene expression between tumor cells with or without treatment of a combination immunotherapy


title: Transcriptional profiling of mouse pancreatic tumor cells I

summary: RNA-seq analysis of sorted WT and Klf5/Smad4/Egfr-KO 6694c2 mouse pancreatic tumor cells from subcutaneously implanted mouse pancreatic tumors

overall_design: Compare gene expression between WT tumor cells and tumor cells with specific knockout of genes


title: Transcriptional profiling of mouse pancreatic tumor cells


title: Expression profiling of lung cancer cells reconstituted with SMARCA4 WT and mutant K785R after SMARCA2 knockdown

summary:
Using RNA-seq, we identified the expression changes in lung cancer cells (NCI-H1944) transduced with control or SMARCA2-targeting hairpins. We also identified the SMARCA2 program that is rescued by SMARCA4 WT and SMARCA4 K785R transduced.
The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech.
The ID of this project in Genentech's ExpressionPlot database is PRJ0034746

overall_design: NCI-H1944 cells were lentivirally transduced with LACZ, SMARCA4 WT and SMARCA4 K785R and selected with blasticidin for 5 d. Cells were then transduced with nontargeting or SMARCA2-targeting hairpins in triplicate. After 72 h puromycin selection, RNA was isolated from cell pellets.


title: Genomic characterization of SMARCA4 mutants in lung cancer


title: A circular RNA generated from an intron of the insulin gene controls insulin secretion

status: Public on Sep 21 2020

city: Lausanne

first: Adriana

last: Rodriguez Trejo

state: Vaud

address: Rue du Bugnon 9

department: DNF

country: Switzerland

institute: UNIL

summary: Fine-tuning of insulin release from pancreatic β-cells is essential to maintain blood glucose homeostasis. Here, we report that insulin secretion is regulated by a circular RNA containing the lariat sequence of the second intron of the insulin gene. Silencing of this intronic circular RNA in pancreatic islets leads to a decrease in the expression of key components of the secretory machinery of β-cells, resulting in impaired glucose- or KCl-induced insulin release and calcium signaling. The effect of the circular RNA is exerted at the transcriptional level and involves an interaction with the RNA-binding protein TAR DNA-binding protein 43 kDa (TDP-43). The level of this circularized intron is reduced in the islets of rodent diabetes models and of type 2 diabetic patients, possibly explaining their impaired secretory capacity. The study of this and other circular RNAs helps understanding β-cell dysfunction under diabetes conditions, and the etiology of this common metabolic disorder.

overall_design: Mouse islet circRNA annotation and RNA-seq of rat islet cells transfected with control or ci-Ins2 gapmeRs (n = 3 samples per treatment).

first: Lisa

last: Stoll

last: Rodríguez-Trejo

first: Claudiane

last: Guay

first: Flora

last: Brozzi

first: Mustafa

middle: B

last: Bayazit

first: Sonia

last: Gattesco

first: Véronique

last: Menoud

first: Jonathan

last: Sobel

first: Ana

middle: C

last: Marques

first: Morten

middle: T

last: Venø

first: Jonathan Lou

middle: S

last: Esguerra

first: Mohammad

last: Barghouth

first: Mara

last: Suleiman

first: Lorella

last: Marselli

first: Jørgen

last: Kjems

first: Lena

last: Eliasson

first: Erik

last: Renström

first: Karim

last: Bouzakri

first: Michel

last: Pinget

first: Piero

last: Marchetti

first: Romano

last: Regazzi


title: Chromatin accessibility of lung cancer cells reconstituted with SMARCA4 WT or SMARCA4 mutants with and without SMARCA2 depletion

first: Robert

last: Piskol

summary:
Using ATAC-seq, we identified the accessibility changes in lung cancer cells (NCI-H1944) reconstituted with SMARCA4 WT or SMARCA4 mutants. We also determined the SMARCA2-regulated accessibility program in NCI-H1944 after SMARCA2 depletion. Lastly, we identified the SMARCA2 accessibility program that is rescued by SMARCA4 WT and mutants.
The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech.

overall_design: NCI-H1944 cells were lentivirally transduced with LACZ, SMARCA4 WT and SMARCA4 mutants (K785R, E882K, T910M, R973L, R1135W, G1159V, G1162C, A1186T, R1192C, G1232S) and selected with blasticidin for 5 d. Cells were then transduced with nontargeting or SMARCA2-targeting hairpins in duplicate. After 72 h puromycin selection, cells were pelleted for ATAC-seq.

first: Tharu

last: Fernando


title: Integration of Innate 1 Immune Signaling by Caspase-8-Mediated Cleavage of N4BP1 (NGS2979 RNA-seq)

status: Public on Sep 09 2020

first: Rohit

last: Reja

summary:
Human mutations in the death receptor Fas or its ligand FasL cause autoimmune lymphoproliferative syndrome (ALPS), whereas mutations in caspase-8 or its adaptor FADD â  which mediate cell death downstream of Fas/FasL â cause severe immunodeficiency in addition to ALPS. Mouse models have corroborated a role for FADD-caspase-8 in promoting inflammatory responses, but the mechanisms underlying immunodeficiency remain undefined. Here, we identify NEDD4-binding protein 1 (N4BP1) as a suppressor of cytokine production
that is cleaved and inactivated by caspase-8. N4BP1 deletion in mice significantly increased production of select cytokines upon Toll-like receptor (TLR) 1/2, TLR7, or TLR9 stimulation, but not upon TLR3 or TLR4 engagement. N4BP1 did not suppress TLR3 or TLR4 responses in wild-type macrophages owing to TRIF- and caspase-8-dependent cleavage of N4BP1. Notably, impaired TLR3 and TLR4 cytokine responses of caspase-8-deficient macrophages were largely rescued by co-deletion of N4BP1. Thus, persistence of intact N4BP1 in caspase-8-deficient macrophages impairs their ability to mount robust cytokine responses. Tumor necrosis factor (TNF), like TLR3 or TLR4 agonists, also induced caspase-8-dependent cleavage of N4BP1, thereby licensing TRIF-independent TLRs to produce higher levels of inflammatory cytokines. Illustrating the importance of this function of TNF in vivo, TNF blockade increased the mortality of mice infected with Streptococcus Pneumoniae, but did not do so when infected mice lacked N4BP1. Collectively, our results identify N4BP1 as a potent suppressor of cytokine responses; reveal N4BP1 cleavage by Caspase-8 as a point of signal integration during inflammation; and offer an explanation for immunodeficiency caused by FADD-caspase-8 mutations.

overall_design:
RNA was extracted from BMDMs for the following genotypes
N4bp1 wild type (N4bp1 WT) and N4bp1 knockout (N4bp1 KO) after 0,1,2,4,8,16 hrs post TLR7 treatment the ligand R837

first: Alexander

last: Gitlin


title: Transcriptomic and functional deficits in human TREM2-/- microglia impair response to Alzheimer’s pathology in vivo [RNA-seq]

city: Irvine

first: Mathew

last: Blurton-Jones

address: 845 Health Sciences Rd

institute: University of California, Irvine

summary: RNA-sequencing of human iPS-microglia isogenic for TREM2 after multiple treatments

overall_design: Comparison of WT and KO TREM2 microglia at baseline and after treatment

first: Amanda

last: McQuade

first: Jonny

last: Hasselmann


title: Expression data from hepatocellular carcinoma cell lines

city: Suwon

first: SO MEE

last: KWON

address: Worldcup-ro 164

country: South Korea

institute: Ajou University School of Medicine

summary: In this study, we demonstrated that mitochondrial respiratory defect enhanced NFE2L1 transcription via reactive oxygen species (ROS)-mediated STAT3 activation and the up-expressed NFE2L1 increased hepatoma cell invasiveness by inducing syntaxin 12 (STX12) expression. Bioinformatic analysis of The Cancer Genome Atlas Liver Hepatocellular carcinoma (TCGA-LIHC) open database showed that NFE2L1 expression is strongly positively correlated with STX12 expression and, furthermore, epithelial-mesenchymal transition (EMT)-related core genes were significantly upregulated in the tumors expressing both NFE2L1 and STX12. The effect of NFE2L1/STX12 axis on lung metastasis of hepatoma cell was proved in nude mice model. Collectively, our results indicate that NFE2L1 was a key mitochondrial retrograde signaling-mediated primary gene product to enhance hepatoma cell invasiveness via STX12 expression

overall_design: To identify for downstream effector gene of NFE2L1, we depleted NFE2L1 in SNU423 and overexpressed it in SNU387. For this, cells were transfected with the plasmids and target siRNA duplexes using FuGENE® HD (Promega) and OligofectamineTM Reagent (Invitrogen), respectively, according to the manufacturer’s instructions. For transfection, we used two siRNA targeting different sequence of NFE2L1 to deplete the NFE2L1 expression in SNU423 and one plasmid to overexpress the NFE2L1 expression in SNU387. Each transfection was duplicated and total 10 samples were used for microarry gene expression profiling.

first: Gyesoon

last: Yoon

first: So

middle: M

last: Kwon


title: NuA3 HAT contributes to the Rpd3 containing HDACs-mediated regulation of mRNA and lncRNA expression dynamics

status: Public on Sep 08 2020

city: Daejeon

first: Yukyung

last: Jun

address: 245 Daehak-ro, Yuseong-gu

department: Center for Supercomputing Applications

institute: Korea Institute of Science and Technology Information

summary: In yeast, NuA3 histone acetyltransferase (NuA3 HAT) enhances H3K14 acetylation and transcription of a subset gene via interaction between the Yng1 PHD finger and H3K4me3. Although NuA3 HAT includes multiple chromatin binding modules with distinct specificities, their interdependencies and combinatorial actions in chromatin binding and transcription remain unknown. Modified peptide pulldown assays reveal that Yng1 n-terminal region is important for the integrity of NuA3 HAT by mediating interaction between core subunits and two methyl-binders, Yng1and Pdp3. We further uncover that NuA3 HAT contributes to both Rpd3S and Rpd3L HDACs-mediated regulation of mRNA and lncRNA expression dynamics. Yng1 n-terminal region, Nto1 PHD finger and Pdp3 PWWP domain are important for optimal induction of mRNA and cryptic transcription repressed by the Set2-Rpd3S HDAC pathway. In contrast, the Yng1 PHD finger-H3K4me3 interaction affects transcriptional repression memory (TREM) regulated by Rpd3L HDAC. These findings suggest that NuA3 HAT utilizes distinct chromatin readers to compete with two Rpd3 containing HDACs for optimal mRNA and lncRNA expression dynamics.

overall_design: Ananysis of gene expression dynamics in wild type and mutants for NuA3 HAT during carbon source shifts.

first: Ji

middle: H

last: Kim

first: Chae

middle: Y

first: TaeSoo


title: A high-throughput CRISPR interference screen for dissecting functional regulators of GPCR/cAMP signaling

city: Durham

first: Nikoleta

last: Tsvetanova

state: NC

address: Department of Pharmacology and Cancer Biology Duke University School of Medicine Box 3813, C334 LSRC, 308 Research Drive

department: Pharmacology and Cancer  Biology

institute: Duke University

summary: G protein-coupled receptors (GPCRs) allow cells to respond to chemical and sensory stimuli through generation of second messengers, such as cyclic AMP (cAMP), which in turn mediate a myriad of processes, including cell survival, proliferation, and differentiation. In order to gain deeper insights into the complex biology and physiology of these key cellular pathways, it is critical to be able to globally map the molecular factors that shape cascade function. Yet, to this date, efforts to systematically identify regulators of GPCR/cAMP signaling have been lacking. Here, we combined genome-wide screening based on CRISPR interference with a novel sortable transcriptional reporter that provides robust readout for cAMP signaling, and carried out a functional screen for regulators of the pathway. Due to the sortable nature of the platform, we were able to assay regulators with strong and weaker phenotypes by analyzing sgRNA distribution among three fractions with distinct reporter expression. We identified 45 regulators with strong and 50 regulators with weaker phenotypes not previously known to be involved in cAMP signaling. In follow-up experiments, we validated the functional effects of seven newly discovered mediators and showed that they control distinct steps of the pathway. Thus, our study provides proof of principle that the screening platform can be applied successfully to identify bona fide regulators of GPCR/second messenger cascades in an unbiased and high-throughput manner, and illuminates the remarkable functional diversity among GPCR regulators.

overall_design: Examination of single guide RNAs (sgRNAs) enrichment in sorted cell populations based on cAMP-reporter expression

first: Khairunnisa

last: Semesta

first: Martin

last: Kampmann

first: Mark

last: von Zastrow

first: Ruilin

last: Tian


title: Single cell RNA sequencing to classify molecularly distinct neuronal and non-neuronal cell types in the mouse ventral posterior hypothalamus

status: Public on Oct 07 2020

city: Farmington

first: William

middle: F

last: Flynn

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

summary: Droplet-based single cell RNA sequencing (scRNA-seq) to classify molecularly distinct neuronal and non-neuronal cell types in the mouse ventral posterior hypothalamus. Cluster analysis of >16,000 single cells revealed 20 neuronal and 18 non-neuronal cell populations, defined by suites of discriminatory markers. We validated differentially expressed genes in a selection of neuronal populations through fluorescence in situ hybridization (FISH). Focusing on the mammillary nuclei, we discovered transcriptionally-distinct clusters that broadly align with neuroanatomical compartments. This single cell transcriptomic analysis of cell types in the VPH provides a resource for interrogating the circuit-level mechanisms underlying the diverse functions of VPH circuits in health and disease.

overall_design: Examination of cells from ventral posterior hypothalamus brain slices from four batches of juvenile B6 mice

first: Laura

middle: E

last: Mickelsen

first: Kristen

last: Springer

first: Lydia

last: Wilson

first: Eric

last: Beltrami

first: Mohan

last: Bolisetty

first: Paul

last: Robson

last: Jackson


title: Unveiling the role of RAB13 localisation in angiogenesis

status: Public on Sep 07 2020

city: Belfast

first: Guilherme

last: Costa

address: 97 Lisburn Road

institute: Queen's University of Belfast

summary: Deciphering the complex biology of cell migration is key to understand human-related disorders. During angiogenesis, endothelial cells engage in coordinated migration events to form new blood vessels from parental counterparts. However, while subcellular localisation of mRNAs and localised translation are fundamental steps between gene transcription and protein activity, whether local regulation of gene expression controls the complex morphogenetic process of angiogenesis has never been addressed. Here, we focused on RAB13 mRNA, a transcript enriched at the leading front of many migratory cell types. We set out to delete regions in the 3'UTR of RAB13 mRNA responsible for its subcellular distribution in vitro and in vivo and to study its localised role during angiogenesis.

sample_organism:
Danio rerio
Homo sapiens

platform_organism:
Danio rerio
Homo sapiens

overall_design:
After identifying regions responsible for the localisation of RAB13 mRNA, we used CRISPR/Cas9 technology with gRNAs targeting the 3'UTR of both human and zebrafish orthologues. We performed RNA-seq experiments using RNA derived from control and mutant samples to 1) investigate whether potential off-target sites were edited by CRISPR/Cas9 and 2) analyse the expression of potential RAB13 splicing variants. Samples analysed: HUVECs - 1x Wild type and 1x Homozygous RAB13 3'UTR; Zebrafish - 2x Wild type and 2x Homozygous RAB13 3'UTR.

Description of RAB13 3'UTR mutations:
Deletion of 190 nucleotides from Human RAB13 3'UTR
Deletion of 482 nucleotides from Zebrafish RAB13 3'UTR

first: Joshua

last: Bradbury

first: Nawseen

last: Tarannum

first: Shane

middle: P

last: Herbert


title: A Cell Atlas of the Drosophila ovary

city: San Francisco

first: Todd

last: Nystul

address: 513 Parnassus Ave, Box 0412

institute: UCSF

summary: Single-cell RNA sequencing of adult Drosophila ovary using the 10X platform.  Ovaries were dissociated to single cells and Single-cell libraries were generated for 435 cells (dataset1), 8326 cells (dataset2) or 5412 cells (dataset3). Cells were sequenced at a depth of~540,000 reads per cell (dataset1),  ~40,000 reads per cell (dataset2) or ~ 70,000 reads per cell (dataset3). We identified transcriptomes of 26 distinct cell populations including the stem cells of the germline and the follicle cell lineage as well as three distinct subtypes inner germarial sheath cells, polar cells, stalk cells and subpopulations of main body follicle cells.

overall_design: Single-cell RNA sequencing of adult ovaries (dataset1: 109-30-Gal4/+; 13CO6-GFP/UAS-CD8::GFP, dataset2 and dataset3: Canton-S)using the 10X platform and HiSeq2500. Live cells were dissociated and run on 1 well of the 10X instrument using the Chromium Single Cell 3' Reagent Version 2 Kit. For dataset1, cells were subjected to MACS prior to loading onto the 10X chip.

middle: G

first: Katja

last: Rust


title: GM-CSF controls Mycobacterium tuberculosis infection by limiting type I IFN-driven neutrophil extracellular trap formation [Lung]

city: London

first: Anne

last: OGarra

address: 1 Midland Road

institute: Francis Crick Insititue

summary: Tuberculosis (TB) remains the world’s top infectious killer. Understanding how immune mediators determine the outcome of Mycobacterium tuberculosis infection could facilitate the design of better therapies against this devastating disease. GM-CSF mediates protective immunity against TB but the underlying mechanisms remain elusive. To determine the molecular mechanisms underlying the protective role of GM-CSF during M. tuberculosis infection we performed RNA-sequencing analyses of whole blood and lung samples obtained from C57Bl/6 mice infected with HN878 and treated with anti-GM-CSF monoclonal antibody or isotype control. Uninfected mice were also treated and used as uninfected controls. Three weeks post-infection, whole blood and lungs were harvested from each individual mouse and processed for RNA-sequencing. Transcriptomic analyses revealed that during M. tuberculosis infection GM-CSF regulates the expression of genes associated with neutrophil recruitment and activation and type I IFN-inducible genes, which have been previously associated with TB pathogenesis. Further mechanistical studies showed  that disease exacerbation driven by GM-CSF blockade during M. tuberculosis infection was type I IFN and neutrophil-dependent and that over-activation of neutrophils by type I IFN induced NET formation at the site of infection. NETs were also found in necrotic lung lesions from patients with pulmonary TB and type I IFN-driven NET formation correlated with increased disease susceptibility in different mouse models of TB. Our findings reveal an important immune network that may play a central role in determining TB outcome.

overall_design: C57Bl/6 female mice were infected with Mycobacterium tuberculosis strain HN878 and treated with anti-GM-CSF monoconal antibody (aGM-CSF) or isotype control (iso) the day prior to infection and then twice a week during the course of the experiment. Uninfected mice were also treated and used as uninfected controls. Three weeks post-infection, whole blood and lungs from each individual mouse were harvested and processed for RNA-sequencing. A total of 39 blood and 39 lung samples were analysed. Experimental groups included: uninfected control mice (5 biological replicates), anti-GM-CSF treated uninfected mice (5 biological replicates), HN878-infected control mice (4 biological replicates), HN878-infected anti-GM-CSF treated mice (5 biological replicates).

first: Lucia

last: Moreira-Teixeira

last: O'Garra


title: Clustering of strong replicators associated with active promoters is sufficient to establish an early-replicating domain

city: Paris

first: Caroline

last: Brossas

address: 15 rue Hélène Brion

country: France

institute: Institut Jacques Monod, Université de Paris, CNRS UMR 7592

summary: Clustering of strong replicators associated with active promoter are sufficient to establish an early-replicating domain

overall_design:
Repli-Seq: A Wt DT40 chicken cell line and one clonal homozygous cell line containing one module of cis-regulatory elements inserted into a mid-late replicating region of chromosome one (chr1:71,981,290-73,532,377 bp, galGal5) on the two alleles were analyzed (See Hassan-Zadeh et al. 2012, Fig.9). Immunoprecipitated nascent strands from the four S-phase fractions collected by flow cytometry or from an asynchronous cell population were sequenced to determine the replication timing profiles of the targeted region.
Hi-C: A Wt DT40 chicken cell line and two clonal cell lines containing two modules of cis-regulatory elements inserted into a mid-late replicating region of chromosome 1 at two genomic positions separated by 30kb (chr1:72,565,520 bp and chr1: 72,536,060 bp, galGal5) on one chromosome (named chromosome 1) and one reporter module inserted in the middle (chr1: 72,548,589 bp, galGal5) on the other chromosome (named chromosome 2) were analyzed. After modification, the chromosome 1 is changing its replication timing toward early replication whereas the chromosome 2 keeps its natural temporal program. Hi-C experiments were used to identify compartment status genome wide. The existence of significant and specific preference of interaction of the allele 1 with different loci was tested.

first: Anne-Laure

last: Valton

first: Sergey

middle: V

last: Venev

first: Sabarinadh

last: Chilaka

first: Antonin

last: Counillon

first: Marc

last: Laurent

first: Coralie

last: Goncalves

first: Bénédicte

last: Duriez

first: Franck

last: Picard

first: Job

last: Dekker

first: Marie-Noëlle

last: Prioleau


title: GM-CSF controls Mycobacterium tuberculosis infection by limiting type I IFN-driven neutrophil extracellular trap formation

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

overall_design: Refer to individual Series


title: GM-CSF controls Mycobacterium tuberculosis infection by limiting type I IFN-driven neutrophil extracellular trap formation [Blood]


title: Identification of mRNAS enriched in endothelial cell protrusions

first: Guilherme

last: Costa

summary:
Deciphering the complex biology of cell migration is key to understand human-related disorders. During angiogenesis, endothelial cells engage in coordinated migration events to form new blood vessels from parental counterparts. However, while subcellular localisation of mRNAs and localised translation are fundamental steps between gene transcription and protein activity, whether local regulation of gene expression controls the complex morphogenetic process of angiogenesis has never been addressed.
Here, we set out to investigate the cytoplasmic distribution of mRNAs in migratory endothelial cells. We isolated RNA from endothelial cell protrusions from their cell bodies and used RNA-sequencing to identify asymmetrically distributed transcripts. These studies identified a set of transcripts enriched in endothelial cell protrusions over cell bodies, which included classically protrusion-enriched mRNAs and other intriguing transcripts encoding proteins implicated in cell migration.

overall_design: To unveil the implications of mRNA localisation in endothelial cell migration during angiogenesis, Human Umbilical Vein Endothelial Cells (HUVECs) were cultured in modified Transwells that permit the segregation of protrusions formed at cell front from their cell body counterparts. In order to investigate whether HUVECs preferentially localise transcripts to their migratory front, RNA was extracted from cell bodies and protrusions to perform a genome-wide transcriptome screen (RNA-seq).

last: Herbert


title: Transcriptome comparison between platyfish jp163A and jp163B strains

status: Public on Sep 05 2020

city: San Marcos

first: Yuan

last: Lu

state: TX

address: university drive

institute: Xiphophorus Genetic Stock Center

summary: Xiphophorus interspecies hybrids represent a valuable model system to study heritable tumorigenesis, and the only model system that exhibits both spontaneous and inducible tumors. Types of tumorigenesis depend on the specific pedigree of the parental species, X. maculatus, utilized to produce interspecies hybrids. Although the ancestors of the two currently used X. maculatus parental lines, Jp163 A and Jp163 B, were originally siblings produced by the same mother, backcross interspecies hybrid progeny between X. hellerii and X. maculatus Jp163 A develop spontaneous melanoma initiating at the dorsal fin due to segregation of an oncogene and a regulator encoded by the X. maculatus genome, while the backcross hybrid progeny with X. hellerii or X. couchianus and Jp163 B exhibit melanoma on the flanks of their bodies, especially after treatment with ultraviolet light. Therefore, dissecting the genetic differences between these two closely related lines may lead to better understanding of functional molecular differences associated with tumorigenic mechanisms. For this purpose, comparative genomic analyses were undertaken to establish genetic variants between these two X. maculatus lines. Surprisingly, given the heritage of these two fish lines, we found genetic variants are clustered together in select chromosomal regions. Among these variants are non-synonymous mutations located in 381 genes. The non-random distribution of genetic variants between these two may highlight ancestral chromosomal recombination patterns that became fixed during subsequent inbreeding. Employing comparative transcriptomics, we also determined differences in the skin transcriptional landscape between the two lines. The genetic differences observed are associated with pathways highlighting fundamental cellular functions including inter-cellular and microenvironment-cellular interactions, and DNA repair. These results collectively lead to the conclusion that diverged functional genetic baselines are present between Jp163 A and B strains. Further, disruption of these fixed genetic baselines in the hybrids may give rise to spontaneous or inducible mechanisms of tumorigenesis.

overall_design: Xiphophorus maculatus strains Jp163 A and Jp163 B skin, and liver gene expression profiling was performed using RNA isolated from respect organs of each strain.

first: Ronald

last: Walter

first: Manfred

last: Schartl

first: Wesley

last: Warren


title: Diel and circadian analysis of clock gene transcripts in central and peripheral tissues in the Atlantic salmon (Salmo salar)

status: Public on Sep 06 2020

city: Tromsø

first: Alexander

middle: Christopher

last: West

state: Troms

address: Framstredet 39, Tromsø

department: Arctic Chronobiology and Physiology

country: Norway

institute: Universitetet i Tromsø

summary:
Atlantic salmon (Salmo salar) pre-smolt optic tectum, saccus vasculosus and gill tissues were collected over a light:dark (LD, 8:16) cycle, constant light (LL) and constant dark (DD) time series at a four hour resolution
Total RNA was extracted, RNA quality was assessed using BIORAD Experion, then submitted to a bespoke clock gene NanoString CodeSet

overall_design: Atlantic salmon (Salmo salar) were raised under LL, then placed under a light dark cycle (LD, 8:16) for 8 weeks before being transferred to constant light or constant darkness. Serial tissue samples were collected (optic tectum, saccus vasculosus and gill; snap frozen) to assess the expression of clock genes in response to fluctuating and constant lighting conditions. Food was removed 48h before the first sampling point, tank water temperature was maintained at 14oC. Dark samples were collected under red light.

first: Shona

last: Wood

first: David

last: Hazlerigg

first: Simen

last: Sandve

first: Even

last: Jørgensen

first: Marianne

last: Iversen


title: c-Jun ChIP-seq analysis of MCF7 cells treated with abemaciclib

status: Public on Sep 03 2020

city: Melbourne

first: Shom

last: Goel

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

summary: We measured changes in AP-1 factors binding after treatment of MCF7 cells with abemaciclib

overall_design: Examination of changes in c-Jun binding in MCF7 cells after treatment with abemaciclib


title: Time-resolved RNA atlas of early human T cell activation (mRNA)

status: Public on Sep 04 2020

city: Saarbrücken

first: Tim

last: Kehl

address: Campus E2.1, P.O. box 151150

department: Center for Bioinformatics

institute: Saarland University

summary: MicroRNAs are central regulators of the T cell function. We explored RNA expression profiles over the initial 24 h of human CD4+ T cell activation. We found high similarity in time-resolved miRNA expression courses comparing independent activations and different donors. The detected miRNA expression patterns could be grouped into six classes only, each with a defined time course. MiR-155-5p known for its role in T cell immunity showed the most prevalent expression changes, quantified with an hourly increase of about 60 molecules/cell. As demonstrated for miRNA-155-5p, the analysis of time-resolved miRNA and mRNA expression data allowed to increase the validation rate of predicted miRNA targets to close to 90 %. Combining our time-resolved expression analysis with an absolute quantification of miRNA expression changes, gives new insights into miRNA regulatory networks and indicates the functional dominance of specific miRNAs within the early T cell activation.

overall_design: Early human T cell activation

first: Caroline

last: Diener

first: Martin

last: Hart


title: FiTAc-seq analysis of PDX 14-07 and MMTV-rtTA/tetO/Her2 tumors treated with abemaciclib

summary: We measured changes in H3K27ac after treatment of PDX 14-07 or MMTV-rtTA/tetO-Her2 tumors implanted in nude mice with abemaciclib

overall_design: Examination of changes in H3K27ac in PDX 14-07 and MMTV-rtTA/tetO-Her2 tumors after treatment with abemaciclib (90 mg/kg) for 21-28 days (PDX) or 40 days (MMTV-Her2)


title: Influence of dietary whole egg  on the transcriptome in Zucker Diabetic Fatty rats

city: Ames

first: Joe

last: Webb

state: IA

address: 2302 Osborn drive, 220 Mackay Hall

institute: Iowa State University

type: Non-coding RNA profiling by high throughput sequencing

summary: Here we analyzed how whole egg consumption in Zucker Diabetic Fatty (ZDF) rats alters microRNA and mRNA expression  across the adipose, liver, kidney, and prefrontal cortex tissue. Male ZDF (fa/fa) rats (n = 12) and their  lean controls (fa/+) (n = 12) were obtained at 6 wk of age. Rats had ad libitum access to water and were  randomly assigned to a modified semi-purified AIN93G casein-based diet or a whole egg-based diet,  both providing 20% protein (w/w). TotalRNA libraries were prepared using QuantSeq 3' mRNA-Seq  and Lexogen smallRNA library prep kits and were further sequenced on an Illumina HighSeq3000.  Differential gene expression was conducted using DESeq2 in R and Benjamini-Hochberg adjusted P-  values controlling for false discovery rate at 5%.We identified 9 microRNAs and 583 genes that were  differentially expressed in response to 8 wk of consuming whole egg-based diets.

overall_design: Examination of two different diets on mRNA and microRNA across multiple tissues in ZDF rats

first: Amanda

last: Bries

first: Elizabeth

last: McNeill

first: Matthew

last: Rowling

first: Kevin

last: Schalinske


title: The immune response and microbiota profiles during co-infection with P. vivax and soil-transmitted helminths

status: Public on Sep 29 2020

first: Alice

last: Easton

state: NY

address: 430 E 29th St

department: Microbiology

institute: NYU Langone

summary: Co-infection with soil transmitted helminths (STH) and Plasmodium spp. parasites is a common occurrence in tropical developing countries, but the consequences of this interaction remain poorly understood. Here, we performed a multi-omic analysis on the peripheral blood and fecal samples of 130 individuals in Tierralta, Córdoba, Colombia who were infected with P. vivax alone (n = 33), co-infected with P. vivax and STH (n = 27), infected with STH alone (n = 39) or were infected with neither P. vivax nor STH (n = 31). In addition to Complete Blood Count (CBC) with differential, transcriptional profiling of peripheral blood samples was performed by RNA-Seq, fecal microbial communities were determined by 16S ribosomal RNA gene sequencing and circulating cytokine levels were measured by bead-based immunoassays. Differences in blood cell counts were driven primarily by P. vivax infection, including an increased percentage of neutrophils that was associated with a transcriptional signature of neutrophil activation in the blood. P. vivax infection was also associated with increased levels of IL-6, IL-8 and IL-10 and these cytokine levels were not affected by STH co-infection.  Surprisingly, P. vivax infection was more strongly associated with changes in the microbiome than STH infection. Children infected with P. vivax exhibited elevated Bacteroides and reduced Prevotella and Clostridiaceae, but these differences were not observed in individuals co-infected with STH. We also observed that P. vivax parasitemia is higher in STH-infected population. When we used machine learning to identify the most important predictors of P. vivax parasite burden from all measured variables, bacterial taxa were the strongest predictors of parasitemia levels in P. vivax infected individuals. In contrast, circulating TGF- β was identified as the strongest predictor of T. trichiura egg burden. This study provides unexpected evidence that the gut microbiota may have a stronger link with P. vivax than with STH infection.

overall_design:
We performed a multi-omic analysis on the peripheral blood and fecal samples of 130 individuals in Tierralta, Córdoba, Colombia who were infected with P. vivax alone (n = 33), co-infected with P. vivax and STH (n = 27), infected with STH alone (n = 39) or were infected with neither P. vivax nor STH (n = 31).

These samples are multiplexed. Pool1 represents 95 samples and Pool2 represents 35 samples. The file sample_metadata.xls includes sample metadata and barcode.

first: Mayra

last: Raciny-Aleman

first: Victor

last: Liu

first: Erica

last: Ruan

first: Maria

last: Yasnot

first: Ana

last: Rodriguez

first: P'ng

last: Loke


title: RNA-seq analysis of human breast cancer cell lines treated with abemaciclib

summary: We measured changes in gene expression after treatment of human breast cancer cell lines with abemaciclib.

overall_design: Examination of changes in gene expression in breast cancer cell lines after treatment with abemaciclib.


title: Enhancer connectome analysis of human breast cancer cell lines treated with abemaciclib

summary: We measured changes in H3K27ac-marked enhancer contacts before and after treatment of human breast cancer cell lines with abemaciclib

overall_design: Performed H3K27ac HiChIP in breast cancer cell lines before and after treatment with abemaciclib


title: Suppressors of PHO regulon hyper-repression by Pol2 CTD Thr4 mutation implicate inositol 1-pyrophosphates as agonists of precocious lncRNA transcription termination

first: Angad

last: Garg

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

summary: This RNA-Seq analysis compares gene expression of the suppressors of RNA polyemrase II CTD-T4A (STF6 and STF9 mutants) contrasting to the parental RNA polymerase II CTD-T4A mutant in the fission yeast S. pombe

overall_design: 2 test samples (suppressor mutants) were analyzed; 1 parental control sample was processed (each sample has 3 replicate experiments)

first: Beate

last: Schwer

first: Stewart

last: Shuman


title: Chemical genetics approach identifies ABNORMAL INFLORESCENCE MERISTEM 1 as a putative target of a novel sulfonamide that protects Arabidopsis against photorespiratory stress [RNA-seq]

city: Wageningen

first: Tom

last: van der Meer

address: Droevendaalsesteeg 1

country: Netherlands

institute: Wageningen University

summary: Alterations of hydrogen peroxide (H2O2) levels have a profound impact on numerous signaling cascades orchestrating stress responses, plant growth and development, including programmed cell death. To expand the repertoire of known molecular mechanisms implicated in H2O2 signaling, we performed a forward chemical screen to identify small molecules that could alleviate the photorespiratory-induced cell death phenotype of Arabidopsis thaliana mutants lacking H2O2 scavenging capacity by peroxisomal CATALASE2. Here, we report the characterization of pakerine, a m-sulfamoyl benzamide from the sulfonamide family. Pakerine alleviates the cell death phenotype of cat2 mutants exposed to photorespiration-promoting conditions and delays dark-induced senescence in wild type Arabidopsis leaves. By using a combination of transcriptomics, metabolomics and affinity purification we identified ABNORMAL INFLORESCENCE MERISTEM 1 (AIM1) as a putative protein target of pakerine. AIM1 is a 3-hydroxyacyl-CoA dehydrogenase involved in β-fatty acid oxidation that contributes to jasmonic acid (JA) and salicylic acid (SA) biosynthesis. Whereas intact JA biosynthesis was not required for pakerine bioactivity, our results point towards a role for β-oxidation-dependent SA production in execution of H2O2-mediated cell death.

overall_design: Gene expression analysis of CATALASES2 deficient Arabidopsis thaliana plants exposed to a combinatorial treatment of photorespiratory inducing growth conditions and a chemical treatment of a chemical alleviating the enhanced cell death phenotype of the mutant plants. Four different treatments are applied to seven day old plants (3 biological replicates per treatment) grown in liquid 1/2 MS media in translucent 96-well plates. Treatments include 1. mock (DMSO) treated plants grown in long day conditions (16 h/8 h light/dark, 100 µmol m-2 s-1 light intensity, 21 oC, 70% relative humidity), 2. mock treated plants grown for 2 days in photorespiratory stress conditions (24 hour light 100 µmol m-2 s-1 light intensity, 21 oC, 70% relative humidity), 3. Chemical treatment, consisting of Pakerine dissolved in DMSO (10 μM final conc.) grown in long day conditions, 4.   Chemical treatment, consisting of Pakerine dissolved in DMSO (10 μM final conc.) grown in photorespiratory stress conditions.

first: Pavel

middle: I

last: Kerchev

first: Frank

last: van Breusegem

first: Christian

last: Stevens

first: Arno

last: Verlee

first: Patrick

last: Willems

first: Francis

last: Impens

first: Kris

last: Gevaert

first: Christa

last: Testerink


title: Chemical genetics approach identifies ABNORMAL INFLORESCENCE MERISTEM 1 as a putative target of a novel sulfonamide that protects Arabidopsis against photorespiratory stress

overall_design: Gene expression analysis of 7 day old Arabidopsis plants subjected to a chemical treatment consisting of pakerine (5 μM in DMSO) or DMSO (mock treatment) for 24 hours in liquid 1/2 MS media in translucent 96 well plates.


title: RNA seq analysis of AR-deleted luminal prostate epithelial cells during organogenesis

city: Newark

first: Antonina

last: Mitrofanova

state: NJ

address: 65 Bergen Street, Rm 923B

institute: Rutgers University

summary: Transcriptome analysis of lineage marked AR-deleted and wild type luminal prostate epithelial cells from prostates from 4 week old males, and bulk wild-type prostates from 3 week old male mice.

overall_design: Pups were treated with of 0.1 mg of tamoxifen at postnatal day (P) 2 for lineage tracing. At 4 weeks, all prostate lobes from a single litter (ranging from 1-5 males per litter) were pooled and dissociated, and YFP-positive CD49flow/- luminal cells were sorted for RNA sequencing. For RNA isolation from bulk wild-type prostates, 2-3 prostates from untreated three-week males (n=6 pools) were collected.

first: Maho

last: Shibata

first: Michael

last: Shen


title: JunB ChIP-seq analysis of MCF7 cells treated with abemaciclib

status: Public on Sep 01 2020

first: Shom

last: Goel

overall_design: Examination of changes in JunB binding in MCF7 cells after treatment with abemaciclib


title: RNA-seq analysis of MCF7 cells treated with abemaciclib, SR11302

summary: We measured changes in gene expression in MCF7 with CDK4/6 and AP-1 inhibition by abemaciclib and SR11302, respectively.

overall_design: Examination of changes in gene expression after treatment of MCF7 with abemaciclib, SR11302 for 7 days


title: An Evolutionary Cancer Epigenetic approach revealed DNA hypermethylation of Ultra-Conserved Non-coding Elements in squamous cell carcinoma of different mammalian species

city: Bologna

first: Luca

last: Morandi

address: via Altura 3

department: DIBINEM

country: Italy

institute: University of Bologna

type: Methylation profiling by high throughput sequencing

summary:
Background: Ultra-Conserved-Non-coding Elements (UCNEs) are genomic sequences that exhibit >95% sequence identity between human, mammals, birds, reptiles and fishes. Recent findings reported their functional role in cancer. Aim of this study was to evaluate their DNA methylation modifications in squamous cell carcinoma (SCC) from different mammal species
Methods: Fifty SCC from 26 humans, 17 cats, 3 dogs, 1 horse, 1 bovine, 1 badger and 1 porcupine were investigated. Fourteen feline stomatitis and normal samples from 36 healthy human donors, 7 cats, 5 dogs, 5 horses, 2 bovines and 1 badger were collected as normal controls. Bisulfite Next Generation Sequencing evaluated the DNA methylation level from seven UCNEs (uc.160, uc.283, uc.416, uc.339, uc.270, uc.299, uc.328).
Results: 57/59 CpGs were significantly different according to the Kruskal-Wallis test (P<0.05) comparing normal vs SCC. A common DNA hypermethylation pattern was observed in SCC from all the species evaluated in this study, with an increasing trend of hypermethylation starting from normal mucosa, through stomatitis to SCC.
Conclusions: Our findings indicate that UCNEs are hypermethylated in human SCC, and this behavior is also conserved among different species of mammals.

sample_organism:
Homo sapiens
Canis lupus familiaris
Meles meles
Felis catus
Equus caballus
Bos taurus
Hystrix cristata

first: Silvia

last: Sabattini

first: Andrea

last: Renzi

first: Antonella

last: Rigillo

first: Giuliano

last: Bettini

first: Eva

last: Dervas

first: Alexandria

last: Schauer

first: Marco

first: Davide

last: Gissi

first: Achille

last: Tarsitano

first: Stefania

last: Evangelisti

first: Caterina

last: Tonon


title: Fra2 ChIP-seq analysis of MCF7 cells treated with abemaciclib

summary: We measured changes in AP-1 binding after treatment of MCF7 cells with abemaciclib

overall_design: Examination of changes in Fra2 binding in MCF7 cells after treatment with abemaciclib


title: 5-hydroxymethylation highlights the heterogeneity in keratinization and cell junctions in head and neck cancers

city: Ann Arbor

first: Siyu

last: Liu

state: MI

address: 100 Washtenaw avenue

department: Bioinformatics

institute: University of Michigan

summary: Purpose: 5hmC is found to be depleted in many human cancers, but its heterogeneity among HNSCC subtypes has not been studied. Experimental Design: we collected18 HPV(+) and 18 HPV(-) HNSCC samples and studied the effect of 5hmC both by HPV status and by HPV(+) subtype.

overall_design: 18 HPV(+) and 18 HPV(-) primary head and neck cancer samples and their matched blood samples were collected and sequenced with hydroxymethylated DNA immunoprecipitation sequencing (hMeDIP-seq)

first: Maureen

last: Sartor

first: Laura

last: Rozek

first: Marcell

last: Costa de Medeiros

first: Evan

last: Fernandez

first: Katie

last: Zarins

first: Raymond

last: Cavalcante

first: Gregory

last: Wolf

first: Tingting

last: Qin

first: Maria

last: Figueroa

first: Nisha

last: D'Silva


title: Interfollicular epidermal differentiation is gradualistic rather than stepwise with GRHL3 controlling progression from stem to transition cell states

city: Irvine

first: Bogi

last: Andersen

address: 205 Sprague Hall

institute: University of California, Irvine

summary: Although interfollicular epidermal (IFE) differentiation is thought to be stepwise as reflected in sharp boundaries between the basal, spinous, granular and cornified layers, this prediction has not been studied at a single cell resolution.  We used single cell RNA-seq to show that IFE differentiation is best described as a single step gradualistic process with a large number of transition cells between the basal and spinous layer. RNA-velocity analysis identifies a commitment point that separates the plastic basal and transition cell state from the unidirectionally differentiating cells. We also show that GRHL3, best known for promoting IFE terminal differentiation, has a major function in suppressing epidermal stem cell expansion and the emergence of an abnormal stem cell state by suppressing Wnt signaling in stem cells.

overall_design: Droplet Based Single Cell RNA sequencing libraries were generated from E14.5 mouse back skin (2 wild type and 2 Grhl3 -/- (KO)), E16.5  mouse back skin (2 wild type and 2 Grhl3 -/- ) and P0 mouse epidermis (3 wild type and 2 Grhl3 -/- ) using the 10X Genomics Chromium Platform and sequenced on the Illumina HiSeq 4000

first: Ziguang

last: Lin


title: Optimized high-order low-dose drug mixtures boost selectivity and efficacy of colorectal carcinoma treatment

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

institute: University of Geneva

summary: Colorectal carcinoma is currently treated with a combination of chemotherapeutics, often supplemented with targeted drugs. Despite recent improvements, an urgent need exists for improved efficacy, especially at late stage disease, and minimized side effects. Therefore, we employed the recently developed mathematical approach of the phenotypically-driven therapeutically guided multidrug optimization (TGMO) technology, to identify individualized optimal drug combinations (ODCs). Using this technology we obtained low dose synergistic and selective ODCs for a panel of human colorectal carcinoma cells, active in 3-dimensional heterotypic co-culture models. RNA sequencing and phosphoproteomics analyses showed that the mechanisms of action of these ODCs converge towards MAP kinase signaling and cell cycle inhibition despite differential cell mutation status, transcript expression levels and protein kinase phosphorylation state. Two cell-specific ODCs were subsequently translated to two in vivo models. Interestingly, the ODCs reduced tumor growth by approximately 80% and significantly outperformed the standard chemotherapy (FOLFOX). Complete lack of toxicity was observed for the ODCs, while still significant after FOLFOX therapy. Pharmacokinetics demonstrated that the drug combinations showed significantly enhanced bioavailability. Finally, the high-order ODCs were also active in freshly isolated cells from patient tumor tissues. Taken together, we show that the TGMO technology efficiently guides towards selective and potent low-dose drug combinations, optimized regardless of tumor mutation status and outperforming conventional chemotherapy.

overall_design: RNA sequencing was conducted for six CRC cell lines treated with CTRL and optimized drug combinations (ODCs), providing samples in duplicate. RNA-seq library preparations was conducted with SMART-Seq v4 Ultra Low Input RNA kit combined with Nextera technology (Illumina). Libraries were sequenced using a HiSeq 4000 Illumina sequencer according to 100 n single read protocol with a minimum of 50 M reads per cell culture sample library.

first: Marloes

last: Zoetemelk

first: George

last: Ramzy

first: Magdalena

last: Rausch

first: Thibaud

last: Koessler

first: Judy

middle: R

last: van Beijnum

first: Andrea

last: Weiss

first: Valentin

last: Mieville

first: Sander

last: Piersma

first: Richard

last: de Haas

first: Céline

last: Delucinge-Vivier

first: Axel

last: Andres

first: Christian

last: Toso

first: Alexander

middle: A

last: Henneman

first: Myléne

last: Docquier

first: Thomas

last: McKee

first: Connie

last: Jimenez

first: Youssef

last: Daali

first: Arjan

middle: W

last: Griffioen

last: Rubbia-Brandt

first: Pierre-Yves

last: Dietrich

first: Patrycja

last: Nowak-Sliwinska


title: H3K27ac ChIP-seq analysis of human breast cancer cell lines treated with abemaciclib, fulvestrant

first: Shom

last: Goel

summary: We measured changes in H3K27ac after treatment of human breast cancer cell lines with abemaciclib, fulvestrant

overall_design: Examination of changes in H3K27ac in breast cancer cell lines after treatment with DMSO (control), abemaciclib, and/or fulvestrant


title: H3K9me3 ChIP-seq analysis of human breast cancer cell lines treated with abemaciclib

status: Public on Aug 31 2020

summary: We measured changes in H3K9me3 after treatment of human breast cancer cell lines with abemaciclib

overall_design: Examination of changes in H3K9me3 in breast cancer cell lines after treatment with abemaciclib


title: Mechanisms of interleukin 4 mediated increase in efficacy of vaccines against opioid use disorders.

city: MINNEAPOLIS

first: Marco

last: Pravetoni

state: Minnesota

address: NILS HASSELMO HALL, 312 CHURCH ST SE, NILS HASSELMO HALL

department: Pharmacology

institute: University of Minnesota

summary: We report our results of RNA-sequencing analysis of mouse lymph nodes and spleens after administration of an anti-oxycodone vaccine (OXY-sKLH) or carrier protein control (sKLH) with and without concurrent antibody-based depletion of interleukin-4 (IL-4)

overall_design: Mice were vaccinated with OXY-sKLH or sKLH (control) with and without depletion of IL-4 using a monoclonal antibody. Lymph nodes and spleens were harvested on day 7 after vaccination and processed into a single cell suspension. Activated T cells were sorted via FACs and were defined as Ghost Dye- CD11c- F4/80- B220- CD8a- CD90.2+ CD4+ CD44+ cells. RNA was extracted from sorted cells using chloroform/trizol and collected using an RNA isolation kit. Samples were processed using a Clontech pico mammalian RNA library preparation. Libraries were sequenced on an Illumina NextSeq with 75 pair-end sequencing with samples acquiring an average of 30 million reads per sample.

first: Bethany

last: Crouse

first: April

last: Kelcher

first: Juan

last: Abrahante


title: Design of an unbiased machine learning workflow to predict Multiple Sclerosis staging from blood transcriptome

city: milan

first: massimo

last: acquaviva

state: mi

address: Via Olgettina, 60

institute: San Raffaele Hospital

summary: Construction of gene expression-based classifiers to predict the different Multiple Sclerosis stages from peripheral blood mononuclear cells (PBMC) transcriptome of MS patients and controls.

overall_design: Total RNA obtained from PBMCs of patients affected with different MS forms was used to build  highly specific gene expression-based classifiers predicting single MS stages and differentiating MS state from healthy controls and other neurological diseases. .

first: Massimo

last: Acquaviva

first: Cinthia

last: Farina


title: ATAC-seq analysis of human breast cancer cell lines treated with abemaciclib

summary: We measured changes in chromatin accessibility after treatment of human breast cancer cell lines with abemaciclib

overall_design: Examination of changes in ATAC-seq signal in duplicate


title: Estrogen Receptor ChIP-seq analysis of MCF7 cells treated with abemaciclib

summary: We measured changes in ER binding after treatment of MCF7 cells with abemaciclib

overall_design: Examination of changes in ER binding in MCF7 cells after treatment with abemaciclib


title: RNA seq analysis of Nfe2 expressing 4T1 and TS/A cells

city: Kanazawa

first: Soichiro

last: Sasaki

address: Kakuma-machi

institute: Cancer Research Institute, Kanazawa University

summary: We founed enhanced Nfe2 mRNA expression in bone tropic mouse breast cancer cell lines, 4T1.3, grown in a bone cavity, compared with in vitro culture condition. Thus, we examined about the function of Nfe2 in tumor growth in bone microenvironment in this study.

overall_design: Total RNA was extracted from mouse breast cancer cell lines 4T1 and TS/A cells which wre transduced Nfe2 gene. The resultant total RNAs were subjected to RNAseq.

first: Sadahiro

last: Iwabuchi

first: Shin-ichi

last: Hashimoto

first: Naofumi

last: Mukaida


title: Massively parallel identification of cis-regulatory variants in yeast promoters

city: Minneapolis

first: Frank

middle: Wolfgang

last: Albert

state: MN

address: 6-160 Jackson Hall, 321 Church St SE

department: Department of Genetics, Cell Biology, & Development

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

sample_organism:
Escherichia coli
Saccharomyces cerevisiae

overall_design: Refer to individual Series


title: G-protein coupled receptor Gpr115 (Adgrf4) is required for enamel mineralization mediated by ameloblasts

city: Sendai

first: Yuta

last: Chiba

state: Miyagi

address: 4-1 Seiryo-cho, Aoba-ku

institute: Tohoku University

summary: Dental enamel, the hardest tissue in the human body, is derived from dental epithelial cell ameloblast-secreted enamel matrices. Enamel mineralization occurs in a strictly synchronized manner along with ameloblast maturation in association with ion transport and pH balance, and any disruption of these processes results in enamel hypomineralization. G-protein coupled receptors (GPCRs) function as transducers of external signals by activating associated G-proteins and regulate cellular physiology. Tissue-specific GPCRs play important roles in organ development, though their activities in tooth development remains poorly understood. The present results show that the adhesion-GPCR Gpr115 (Adgrf4) is highly and preferentially expressed in mature ameloblasts and plays a crucial role during enamel mineralization. To investigate the in vivo function of Gpr115, knockout (Gpr115-KO) mice were created and found to develop hypo-mineralized enamel, with a larger acidic area due to the dysregulation of ion composition. Transcriptomic analysis also revealed that deletion of Gpr115 disrupted pH homeostasis and ion transport processes in enamel formation. In addition, in vitro analyses using the dental epithelial cell line Cervical Loop-Derived Dental Epithelial (CLDE) cell demonstrated that Gpr115 is indispensable for the expression of carbonic anhydrase 6 (Car6), which has a critical role in enamel mineralization. Furthermore, an acidic condition induced Car6 expression under the regulation of Gpr115 in CLDE cells. Thus, we concluded that Gpr115 plays an important role in enamel mineralization via regulation of Car6 expression in ameloblasts. The present findings indicate a novel function of Gpr115 in ectodermal organ development and clarify the molecular mechanism of enamel formation.

overall_design: Tooth germ mRNA profiles of 7-day old wild type (WT) and Gpr115-/- mice were generated by RNA-sequencing, in triplicate, using Illumina Hiseq1500.

first: Keigo

last: Yoshizaki

first: Kan

last: Saito

first: Tomoko

last: Ikeuchi

first: Tsutomu

last: Iwamoto

first: Craig

last: Rhodes

first: Takashi

last: Nakamura

first: Susana

last: de Vega

first: Robert

middle: J

last: Morell

first: Erich

last: Boger

first: Daniel

last: Martin

first: Ryoko

last: Hino

first: Hiroyuki

last: Inuzuka

first: Christopher

middle: K

last: Bleck

first: Aya

last: Yamada

first: Yoshihiko

first: Satoshi

last: Fukumoto


title: Massively parallel identification of cis-regulatory variants in yeast promoters - Experimental measurements

first: Frank

last: Albert

summary: Sequence variation in regulatory DNA alters gene expression and shapes genetically complex traits. However, the identification of individual, causal regulatory variants is challenging. Here, we used a massively parallel reporter assay to measure the cis-regulatory consequences of 5,832 natural DNA variants in the promoters of 2,503 genes in the yeast Saccharomyces cerevisiae. We identified 451 causal variants, which underlie genetic loci known to affect gene expression. Several promoters harbored multiple causal variants. In five promoters, pairs of variants showed non-additive, epistatic interactions. Causal variants were enriched at conserved nucleotides, tended to have low derived allele frequency, and were depleted from promoters of essential genes, consistent with the action of negative selection. Causal variants were enriched for alterations in transcription factor binding sites. Models integrating these features provided modest, but statistically significant, ability to predict causal variants. This work revealed a complex molecular basis for cis-acting regulatory variation.

overall_design: This study used a massively parallel reporter assay to study cis-effects of yeast promoter variants on gene expression. This repository provides the experimental measurements. The project used designed, synthetic DNA oligos. Each oligo was tagged with multiple, randomly assigned DNA barcodes. There were two sub-libraries ("TSS" and "Upstream"). Each of these sub-libraries had multiple replicates from separate growth cultures. For each replicate, we sequenced barcodes from cDNA (to measure expression driven by the given oligo; indicated here by a “treatment” called “RNA”) and plasmid DNA (to normalize for unequal library composition; treatment “DNA”). In the TSS library, two samples (TSS_2016_A1 and TSS_2016_A2) are technical replicates, as are TSS_2016_B1 and TSS_2016_B2. Each sub-library has two processed data files.

first: Rocky

last: Cheung

first: Kaushik

last: Renganaath

first: Laura

last: Day

first: Sriram

last: Kosuri

first: Leonid

last: Kruglyak


title: Gene expression analysis of the apical portion of pterygium and control conjunctiva tissues to screen the comprehensive gene expression levels

city: Kahoku

first: Eri

last: Kubo

state: Ishikawa

address: 1-1 Daigaku, Uchinada

department: Ophthalmology

institute: Kanazawa Medical University

summary: A sight threatening, pterygium is a common ocular surface disorders identified by fibrovascular growth of the cornea and induced by variety of stress factors, like ultraviolet (UV) exposure. However, the genes involved in the etiopathogenesis of this disease is not well studied.

overall_design: Relative gene expression profiles that are modulated in apical portion of pterygium compared to normal uninvolved conjunctival tissues were analyzed

first: Naoko

last: Shibata


title: FGFR4 is a regulator of tumor subtype differentiation in luminal breast cancer and metastatic disease II

city: Chapel Hill

first: Charles

middle: M.

last: Perou

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

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

institute: University of North Carolina at Chapel Hill

summary: Mechanisms driving tumor progression from less aggressive subtypes to more aggressive states represent key targets for breast cancer therapy. We identified a subset of Luminal A primary breast tumors to give rise to HER2-enriched (HER2E) subtype metastases, but remain clinically HER2 negative (cHER2-). By testing the unique genetic and transcriptomic features of these cases, we developed the hypothesis that fibroblast growth factor receptor 4 (FGFR4) likely participates in this subtype switching. To evaluate this, we developed two FGFR4 genomic signatures using a PDX model treated with a FGFR4 inhibitor (BLU9931), which inhibited PDX growth in vivo. Bulk tumor gene expression analysis, and single cell RNAseq demonstrated that the inhibition of FGFR4 signaling caused molecular switching. Examining patient outcomes in the METABRIC breast cancer cohort showed that the FGFR4-induced and FGFR4-repressed signatures each predicted overall survival (OS) (HR=6.30, P<0.0001; HR=0.33; P<0.0001, respectively). Multivariate analysis showed that the FGFR4-induced signature was also an independent prognostic factor beyond subtype and stage for OS (HR=2.34, P=0.014). Supervised analysis of 77 primary tumors with paired metastasis revealed that the FGFR4-induced signature was significantly higher in luminal/ER+ tumor metastases compared with their primaries. Finally, multivariate analysis demonstrated that the FGFR4-induced signature also predicted site-specific metastasis for lung, liver and brain, but not for bone or lymph nodes. These data identify a link between FGFR4-regulated genes and metastasis, suggesting treatment options for FGFR4-positive patients, whose high expression is not caused by mutation or amplification.

overall_design: **Raw data are available at dbGAP phs001866 **

first: Matthew

last: Soloway


title: Batf3 programs CD8 T cell memory

city: Würzburg

first: Wolfgang

last: Kastenmüller

address: Versbacher Str. 9

institute: University of Wuerzburg

summary: Anti-viral CD8 T cell responses are characterized by an initial activation/priming of T lymphocytes followed by a massive proliferation, subset differentiation, population contraction and the development of a stable memory pool. The transcription factor BATF3 has been shown to play a central role in the development of conventional dendritic cells (cDC1), which in turn are critical for the optimal priming of CD8 T cells. Here we show that BATF3 is expressed within the first days after priming but has long-lasting T cell intrinsic effects. We found that T cells that lack Batf3 show a normal expansion and differentiation, yet succumbed to an aggravated contraction and had a diminished memory response. Vice versa BATF3-overexpression in CD8 T cells promoted their survival and transition to memory. Mechanistically, BATF3 regulates T cell apoptosis and longevity via the proapoptotic factor BIM. By programing CD8 T cell survival and memory, BATF3 is a promising molecule to optimize adoptive T cell therapy in patients.

overall_design: CD8+ T cells were isolated from spleen of TCR transgenic OT-I mice. Cells were transduced either with an empty or Batf3 expressing vector (see the Retroviral transduction M&M session). Successfully transduced CD8 T cells were FACS sorted and cultured for 6h in supplemented medium with IL-15 (100ng/ml) (non-stimulated) or supplemented medium plus anti-CD3/CD28 (1ug/ml) (stimulated). Three technical replicates from each condition were used for the bulk sequencing.

first: Marco

last: Ataide

last: Kastenmueller


title: Agonist-Induced Functional Analysis and Cell Sorting is a novel tool to uncover interneuron impairment: Fragile X Syndrome as a proof of concept

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: We created the agonist-induced Functional Analysis and Cell Sorting (aiFACS) technique to simultaneously stimulate, record and sort neurons from mouse whole brains upon pharmacological stimulation in real time.

overall_design: Single cell transcriptomics of neuronal cells aiFACS baseline and AMPA stimulation.

first: Sara

last: Castagnola

first: Julie

last: Cazareth

first: Virginie

last: Magnone

first: Barbara

last: Bardoni

first: Thomas

last: Maurin


title: Batf3 programs CD8 T cell memory

overall_design: CD8+ T cells were isolated from spleen of either WT or Batf3-/-  mice. Splenocytes were enriched for CD8 T cells and cultured for either 48h or 72h in supplemented medium with IL-15 (50ng/ml)  plus anti-CD3/CD28 (1µg/ml). Four technical replicates from each condition were used for the bulk sequencing.


title: Chronic Inflammation Prediction for Inhaled Particles, the Impact of Material Cycling and Quarantining in the Lung Epithelium

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary: We are daily exposed to a multitude of health hazardous airborne particulate matter with notable deposition in the fragile alveolar region of our lungs. Hence, there is a great need for identification and prediction of material-associated diseases, currently hindered due to the lack of in-depth understanding of causal relationships, in particular between acute exposures and chronic symptoms. By applying advanced microscopies and omics to in vitro and in vivo systems, together with in silico molecular modelling, we have here determined that the long-lasting response to a single exposure can originate from the interplay between the newly discovered nanomaterial quarantining and nanomaterial cycling between different lung cell types. This new insight finally allows us to predict the spectrum of lung inflammation associated with materials of interest using only in vitro measurements and in silico modelling potentially relating outcomes to material properties for large number of materials thus boosting safe-by-design-based material development. Because of its profound implications for animal-free predictive toxicology, our work paves the way to a more efficient and hazard-free introduction of numerous new advanced materials into our lives.

overall_design: We performed gene expression microarray analysis of LA-4 cells, MH-S cells or cocultures treated with TiO2 nanotubes (for 4h or 48h) or controls (for 0h or 48h)

first: Hana

last: Majaron

first: Boštjan

last: Kokot

first: Aleksandar

last: Sebastijanović

first: Carola

last: Voss

first: Rok

last: Podlipec

first: Patrycja

last: Zawilska

first: Trine

last: Berthing

first: Carolina

last: Ballester

first: Pernille

last: Danielsen

first: Claudia

last: Contini

first: Mikhail

last: Ivanov

first: Ana

last: Krišelj

first: Petra

last: Čotar

first: Qiaoxia

last: Zhou

first: Jessica

last: Ponti

first: Vadim

last: Zhernovkov

last: Schneemilch

first: Mojca

last: Pušnik

first: Polona

last: Umek

first: Stane

last: Pajk

first: Olivier

last: Joubert

first: Otmar

last: Schmid

first: Iztok

last: Urbančič

first: Martin

last: Irmler

first: Vladimir

last: Lobaskin

first: Sabina

last: Halappanavar

first: Nicholas

last: Quirke

first: Alexander

last: Lyubartsev

first: Ulla

last: Vogel

first: Tilen

last: Koklič

first: Tobias

last: Stöger

first: Janez

last: Štrancar


title: A latent lineage potential in resident neural stem cells

city: Stockholm

first: Enric

last: Llorens Bobadilla

address: Solnavägen 9

country: Sweden

institute: Karolinska Institutet

summary: Injuries to the central nervous system (CNS) are inefficiently repaired. Resident neural stem cells exist, but manifest a very limited contribution to cell replacement. Here we uncover a latent potential in neural stem cells to replace large numbers of oligodendrocytes in the injured mouse spinal cord. Using single cell genomics we found that neural stem cells are in a permissive chromatin state that enables the unfolding of a normally latent gene expression program for oligodendrogenesis after injury. Once unveiled, stem cell-derived oligodendrogenesis is abundant, follows the natural progression of oligodendrocyte differentiation, contributes to axon remyelination and stimulates functional recovery of axon conduction. Resident stem cells can thus serve as a meaningful reservoir for cellular replacement and constitute an alternative to cell transplantation after CNS injury.

overall_design: Interrogation via single cell RNA and open chromatin sequencing experiments of cells isolated from the mouse central nervous system

middle: L

last: Bobadilla

first: Margherita

last: Zamboni

first: Joseph

last: Bergenstrahle

first: Jonas

last: Frisén


title: Comparative analysis of cellular heterogeneity in the LAM lung using scRNA-seq

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary: Investigate detailed cellular composition of the LAM lung compared to the age and sex matched healthy control, in order to isolate LAM-lung-specific cellular states or subtypes.

overall_design: Age-and sex-matched donor lung explants from control healthy and LAM patients were subjected to the single cell transcriptomocs analysis in parallel (n=1 each). Sample prepartion included creating a single cell suspension and immune cell pre-depletion using human anti-CD45 MACS beads. 10% of CD45+ cells were addded back to the samples to comprise 20K cells for the 10x genomics capture. Obtained libraries were sequenced in 2 repeats using Illumina HiSeq

first: Maria

last: Basil

first: Justine

last: Carl

first: Kseniya

last: Obraztsova


title: Investigation of the gene expression changes triggered by the lung mesenchymal Tsc2KO in each major cell subpopulation of the adult mouse lung

summary: Tumor suppressor Tuberous sclerosis complex 2 (TSC2) is a key negative regulator of mammalian target of rapamycin (mTOR), a central controller of cell growth and metabolism in health and disease. Loss of TSC2 induces the constitutive activation of mTORC1 in rare lung disease pulmonary Lymphangioleiomyomatosis (LAM), which affects only women of childbearing age and characterized by lung destruction and progressive loss of pulmonary function. Little is known how TSC2 loss induces LAM and what is the LAM cell of origin. To determine cell-type specific effects of TSC2 loss and mTORC1 activation on lung homeostasis we generated new transgenic mice with targeted Tsc2 deletion in lung mesenchyme Tbx4-Cre+Tsc2flox/flox and lung epithelium Shh-Cre+Tsc2flox/flox. Both Tbx4-Cre+, Tsc2flox/flox and Shh-Cre+, Tsc2flox/flox mice were viable and fertile. Adult Tbx4-Cre+Tsc2flox/flox mice demonstrated mTORC1 activation in lung mesenchyme, progressive alveolar enlargement, female-specific pulmonary function decline and prgenancy-induced lesion growth. To investigate molecular mechanism underlying observed phenotypic changes in the Tsc2KO lungs  we performed comparative bulk-RNAseq analysis of the gene expression changes in the major cell subpopulations of the adult female 8-week-old Tsc2KO mouse lungs compared to the age- and sex-matched WT controls.

overall_design: Cell population RNA-seq was performed in 3 biological replicates. 3 Tbx4CreTsc2KO and 3 Tbx4CreTsc2WT muse lungs were subjected to the digest and consecutive-depletion-based  magnetic beads sort using antibodies against the appropriate cell surface markers: 1) CD45+ (immune cells), 2) CD45-EpCAM+ (Epithelilal cells), 3) CD45-, EpCAM-, CD31+ (Vascular endothelial cells), 4) CD45-, EpCAM-, CD31-, PDPN+ (Lymphatic endothelial cells) and 5) All negative(CD45-, EpCAM-, CD31-, PDPN-) Mesenchymal cells. Total RNA was isolated from all cell subpopulations and subjected to the bulk mRNA sequencing using Illumina HiSeq2500.

first: Ryan

last: Rue


title: Large-scale Multi-omic Analysis of COVID-19 Severity

status: Public on Aug 29 2020

city: Albany

first: Adolfo

middle: Ariel

last: Jaitovich

address: 47 New Scotland Av

department: Molecular and Cellular Physiology

institute: Albany Medical Center

summary: Using RNA-seq and high-resolution mass spectrometry we performed a comprehensive systems analysis on 128 plasma and leukocyte samples from hospitalized patients with or without COVID-19 (n=102 and 26 respectively) and with differing degrees of disease severity. We generated abundance measurements for over 17,000 transcripts, proteins, metabolites, and lipids and compiled them with clinical data into a curated relational database. This resource offers the unique opportunity to perform systems analysis and cross-ome correlations to both molecules and patient outcomes. In total 219 molecular features were mapped with high significance to COVID-19 status and severity, including those involved in processes such as complement system activation, dysregulated lipid transport, and B cell activation. In one example, we detected a trio of covarying molecules – citrate, plasmenyl-phosphatidylcholines, and gelsolin (GSN) – that offer both pathophysiological insight and potential novel therapeutic targets. Further, our data revealed in some cases, and supported in others, that several biological processes were dysregulated in COVID-19 patients including vessel damage, platelet activation and degranulation, blood coagulation, and acute phase response. For example, we observed that the coagulation-related protein, cellular fibronectin (cFN), was highly increased within COVID-19 patients and provide new evidence that the upregulated proteoform stems from endothelial cells, consistent with endothelial injury as a major activator of the coagulation cascade. The abundance of prothrombin, which is cleaved to form thrombin during clotting, was significantly reduced and correlated with severity and might help to explain the hyper coagulative environment of SARS-CoV-2 infection. From transcriptomic analysis of leukocytes, we concluded that COVID-19 patients with acute respiratory distress syndrome (ARDS) demonstrated a phenotype that overlapped with, but was distinct from, that found in patients with non-COVID-19-ARDS. To aid in the global efforts toward elucidation of disease pathophysiology and therapeutic development, we created a web-based tool with interactive visualizations allowing for easy navigation of this systems-level compendium of biomolecule abundance in relation to COVID-19 status and severity. Finally, we leveraged these multi-omic data to predict COVID-19 patient outcomes with machine learning, which highlighted the predictive power of these expansive molecular measurements beyond the standardized clinical estimate of 10-year survival Charlson score.

overall_design: 126 samples were analyzed in total with 100 COVID-19 patients and 26 non-COVID-19

first: Ariel

last: Jaitovitch

last: Balnis

first: Scott

last: Swanson


title: Comparative analysis of cellular heterogeneity in the LAM lung using bulk RNA-seq and scRNA-seq

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Massively parallel identification of cis-regulatory variants in yeast promoters - Annotation runs

first: Frank

last: Albert

overall_design: This study used a massively parallel reporter assay to study cis-effects of yeast promoter variants on gene expression. This repository provides sequencing data used in barcode annotation. Specifically, the project used designed, synthetic DNA oligos, each tagged with multiple DNA barcodes of length 20 bp that were randomly assigned by PCR. The annotation runs mapped each barcode to the oligo it tagged. There were two sub-libraries ("TSS" and "Upstream"). Each sub-library has its own annotation run, with separate raw data and processed data.

first: Rocky

last: Cheung

first: Kaushik

last: Renganaath

first: Laura

last: Day

first: Sriram

last: Kosuri

first: Leonid

last: Kruglyak


title: Molecular basis of CTCF binding polarity in genome folding

status: Public on Aug 30 2020

city: San Francisco

first: Elphege

last: Nora

state: CA

address: 555 Mission Bay Boulevard South

department: Cardiovascular Research Institute

institute: University of California San Francisco

summary: Current models propose that boundaries of mammalian topologically associating domains (TADs) arise from the ability of the CTCF protein to stop extrusion of chromatin loops by cohesin. While the orientation of CTCF motifs determines which pairs of CTCF sites preferentially stabilize loops, the molecular basis of this polarity remains mysterious. Here we report that CTCF positions cohesin but does not control its overall binding dynamics on chromatin by single molecule live imaging. Using an inducible complementation system, we found that CTCF mutants lacking the N-terminus cannot insulate TADs properly. Cohesin remained at CTCF sites in this mutant, albeit with reduced enrichment. Given that the orientation of the CTCF motif presents the CTCF N-terminus towards cohesin as it translocates from the interior of TADs, these observations explain how the orientation of CTCF binding sites determines the genomic distribution of chromatin loops.

overall_design: ChIP-seq, Hi-C and 5C in mouse ES cells harboring an auxin-inducible degron on endogenous CTCF alleles and expressing dox-inducible mutant CTCF transgenes. WT parental cells are E14tg2a (129 X,Y background).

first: Elphège

last: Caccianini

first: Geoffrey

last: Fudenberg

first: Kevin

last: So

first: Vasumathi

last: Kameswaran

first: Abigail

last: Nagle

first: Alec

last: Uebersohn

first: Bassam

last: Hajj

first: Agnès

last: Le Saux

first: Antoine

last: Coulon

last: Mirny

first: Katherine

middle: S

last: Pollard

first: Maxime

last: Dahan

first: Benoit

last: Bruneau