title: The BRD9/7 Inhibitor TP-472 Blocks Melanoma Tumor Growth by Suppressing ECM-Mediated Oncogenic Signaling and Inducing Apoptosis

city: Birmimgham

first: Romi

last: Gupta

address: 720, 20th street south

institute: University of Alabama at Birmingham

summary: Melanoma accounts for the majority of all skin cancer-related deaths and only 1/3rd of melanoma patients with distal metastasis survive beyond five years. However, current therapies including BRAF/MEK targeted therapies or immunotherapies only benefit a subset of melanoma patients due to the emergence of intrinsic or extrinsic resistance mechanisms. Effective treatment of melanoma will thus require new and more effective therapeutic agents. Towards the goal of identifying new therapeutic agents, we conducted an unbiased, druggable epigenetic drug screen using a library of 32 epigenetic inhibitors obtained from the Structural Genome Consortium that targets proteins encoding for epigenetic regulators. This chemical genetic screening identified TP-472, which targets bromodomain-7/9, as the strongest inhibitor of melanoma growth in both short- and long-term survival assays and in mouse models of melanoma tumor growth. Mechanistically, using a transcriptome-wide mRNA sequencing profile we identified TP-472 treatment downregulates genes encoding various extracellular matrix (ECM) proteins, including integrins, collagens, and fibronectins. Reactome-based functional pathway analyses revealed that many of the ECM proteins are involved in extracellular matrix interactions required for cancer cell growth and proliferation. TP-472 treatment also upregulated several pro-apoptotic genes that can inhibit melanoma growth. Collectively, our results identify BRD7/9 inhibitor TP-472 as a potentially useful therapeutic agent for melanoma therapy.

overall_design: A375 cells treated with either DMSO, 5 microMolar and 10 microMolar  of TP-472 for 24 hours and these cells were used to prepare the total RNA, followed by RiboRNA depletion with random priming and RNASeq Illumina Hi-Seq 2500 platform, with three biological replicates for each sample.

first: Suresh

last: Chava


title: ∆Np63 executes an oncogenic program through the regulation of a common landscape of super-enhancer associated genes in non-small cell lung cancer

status: Public on Dec 23 2021

city: Tampa

first: Elsa

middle: Renee

last: Flores

state: FL

address: 12902 USF Magnolia Drive

department: Department of Molecular Oncology

country: USA

institute: Moffit Cancer Center

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Distinct lung stem cells give rise to lung adenocarcinoma (ADC) and squamous cell carcinoma (SCC). ΔNp63 guides development of these cells through regulation of terminal differentiation; however, its mechanistic role in lung cancer development has remained elusive. We utilized a ΔNp63-specific conditional knockout mouse model and found that ∆Np63 maintains lung ADC and SCC by keeping lung stem cells in quiescence. ChIP-seq analysis of lung basal cells and alveolar type 2 (AT2) cells lacking ∆Np63 revealed a robust loss of activating histone marks at super enhancers of cell identity genes defining a unifying oncogenic role for ∆Np63 in non-small cell lung cancer.

overall_design: Basal cells and AT2 cells isolated from ΔNp63fl/fl and ΔNp63Δ/Δ mice were analyzed by RNA-seq and ChIP-seq.

first: Cristian

last: Coarfa


title: The evolution, evolvability, and engineering of gene regulatory DNA [RNA-seq]

city: Cambridge

first: Carl

middle: G

last: de Boer

state: MA

address: 415 Main St

institute: The Broad Institute

summary: Here, we used RNA-seq to quantify expression conservation across many Ascomycete yeasts.

sample_organism:
Schizosaccharomyces pombe
Schizosaccharomyces japonicus
Schizosaccharomyces octosporus
Lachancea waltii
Saccharomyces bayanus
Saccharomyces cerevisiae
Yarrowia lipolytica
Candida albicans
Nakaseomyces glabratus
Naumovozyma castellii
Kluyveromyces lactis

overall_design: We used strand-specific RNA-seq (dUTP) to quantify mRNA expression in each species. There was one replicate per species, and all species were grown in BMW media to log phase. With the exception of N. castellii (25C), all others were grown at 30C. Expression conservation was calculated using the RPKM for each species using orthologous genes.

first: Lin

last: Fan

first: Xian

last: Adiconis

first: Joshua

middle: Z

last: Levin

first: Eeshit Dhaval

last: Vaishnav

first: Moran

last: Yassour


title: Batf-mediated Epigenetic Control of Effector CD8+ T Cell Differentiation (RNA-Seq)

status: Public on Dec 22 2021

city: Boston

first: Jim

last: Kaminski

address: 1 Blackfan Circle

institute: Boston Children's Hospital

summary: The response of naive CD8+ T cells to their cognate antigen involves rapid and broad changes in gene expression that are coupled with extensive chromatin remodeling, but the mechanisms governing these changes are not fully understood. In this study, we investigated how this process depends on the activity of the basic leucine zipper ATF-like transcription factor Batf, which is essential for the earliest phase of effector CD8+ T cell differentiation. Through genome scale profiling of multiple modalities, we characterized the role of Batf in chromatin organization at several levels, including the accessibility of key regulatory regions, the expression of nearby genes, and the interactions these regions make with each other and with key transcription factors. We quantified the dependencies between Batf and other transcription factors and identified a core transcription factor network that cooperated with Batf, including Irf4, and the transcription factors Runx3 and T-bet, which tended to co-localize with Batf and bind in regions whose accessibility and long-range interactions were mediated by Batf. We functionally demonstrated the synergistic activity of this network in initiating aspects of the effector T cells’ transcriptional and chromatin accessibility profiles in an ectopically-induced fibroblast system. Using HiChIP, we further found that overexpressing all four factors in fibroblasts was required to recapitulate important aspects of the CD8+ T cell chromatin architecture. Our results provided a comprehensive resource for studying the epigenomic and transcriptomic landscape of effector differentiation of cytotoxic T cells and suggested various modes of dependencies between transcription factors in this process.

overall_design: This submission contains the RNA-Seq portion of the data. There are three datasets, described below.     Ectopic_Expression_In_Fibroblasts  These samples are NIH/3T3 fibroblasts which were transduced with a doxycycline-inducible lentivirus consisting of any combination of Batf, Irf4, Runx3 and T-bet (16 combinations altogether). Ectopic expression of the respective TFs in a given sample were induced with doxycycline. Samples with and without doxycycline are included, resulting in 32 different conditions, with two replicates each, resulting in 64 samples.      CD8_In_Vitro_Timecourse   These samples are in vitro P14 CD8+ T Cells measured daily after stimulation at Day 1. Samples with and without restimulation are included for Day 6. A pre-stimulation sample at Day 0 is also included.    CD8_TCell_In_Vivo  These samples are in vivo P14 CD8+ T Cells with a Cre-Lox system enabling conditional knockout of Batf or Irf4. The samples were obtained 3.5 days after infection with an acute strain of LCMV.

first: Hsiao-Wei

last: Tsao


title: Mouse Embryo E11, E13, E15, E18 conditional knockout of EED, with wt controls

city: Brisbane

first: Stefan

last: Thor

state: QLD

address: Skerman Bldg (65) room 506  Faculty of Medicine

department: School of Biomedical Sciences

country: Australia

institute: The University of Queensland

summary: Floxed EED homozygote mice are knocked-out by Sox1-driven Cre to remove H3K27me3 during neurogenesis

overall_design: Control mice are compared to EED-cKO mice in bulk RNAseq, in dissected forebrain, midbrain, hindbrain and spinal cord, across embryonic time E11-E18

first: Jonathan

last: Rakar

first: Ariane

last: Mora

first: Ignacio

last: Monedero Cobeta

first: Behzad

last: Yaghmaeian Salmani

first: Annika

last: Starkenberg

first: Mikael

last: Boden


title: Intron-based inference of transcription factor activity allows accurate decoding of dynamic cellular processes

city: Beijing

first: Yan

last: WU

state: Beijing

address: No.5 Yiheyuan Road Haidian District, Beijing, P.R.China

department: Academy for Advanced Interdisciplinary Studies

country: China

institute: Peking University

summary: Activities of transcription factors (TFs) are temporally modulated to regulate dynamic cellular processes, including development, homeostasis, and disease. Understanding how these processes are regulated thus requires accurate analysis of TF activities. To analyze TF activities, existing methods often leverage the expression levels of the TF’s target genes using transcriptome data. However, because these methods typically use exon-based target expression levels, the estimated TF activities reflect multiple sources of regulation on target genes besides TF activity-dependent regulation, and thus may not faithfully recapitulate actual TF activities. To address this, we devised a TF activity measure using intron-based target expression levels, and implemented it to decode the temporal control of TF activities during dynamic biological processes. Using simulations and public datasets, we first showed that, compared to exon-based estimates, intron-based TF activities display higher correlations with input TF activities, TF nuclear localization levels, and TF chromatin occupancies, suggesting that intron-based measure can better recapitulate instantaneous TF activities. By analyzing public transcriptome data on circadian rhythm and by collecting time-series transcriptome data of T cell response, we found that intron-based TF activities provide an improved characterization of the circadian phasing for cycling TFs in circadian rhythm, and uncover two temporally opposing modules of TFs during T cell’s response to chemical mimics of antigens. Collectively, we anticipate that the proposed approach should be broadly applicable for decoding TF-mediated control of dynamic processes.

overall_design: Two biological replicates of Jurkat T-cells were stimulated with 50 ng/mL PMA and 1 uM Ionomycin for different durations (i.e., 3/6/9/12/15/30/45/60 min) and sequenced. Cells without stimulation were also sequenced and annotated as 0 min. Note that one replicate with 15 min treatment showed abnormal profile and was thus discarded.

last: Wu

first: Lingfeng

last: Xue

first: Wen

last: Huang

first: Minghua

last: Deng

first: Yihan

last: Lin


title: Analysis of miRNA expression in human Oral epithelial cells induced by S. gordonii

city: Lexington

first: kuey

middle: Chu

last: Chen

state: KENTUCKY

address: 800 Rose Street, UK Med Ctr

department: Pharmacology and Nutritional Sciences

institute: University of Kentucky

summary:
The mechanisms through which oral commensal bacteria mitigates uncontrolled inflammatory responses in the oral mucosa remain unknown. Here we evaluated the ability of S. gordonii to stimulate the expression of miRNAs in oral epithelial cells with potential to target chemokine expression.
The human oral epithelial cell line (OKF6) was exposed to different MOIs of S. gordonii for 24h and expression analysis of miRNAs performed using the Affymetrix platform.

overall_design: Oral epithelial cells (OKF6) were grown in 24-well plates overnight and exposed to different OEC:S. gordonii MOIs (1:10; 1:50; 1:100) for 24h, followed by RNA isolation and miRNA expression analysis using the GeneChip miRNA 4.0 Array.

first: Octavio

middle: A

last: Gonzalez


title: Expression profiling of prognostic liver signature in clinical fibrotic liver tissues cultured with various anti-fibrotic and chemopreventive agents

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary:
Background/Aims: There is a major unmet need to assess prognostic impact of anti-fibrotics in clinical trials due to the slow rate of liver fibrosis progression. We aimed to develop a surrogate biomarker to predict future fibrosis progression.
Methods: A Fibrosis Progression Signature (FPS) was defined to predict fibrosis progression within 5 years in HCV and NAFLD patients with no to minimal fibrosis at baseline (n=421), and validated in an independent NAFLD cohort (n=78). The FPS was used to assess response to 13 candidate anti-fibrotics in organotypic ex vivo cultures of clinical fibrotic liver tissues (n=78), and cenicriviroc in NASH patients enrolled in a clinical trial (n=19, NCT02217475). A serum-protein-based surrogate FPS (FPSec) was developed and technically evaluated in a liver disease patient cohort (n=79).
Results: A 20-gene FPS was defined and validated in an independent NAFLD cohort (aOR=10.93, AUROC=0.86). Among computationally inferred fibrosis-driving FPS genes, BCL2 was confirmed as a potential pharmacological target using clinical liver tissues. Systematic ex vivo evaluation of 13 candidate anti-fibrotics identified rational combination therapies based on epigallocatechin gallate, some of which were validated for enhanced anti-fibrotic effect in ex vivo culture of clinical liver tissues. In NASH patients treated with cenicriviroc, FPS modulation was associated with 1-year fibrosis improvement accompanied by suppression of the E2F pathway. Induction of PPAR-alfa pathway was absent in patients without fibrosis improvement, suggesting benefit of combining PPAR-alfa agonism to improve anti-fibrotic efficacy of cenicriviroc. A 7-protein FPSec panel showed concordant prognostic prediction with FPS.
Conclusion: FPS predicts long-term fibrosis progression in an etiology-agnostic manner, which can inform anti-fibrotic drug development.

overall_design: Gene expression profiling of snap-frozen surgical liver tissues treated with various anti-fibrotic and chemopreventive agents in ex vivo precision-cut liver slice (PCLS) culture. The samples in the FPS validation set 2.

first: Tongqi

last: Qian

first: Naoto

last: Fujiwara

first: Bhuvaneswari

last: Koneru

first: Shijia

last: Zhu


title: Batf-mediated Epigenetic Control of Effector CD8+ T Cell Differentiation (ATAC-Seq)

first: Jim

last: Kaminski

overall_design: This submission contains the ATAC-Seq portion of the data. There are three datasets, described below.     Ectopic_Expression_In_Fibroblasts  These samples are NIH/3T3 fibroblasts which were transduced with a doxycycline-inducible lentivirus consisting of any combination of Batf, Irf4, Runx3 and T-bet (16 combinations altogether). Ectopic expression of the respective TFs in a given sample were induced with doxycycline. Samples with and without doxycycline are included, resulting in 32 different conditions, with two replicates each, resulting in 64 samples.      CD8_TCell_In_Vitro  These samples are in vitro P14 CD8+ T Cells measured six days after initial stimulation. Samples with and without restimulation are included for Day 6 for WT and Batf KO    CD8_TCell_In_Vivo  These samples are in vivo P14 CD8+ T Cells with a Cre-Lox system enabling conditional knockout of Batf or Irf4. The samples were obtained 3.5 days after infection with an acute strain of LCMV.

first: Hsiao-Wei

last: Tsao


title: Gibberellins regulate ovule number through a DELLA-CUC2 complex in Arabidopsis

city: Valencia

first: Javier

last: Forment

state: Valencia

address: Ingeniero Fausto Elio, s/n

department: Biotecnología

country: Spain

institute: Instituto de Biología Molecular y Celular de Plantas, IBMCP (UPV-CSIC)

summary: Ovule development is a key process for plant reproduction that ensures correct seed production. Understanding the molecular mechanisms that control ovule formation will also provide new approaches to increase crop yield for breeding. Several molecular factors and plant hormones, including gibberellins, are involved in ovule initiation and development. Gibberellins control ovule development by the destabilization of DELLA proteins, whereas DELLA activity has been proved to act as a positive factor for ovule primordia emergence. But the molecular mechanism by which DELLA act remained unknown. Here we have proved that DELLA proteins control ovule initiation by the formation of a protein complex with the CUC2 transcription factor. The DELLA protein GAI requires CUC2 to promote ovule primordia formation, thus GAI would function by its direct protein-protein interaction with CUC2 in cells of the placenta that determine the boundary regions between ovules during pistil development. Analysis of GAI-CUC2 interaction and colocalization in placenta support this hypothesis. Moreover, molecular analysis of the loci at which GAI protein may act as transcriptional co-regulators in a CUC2-dependent manner identified a subset of target genes that would be regulated by the GAI-CUC2 complex and contribute to regulate ovule primordia emergence.

overall_design: ChIP-Seq of chromatin from inflorescences of pGAI:gai∆17-3xYPet, pGAI:gai∆17-3xYPet cuc2-1, and non-transgenic Arabidopsis thaliana plants.

first: Barro-Trastoy

last: Daniela

first: Gomez

last: Maria Dolores

first: Tornero

last: Pablo

first: Perez-Amador

last: Miguel A.


title: Prognostic liver signature profiles in biopsy tissues from non-alcoholic fatty liver disease patients followed for fibrosis progression

overall_design: Gene expression profiling of formalin-fixed paraffin-embedded liver biopsy tissues obtained at the time of enrollment and follow-up. The samples in the FPS validation set 1.

first: Atsushi

last: Ono

first: Kazuaki

last: Chayama


title: Batf-mediated Epigenetic Control of Effector CD8+ T Cell Differentiation

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

overall_design: Refer to individual Series


title: Prognostic Liver Signature profiles in biopsy tissues from non-alcoholic fatty liver disease (NAFLD) patients in Japan

summary: Background/Aims: There is a major unmet need to assess prognostic impact of anti-fibrotics in clinical trials due to the slow rate of liver fibrosis progression. We aimed to develop a surrogate biomarker to predict future fibrosis progression.  Methods: A Fibrosis Progression Signature (FPS) was defined to predict fibrosis progression within 5 years in HCV and NAFLD patients with no to minimal fibrosis at baseline (n=421), and validated in an independent NAFLD cohort (n=78). The FPS was used to assess response to 13 candidate anti-fibrotics in organotypic ex vivo cultures of clinical fibrotic liver tissues (n=78), and cenicriviroc in NASH patients enrolled in a clinical trial (n=19, NCT02217475). A serum-protein-based surrogate FPS (FPSec) was developed and technically evaluated in a liver disease patient cohort (n=79).  Results: A 20-gene FPS was defined and validated in an independent NAFLD cohort (aOR=10.93, AUROC=0.86). Among computationally inferred fibrosis-driving FPS genes, BCL2 was confirmed as a potential pharmacological target using clinical liver tissues. Systematic ex vivo evaluation of 13 candidate anti-fibrotics identified rational combination therapies based on epigallocatechin gallate, some of which were validated for enhanced anti-fibrotic effect in ex vivo culture of clinical liver tissues. In NASH patients treated with cenicriviroc, FPS modulation was associated with 1-year fibrosis improvement accompanied by suppression of the E2F pathway. Induction of PPARalpha pathway was absent in patients without fibrosis improvement, suggesting benefit of combining PPARalpha agonism to improve anti-fibrotic efficacy of cenicriviroc. A 7-protein FPSec panel showed concordant prognostic prediction with FPS.  Conclusion: FPS predicts long-term fibrosis progression in an etiology-agnostic manner, which can inform anti-fibrotic drug development.

overall_design: Gene expression profiling of formalin-fixed paraffin-embedded liver biopsy tissues obtained from NAFLD patients. The samples for the FPS derivation set 3.


title: Regulation of retinal amacrine cell generation by miR-216b and Foxn3 [PAR-CLIP]

city: Ann Arbor

first: David

last: Turner

state: MI

address: 109 Zina Pitcher Place

department: Michigan Neuroscience Institute

institute: University of Michigan

summary: The mammalian retina contains a complex mixture of different types of neurons. We find that the microRNA miR-216b is preferentially expressed in postmitotic retinal amacrine cells in the mouse retina, and expression of miR-216a/b and miR-217 in the retina depend in part on Ptf1a, a transcription factor required for amacrine cell differentiation. Surprisingly, ectopic expression of miR-216b, or the related miR-216a, can direct the formation of additional amacrine cells in the developing retina. In addition, we observe the loss of bipolar neurons in the retina after miR-216b expression. We identify the mRNA for the transcriptional regulator Foxn3 as a retinal target of miR-216b by Argonaute PAR-CLIP and reporter analysis. Inhibition of Foxn3 in the postnatal developing retina by RNAi also increases the formation of amacrine cells and reduces bipolar cell formation, while overexpression of Foxn3 inhibits amacrine cell formation prior to the expression of Ptf1a. Disruption of Foxn3 by CRISPR in embryonic retinal explants also reduces amacrine cell formation. Co-expression of Foxn3 partially reverses the effects of ectopic miR-216b on retinal cell type formation. Our results identify Foxn3 as a novel regulator of interneuron formation in the developing retina and suggest that miR-216b likely regulates expression of Foxn3 and other genes in amacrine cells.

overall_design: Identification of consistent Argonaute binding sites with miR-216a/b seed matches in developing neural retinas

middle: L

first: Huanqing

last: Zhang


title: Regulation of retinal amacrine cell generation by miR-216b and Foxn3 [miRNA-seq P0]

type: Non-coding RNA profiling by high throughput sequencing

overall_design: Retina microRNA profiles of P0 wild-type mice


title: Regulation of retinal amacrine cell generation by miR-216b and Foxn3 [miRNA-seq Ptf1a]

overall_design: Retina microRNA profiles of E18.5 Ptf1a+/- and Ptf1a-/- mice


title: Batf-mediated Epigenetic Control of Effector CD8+ T Cell Differentiation (HiChIP)

overall_design: This submission contains the HiChIP portion of the data.    P14 CD8+ T Cells and NIH/3T3 fibroblasts ectopically expressing Batf, Batf/Irf4, and Batf/Irf4/Runx3/T-bet were subjected to HiChIP for Batf. Additional samples were subjected to HiChIP for Ctcf.


title: BCL-XL inhibition induces an FGFR4 mediated rescue response in colorectal cancer

city: Amsterdam

first: Arezo

last: Torang

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

summary: The heterogeneous therapy response observed in colorectal cancer is in part due to cancer stem cells (CSCs) that resist chemotherapeutic insults. The anti-apoptotic protein BCL-XL plays a critical role in protecting CSCs from cell death, where its inhibition with high doses of BH3-mimetics can induce apoptosis. To identify pathways that can regulate sensitivity to BCL-XL inhibition, we screened a compound library for synergy with low dose BCL-XL inhibitor A-1155463 and reveal that FGFR4 inhibition effectively sensitizes to A-1155463 both in vitro and in vivo. Mechanistically, we identify a rescue response that is activated upon BCL-XL inhibition and leads to rapid FGF2 secretion and subsequent FGFR4-mediated post-translational stabilization of MCL-1. FGFR4 inhibition prevents MCL-1 upregulation and thereby sensitizes CSCs to BCL-XL inhibition. Altogether, our findings suggest a cell transferable induction of a FGF2/FGFR4 rescue response in CRC that is induced upon BCL-XL inhibition and leads to MCL-1 upregulation.

overall_design: mRNA profile of CRC derived spheroid culture Co01

first: P

last: Ramesh

first: J

middle: P

last: Medema

first: S

middle: R

last: van Hooff


title: Batf-mediated Epigenetic Control of Effector CD8+ T Cell Differentiation (ChIP-Seq)

overall_design: This submission contains the ChIP-Seq portion of the data. These samples are from P14 CD8+ T cells, either WT of BatfKO. The cells were stimulated anti-CD3, anti-CD28 and IL-2 and restimulated with PMA + ionomycin for 3h before being subjected to the ChIP-Seq protocol.


title: Flowering time and inflorescence architecture are regulated by FRUITFULL-like genes in tomato

city: Wageningen

first: Xiaobing

last: Jiang

address: Droevendaalsesteeg 1

department: Bioscience

institute: Wageningen University

summary: Null mutations of tomato FRUITFULL-like genes FUL1, FUL2, MBP10, MBP20 caused delayed flowering and branched inflorescence, so we sequenced mRNA from vegetative meristems (VM), transition meristems (TM), floral meristems (FM), and FM of the first sympodial shoot of tomato mutant ful1/ful2/mbp10/mbp20 (slful) as well as the wild type Moneyberg (WT) to see genome-wide expression changes affected by the mutations.

overall_design: Meristems at the same developmental stages were collected from many plants of both mutants and wild types and then pooled together for mRNA extractions and then sequencing library construction. Three biological replicates were analyzed for each stage.

first: Marian

last: Bemer


status: Public on Dec 21 2021

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

summary: Transcriptome analysis of spinal cord microglia and total spinal cord from Lewis rats intratracheally treated with PBS, neomycin or vancomycin.

overall_design: In order to investigate the effect of antibiotics on the CNS, we performed a RNA-Seq analysis on spinal cord-derived microglia and total spinal cord from wild type LEW/Crl rats (Rattus norvegicus) after 7 days of intratracheal treatment with PBS, neomycin (NEO) or vancomycin (VANCO).

first: Shomroni

last: Orr

first: Leon

last: Hosang

first: Francesca

last: Odoardi


title: Expression profiling of Prognostic Liver Signature and fibrosis-related genes in clinical fibrotic liver tissue cultured with various anti-fibrotic agents

first: Yujin

last: Hoshida

overall_design: Gene expression profiling of a snap-frozen surgical liver tissue (HCV-infected, F2 fibrosis) treated with various compounds in ex vivo precision-cut liver slice (PCLS) culture..

first: Tongqi

last: Qian

first: Naoto

last: Kubota

last: Fujiwara

first: Shijia

last: Zhu


title: Prognostic Liver Signature profiles in biopsy tissues from non-alcoholic fatty liver disease (NAFLD) patients in the U.S.

overall_design: Gene expression profiling of formalin-fixed paraffin-embedded liver biopsy tissues. The samples for the FPS derivation set 4.

first: Andrew

last: Warren

first: Kathleen

last: Corey

first: Raymong

last: Chung


title: LKB1 drives stasis and C/EBP-mediated reprogramming to an alveolar type II fate in lung cancer

city: Stanford

first: Christopher

last: Murray

state: California

address: 1291 Welch Rd. B261, Beckman Center

department: Genetics

institute: Stanford University


title: Prognostic Liver Signature profiles in biopsy tissues from chronic hepatitis C patients followed for fibrosis progression

overall_design: Gene expression profiling of formalin-fixed paraffin-embedded liver biopsy tissues obtained at the time of enrollment. The samples in the PLS validation set 1/FPS derivation set 1 from MGH.

first: Shigeki

last: Nakagawa

first: Matthew

last: Tung

first: Raymond


title: Prognostic Liver Signature profiles in post-transplant liver biopsy tissues from chronic hepatitis C patients

overall_design: Gene expression profiling of formalin-fixed paraffin-embedded liver biopsy tissues obtained at the time of enrollment. The samples in the PLS validation set 2/FPS derivation set 2.

first: Jacqueline

last: O'Leary


title: Gene expression in Jaltomata (species herrerae and procumbens) nectaries

city: Duluth

first: Marshall

last: Hampton

state: MN

address: 1117 University Drive

institute: University of Minnesota Duluth

summary: RNA-Seq of nectary and leaf samples of Jaltomata herrerae, and Jaltomata procumbens

sample_organism:
Jaltomata procumbens
Jaltomata herrerae

platform_organism:
Jaltomata procumbens
Jaltomata herrerae

overall_design: Jaltomata procumbens and Jaltomata herrerae plants were grown in Sun Gro LC8 soil in the MAES/MDA Plant Growth Facilities at the University of Minnesota with typical daytime highs of 25C and nighttime lows of 15C. Three types of RNA samples were separately prepared in triplicate from the floral nectaries of both species, including: ‘pre-secretory’ (~24-48 hours prior to anthesis/nectar secretion), ‘secretory’ (full anthesis, at ~3-6 hours after dawn), and ‘post-secretory’ (after petal abscission). RNA from fully expanded leaf tissue was also isolated in triplicate for both species. All tissues were manually dissected by hand with the RNA being immediately extracted by mechanical disruption with a microcentrifuge pestle and using an RNAqueous® RNA isolation kit (Thermo Fisher) with Plant RNA Isolation Aid (Thermo Fisher). Agarose gel electrophoresis and UV spectrophotometry were used to assess RNA quality for all samples prior to submission to the University of Minnesota Genomics Center for mRNA isolation, barcoded library creation and Illumina NovaSeq 6000 sequencing. Twenty-four TruSeq stranded mRNA libraries were created (triplicate samples for nectaries at three timepoints each, as well as leaf tissue, for each species) and sequenced via 150 bp, paired-end runs on the NovaSeq 6000 using Rapid chemistry. All libraries were pooled and sequenced. All expected barcodes were detected and mean depth for the libraries was ≥ 20 M reads. The average quality scores were all above Q30.

first: Clay

middle: J

last: Carter

first: Evin

last: Magner


title: Gene expression profiling of teloHAEC cells with CRISPR-Cas9-mediated deletion of candidate enhancer regions

city: Kuopio

first: Tiit

last: Örd

address: Neulaniementie 2

country: Finland

institute: A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland

summary: Functional consequences of genetic variation in the non-coding human genome are difficult to ascertain despite demonstrated associations to common, complex disease traits. To elucidate properties of functional non-coding SNPs with effects in human endothelial cells (EC), we utilized our previous molecular Quantitative Trait Locus (molQTL) analysis for transcription factor binding, chromatin accessibility, and H3K27 acetylation to nominate a set of likely functional non-coding SNPs. Together with information from Genome-Wide Association Studies (GWAS) for vascular disease traits, we tested the ability of more than 34,000 genetic variants to perturb enhancer function in ECs using the highly multiplexed reporter assay. Based on these results, CRISPR-mediated deletion followed by mRNA-Seq was carried out for SNP-containing regulatory elements near SMAD3 and LDAH (C2orf43) in order to functionally verify the target genes of the regulatory elements.

overall_design: mRNA expression profiling of teloHAEC cells following CRISPR treatment

first: Anu

last: Toropainen

first: Paula

last: Martí Torrell

first: Minna

middle: U

last: Kaikkonen


title: Prognostic Liver Signature profiles in biopsy tissues from chronic hepatitis C patients with HIV co-infection followed for fibrosis progression

first: Yujin

last: Hoshida

overall_design: Gene expression profiling of formalin-fixed paraffin-embedded liver biopsy tissues obtained at the time of enrollment. The samples in the PLS validation set 1/FPS derivation set 1 from JHU.

first: Tongqi

last: Qian

first: Naoto

first: Shujia

first: David

last: Thomas


title: RNA-seq profiles of Tp53, Prkar1a and Axin1 edited basal organoids from a mouse model of breast cancer

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

summary: This study demonstrates the applicability of an in vivo CRISPR/Cas9 genome-wide screen in the BALB/c-Trp53+/– mouse model of breast cancer to identify novel tumor suppressor genes involved in mammary tumorigenesis. Preneoplastic mammary organoids were established from using sorted basal cells isolated from BALB/c-Trp53+/– mice. CRISPR/Cas9 screening was used to target Trp53, Axin1 and Prkar1a. To explore the potential molecular basis of the morphological differences, RNA-seq analysis was used to compare the Axin1/Trp53 and Prkar1a/Trp53-edited organoids and to organoids targeted by Trp53-only guides.

overall_design: Three biological replicates were prepared of Tp53, Tp53/Prkar1a and Tp53/Axin1 edited organoids. RNA-seq profiles of the 9 independent samples were sequenced on an Illumina NextSeq 500 to produce 75bp paired-end reads. Two sequencing runs were performed to increase sequencing depth for all the samples.

first: Yunshun

last: Chen

first: Luuk

last: Heitnik

first: Jane

middle: E

last: Visvader


title: Single-cell RNA sequencing of zebrafish hematopoietic stem cells and endothelial cells

city: Madison

first: Owen

middle: James

last: Tamplin

state: WI

address: 1111 Highland Ave

department: Cell and Regenerative Biology

institute: University of Wisconsin-Madison

summary: Assessing gene changes in endothelial to hematopoietic transition in control zebrafish embryos and comparing gene changes to those seen in vegfc knock-down embryos.

overall_design: 52 hours post fertilization (hpf) embryos were dissociated for FACs sorting to isolate GFP+ HSPCs, mCherry+ ECs and double positive cells undergoing EHT. Following the sort, cells underwent standard 10x encapsulation.

first: Rebecca

last: Schiavo


title: RNA-seq and ATAC-seq profiling of thymic epithelial cells from wildtype and Kat7 knockout mice

summary: The autoimmune regulator, AIRE, induces the transcription of thousands of peripheral tissue genes (PTGs) in thymic epithelial cells (TECs) to mediate immunological tolerance. The chromatin state required for optimal AIRE function in TECs and how this state is induced remains unclear. Using RNA-seq and ATAC-seq, we tested the role of the histone acetyltransferase, KAT7 (also known as HBO1 or MYST2), which is essential for acetylation of histone 3 lysine 14 (H3K14), in TEC differentiation, AIRE-mediated PTG expression and thymic tolerance. We find that KAT7 is required for optimal expansion of medullary TEC and has a major role in the expression of AIRE-dependent PTGs, associated with enhanced chromatin accessibility at these gene loci in TECs. Mice with TEC-specific Kat7 deletion develop organ-specific autoimmunity with features resembling those observed in Aire-deficient mice. These findings highlight critical roles for KAT7-mediated acetylation in promoting a chromatin state at PTG loci that enables AIRE function and the establishment of immunological tolerance.

overall_design: See individual series.

first: Luke

middle: C

last: Gandolfo

first: Melanie

last: Heinlein

first: Daniel

middle: D

last: Gray


title: ATF7ip targets transposable elements for H3K9me3 deposition to modify CD8+ T cell effector and memory responses

city: SAN FRANCISCO

first: SUJIT

last: KASHYAP

state: CA

address: 513 Parnassus Ave

department: Pediatric Rheumatology

institute: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO

summary:
Method: To study the effector response of Atf7ip, a) we infected Atf7ip+/fl and  Atf7ipfl/fl  mice with lcmv . RNAseq was performed using CD8 T cells isolated from Lymph node and Spleen of Het and KO mice.  RNA was isolated using Qiagen RNeasy Mini Kit as per manufacturers protocol. The RNA-Seq was performed by UCSF core using Illumina Platform. RNAseq was also carried out using naive CD8 T cells isolated from Atf7ip+/fl and  Atf7ipfl/fl mice along with Atf7ip+/fl and  Atf7ipfl/fl  CD8 T cells stimulated for 72 hrs. This set of samples were sequenced using commercial facility from Genewiz, USA.
Results: Our transcriptome analysis (RNA-seq) identified, Il7r, Runx3 etc. to be upregulated in the Atf7ipfl/fl  CD8 T cells as compared to the Atf7ip+/fl CD8 T cells.

overall_design: Spleenocyte and lymph node mRNA profiles of  Atf7ip+/fl and  Atf7ipfl/fl  mice

first: Sujit

last: Kashyap

first: Jun

last: Sin

first: Michael

last: Waterfield


title: ATF7ip targets transposable elements for H3K9me3 deposition to modify CD8+ T cell effector and memory responses [ChIP-seq]

summary: CD8+ T cells are critical for the adaptive immune response to infection and tumors.  Moreover, CD8+ T cell memory is important for the immune systems response to repeat infections.  Here, we identify the activating transcription factor 7 interacting protein as a critical regulator of CD8+ T cell memory and effector responses.  Mice with a T cell specific deletion of ATF7ip have a CD8+ T cell intrinsic enhancement of Il7r expression and Il2 expression leading to enhanced memory responses.  ChIP-seq studies identified ATF7ip as an inhibitor of Il7r and Il2 gene expression through the deposition of the repressive histone mark H3K9me3 in the Il7r gene loci and Il2-Il21 intergenic region. Interestingly, ATF7ip targeted transposable elements (TE) for H3K9me3 in these regions.  These results demonstrate a new epigenetic pathway by which IL7r and IL-2 production are constrained in CD8+ T cells, and this may open up new avenues for modulating their production.

overall_design: Naïve  CD8 T cells were isolated by flow cytometry and H3K9me3 ChIP-seq was performed in duplicate CD8Cre/ATF7ip+/fl vs CD8-Cre/ATF7ipfl/fl naïve T cells

last: sin


title: Identification and tracking of alloreactive T cell clones in Rhesus Macaques (RM) through the RM-scTCR-Seq platform

first: Jim

last: Kaminski

summary: T cell receptor clonotype tracking is a powerful tool for interrogating T cell mediated immune processes We apply this method to a Rhesus Macaque model of Graft Versus Host Disease (GvHD), and identify and track in vitro detected alloreactive clonotypes in GvHD target organs and explore their GvHD driven cytotoxic T cell signature.

overall_design: Examination of scTCR-Seq and scRNA-Seq of T cells in RM model of GvHD and in vitro MLR experiments.

first: Ulrike

last: Gerdemann

first: Ryan

last: Fleming


title: Early-life thermal stress mediates long-term alterations in hypothalamic microglia [RNA-Seq]

city: Rishon LeZion

first: Tatiana

last: Kisliouk

address: 68 HaMaccabim Road

department: Animal Sciences

country: Israel

institute: ARO

summary: We identified the microglial population in the chick anterior hypothalamus (AH) and showed that early-life thermal stress (on day 3 post-hatch) influences the inflammatory process in the AH, altering microglial transcriptomic signature in response to LPS treatment (on day 10 post-hatch).

overall_design: Microglial mRNA profile of 11-day-old non-conditioned/heat-conditioned saline-injected and non-conditioned/heat-conditioned LPS-injected chicks 24 h after the injection by 3'-mRNA- sequencing (RNA-seq)

first: Osher

last: Ben-Nun

first: Asaf

last: Marco

first: Tali

last: Rosenberg

first: Noam

last: Meiri


title: Early-life thermal stress mediates long-term alterations in hypothalamic microglia [RRBS]

type: Methylation profiling by high throughput sequencing

summary: We identified the microglial population in the chick anterior hypothalamus (AH) and showed that early-life thermal stress (on day 3 post-hatch) influences the inflammatory process in the AH. We described alterations in genome-wide CpG methylation profile of hypothalamic microglia between heat-conditioned and non-conditioned 10-day-old chicks prior LPS challenge. We suppose that changes in CpG DNA methylation might be involved in reprogramming microglial function.

overall_design: Microglial total CpG-methylation profile of 10-day-old heat-conditioned and non-conditioned chicks before LPS-challenge by reduced representation bisulfite sequencing (RRBS)


title: RNA-seq profiling of cortical and medullary thymic epithelial cells from wildtype and Kat7 knockout mice

first: Gordon

last: Smyth

summary: Thymic epithelial cells (TECs) govern thymic T lymphocyte differentiation and selection. They can be divided into cortical and medullary TECs based on their anatomical location, function and molecular features. Cortical TECs (cTECs) provide the microenvironment for the commitment of haematopoietic precursors to the T lymphoid lineage and mediate the positive selection of CD4+CD8+ double-positive thymocytes. Medullary TECs (mTECs) facilitate the negative selection of self-reactive thymocytes and the differentiation of FOXP3+ regulatory T (Treg) cells2. Medullary TECs are also distinctive for their "promiscuous" gene expression, transcribing thousands of peripheral tissue genes (PTG) that are otherwise only expressed highly in one or two other organs. Much of this PTG expression by mTECs is controlled by the autoimmune regulator, AIRE. To determine the transcriptional impact of Kat7 loss, we purified mTECs and cTECs from Kat7-knockout and control mice and performed RNA-seq. The mTECs were further divided into MHCII-high and MHCII-low subsets.

overall_design: cTEC, mTEC-high and mTEC-low populations were sorted from three biological replicates of wildtype mice and three biological replicates of Kat7 knockout mice to produce in 18 RNA-seq libraries in all. Sequencing was conducted on an Illumina NextSeq 500 to produce 75bp paired-end reads.


title: Transcriptomics data of blood and brain from the YAC128 Huntington's disease mouse model [blood]

city: Leiden

first: Elsa

last: Kuijper

address: Albinusdreef 2

department: Human Genetics

institute: Leiden University Medical Center

summary: Therapeutic development for Huntington's disease (HD) would benefit from a method to monitor disease progression and treatment efficacy, ideally using blood biomarkers. Previously, HD-specific signatures were identified in human blood which adequately represented signatures in human brain, showing biomarker potential. Since drug candidates are normally first screened in rodent models, we aimed to identify HD-signatures in blood and brain of YAC128 HD mice and validate these with our previously identified human signatures. In both brain and blood, we identified HD-associated modules using Weighted Gene Co-expression Network Analysis (WGCNA) representing various biological processes previously associated with HD. Disease-related processes in blood and brain showed substantial overlap, including processes related to protein modification, cell cycle, RNA splicing, nuclear transport and vesicle-mediated transport. Moreover, the disease-associated processes shared between mouse blood and brain were highly comparable to those previously identified in human blood and brain. In addition to shared pathology, we identified HD-associated blood modules showing blood-specific pathology.

overall_design: Blood samples were collected at two time points (around 12 and 20 months) from YAC128 and control mice for RNA isolation and sequencing.

first: Willeke

last: van Roon-Mom

first: Lodewijk

last: Toonen


title: Transcriptomics data of blood and brain from the YAC128 Huntington's disease mouse model [brain]

overall_design: Brain RNAseq data from four brain regions collected from YAC128 and control mice around 20 months of age.


title: Butyrate protects against diet-induced liver fibrosis and suppresses non-canonical TGF-β signaling in human stellate cells

city: Rijswijk

first: Eveline

last: Gart

state: Zuid-Holland

address: Van vredenburchweg 659

institute: TNO

summary: Background & Aims: In obesity-associated non-alcoholic steatohepatitis (NASH), persistent hepatocellular damage and inflammation are key drivers of fibrosis, the main determinant of NASH-associated mortality. The short chain fatty acid butyrate can exert metabolic improvements and anti-inflammatory activities in NASH. However, its effects on NASH-associated liver fibrosis remains unclear.    Methods: Putative antifibrotic effects of butyrate were studied in Ldlr-/-.Leiden mice fed an obesogenic NASH-inducing diet (HFD) containing 2.5% (w/w) butyrate for 38 weeks and compared to an HFD control group. Antifibrotic mechanisms of butyrate were further investigated in TGF-β-stimulated primary human hepatic stellate cells (HSC).   Results: HFD-fed mice developed obesity, insulin resistance, increased levels of plasma leptin, adipose tissue inflammation, gut permeability, dysbiosis and NASH-associated fibrosis. Butyrate corrected hyperinsulinemia, lowered plasma leptin levels and attenuated adipose tissue inflammation, without affecting gut permeability or microbiota composition. Butyrate lowered plasma ALT and CK-18M30 and attenuated hepatic steatosis and inflammation. Butyrate inhibited fibrosis development as demonstrated by decreased hepatic collagen content and Sirius-red-positive area. In TGF-β-stimulated HSC, butyrate dose-dependently reduced collagen deposition and decreased procollagen1α1 and PAI-1 protein expression. Transcriptomic analysis and subsequent pathway and upstream regulator analysis revealed deactivation of specific non-canonical TGF-β signaling pathways RhoA/Rock and PI3K/AKT and other important pro-fibrotic regulators (e.g. YAP/TAZ and MYC) by butyrate, providing a potential rationale for its antifibrotic effects.   Conclusions: Butyrate protects against the development of obesity and insulin resistance-associated NASH and liver fibrosis. These antifibrotic effects are at least in part attributable to a direct effect on collagen production in hepatic stellate cells, as a result of inhibiting non-canonical TGF-β signaling.

overall_design: Antifibrotic mechanisms of butyrate were investigated in TGF-β-stimulated primary human hepatic stellate cells (HSC). There were 3 HSC treatments, for 4 days: (i) Unstimulated Control, (ii) TGF-β1 (2 ng/mL), (iii) TGF-β1 (2 ng/mL) + Sodium Butyrate (1mM)

first: Wim

last: van Duyvenvoorde

first: Karin

last: Toet

first: Martien

middle: M

last: Caspers

first: Lars

last: Verschuren

first: Everton

middle: S

last: Lima

first: Aswin

last: Menke

first: Roeland

last: Hanemaaijer

first: Jaap

last: Keijer

first: Kanita

last: Salic

first: Robert

last: Kleemann

first: Martine

last: Morrison


title: Functionally distinct roles for TET-oxidized 5-methylcytosine bases in somatic reprogramming to pluripotency

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

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

overall_design: Refer to individual Series


title: RNA-seq profiling of epithelial cells from fetal thymic organ cultures from Kat7 knockout and wildtype mice

first: Gordon

last: Smyth

summary: Thymic epithelial cells (TECs) govern thymic T lymphocyte differentiation and selection. Medullary TECs are distinctive for their "promiscuous" gene expression, transcribing thousands of peripheral tissue genes (PTG) that are otherwise only expressed highly in one or two other organs. Much of this PTG expression by mTECs is controlled by the autoimmune regulator, AIRE. This experiment was part of a larger study in which we examined the impact of Kat7 loss on AIRE-mediated PTG expression. Despite the apparently normal differentiation of AIRE+ TECs in Kat7-knockout mice, it was possible that the defect in AIRE-mediated PTG expression was secondary to the developmental loss of this histone acetyltransferase. To address this hypothesis, we employed fetal thymic organ cultures (FTOC) depleted of thymocytes where AIRE+ mTEC and PTG expression was induced by an agonist anti-RANK antibody. We then used two different approaches to acutely block KAT7 function and subsequently sort purified TECs for RNA-seq analysis to assess the impact on AIRE-mediated PTG transcription. AIRE+ mTECs exhibit relatively low turnover in organ culture; therefore, this approach uncouples KAT7 impacts on AIRE function from potential influences on TEC differentiation. Our first approach employed a new small molecule inhibitor of KAT7 function, WM-3835. The second approach was an inducible genetic deletion system. FTOC established with thymi from control (Kat7fl/fl) or RosaCre-ERT2 Kat7fl/fl mice were treated with tamoxifen to activate CRE-mediated deletion of Kat7.

overall_design: Three biological replicates of TECs from control and RosaCre-ERT2 Kat7fl/fl FTOCs or DMSO and WM-3835 treated wildtype FTOCs.

first: Luke

last: Gandolfo

first: Melanie

last: Heinlein

first: Daniel

last: Gray


title: Massively parallel profiling of human regulatory variants in endothelial cells

first: Tiit

last: Örd

summary: Genome-wide association studies (GWAS-s) have linked thousands of genetic variants with complex diseases and traits. However, most genetic variants identified reside in non-coding regions of the genome making it hard to predict and understand the molecular mechanisms underlying causal alleles. We have previously performed molecular Quantitative Trait Locus (molQTL) analysis for transcription factor binding, chromatin accessibility, and H3K27 acetylation across primary Human Aortic Endothelial Cell (HAEC) samples. Here we expand this analysis to study more than 30,000 genetic variants using the massively parallel reporter assay (MPRA) STARR-Seq in immortalized HAEC cells (teloHAEC). We demonstrate that more than 5,000 variants exhibit differential expression between alleles and identify ETS and AP-1 motifs as the strongest sequence attributes—and cell type-specific chromatin accessibility as the strongest epigenetic attribute—associated with allele-specific regulatory activity. Using interleukin 1-beta (IL1b) as a modulator of cell state and environment, we observe robust evidence for context-specific SNP effects, thereby underscoring the prevalence of GxE effects on noncoding variant function. We integrate results from molQTL mapping and STARR-seq with eQTL data from HAECs and GTEx tissues to fine-map functional non-coding SNPs at GWAS loci for vascular diseases.

overall_design: STARR-Seq massively parallel reporter assay (MPRA) to study SNP effects on regulatory region activity in human endothelial cells

first: Anu

last: Toropainen

first: Lindsey

last: Stolze

first: Michael

last: Whalen

first: Paula

last: Torrell

first: Verena

last: Link

first: Minna

last: Kaikkonen

first: Casey

last: Romanoski


title: Functionally distinct roles for TET-oxidized 5-methylcytosine bases in somatic reprogramming to pluripotency [ATAC-seq]

summary: Active DNA demethylation via Ten-eleven Translocation (TET) family enzymes is essential for epigenetic reprogramming in cell state transitions. TET enzymes catalyze up to three successive oxidations of 5-methylcytosine (5mC), generating 5- hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), or 5-carboxycytosine (5caC). Although these bases are known to contribute to distinct demethylation pathways, the lack of tools to uncouple these sequential oxidative events has constrained our mechanistic understanding of TET’s role in reprogramming. Here, we employ biochemically engineered TET mutants to examine their effects on the reprogramming efficiency of mouse embryonic fibroblasts (MEFs). We show that only TET mutants proficient for oxidation to 5fC/5caC are able to rescue the reprogramming potential of Tet2 -deficient MEFs. This effect correlated with an increased capacity to drive DNA demethylation at reprogramming enhancers, ultimately accelerating chromatin opening in these regions. Together, these experiments demonstrate that DNA demethylation through 5fC/5caC intermediates is critical for iPSC reprogramming.

overall_design: ATAC-seq of Dox-inducible Tet2-/- ; OKSM-rtTA mouse embryonic fibroblasts (MEFs) transduced with empty vector (pMXs), Tet2-WT, or Tet2-E (stalling mutant) at three timepoints of iPSC reprogramming (Day 0, Day 5, and Day 10), each with four replicates.

first: Blake

last: Caldwell

first: Rahul

last: Kohli

first: Marisa

last: Bartolomei


title: ATAC-seq profiling of medullary thymic epithelial cells from wildtype and Kat7-knockout mice

summary: Thymic epithelial cells govern thymic T lymphocyte differentiation and selection. Medullary TECs (mTECs) facilitate the negative selection of self-reactive thymocytes and the differentiation of FOXP3+ regulatory T cells. Medullary TECs are also distinctive for their “promiscuous” gene expression, transcribing thousands of peripheral tissue genes (PTG) that are otherwise only expressed highly in one or two other organs. Much of this PTG expression by mTECs is controlled by the autoimmune regulator, AIRE. To probe the mechanism by which KAT7 promotes AIRE function, we performed ATAC-seq to compare chromatin accessibility in MHCII-high medullary thymic epithelial cells from Kat7-knockout and wildtype mice.

overall_design: Three biological replicates were prepared from wildtype and from Kat7 knockout mice to produce in six ATAC-seq libraries in all. Sequencing was conducted on an Illumina NextSeq 500 to produce 75bp paired-end reads.


title: BCL11A promotes myeloid leukemogenesis by abrogating the transcriptional activity of PU.1 [array]

city: Tokyo

first: Takuro

last: Nakamura

address: 3-8-31 Ariake, Koto-ku

department: The Cancer Institute

country: Japan

institute: Japanese Foundation for Cancer Research

summary:
The transcriptional repressor Bcl11a is involved in hematological malignancies, B-cell development and fetal to adult hemoglobin switching, however, the molecular mechanism how Bcl11a promotes development of myeloid leukemia remains largely unknown. We found that Bcl11a cooperates with the pseudokinase Trib1 in AML development. Bcl11a promotes proliferation of Trib1-expressing AML cells both in vitro and in vivo. ChIP-seq analysis showed that Bcl11a is significantly associated on DNA-binding with PU.1 that promotes myeloid differentiation, and Bcl11a represses a number of PU.1 target genes such as Clec5a, Fcgr3 and Csf1r. The repression of PU.1 target genes by Bcl11a is achieved by both sequence-specific DNA binding activity and recruitment of corepressors by Bcl11a, and suppression of corepressor components HDAC1 and LSD1 cancelled the repressive activity. Association of high level of expression of BCL11A and worse prognosis is observed in human AML patients, and blocking of BCL11A expression upregulates PU.1 target expression, inhibits engraftment to bone marrow, and enhances myeloid differentiation of HL-60 cells, suggesting that BCL11A is involved in human myeloid malignancies via the PU.1 transcriptional activity.
We used microarrays to detail the global program of gene expression in mouse AML

overall_design: Murine AML cell lines expressing Trib1 with or without Bcl11a were examined.

first: Yoshitaka

last: Sunami


title: BCL11A promotes myeloid leukemogenesis by abrogating the transcriptional activity of PU.1 [ChIP-seq]

summary: The transcriptional repressor Bcl11a is involved in hematological malignancies, B-cell development and fetal to adult hemoglobin switching, however, the molecular mechanism how Bcl11a promotes development of myeloid leukemia remains largely unknown. We found that Bcl11a cooperates with the pseudokinase Trib1 in AML development. Bcl11a promotes proliferation of Trib1-expressing AML cells both in vitro and in vivo. ChIP-seq analysis showed that Bcl11a is significantly associated on DNA-binding with PU.1 that promotes myeloid differentiation, and Bcl11a represses a number of PU.1 target genes such as Clec5a, Fcgr3 and Csf1r. The repression of PU.1 target genes by Bcl11a is achieved by both sequence-specific DNA binding activity and recruitment of corepressors by Bcl11a, and suppression of corepressor components HDAC1 and LSD1 cancelled the repressive activity. Association of high level of expression of BCL11A and worse prognosis is observed in human AML patients, and blocking of BCL11A expression upregulates PU.1 target expression, inhibits engraftment to bone marrow, and enhances myeloid differentiation of HL-60 cells, suggesting that BCL11A is involved in human myeloid malignancies via the PU.1 transcriptional activity.

overall_design: Examination of binding sites of 2 transcription factors and Histone H3K27ac in a single cell line


title: Transcriptomics data of blood and brain from the YAC128 Huntington's disease mouse model

first: Elsa

last: Kuijper


title: Functionally distinct roles for TET-oxidized 5-methylcytosine bases in somatic reprogramming to pluripotency [RNA-Seq]

first: Yemin

last: Lan

overall_design: RNA-seq of Dox-inducible Tet2-/- ; OKSM-rtTA mouse embryonic fibroblasts (MEFs) transduced with empty vector (Untreated and pMXs), Tet2-WT, or Tet2-E (stalling mutant), either untreated or at iPSC reprogramming day5, each with 3-4 replicates


title: BCL11A promotes myeloid leukemogenesis by abrogating the transcriptional activity of PU.1


title: Transcriptional program of regulatory T cells in transplanted mice treated with interferon beta

status: Public on Dec 20 2021

city: New York

first: Miguel

last: Fribourg

state: NY

address: 1 Gustave Levy Pl

department: Medicine

institute: Icahn School of Medicine at Mount Sinai

summary: We report the differences in transcriptional program of Foxp3+ cells in mice B6 mice recipients of a BALB/c heart treated with CTLA-4 Ig and either vehicle or interferon beta (IFNb)

overall_design: We compare transplant recipients either treated with vehicle or IFNb (10,000 U/ml) on days -1,1,2,3,4 and 11 post transplant.

first: Francisco

last: Fueyo-Gonzalez


title: Gene expression analysis of astrocytes differentiated from iPS cells generated from monozygotic twins discordant for schizophrenia

city: Helsinki

first: Iiris

last: Hovatta

address: Haartmaninkatu 3

department: Department of Psychology and Logopedics

institute: University of Helsinki

summary: Previous studies have implicated several brain cell types in schizophrenia, but the genetic impact of astrocytes is unknown. Considering their high complexity in humans, astrocytes are likely key determinants of neurodevelopmental diseases. Human induced pluripotent stem cell (hiPSC) -derived astrocytes differentiated from five monozygotic twin pairs discordant for schizophrenia and five healthy subjects were studied for alterations related to high genetic risk and clinical manifestation of SCZ in astrocyte transcriptomics.

overall_design: Ribo-depleted RNA was sequenced with Illumina Next-seq 500 from iPS derived astrocytes

first: Jari

last: Koistinaho

last: Tiihonen


title: Contribution of astrocytes to familial risk and clinical manifestation of Schizophrenia

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: PRP4KA phosphorylates Serrate/Ars2 for degradation vs 20S proteasome to fine-tune RNA processing

city: College Station

first: Lin

last: WANG

state: Texas

address: 2123 Norman Borlaug Center Rm112A

institute: Texas A&M University

summary: We examined global expression profiles of 3-week-old prp4k3(amiR-PRP4K3) leaves compared to Col-0 using illumina sequencing. PRP4KA and its paralogs interact with Serrate (SE), a key factor in miRNA metabolism.phosphorylation of SE via PRP4KA can quickly clear accumulated SE to secure its proper amount. This study provides new insight into how protein phosphorylation regulates RNA metabolism through controlling homeostasis of SE accumulation in miRNA metabolism.

overall_design: Examination of RNA and small RNA in prp4k3(amiR-PRP4K3) and Col-0 profiling by high throughput sequencing

last: Wang

first: Yanjun

last: Li

first: Zhiye


title: Gene expression analysis of transplanted hiPSC-astrocyte progenitors generated from monozygotic twin pair discordant for schizophrenia into mouse brain

summary: The humanized mice's frontal cortical tissues were used for transcriptomic analysis, as this brain area shows early involvement in pathophysiology of schizophrenia. We transplanted hiPSC-astrocyte progenitors from one monozygotic twin pair discordant for schizophrenia and one healthy control into neonatal mouse forebrains and analyzed mouse behavior at five and ten months, followed by gene expression profiling of the frontal cortices seven days later.

overall_design: Ribo-depleted RNA was sequenced with Illumina Next-seq 500 from transplanted mouse cortical samples


title: RNA-seq of HSF1 phase separation in heat shock and non-heat shock cells.

status: Public on Dec 19 2021

city: Beijing

first: Hongchen

last: Zhang

state: Please Select

address: No.5 Yiheyuan Road Haidian District, Bei, jing,china

institute: Peking University

summary: We investigated whether interfering with HSF1 LLPS affected the expression of its target genes using RNA sequencing. We found HS induced HSPs gene expression in LLPS-dependent manner. LLPS-dependent gene activation was also observed in M1 cells under NHS condition. In addition, LLPS-incompetent M3 infected cells showed less HSP gene expression even under HS condition. Thus, these data collectively support a crucial role for LLPS of HSF1 in activating HSP genes expression.

overall_design: Examination of gene expression of LLPS-competent versus LLPS-incompetent HSF1 mutants under both HS and NHS conditions.

first: Shipeng

last: Shao

first: Yujie

last: Sun


title: M249 melanoma cells: Vemurafenib and Selumetinib resistant through BRAF double minutes vs. parental

city: Foster City

first: Kai

last: Song

address: 333 Lakeside Dr

institute: Gilead Sciences, Inc

summary: CGH profiling of M249 melanoma cell line treated with step-wise increasing Vemurafenib and Selumetinib to develop resistance (VSR). The resistance mechanims was through BRAF amplification in double minute (DM) format. The control cell line is untreated M249.

overall_design: Two-condition experiment, M249 Parental vs M249 VSR DM. Biological replicates: 1 control replicate, 1 treated replicate.

first: Thomas

last: Graeber


title: Multi-objective Optimization Reveals Time- and Dose-Dependent Inflammatory Cytokine-Mediated Regulation of Human Stem Cell Derived T-cell Development

city: Vancouver

first: John

last: Edgar

state: BC

address: 2222 Health Sciences Mall, Room 404

department: School of Biomedical Engineering

country: Canada

institute: University of British Columbia

summary: The generation of T-cells from stem cells in vitro could provide an alternative source of cells for immunotherapies. T-cell development from hematopoietic stem and progenitor cells (HSPCs) is tightly regulated through Notch pathway activation by ligands Delta-like (DL) 1 and 4. Other molecules, such as stem cell factor (SCF) and interleukin (IL)-7, play a supportive role in regulating the survival, differentiation, and proliferation of developing T-cells. Numerous other signaling molecules influence T-lineage development in vivo, but little work has been done to understand and optimize their use for T-cell production. Using a defined engineered thymic niche system, we undertook a multi-stage statistical learning-based optimization campaign and identified IL-3 and tumor necrosis factor α (TNFα) as stage- and dose-specific enhancers of cell proliferation and T-lineage differentiation. We used this information to construct an efficient three-stage process for generating conventional TCRab+CD8+ T-cells expressing a diverse TCR repertoire from blood stem cells. Our work provides new insight into T-cell development and a robust system for generating T-cells to enable clinical therapies for treating cancer and immune disorders.

overall_design: T-cells were differentiated from umbilical cord blood (UCB)-derived CD34+ cells. Five UCB donors were included as replicates. One postnatal thymocyte donor was included as a control.

first: Yale

last: Michaels

first: Peter

middle: W

last: Zandstra


title: A late-stage assembly checkpoint of the human mitochondrial ribosome large subunit

city: Tel Aviv

first: Aldema

last: Sas-Chen

state: Israel

address: Tel Aviv University

department: Shmunis School of Biomedicine and Cancer Research

institute: Tel Aviv University

summary: The epitranscriptome plays a key regulatory role in cellular processes in health and disease, including ribosome biogenesis. Here, analysis of the human mitochondrial transcriptome shows that 2’-O-methylation is limited to residues of the mitoribosomal large subunit (mtLSU) 16S mt-rRNA, modified by MRM1, MRM2, and MRM3. Ablation of MRM2 leads to a severe impairment of the oxidative phosphorylation system, caused by defective mitochondrial translation and accumulation of mtLSU assembly intermediates. Structures of these particles (2.58Å) present disordered RNA domains, partial occupancy of bL36m and bound MALSU1:L0R8F8:mtACP anti-association module. Additionally, we present five mtLSU assembly states with different intersubunit interface configurations. Complementation studies demonstrate that the methyltransferase activity of MRM2 is dispensable for mitoribosome biogenesis. The Drosophila melanogaster orthologue, DmMRM2, is an essential gene, with its knock-down leading to developmental arrest. This work identifies a key late-stage quality control step during mtLSU assembly, ultimately contributing to the maintenance of mitochondrial homeostasis.

overall_design: WT HEK-293T cells, and cells knocked-out of either MRM1, MRM2 or MRM3 were harvested. Mitochondria isolation and RNA extraction was conducted as previously described (Sas-Chen, Nir and Schwartz, 2021; doi: 10.1007/978-1-0716-0834-0_9). Strand-specific libraries were generated using low and high concentration of dNTPs. Libraries were sequenced using a NextSeq 500 platform generating short paired-end reads, ranging from 25 to 55 bp from each end.

first: Schraga

last: Schwartz


title: The Asymmetric Distribution of RNAPII and Nucleosomes on Replicated Daughter Genomes is caused by Differences in Replication Timing between the Lagging and the Leading Strand [RNA-seq]

status: Public on Dec 18 2021

city: Montpellier

first: Marta

last: Radman-Livaja

address: 1919 route de Mende

department: IGMM

country: France

institute: CNRS

summary: Chromatin features are thought to have a role in the epigenetic transmission of transcription states from one cell generation to the next. It is unclear how chromatin structure survives disruptions caused by genomic replication or if chromatin features are instructive of the transcription state of the underlying gene. We developed a method to monitor budding yeast replication, transcription and chromatin maturation dynamics on each daughter genome in parallel, with which we identified clusters of secondary origins surrounding known origins. We find a difference in the timing of lagging and leading strand replication on the order of minutes at most yeast genes. We propose a model in which the majority of old histones and RNAPII bind to the gene copy that replicated first, while newly synthesized nucleosomes are assembled on the copy that replicated second. RNAPII enrichment then shifts to the sister copy that replicated second. The order of replication is largely determined by genic orientation: if transcription and replication are co-directional the leading strand replicates first; if they are counter-directional the lagging strand replicates first. A mutation in the Mcm2 subunit of the replicative helicase Mcm2-7 which impairs Mcm2 interactions with histone H3 slows down replication forks but does not qualitatively change the asymmetry in nucleosome distribution observed in the WT. Active transcription states are inherited simultaneously and independently of their underlying chromatin states through the recycling of the transcription machinery and old histones, respectively. Transcription thus actively contributes to the reestablishment of the active chromatin state.

overall_design: We have measured the genome-wide mRNA levels in wt, rtt109D and hst3,4DD. S. cerevisiae mRNA counts were normalized to S.pombe mRNAs that were "spiked" into each sample.

first: Rahima

last: Ziane

first: Alain

last: Camasses


title: Endothelial Shp2 deficiency controls alternative activation of macrophage preventing radiation-induced lung injury through Notch signaling

city: Hangzhou

first: Pan

last: Liu

state: Zhejiang

address: Yuhangtang road 866

institute: Zhejiang university school of medicine

summary: Radiation-induced lung injury is a common late side-effect of thoracic radiotherapy. The inflammatory microenvironment plays a key role in this process. Endothelial cells are the goalkeeper of inflammation. Endothelial dysfunction following leukocytes infiltrated is a prominent feature in the pathogenesis of radiation-induced lung injury. Tyrosine phosphatase Shp2 is a key regulator of endothelial functions and inflammation. Here, we established a clinical-mimicking mouse model of radiation-induced lung injury and found that Shp2 activity was elevated in endothelium after injury. Mice with endothelium-specific Shp2 deletion showed relieved collagen deposition along with disrupted radiation-induced Jag1 expression in the endothelium. Furthermore, endothelium-derived Jag1 activated the alternative activation of macrophages in vitro and in vivo by paracrine Notch signaling. Consistently, Notch pathway was significant activated by chest irradiation in the peripheral blood leukocytes of cancer patients. Collectively, this is the first demonstration of radiation-induced lung injury regulation by endothelial Shp2. Shp2 participates in the radiation-induced endothelial dysfunction and subsequently inflammatory microenvironment producing.

overall_design: Relative mRNA level in irradiated shScr and shShp2 HUVECs.

first: Xue


title: The Asymmetric Distribution of RNAPII and Nucleosomes on Replicated Daughter Genomes is caused by Differences in Replication Timing between the Lagging and the Leading Strand [ChIP]

type: Genome binding/occupancy profiling by genome tiling array

overall_design: two Rpb3-HA ChIP samples on sonicated chromatin from S-phase cells 25 and 32 min after release from alpha factor G1 arrest with a dye flip technical replicate foreach sample


city: Loughborough

first: Nathan

last: Archer

state: East Midlands

address: Sutton Bonington

department: School of Veterinary Medicine and Sciences

country: United Kingdom

institute: University of Nottingham

summary: The mRNA cap structure consists of the m7G "cap0" linked to the 5'-most nucleotide of the initial mRNA. The first two nucleotides of mRNA can be 2'-O-Ribose modified to form cap1 or cap2 structures. Here, mRNA was sequenced after CLIP with tagged recombinant CMTR1 and compared to input RNA.

overall_design: CLIP of mRNA capping enzyme CMTR1 in Drosophila melanogaster embryo

first: Zsuzsa

last: Bodi

first: Rupert

last: Fray

first: Matthias

last: Soller


title: Identification of the dismal subtype of B-ALL with dysregulation of CDX2 and UBTF

status: Public on Dec 17 2021

city: MEMPHIS

first: QINGSONG

last: GAO

state: Tennessee

address: 262 DANNY THOMAS PLACE

institute: ST JUDE CHILDREN'S RESEARCH HOSPITAL

summary: A new subtype of B-ALL was identified through integrative genomic analysis and H3K27ac HiChIP was used to investigate impact of structural variants on the CDX2-FLT3-PAN3 genomic region

overall_design:
Chromatin interactions in leukemia cell lines using H3K27ac HiChIP
----------------------------
Authors state the following:
Raw data for the following 3 samples have been submitted to EGA (EGAS00001005863, submission in progress) because these are generated from patients samples:
SJALL060150
SJBALL020169
SJBALL113
SJALL060150_HiChIP, primary sample, leukemia, H3K27ac (Active Motif am91193 lot#22420004)
SJBALL020169_HiChIP, primary sample, leukemia, H3K27ac (Active Motif am91193 lot#22420004)
SJBALL113_HiChIP, primary sample, leukemia, H3K27ac (Active Motif am91193 lot#22420004)

first: Shunsuke

last: Kimura

first: Lindsey

last: Montefiori

first: Charles

last: Mullighan


title: SARS-CoV-2 Nucleocapsid protein attenuates stress granule formation and interacts directly with mRNAs to impair host stress response

city: Toronto

first: Jack

last: Greenblatt

address: 160 College Street

institute: University of Toronto

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

overall_design: Refer to individual Series


title: CLIP of mRNA capping enzyme CMTR2 in drosophila melanogaster

summary: The mRNA cap structure consists of the m7G "cap0" linked to the 5'-most nucleotide of the initial mRNA. The first two nucleotides of mRNA can be 2'-O-Ribose modified to form cap1 or cap2 structures. Here, mRNA was sequenced after CLIP with tagged recombinant CMTR2 enzyme and compared to input RNA.

overall_design: CLIP of mRNA capping enzymes CMTR2 in drosophila melanogaster


title: A fast Myh super enhancer dictates adult muscle fiber phenotype through competitive interactions with the fast Myh genes

city: Paris

first: Matthieu

last: Dos Santos

state: Paris

address: 24 rue du Faubourg Saint Jacques

institute: Institut Cochin

summary: The contractile properties of adult myofibers are shaped by their Myosin heavy chain (MYH) isoform content. We identify by snATAC-seq a 42kb super-enhancer (SE) at the locus regrouping the fast Myh (fMyh) genes. By 4C-seq we show that active fMyh promoters interact with the SE by DNA looping, leading to the activation of a single promoter per nucleus. A rainbow mouse transgenic model of the locus including the SE recapitulates the endogenous spatio-temporal expression of adult fMyh genes. In situ deletion of the SE by CRISPR/Cas9 editing demonstrates its major role in the control of associated fMyh genes, and deletion of two fMyh genes at the locus reveals an active competition of the promoters for the shared SE. Last, by disrupting the organization of fMyh, we uncover positional heterogeneity within limb skeletal muscles that may underlie selective muscle susceptibility to damage in certain myopathies.

overall_design: Circular Chromosome Conformation Capture (4C-seq) samples from mouse aged 8 weeks at different anatomical positions.

last: dos Santos

first: Daan

last: Noordermeer

first: Pascal

last: Maire


title: Transcriptional regulation by SETBP1 and SETBP1(D/N) in mouse hematopoietic stem and progenitor cells

city: Bethesda

first: Yang

last: Du

state: MD

address: 4301 Jones Bridge Road

department: Pediatrics

institute: Uniformed Services University of the Health Sciences

summary: Global gene expression changes induced by Setbp1 and Setbp1(D/N) in purified mouse hematopoietic stem and progenitor cells were characterized by RNA-seq analysis; ChIP-seq studies to identify cooperation between SETBP1/SETBP1(D/N) and MLL1 in regulating gene transcription in hematopoietic stem and progenitor cells.

overall_design: For characterizing gene expression changes, Lin-Sca-1+c-kit+(LSK) cells from bone marrow of C57BL/6 mice were infected with control empty pMYs retrovirus (pMYs-IRES-GFP, 2105) or pMYs virus expressing Setbp1 cDNA (pMYs-Setbp1-IRES-GFP, WT) or Setbp1(D/N) cDNA (pMYs-Setbp1(D/N)-IRES-GFP, DN). After a brief expansion in methylcellulose medium, the transduced cells were purified based on GFP expression and their expression proflies analyzed by RNA-seq. For identifying cooperation in transcriptional regulation, LSK cells were infected with pMYs-3xFLAG-Setbp1-IRES-GFP (2PL) or pMYs-3xFLAG-Setbp1(D/N)-IRES-GFP (DPL) virus and genomic occupancy of SETBP1 (M2), SETBP1(D/N) (M2), Mll1 (MLN), H3K4me3, and H4K16ac analyzed by ChIP-seq.

first: Nhu

last: Nguyen


title: Cap 2’-O-ribose methylation is required for reward learning in Drosophila melanogaster

summary: RNA-seq Quant-seq FWD performed on cap-adjacent methylatransferase mutants and wildtype of drosophila melanogaster.

overall_design: 3'-Quant-seq fwd performed on three replicates of WT and four replicates of drosophila mutant for cap-adjacent methyltransferases.

first: Zsuzsanna

middle: G

first: Daniel

last: Hebenstreit


city: Nanjing

first: Yuyu

last: Zhu

address: Xianlin

institute: Nanjing University of Chinese Medicine

summary: We report the application of RNA sequencing technology for high-throughput profiling in mouse peritoneal macrophages derived from wild type and SHP2lyz2-/- mice. The goal of this study is to search differential gene in indicated groups. Through differential gene analysis, we can find out the specific mechanism of SHP2 deficiency to alleviate disease development.

overall_design:
RNA sequencing of peritoneal macrophages from wild-type and SHP2lyz2-/- mice
Finding out differential gene

last: Sun


title: SARS-CoV-2 Nucleocapsid protein attenuates stress granule formation and interacts directly with mRNAs to impair host stress response (iCLIP-Seq)

summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid (N) protein is highly expressed upon infection and is essential for viral replication, making it a promising target for antiviral drug and vaccine development. Here, starting from a functional proteomics workflow, we catalogued the protein-protein interactions of 28 SARS-CoV-2 proteins in HEK293 cells, including an evolutionarily conserved specific interaction of N with the stress granule resident proteins G3BP1 and G3BP2. N protein localizes to stress granules and sequesters G3BP1 and G3BP2 away from their normal interaction partners, thus attenuating stress granule formation. N also binds directly to host mRNAs, with a preference for 3´ UTRs, and modulates target mRNA stability. We show that SARS-CoV-2 N protein rewires the G3BP1 mRNA-binding profile, thereby suppressing host gene expression changes induced in response to cellular stress.

overall_design: iCLIP-seq of GFP-tagged SARS-CoV-2 N protein in HEK293 cells treated with or withour Sodium Arsenite. iCLIP-seq of G3BP1 in n HEK293 cells treated with or withour Sodium Arsenite.iCLIP-seq of G3BP1 in N-expressing HEK293 cells treated with or withour Sodium Arsenite. Each experiment was performed in biological duplicate. Control libraries for size-match inputs (SMI) were prepared in parallel

first: Syed

last: Nabeel-Shah

first: Hyunmin

last: Lee

first: Nujhat

last: Ahmed

first: Giovanni

last: Burke

first: Shaghayegh

last: Farhangmehr

first: Kanwal

last: Ashraf

first: Shuye

last: Pu

first: Ulrich

last: Braunschweig

first: Guoqing

last: Zhong

first: Hong

last: Wei

first: Hua

last: Tang

first: Jianyi

last: Yang

first: Edyta

last: Marcon

first: Benjamin

last: Blencowe

first: Zhaolei

last: Zhang

middle: F


title: Gfi1aa/Lsd1 facilitates hemangioblast differentiation into primitive erythrocytes by targeting etv2 and sox7 in zebrafish

city: Guangzhou

first: Mei

last: Wu

state: Guangdong

address: Waihuan Dong Road

department: School of Medicine

institute: South China University of Technology

summary: The first wave of hematopoiesis is the primitive hematopoiesis, which produces embryonic erythroid and myeloid cells. Primitive erythrocytes are thought to be generated from bipotent hemangioblasts, but the molecular basis remains unclear. Transcriptional repressors Gfi1aa and Gfi1b have been shown to cooperatively promote primitive erythrocytes differentiation from hemangioblasts in zebrafish. However, the mechanism of these repressors during the primitive wave is largely unknown. Herein, by functional analysis of zebrafish gfi1aasmu10, gfi1bsmu11, gfi1absmu12 single, double, and triple mutants, we found that Gfi1aa not only plays a predominant role in primitive erythropoiesis but also synergizes with Gfi1ab. To screen Gfi1aa downstream targets, we performed RNA-seq and ChIP-seq analysis and found two endothelial transcription factors, etv2 and sox7, to be repressed by Gfi1aa. Genetic analysis demonstrated Gfi1aa to promote hemangioblast differentiation into primitive erythrocytes by inhibiting both etv2 and sox7 in a Lsd1-dependent manner. Moreover, the H3K4me1 level of etv2 and sox7 were increased in gfi1aa mutant. Taken together, these results suggest that Gfi1aa/Lsd1-dependent etv2/sox7 downregulation is critical for hemangioblast differentiation during primitive hematopoiesis by inhibition of endothelialization. The different and redundant roles for Gfi1(s), as well as their genetic and epigenetic regulation during primitive hematopoiesis, help us to better know the molecular basis of the primitive hematopoiesis and sheds light on the understanding the Gfi1(s) related pathogenesis.

overall_design: Whole embryos mRNA profiles of Gfi1(s) mutant and WT in zebrafish

first: Junwei

last: Lian

first: Yiyue


title: Pathogen infection and cholesterol deficiency activate the C. elegans p38 immune pathway through a TIR-1/SARM1 phase transition

status: Public on Dec 16 2021

city: Worcester

first: Read

last: Pukkila-Worley

state: Massachusetts

address: 55 N Lake Ave

institute: University of Massachusetts Medical School

summary: Intracellular signaling regulators can be concentrated into membrane-free, higher-ordered protein assemblies to initiate protective responses during stress — a process known as phase transition. Here, we show that a phase transition of the Caenorhabditis elegans Toll/interleukin-1 receptor domain protein (TIR-1), an NAD+ glycohydrolase homologous to mammalian sterile alpha and TIR motif-containing 1 (SARM1), underlies p38 PMK-1 immune pathway activation in C. elegans intestinal epithelial cells. Through visualization of fluorescently labeled TIR-1/SARM1 protein, we demonstrate for the first time that physiologic stresses, both pathogen and non-pathogen, induce multimerization of TIR-1/SARM1 into visible puncta within intestinal epithelial cells. In vitro enzyme kinetic analyses revealed that, like mammalian SARM1, the NAD+ glycohydrolase activity of C. elegans TIR-1 is dramatically potentiated by protein oligomerization and a phase transition. Accordingly, C. elegans with genetic mutations that specifically block either multimerization or the NAD+ glycohydrolase activity of TIR-1/SARM1 fail to induce p38 PMK phosphorylation, are unable to increase immune effector expression, and are dramatically susceptible to bacterial infection. Finally, we demonstrate that low cholesterol stress causes TIR-1/SARM1 to oligomerize into puncta in intestinal epithelial cells and engages its NAD+ glycohydrolase activity, which increases p38 PMK-1 phosphorylation, and primes immune effector induction in a manner that leads to reduced pathogen accumulation in the intestine during a subsequent infection. These data reveal a new adaptive response that allows a metazoan host to anticipate pathogen threats during micronutrient deprivation, a time of relative susceptibility to infection. Thus, a phase transition of TIR-1/SARM1 as a prerequisite for its NAD+ glycohydrolase activity is strongly conserved across millions of years of evolution and is essential for diverse physiological processes in multiple cell types.

overall_design: RNA-seq of uninfected C. elegans wild-type (N2) animals grown on either 0 μg/mL or 5 μg/mL cholesterol supplemented medium.

first: Nicholas

last: Peterson


title: SARS-CoV-2 Nucleocapsid protein attenuates stress granule formation and interacts directly with mRNAs to impair host stress response (RNA-Seq)

first: Jack

last: Greenblatt

overall_design: RNA-seq analysis of WT type and SARS-CoV-2 N expressing HEK293 cells treated with or without Sodium Arsenite

first: Syed

last: Nabeel-Shah

first: Hyunmin

last: Lee

first: Nujhat

last: Ahmed

first: Giovanni


title: The Asymmetric Distribution of RNAPII and Nucleosomes on Replicated Daughter Genomes is caused by Differences in Replication Timing between the Lagging and the Leading Strand [ChIP-seq]

first: Marta

last: Radman-Livaja

overall_design: We have measured the genome-wide dynamics of H3K4me3, H3, H3K36me3, H3K56ac and RNAPol2 (Rpb3) distribution on both replicated daughter genomes in a timecourse during budding yeast S-phase in wt and mutant backgrounds. We  used EdU (ethylene deoxy uridine) to mark nascent (replicated) DNA strands. We have enriched for DNA fragments bound by the above proteins by immunoprecipitation at different times in budding yeast S-phase. EdU incorporated into nascent ChIPed (the ChIP-NChAP (Nascent Chromatin Avidin Pulldown) fraction) and nascent bulk DNA ( the NChAP fraction) strands was biotinylated using Click chemistry and nascent DNA strand fragments were subsequently isolated by pulldown on Streptavidin coated magnetic beads for strand specific NGS library preparation.

first: Rahima

last: Ziane

first: Alain

last: Camasses


title: The Asymmetric Distribution of RNAPII and Nucleosomes on Replicated Daughter Genomes is caused by Differences in Replication Timing between the Lagging and the Leading Strand


title: High-affinity, neutralizing antibodies to SARS-CoV-2 can be made in the absence of T follicular helper cells

city: West Haven

first: Ryan

last: Chow

state: CT

address: 850 West Campus Drive

institute: Yale University

overall_design: BCR repertoire sequencing of SARS-CoV-2 S-specific plasmablasts from mediastinal lymph nodes of K18-hACE2 Bcl6f/f or K18-hACE2 Bcl6f/f Cd4Cre mice, 14 days post infection with SARS-CoV-2. 4 independent mice per condition.

first: Jennifer

last: Chen

first: Craig

middle: B

last: Wilen

first: Stephanie

last: Eisenbarth


title: SARS-CoV-2 infects the human kidney and drives fibrosis in kidney organoids

city: Aachen

first: Ivan

middle: Gesteira

last: Costa

state: Northrhine-Westphalia

address: Pauwelsstr. 19

department: Joint Research Center for Computational Biomedicine

institute: UKA RWTH Aachen

summary: Single-cell RNA-seq of iPSC derived human kidney organoids. Single-nuclei RNA-seq data of COVID-19 patient autopsy kidney tissue. The current data was used to suggest that SARS-CoV-2 can directly infect kidney cells and induce cell injury as well as a pro-fibrotic environment which could explain acute kidney injury in COVID-19 patients and also long-term effects potentially leading to the development of chronic kidney disease.

overall_design:
CTR, iPSC kidney organoids; COVID, SARS-CoV-2 infected kidney organoids; COVID-19, SARS-CoV-2 infected kidney autopsy.

>>>Submitter states that raw data are not available due to patient privacy concerns<<<

first: Jitske

last: Jansen

first: Katharina

last: Reimer

first: James

last: Nagai

first: Rebekka

last: Schneider

first: Bart

last: Smeets

first: Rafael

last: Kramann


title: Human prostate luminal epithelia adopt a club-like state in response to low androgen levels

city: Dallas

first: Gervaise

middle: H.

last: Henry

address: 5323 Harry Hines Blvd, Mail Code:9110

department: Urology

institute: UT Southwestern Medical Center

summary: Spatial transcriptomics of treatment naive and 5-alpha reductase inhibitior treated human BPH tissue

overall_design: Fresh human prostate specimens were embedded in OCT, slides were H&E stained and processed for 10x Genomics Visium spatial transcriptomics.

first: Douglas

last: Strand

middle: H


title: Transcriptional changes associated with chemical induction of adenylyl cyclase activity in Mtb

city: Ithaca

first: Brian

last: VanderVen

state: New York

address: 930 Campus Road

department: Microbiology and Immunology

institute: Cornell University

summary: Goal: Assess transcriptional changes in Mtb associated with activation of adenylyl cyclase activity in the bacterium, by treatment with the Rv1625c agonist V-59 or activation of the TetOn-cAMP construct. Specifically, address changes in transcription of cholestrrol utilization genes, during growth of Mtb in cholesterol media. Method: WT, Rv1625c knockout, and Rv1625c Complement strains of Mtb were grown in cholesterol-based media and treated with V-59 or vehicle control (DMSO). V-59 is known to increase cAMP synthesis in WT, but not in Rv1625c knockout Mtb. V-59 increases cAMP synthesis above that observed in WT in the Complement strain, due to Rv1625c overexpression in this strain. Also, utilized TetOn-cAMP Mtb strain, to induce cAMP synthesis independent of V-59 and Rv1625c. Treatment with Atc induces expression of catalytic domain of Rv1264 in this strain. We grew the TetOn-cAMP strain in cholesterol-based media, treated with Atc or EtOH (vehicle control). Conclusions: Transcriptional changes to cholesterol utilization genes associated with V-59 treatment in WT Mtb were similar to those associated with TetOn-cAMP induction. The transcriptional changes associated with blockade of cholesterol degradation following V-59 treatment in WT Mtb were not observed in the Rv1625c knockout strain. The Rv1625c knockout strain had intrinsic defects in induction of cholesterol utilization genes. The Complement strain showed enhanced transcriptional changes in response to V-59 treatment.

overall_design: RNA profiles of adenylyl cyclase inducing compound vs. vehicle control in Mtb during culture in cholesterol-based media for four hours

first: Kaley

last: Wilburn


title: Next generation RNA sequencing of embryonic dorsal root ganglions to study the effects of electrical stimulation.

status: Public on Dec 15 2021

city: Daegu

first: Aseer

last: Intisar

address: 333, Techno Jungang-daero, Hyeonpung-myeon, Dalseong-gun

country: South Korea

institute: Daegu Gyeongbuk Institute of Science and Technology

summary:
Purpose: This study aimed to investigate the effectiveness of electrical stimulation to enhance myelination in the mouse dorsal root ganglion (DRG) – an ex vivo model of the peripheral nervous system.
Method: DRG mRNA profiles were generated by high-throughput NGS at 11 DIV (1 day after ES) and 19 DIV (9 days after ES).
Results: ES upregulated the expression of genes involved in peripheral nervous system myelination and lipid biosynthesis, while downregulating the expression of genes involved in fatty acid oxidation. The extent of changes in gene expression after ES were generally greater at 11 DIV than at 19 DIV.

overall_design: ES DRGs were given electrical stimulation at DIV 10. Control DRGs were not given any electrical stimulation. For each condition, RNA was harvested from three dorsal root ganglion explants pooled together.

first: Woon-Hae

last: Kim

first: Hyun

middle: Y

last: Shin

first: Minseok


title: Phosphorylation-resistant Rb knockin mice develop diabetes that can be attenuated by vitamin C

first: Eldad

last: Zacksenhaus

state: Ontario

address: 101 College Street

institute: University Health Network

summary: While the effect of phosphorylation of the tumor suppressor pRB on cell cycle progression has been analyzed extensively in vitro, little is known about the consequences of blocking the phosphorylation of endogenous pRB on development and homeostasis. Here we show that homozygous RbΔK4 and RbΔK7 knockin mice, with Ser/Thr-to-Ala substitutions in four or all seven CDK sites in the C-terminus of pRb, undergo normal embryogenesis and early development. This is despite inhibition of pRb phosphorylation on additional but not all other upstream sites. Remarkably, adult RbΔK7 but not RbΔK4 mice are smaller than control littermates and exhibit hallmarks of accelerated aging including short telomeres, infertility, kyphosis and diabetes.Diabetes is insulin-sensitive and associated with failure of quiescent pancreatic -cells to re-enter the cell cycle in response to mitogens, leading to induction of DNA damage response (DDR), senescence-associated secretory phenotype, and diminished islet mass. The epigenetic regulator vitamin C decreased pancreatic islet DDR, increased cell cycle re-entry, and attenuated diabetes in RbΔK7 mice. These results have direct implications for cell-cycle regulation, anti-CDK therapy, diabetes and longevity.

overall_design: Two-condition experiment, RbΔK7 mutant vs. control pancreatic islet cells. Biological replicates: 2 control, 2 mutant, independently grown and harvested. One replicate per array.

first: Zhe

last: Jiang


title: Single-cell transcriptomics  of the mouse skin  reveal potential target of psoriasis

first: Dijun

last: Chen

state: Jiangsu

department: Life Sciences

institute: Nanjing University

summary: Psoriasis is a complex chronic inflammatory skin disease, but the exact mechanism underlying its development remains elusive. We found the expression of SHP2 was significantly higher in skin lesions and human peripheral blood mononuclear cells derived from psoriatic patients than those from normal controls.  determine whether SHP2 activity affects psoriasis pathogenesis, we treated the murine psoriatic model with SHP099, a potent allosteric inhibitor of SHP2. SHP099 ameliorates the IMQ-induced psoriatic development in mice with unclear molecular mechanism. To address that, single-cell RNA sequencing was performed to explore the role of SHP2 in all cell types in IMQ-induced mouse skin upon SHP099 treatment.

overall_design: Examination of 6  skin samples in IMQ-induced psoriasis-like mouse model

first: Yang

last: Sun

first: Yuyu

last: Zhu

first: Zhigui

last: Wu


title: Dynamic Runx1 chromatin boundaries affect gene expression in hematopoietic development

city: Oxford

first: Dominic

last: Owens

address: John Radcliffe Hospital

department: MRC WIMM

institute: University of Oxford

summary: The transcription factor RUNX1 is a critical regulator of developmental hematopoiesis and is frequently disrupted in leukemia. Runx1 is a large, complex gene that is expressed from two alternative promoters under the spatiotemporal control of multiple hematopoietic enhancers. To dissect the dynamic regulation of Runx1 in hematopoietic development, we analyzed its three-dimensional chromatin conformation in mouse embryonic stem cell (ESC) differentiation cultures. Runx1 resides in a 1.1 Mb topologically associating domain (TAD) demarcated by convergent CTCF motifs. As ESCs differentiate to mesoderm, chromatin accessibility, Runx1 enhancer-promoter (E-P) interactions, and CTCF-CTCF interactions increased in the TAD, along with initiation of Runx1 expression from the P2 promoter. Differentiation to hematopoietic progenitor cells was associated with the formation of tissue-specific sub-TADs over Runx1, a shift in E-P interactions, P1 promoter demethylation, and robust expression from both Runx1 promoters. Deletions of promoter-proximal CTCF sites at the sub-TAD boundaries had no obvious effects on E-P interactions but led to partial loss of domain structure, mildly affected gene expression, and delayed hematopoietic development. Together, our analyses of gene regulation at a large multi-promoter developmental gene revealed that dynamic sub-TAD chromatin boundaries play a role in establishing TAD structure and coordinated gene expression.

overall_design: Tiled-C, poly-A-minus-RNA-seq, ATAC-seq, CTCF-ChIP-seq

first: Giorgio

last: Anselmi

first: Jim

middle: R

last: Hughes

first: Marella

last: de Bruijn


title: Dynamic FMR1 granule phase switch instructed by m6A modification contributes to maternal RNA decay

city: Beijing

first: Guoqiang

last: Zhang

address: 1 Beichen West Road, Chaoyang District

institute: INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES

summary: Maternal RNA degradation is critical for embryogenesis and is tightly controlled by maternal RNA-binding proteins. Fragile X mental-retardation protein (FMR1) binds target mRNAs to form ribonucleoprotein (RNP) complexes/granules that control various biological processes, including early embryogenesis. However, how FMR1 recognizes target mRNAs and how FMR1-RNP granule assembly/disassembly regulates FMR1-associated mRNAs remain elusive. Here we show that Drosophila FMR1 preferentially binds mRNAs containing m6A-marked “AGACU” motif with high affinity to contributes to maternal RNA degradation. The high-affinity binding largely depends on a hydrophobic network within FMR1 KH2 domain. Importantly, this binding greatly induces FMR1 granule condensation to efficiently recruit unmodified mRNAs. The degradation of maternal mRNAs then causes granule de-condensation, allowing normal embryogenesis. Our findings reveal that sequence-specific mRNAs instruct FMR1-RNP granules to undergo a dynamic phase-switch, thus contributes to maternal mRNA decay. This mechanism may represent a general principle that regulated RNP-granules control RNA processing and normal development.

overall_design: RNA-seq of embryos at the indicated stages were generated by deep sequencing, in duplicate, using NovaSeq platform. MeRIP-Seq of embryos at the indicated stages were generated by deep sequencing, in duplicate, using illumina Hiseq instrument.

first: Yongru

last: Xu

first: Xiaona

last: Wang

first: Yuanxiang

first: Liangliang

first: Wenxin

first: Yiru

first: Yajie

last: Gao

first: Xuna

first: Ying

last: Cheng

first: Qinmiao

first: Dahua


title: Genome-scale Screening in a Rat Haploid System Identifies Thop1 as a Modulator of Pluripotency Exit II

city: Tianjin

first: Ling

last: Shuai

address: 38 Tong Yan Road, Jinnan district

department: State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy

institute: Nankai University

summary: Rat embryonic stem cells (ESCs), which are widely studied, can self-renew and exhibit pluripotency in long-term culture, but the mechanism underlying how they exit pluripotency remains obscure. Rat haploid ESCs (haESCs) enable advances in the discovery of unknown functional genes owing to their homozygous and pluripotent characteristics. Herein, we performed genome-wide mutation using piggyBac transposons in rat haESCs and obtained differentiation-retarded mutants assisted by Rex1-GFP reporter selection. High-throughput sequencing analysis further revealed numerous insertions related to various pathways affecting random differentiation. Thereafter, deletion of Thop1 (one candidate gene in the screened list) arrested the differentiation of rat ESCs by inhibiting the phosphorylation of ERK1/2, whereas overexpression of Thop1 promoted rat ESCs exit from pluripotency. Our findings provide an ideal tool to study functional genomics in rats: a homozygous haploid system carrying a pluripotency reporter that facilitates robust discovery of the mechanisms involved in the self-renewal or pluripotency of rat ESCs.

overall_design: Comparation of the transcriptomes between and rat WT-haESCs and Thop1-KO haESCs by RNA-seq analysis

first: Mei

first: Wenhao

first: Yiding

last: Zhao