title: A DNA adenine demethylase impairs PRC2-mediated repression of genes marked by a specific chromatin signature

city: Wuhan

first: Qingxiao

last: Jia

state: Hubei

address: No.1,Shizishan Street

institute: HZAU

summary: The Fe(II)- and α-ketoglutarate-dependent AlkB family dioxygenases are implicated in nucleotide demethylation. AlkB homolog1 (ALKBH1) is shown to demethylate DNA adenine methylation (6mA) preferentially from single-stranded or unpaired DNA, while its demethylase activity and function in the chromatin context are unclear. In this work we found that loss-of-function of the rice ALKBH1 gene led to increased 6mA in R-loop regions of the genome but had a limited effect on the overall 6mA level. However, the ALKBH1 mutation or over-expression mainly affected the expression of genes with a specific combination of chromatin modifications in the body region marked with H3K4me3 and H3K27me3 but depleted of DNA CG methylation. Further analysis revealed that the ALKBH1 protein preferentially binds to genes marked by the chromatin signature and has a function to maintain a high H3K4me3/H3K27me3 ratio by impairing the binding of Polycomb Repressive Complex2 (PRC2) to the targets, which is required for both the basal and stress-induced expression of the genes.These results unravel a function of ALKBH1 to control the balance between the antagonistic histone methylations for gene activity and provide insight into the regulatory mechanism of PRC2-mediated H3K27me3 deposition within the gene body region.

overall_design: We used rice demethylase ALKBH1 mutant and overexpression materials to carry out 6mA-seq, RNA-seq and ChIP-seq, the dynamic regulation of 6mA and the mechanism of its influence on gene expression and the relationship between other chromatin modifications were analyzed.

first: Xinran

last: Zhang

first: Dao-Xiu

last: Zhou


title: Transcriptional down-regulation of the TGFB2 gene by multiple Fra-1-bound enhancers showing different molecular and functional features in a Triple Negative Cancer (ChIP-Seq)

status: Public on Jul 25 2023

city: Montpellier

first: Isabelle

last: Jariel-Encontre

state: Montpellier Cedex5

address: 208 Avenue des Apothicaires

country: France

institute: IRCM-U1194- INSERM

type: Genome binding/occupancy profiling by high throughput sequencing

summary: genome-wide mapping of H3K36me3 histone mark in the MDA-MB-231 cell line

overall_design: ChIP-seq against H3K36me3 histone mofification in MDA-MB-231 triple negtive breast cancer cell line

first: Fabienne

last: BEJJANI

first: Claire

last: TOLZA

first: Marc

last: PIECHACZYK

last: JARIEL-ENCONTRE


title: Transcriptional profiling of primary human erythroblasts infected with Plasmodium falciparum

city: Palo Alto

first: Tamar

middle: P

last: Feldman

state: CA

address: 240 Pasteur Dr

country: USA

institute: Stanford University

type: Expression profiling by high throughput sequencing

summary: In malaria infection, Plasmodium spp. parasites accumulate in the bone marrow near sites of erythroid development. While it has been observed that Plasmodium falciparum infection of late-stage erythroblasts can delay terminal erythroid differentiation and enucleation, the mechanism(s) underlying this phenomenon are unknown. Here, we apply RNA-seq after fluorescence-activated cell sorting (FACS) of infected erythroblasts to identify transcriptional responses to direct and indirect interaction with P. falciparum.

sample_organism:
Plasmodium falciparum
Homo sapiens

platform_organism:
Plasmodium falciparum
Homo sapiens

overall_design: Comparative gene expression profiling analysis of human erythroblasts sorted into populations and analyzed by RNA-seq. Transcriptomic profiles (4-6 biological replicates) were obtained from four cell types (proerythroblast, basophilic erythroblast, polychromatic erythroblast, orthochromatic erythroblast) in four treatment conditions (media-only, dead parasite (SRS, syringe-ruptured schizont), uninfected, infected).

first: Yana

last: Ryan

first: Elizabeth

middle: S

last: Egan


title: Transcriptional down-regulation of the TGFB2 gene by multiple Fra-1-bound enhancers showing different molecular and functional features in a Triple Negative Cancer

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

overall_design: Refer to individual Series


title: ATAC-seq of microglia from 3-, 14- and 24-month-old female mouse brains treated by LPS or PBS

city: Shanghai

first: Bo

last: Peng

address: 138 Yixueyuan Road

department: Institute for Translational Brain Research

country: China

institute: Fudan University

summary: Microglia are important immune cells in the brain. Microglia undergo a series of alterations during aging and increase the susceptibility to brain dysfunctions. However, the characteristics of microglia during the aging process are not fully understood. In this study, we mapped transcriptional and epigenetic profiles of microglia from 3- to 24-month-old mice. We observed unexpected gender divergences and identified age-dependent microglia (ADEM) genes in the aging process. We then compared characteristics between microglial aging and activation. To dissect the function of aged microglia excluding the influence from other aged brain cells, we established an accelerated microglial turnover model without directly affecting other brain cells. By this model, we achieved aged microglia in non-aged brains and confirmed that aged microglia per se contribute to cognitive decline. Collectively, we provide a comprehensive resource to decode the aging process of microglia, shedding light on how microglia maintain brain functions.

overall_design: After administration of PBS or LPS for 1.5 hours, microglia from 3-month, 14-month, and 24-month female mouse brains were purified for sequencing.

first: Yanxia

last: Rao

first: Xiaoyu

last: Li


title: Transcriptional down-regulation of the TGFB2 gene by multiple Fra-1-bound enhancers showing different molecular and functional features in a Triple Negative Cancer (ATAC-Seq)

summary: mapping of chromatin accessibility in MDA-MB-231 cells in presence and absence of Fra-1 by ATAC-seq experiments

overall_design: ATAC-seq was carried out on biological triplicate of MDA-MB-231 cells transfected for 72 hours by either a control siRNA or an siRNA directed against Fra-1.


title: Bulk RNA-seq of microglia at different ages

overall_design: Microglia from 3- to 24-month-old female and male mouse brains were purified for RNA sequencing.


title: Gene expression profile at single-cell level of microglia from 3-, 14- and 24-month-old female mouse brains

overall_design: After injecting PBS or LPS for 1.5 hours, microglia from 3-, 14- and 24-month-old female mouse brains were purified for sequencing.


title: scRNA-seq of brain cells from 3- and 24-month-old mouse brains

overall_design: Whole brain cells from 3- and 24-month-old female mice were purified for sequencing.


title: HMGB2 regulates the differentiation and stemness of exhausted CD8+ T cells during chronic viral infection and cancer [RNA-seq]

status: Public on Jul 24 2023

city: Irvine

first: Roberto

last: Tinoco

address: 3444 McGaugh Hall

department: Molecular Biology and Biochemistry

institute: University of California, Irvine

summary: Transcriptional and epigenetic features were detected in WT versus HMGB2-/- P14 T cells following LCMV Arm and Cl13 infection.

overall_design: Transcriptional features of WT and HMGB2-/- P14 T cells following adoptive co-transfer into hosts and subsequent infection with either LCMV Arm (8dpi) or Cl13 (8dpi, 20dpi).

first: Emily

middle: N

last: Neubert

first: Sloan

middle: A

last: Lewis


title: Dedifferentiation of Gata6+ epidermal cells

city: London

first: Fiona

middle: Mary

last: Watt

address: Great Maze Road

country: United Kingdom

institute: Kings College London

summary: In the present study, we have integrated lineage tracing with single-cell mRNA-Sequencing to get insights into the molecular mechanisms underlying dedifferentiation of Gata6+ epidermal cells within wounded adult mouse epidermis.

overall_design: Gata-lineage positive and negative epidermal cells from wounded and unwounded skin were isolated by flow sorting, profiled by Smart-seq2 and sequenced by Illumina HiSeq4000. Time points include days 0, 6, 9 and 11 after wounding".

first: Miguel

last: Bernabe-Rubio

middle: M

first: Shahnawaz

last: Ali


title: HMGB2 regulates the differentiation and stemness of exhausted CD8+ T cells during chronic viral infection and cancer [ATAC-seq]

overall_design: Epigenetic features of WT and HMGB2-/- P14 T cells following adoptive co-transfer into hosts and subsequent infection with LCMV Cl13 for 8 days.


title: Periplasmic stress contributes to a tradeoff between protein secretion and cell growth in E. Coli Nissle

city: Boston

first: Neel

last: Joshi

state: MA

address: 10 Gainsborough St

department: Chemistry and Chemical Biology

institute: Northeastern University

summary: To investigate changes in E. coli Nissle 1917 gene expression when engineered to secrete a large amount of protein via the curli (Type VIII) secretion system.

overall_design: To investigate variants of protein secretion and conduct gene expression profiling analysis to determine genes that are upregulated due to cellular burden from protein secretion. The different variants derived include: no protein expression or secretion, localized protein expression in the cytoplasm, and protein expression with secretion to the extracellular space (i.e., secretion through the inner and outer membrane).

first: Siva

last: Emani

first: Timothy

last: Storms

first: Anton

last: Kan

first: Shanna

last: Bonanno

first: Jade

last: Law

first: Sanhita

last: Ray


title: Efficient genome editing in erythroid cells unveils novel MYB target genes and regulatory functions

city: Montpellier cedex 5

first: Eric

last: Soler

address: 1919 route de Mende

institute: IGMM

summary: Targeted genome editing holds great promise in biology. However, efficient genome modification, including gene knock-in, remains an unattained goal in multiple cell types and loci due to poor transfection efficiencies and low target genes expression, impeding the positive selection of recombined cells. Here, we describe a genome editing approach to achieve efficient gene targeting using hard to transfect erythroid cell lines. We demonstrate robust fluorescent protein knock-in efficiency in low expressed transcription factor gene loci (e.g. Myb or Zeb1). We further show the ability to target several genes in individual cells, exemplified by MYB-GFP and NuMA-Cherry double knock-in, allowing multicolor labeling of regulatory factors at physiological endogenous levels. Our knock-in tagging approach allowed us to perform genome-wide TF analysis at increased signal-to-noise ratios, and highlighted previously unidentified MYB target genes and pathways. Overall, we establish a versatile CRISPR-Cas9-based platform, offering attractive opportunities for the dissection of the erythroid differentiation process.

overall_design: CUT&RUN

first: Virginie

last: Deleuze

first: Léonor

last: Garcia

first: Betty

last: Rouaisnel

first: Mohammad

last: Salma

first: Alexia

last: Kinoo

first: Charlotte

last: Andrieu-Soler


title: Real-time quantitative PCR analysis of mouse dendritic cells treated with Ac4ManNAz or PBS

status: Public on Jul 22 2023

city: Urbana

first: Hua

last: Wang

state: IL

address: 202 MSE Building, 1304 West Green Street

institute: University of Illinois at Urbana Champaign

summary: Dendritic cell (DC) vaccine was among the first FDA-approved cancer immunotherapies, but has been limited by the modest cytotoxic T lymphocyte (CTL) response and therapeutic efficacy. Here we report a facile metabolic labeling approach that enables targeted modulation of adoptively transferred DCs for developing enhanced DC vaccines. We show that metabolic glycan labeling can reduce the membrane mobility of DCs, which activates DCs and improves the antigen presentation and subsequent T cell priming property of DCs. Metabolic glycan labeling itself can enhance the antitumor efficacy of DC vaccines. In addition, the cell-surface chemical tags (e.g., azido groups) introduced via metabolic glycan labeling also enable in vivo conjugation of cytokines onto adoptively transferred DCs, which further enhances CTL response and antitumor efficacy. Our DC labeling and targeting technology provides a new strategy to improve the therapeutic efficacy of DC vaccines, with minimal interference upon the clinical manufacturing process.

overall_design: Mouse dendritic cells that were treated with Ac4ManNAz or PBS (1 million cells per sample) were collected, washed, frozen at -80oC, and transferred to the sequencing Core at UIUC. The staff then extract RNA and treat it with DNAse, run it on a fragment analyzer so that you get the RIN, make individually barcoded polyA+ selected RNAseq libraries, sequence them on an SP lane with 1x100nt single-reads, which produces ~ 400 million reads

first: Joonsu

last: Han

first: Rimsha

last: Bhatta

first: Yusheng

last: Liu

first: Yang

last: Bo

first: Alberto

last: Elosegui Artola


title: HMGB2 regulates the differentiation and stemness of exhausted CD8+ T cells during chronic viral infection and cancer.

first: Roberto

last: Tinoco


title: TOX2 coordinates with TET2 to positively regulate central memory differentiation in human CAR T cells

city: Philadelphia

first: Sierra

middle: Marie

last: Collins

state: PA

address: 3400 Civic Center Blvd. Rm 9-164 SCTR BLDG 421/CD

department: Perelman School of Medicine

institute: University of Pennsylvania

summary:
To investigate the effects of TOX and TOX2 on memory T cell differentiation in human CAR T cells, we used shRNA to knock down TOX2 or TOX, or overexpress FLAG-TOX2.
We then performed gene expression profiling analysis using RNAseq, plus examined the binding of TOX2 to chromatin using ChIPseq.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for shNT vs. shTOX2 or shTOX2, or FLAG vs. FLAG-TOX2.
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for TOX2 in WT or TOX2-overexpressing human CAR T cells.

first: Katherine

last: Alexander

first: Shelley

middle: L

last: Berger


title: Rege-1 promotes C. elegans survival by modulating the metabolic pathways

status: Public on Jul 21 2023

city: Taipei

first: Yi-Ting

last: Tsai

address: No.1 Jen Ai road section 1

country: Taiwan

institute: National Taiwan University

summary: To understand how excess amount of ets-4 contributed to poor survival of rege-1(ht070) fed with PA14, we performed mRNA-seq on the adult worms after 48 hours exposure to either OP50 or PA14 in all four strains.

overall_design: 4 genotypes exposed to two different treatments

first: Hsin-Yue


title: Targeting Duchenne Muscular Dystrophy by Skipping DMD Exon 45 with Base Editors

status: Public on Jul 20 2023

first: Michael

last: Gapinske

address: 1406 W Green Street

department: BIOE

institute: University of Illinois at Urbana-Champaign

summary: Duchenne muscular dystrophy is an X-linked monogenic disease caused by mutations in the dystrophin gene (DMD) and characterized by progressive muscle weakness leading to loss of ambulation and significantly decreased life expectancy. Since the current standard of care for Duchenne muscular dystrophy is to merely treat symptoms, there is a dire need for novel treatment modalities that can correct the underlying genetic mutations. While several gene replacement therapies are being explored in clinical trials, one emerging approach that can directly correct mutations in genomic DNA is base editing. We have recently developed CRISPR-SKIP, a base editing strategy to induce permanent exon skipping by introducing C>T or A>G mutations at splice acceptors in genomic DNA, which can be utilized therapeutically to recover dystrophin expression when a genomic deletion leads to an out-of-frame DMD transcript. We now demonstrate that CRISPR-SKIP can be adapted to correct some forms of Duchenne muscular dystrophy by disrupting the splice acceptor in human DMD exon 45 with high efficiency, which enables open reading frame recovery and restoration of dystrophin expression. We also demonstrate that AAV-delivered split-intein base editors edit the splice acceptor of DMD exon 45 in cultured human cells and in vivo, highlighting the therapeutic potential of this strategy.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Determining the ability of CRISPR base editors to edit the splice acceptor of DMD exon 45, and the effect that that editing has on exon skipping. Sequencing data from targeted amplicon sequencing of edited genomic DNA from cell lines and mouse tissues, as well sequencing of RNA from engineered tissue

first: Jackson

last: Winter

first: Devyani

last: Swami

first: Lauren

first: Wendy

last: Woods

first: Shraddha

last: Shirguppe

first: Angelo

last: Miskalis

first: Anna

last: Busza

first: Dana

last: Joulani

first: Collin

last: Kao

first: Kurt

last: Kostan

first: Anne

last: Bigot

first: Rashid

last: Bashir

first: Pablo

last: Perez-Pinera


title: Effect of depletion of TFPI2 on gene expression in glioma stem cells

city: Cleveland

first: Lizhi

last: Pang

state: OH

address: 9500 Euclid Avenue

department: Department of Cancer Biology

institute: Cleveland Clinic

summary:
To investigate the mechanism of TFPI2 in regulation of glioblastoma stemness, we established GSC272 cell line in which TFPI2 gene has been knocked down by shRNA.
We then performed gene expression profiling analysis using data obtained from RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for GSC272 cells KD derivatives (shC and shTFPI2).

first: Pang

last: Lizhi

first: Peiwen

last: Chen


title: Translocator protein is a marker of activated microglia in rodent models but not human neurodegenerative diseases

status: Public on Jul 19 2023

first: Nurun

last: Fancy

address: 726 Sir Michael Uren Hub

department: Brain Sciences

institute: Imperial College London


title: Translocator protein is a marker of activated microglia in rodent models but not human neurodegenerative diseases I

summary: Microglial activation plays central roles in neuro-inflammatory and neurodegenerative diseases. Positron emission tomography (PET) targeting 18kDa Translocator Protein (TSPO) is widely used for localising inflammation in vivo, but its quantitative interpretation remains uncertain. We show that TSPO expression increases in activated microglia in mouse brain disease models but does not change in a non-human primate disease model or in common neurodegenerative and neuroinflammatory human diseases. We describe genetic divergence in the TSPO gene promoter, consistent with the hypothesis that the increase in TSPO expression in activated myeloid cells depends on the transcription factor AP1 and is unique to a subset of rodent species within the Muroidea superfamily. Finally, we identify LCP2 and TFEC as potential markers of microglial activation in humans. These data emphasise that TSPO expression in human myeloid cells is related to different phenomena than in mice, and that TSPO-PET signals in humans reflect the density of inflammatory cells rather than activation state.

overall_design:
Human monocyte derived macrophages (MDMs) were obtained from fresh blood of male and female
healthy donors (n = 6) between 20 and 60 years after CD14-affinity purification. Cells were then treated with or without LPS (100ng/ml) for 24 hours. Total RNA was collected by rRNA depletion before generating cDNA libraries. Illumina sequencing was used to obtain a minimum of 40 million paired-end reads per sample.

first: Erik

last: Nutma

first: Maria

last: Weinert

first: Stergios

last: Tsartsalis

first: Manuel

middle: C

last: Marzin

first: Robert

middle: J

last: Muirhead

first: Irene

last: Falk

first: Marjolein

last: Breur

first: Joy

last: de Bruin

first: David

last: Hollaus

first: Robin

last: Pieterman

first: Jasper

last: Anink

last: Story

first: Siddharthan

last: Chandran

first: Jiabin

last: Tang

last: Trolese

first: Takashi

last: Saito

first: Takaomi

last: Saido

first: Katharine

middle: H

last: Wiltshire

first: Paula

last: Beltran-Lobo

first: Alexandra

last: Phillips

first: Jack

last: Antel

first: Luke

last: Healy

first: Marie-France

last: Dorion

first: Dylan

last: Galloway

first: Rochelle

middle: Y

last: Benoit

first: Quentin

last: Amosse

first: Kelly

last: Ceyzériat

first: Aurélien

last: Badina

first: Eniko

last: Kovari

first: Caterina

last: Bendotti

first: Eleonora

last: Aronica

first: Carola

middle: I

last: Radulescu

first: Jia

last: Wong

last: Barron

first: Amy

last: Smith

first: Samuel

last: Barnes

middle: W

last: Hampton

first: Paul

last: van der Valk

first: Steven


title: Lorazepam stimulates IL-6 production and is associated with poor survival outcomes in pancreatic cancer

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

summary: LOR is associated with worse progression-free survival (PFS) while alprazolam (ALP) is associated with improved PFS, in pancreatic cancer patients receiving chemotherapy. LOR promotes desmoplasia (fibrosis and extracellular matrix protein deposition), inflammatory signaling, and ischemic necrosis. GPR68 is preferentially expressed on human PDAC CAFs, and n-unsubstituted BZDs, such as LOR, significantly increase IL-6 expression and secretion in CAFs in a pH and GPR68-dependent manner. Conversely, ALP, and other GPR68 n-substituted BZDs decrease IL-6 in human CAFs in a pH and GPR68-independent manner. Across many cancer types, LOR is associated with worse survival outcomes relative to ALP and patients not receiving BZDs. We demonstrate that LOR stimulates fibrosis and inflammatory signaling, promotes desmoplasia and ischemic necrosis, and is associated with decreased pancreatic cancer patient survival.

overall_design:
This research investigates the association between benzodiazepines (BZDs) and cancer patient survival outcomes, the pancreatic cancer tumor microenvironment, and cancer-associated fibroblast (CAF) signaling.
Multivariate Cox regression modeling was used to retrospectively measure associations between Roswell Park cancer patient survival outcomes and BZD prescription records. Immunohistochemistry, H&E, Masson’s trichrome, RNAscope, and RNA sequencing were used to evaluate the impact of lorazepam (LOR) on the murine PDAC tumor microenvironment. ELISA and qPCR were used to determine the impact of BZDs on IL-6 expression or secretion by human immortalized pancreatic CAFs. PRESTO-Tango assays, reanalysis of PDAC single cell sequencing/TCGA datasets, and GPR68 CRISPRi knockdown CAFs were used to determine the impact of BZDs on GPR68 signaling.
8 samples. Four from DMSO and LOR conditions

first: Abigail

last: Cornwell

first: Arwen

last: Tisdale

first: Swati

last: Venkat

first: Kathry

middle: E

last: Maraszek

first: Abdulrahman

last: Alahmari

first: Anthony

last: George

first: Kristopher

last: Attwood

first: Madison

first: Donald

last: Rempinski

first: Janusz

last: Franco-Barraza

first: Mukund

last: Seshadri

first: Mark

middle: D

last: Parker

last: Cortes-Gomez

first: Christos

last: Fountzilas

first: Edna

last: Cukierman

first: Nina

middle: G

last: Steele

first: Michael

last: Feigin


title: Effect of knockout of and pathogenic mutations in Hnrnph2 on gene expression in mouse cortex

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

summary: To investigate the effect of knockout of and pathogenic mutatations in Hnrnph2, we generated mouse lines in which endogenous Hnrnph2 has been knocked out, or 2 pathogenic mutations (R206W, P209L) have been knocked into the endogenous Hnrnph2 using CRISPR Cas-9.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of bulk cortex from male mice aged 8 weeks (knockout and R206W knockin lines) or 3 weeks (P209L knockin line) and age matched littermate controls (n=3 per grpup).

first: Hong

last: Kim

first: Ane

last: Korff

first: J

middle: P

last: Taylor


title: Translocator protein is a marker of activated microglia in rodent models but not human neurodegenerative diseases II

first: Nurun

last: Fancy

first: Erik

last: Nutma

first: Maria

last: Weinert

first: Stergios

last: Tsartsalis

first: Manuel

last: Marzin

first: Robert

last: Muirhead

first: Irene

last: Falk

first: Marjolein

last: Breur

first: Joy

last: de Bruin

first: David

last: Hollaus

first: Robin

last: Pieterman

first: Jasper

last: Anink

last: Story

first: Siddharthan

last: Chandran

first: Jiabin

last: Tang

last: Trolese

first: Takashi

last: Saito

first: Takaomi

last: Saido

first: Katharine

last: Wiltshire

first: Paula

last: Beltran-Lobo

first: Alexandra

last: Phillips

first: Jack

last: Antel

first: Luke

last: Healy

first: Marie-France

last: Dorion

first: Dylan

last: Galloway

first: Rochelle

last: Benoit

first: Quentin

last: Amosse

first: Kelly

last: Ceyzériat

first: Aurélien

last: Badina

first: Eniko

last: Kovari

first: Caterina

last: Bendotti

first: Eleonora

last: Aronica

first: Carola

last: Radulescu

first: Jia

last: Wong

first: Anna

last: Barron

first: Amy

last: Smith

first: Samuel

last: Barnes

last: Hampton

first: Paul

last: van der Valk

first: Steven


title: Effect of erythritol on gene expression of Staphylococcus pseudintermedius

city: Toyoake

first: Tadashi

last: Fujii

state: Aichi

address: 1-98 Dengakugakubo Kutsukake-cho

department: School of Medicine, Gastroenterology and Hepatology

country: Japan

institute: FUJITA HEALTH UNIVERSITY

summary: We performed a transcriptome analysis of Staphylococcus pseudintermedius with and without 5% (w/w) erythritol exposure to validate the mechanism of growth inhibition.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Staphylococcus pseudintermedius with and without 5% (w/w) erythritol exposure

first: Takumi

last: Tochio

first: Koji

last: Nishifuji


title: The master energy homeostasis regulator PGC-1α exhibits a novel mRNA nuclear export function

first: Simeon

middle: R.

last: Mihaylov

address: 1 Midland Road

institute: The Francis Crick Institute

overall_design: Refer to individual Series


title: Effect of knockout of and pathogenic mutations in HNRNPH2 on gene expression in human and mouse

first: Yong-Dong

last: Wang


title: The master energy homeostasis regulator PGC-1α exhibits a novel mRNA nuclear export function [ChIP-Seq]

summary: PGC-1α plays a central role in maintaining mitochondrial and energy metabolism homeostasis, linking external stimuli to transcriptional co-activation of genes involved in adaptive and age-related pathways. The carboxyl-terminus encodes a serine/arginine-rich (RS) region and a putative RNA recognition motif, however the potential RNA-processing function(s) remained elusive for the past 20 years. Here, we show that the RS domain of human PGC-1α directly interacts with RNA and the nuclear RNA export receptor NXF1. Inducible depletion of PGC-1α and expression of RNAi-resistant RS-deleted PGC-1α further demonstrated that its RNA/NXF1-binding activity is required for the nuclear exportof a subset of mRNAsand mitochondrial homeostasis.Genome-wide investigations revealed that the nuclear export function is not strictly linked to PGC-1α-binding promoters, identifyingin turnnovel mRNA nuclear export targets inmRNA- and age-related pathways.These findingsprovide new directions to further elucidate the roles of PGC-1α in gene expression, metabolic disorders, ageing andneurodegeneration.

overall_design: Comparative chromatin immuniprecipitation DNA seqeuncing (ChIP-seq) analysis using data from 18 samples from stable inducible Flp-In T-REx 293 cell lines. The cells lines included (i) Sham - a negative control line which has undergone the same procedures for generation of stable inducible cell lines but does not have a GOI inserted; (ii) PGC-1α WT-res - a cell line with endogenous depletion of PGC-1α and replacement with wild-type cDNA; (iii) PGC-1α ΔRS-res - a cell line with endogenous depletion of PGC-1α and replacement with deletion construct of PGC-1α lacking amino acids 595-633. For each group, cells from three consecutive passages were used.

middle: R

first: Guillaume

last: Hautbergue


title: An engineered Sox17 induces somatic to neural stem cell fate transition independently from pluripotency reprogramming [RNA-seq II]

city: Hong Kong

first: Mingxi

last: WENG

state: Not Applicable

address: L408A, Laboratory Block, 21 Sassoon Road, Pokfulam, Hong Kong

country: Hong Kong

institute: School of Biomedical Sciences, The University of Hong Kong

summary: Advances in molecular strategies to reprogram cell fate is a promising avenue for cell-based therapies. Methods to generate induced neural stem cells (iNSCs) are often slow with limited reprogramming events and it is unclear whether cells transit via a pluripotent state. We report an iNSC reprogramming approach from embryonic and aged mouse fibroblasts using an engineered Sox17 (eSox17FNV). eSox17FNV efficiently drives iNSC reprogramming while Sox2 or Sox17 fails to do so. eSox17FNV acquires the capacity to bind new protein partners to scan the genome more efficiently and possesses a more potent transactivation domain than Sox2. At the onset of reprogramming, in the presence of eSox17FNV, fibroblasts divert from a iPSC route towards iNSC fate. Further, lineage tracing shows that emerging iNSCs do not transit through a pluripotent state if POU factors are excluded. This reveals new molecular and physiological framework for iNSC generation and contrasts with lineage from pluripotency reprogramming.

overall_design: We analyzed the gene expression profiles of mouse iNSCs reprogrammed from embryonic, adult and old mouse fibroblasts using transcription factor combination containing eSox17FNV by RNA-seq.

last: Weng

first: Ralf

last: Jauch


title: Effect of knockout of and pathogenic mutations in HNRNPH2 on gene expression in human iPSC-derived neurons

summary: To investigate the effect of knockout of and pathogenic mutatations in HNRNPH2, we generated human iPSC lines in which endogenous HNRNPH2 has been knocked out, or 3 pathogenic mutations (R206W, R206Q, and P209L) have been knocked into the endogenous HNRNPH2 using CRISPR Cas-9.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of undifferentiated iPSCs or 3 weeks old neurons.

first: Hong

last: Kim

first: Ane

last: Korff

first: J

last: Taylor


title: An engineered Sox17 induces somatic to neural stem cell fate transition independently from pluripotency reprogramming [RRBS]

type: Methylation profiling by high throughput sequencing

overall_design: We used reduced representation bisulfite sequencing (RRBS) to analyze the genomic DNA methylation of young and old primary NSCs and fibroblasts and mouse iNSCs generated from old fibroblasts.


title: An engineered Sox17 induces somatic to neural stem cell fate transition independently from pluripotency reprogramming [scRNA-seq]

overall_design: We analyzed mouse primary NSC isolated from mouse embryos and iNSCs reprogrammed from mouse embryonic fibroblasts using transcription factor combination containing eSox17FNV by scRNA-seq.


title: An engineered Sox17 induces somatic to neural stem cell fate transition independently from pluripotency reprogramming [RNA-seq III]

overall_design: We analyzed the gene expression profiles of C-MYC/eSOX17FNV reprogramme human iNSCs from human erythroid progenitor cells (EPCs) by RNA-seq.


title: Transcriptome analysis Arabidopsis Col-0 plants grown in presence of SynComCol-0, SynCommfec and under axenic condition in Gnotopot growth system

city: Durham

first: Reza

last: Sohrabi

state: NC

address: FFSC Bldg rm 4305, 124 Science Dr,

department: Biology

institute: Duke University

summary: We performed RNA-Seq based gene expression analysis of Arabidopsis Col-0 plants grown in presence of SynComCol-0 (eubiotic bacterial community), SynCommfec (dysbiotic bacterial community) and Axenic conditions in GnotoPot plant gnotobiotic growth system. SynCom preparation was done by mixing equal ratio of the each strain measured based on optical density of (OD600) in 10 mM MgCl2 and adjusting to the final combined OD600 of 0.04. Plants were grow in GnotoPots as described in (Chen et al, Nature 2020). We identified genes differentially enriched in response to presence of eubiotic and dysbiotic bacterial communities.  Our results suggested that in presence of dysbiotic community there is over abundance of gene expression for immunity/defense-related genes in SynCommfec compared SynComCol-0 colonized plants.

overall_design: Three biological samples for each of the treatments were analyzed.

first: James

last: Kremer

first: Bradley

last: Paasch

first: Sheng

last: He


title: Transcriptome analysis Arabidopsis Col-0 plants grown in gnotobiotic growth system

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


title: An engineered Sox17 induces somatic to neural stem cell fate transition independently from pluripotency reprogramming [ATAC-Seq]

overall_design: We analyzed the chromatin accessibility profiles of Sox2, Sox17, Sox17FNV in replicates at day 4 of doxycycline-induced lentivirus based somatic cell reprogramming to iNSC in NSC medium


title: Transcriptome analysis Arabidopsis Col-0 plants grown under axenic and holoxenic conditions in FlowPot gnotobiotic growth system

summary: We performed RNA-Seq based gene expression analysis of Arabidopsis Col-0 plants grown under axenic and holoxenic conditions in FlowPot system. Holoxenic plants were grown in the presence of soil slurries containing microbial communities derived from natural soils and under axenic condition in presence of heat-killed soil slurries for three weeks. We identified genes differentially enriched in response to presence of microbial communities.  Our results suggested that in presence of microbiota there is a differential expression of immunity/defense-related genes in holoxenic compared to axenic plants.

overall_design: Whole rosette tissues of 21-days old plants from three biological replicates each defined as a pool of eight rosettes were collected from four FlowPots within the same microbox. For holoxenic experiments, natural community inputs harvested from soils obtained from two geographical locations (MSU and Laurel) were used. For axenic mock-inoculated plants corresponding autoclaved soil slurries were used.


title: An engineered Sox17 induces somatic to neural stem cell fate transition independently from pluripotency reprogramming [RNA-seq]

overall_design: We analyzed the gene expression profiles of Sox2, Sox17 and Sox17FNV mediated somatic cell reprogramming towards iNSCs in NSC medium at different reprogramming time points (Days 4, 8, 12, 18, 24, 30) by RNA-seq. In addition, we also sequenced a Sox17FNV mediated iNSC and iPSC reprogramming in parallel at day 4, 8, 12, 16, 20, 24 in chemically defined medium.


title: Optimized minimal genome-wide human sgRNA library

status: Public on Jul 18 2023

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

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

department: School of Life Sciences

institute: Westlake university

summary:
To minimize the human genome-wide CRISPR/Cas9 library size, we established H-mLib which recruited a novel sgRNA design  method and applied with dual plasmid based strategy.
The performance of the H-mLib was benchmarked to other CRISPR libraries in a proliferation screening conducted in K562 cells.
We also identified human core essential genes and cell-type specific essentials genes in K562 and Jurkat cells.

overall_design: CRISPR screen

first: Yangfan

last: Zhou

first: Lixia

first: Zhike

last: Lu

first: Zhenxing

last: Yu


title: RNA-seq analysis about Dot1l knocked out  samples

city: Tianjin

first: Haiyang

last: Sun

address: No.38 Tongyan Road, Jinnan District

institute: Nankai University

summary: Endogenous retroviruses (ERVs) are suppressed to maintain genome stability and it’s regulatory mechanism remains unclear. To determine the restrain mechanism of MERVL, we knocked out Dot1l and analyzed the effect on the expression of transposable elements and coding genes. Our results showed Dot1l as a repressor of MERVL and 2-cell genes in ESCs.

overall_design: We knocked out Dot1l in E14 ESCs by CRISPR/Cas9 gene editing technology and performed RNA-seq analysis in order to exam the transcriptome after Dot1l  knock out.

first: Xinyi

first: Xin

last: Zhao

first: Xuan


title: An engineered Sox17 induces somatic to neural stem cell fate transition independently from pluripotency reprogramming

first: Mingxi


title: MYC Deregulation and PTEN Loss Model Tumor and Stromal Heterogeneity of Aggressive Triple-Negative Breast Cancer

city: Portland

first: Zinab

last: Doha

state: OR

address: 2730 S MOODY AVE

institute: Oregon Health & Science University

summary: Triple-negative breast cancer (TNBC) patients have a poor prognosis and few treatment options. Mouse models of TNBC are important for development of new therapies, however, few mouse models represent the complexity of TNBC. Here, we develop a female TNBC murine model by mimicking two common TNBC mutations with high co-occurrence: amplification of the oncogene MYC and deletion of the tumor suppressor PTEN. This Myc;Ptenfl model develops heterogeneous triple-negative mammary tumors that display histological and molecular features commonly found in human TNBC. Our research involves deep molecular and spatial analyses on Myc;Ptenfl tumors including bulk and single-cell RNA-sequencing, and multiplex tissue-imaging. Through comparison with human TNBC, we demonstrate that this genetic mouse model develops mammary tumors with differential survival and therapeutic responses that closely resemble the inter- and intra-tumoral and microenvironmental heterogeneity of human TNBC, providing a pre-clinical tool for assessing the spectrum of patient TNBC biology and drug response.

overall_design:
- RNA was extracted from Myc;Ptenfl tumor tissue (n = 13) or normal mammary gland as control (n=3) using Trizol (Invitrogen). Normalized count data was generated using the standard DESeq2 (v1.36.0) workflow with Variance Stabilizing Transformation.
- Single-cell suspensions of 11 Myc;Ptenfl tumors were obtained by enzymatic digestion. Library prepared with the Chromium Single Cell 3’ V3 (10X Genomics) following the manufacturer’s protocol with a targeted recovery of 20,000 cells per library. Libraries were sequenced on an Illumina NovaSeq. BCL files were converted to fastq format with bcl2fastq2 (Illumina), and then aligned to mouse genome build mm10-2020-A (10X Genomics) using Cellranger (10X Genomics, version 6.0.2).

first: Doha

last: Zinab

first: Wang

last: Xiaoyan

first: Sears

last: Rosalie


title: Changes in the transcriptome of Arabidopsis thaliana after ethylene-mediated metabolic priming

city: Knoxville

first: Brad

last: Binder

state: Tennessee

address: 309 Ken and Blaire Mossman Bldg.

department: Biochemistry & Cellular and Molecular Biology

institute: University of Tennessee

summary: We demonstrated that pretreatment of darkgrown seedlings with ethylene followed by removal of ethylene and transfer to light results in long-term increases in growth. Tolerance to abiotic stresses also increases. Correlating with these changes are increases in photosynthesis and carbohydrate levels. The goal of this transcriptomic analysis was to gain insights into the transcriptional changes that occur to cause these changes in growth and stress tolerance.

overall_design: Arabidopsis thaliana seedlings were germinated on agar plates with 1/2 MS-NS in darkness for 3 d in the presence or absence of 0.7 ppm ethylene. At this time, seedlings were transferred to light and ethylene-free conditions for 5 d. At this time RNA extraction was carried out. Three replicates of each condition were obtained.

first: Eric

last: Brenya


title: ChIP-seq analysis about Dot1l and Npm1 samples

summary: To identify whether Dot1l or Npm1 were enriched in MERVL directly, we performed Dot1l and Npm1 ChIP-seq in wildtype ESCs. We conclude that Dot1l and Npm1 binding were enriched on MERVL-int region, suggesting a direct regulatory role of Dot1l and Npm1 on MERVL expression.

overall_design: We carried out  Dot1l and Npm1 ChIP-seq with anti-Dot1l, anti-Npm1 antibodies in wildtype ESCs in order to  identify whether Dot1l or Npm1 were enriched in MERVL.


title: miRNA profiling from peripheral white blood cells in fertile and subfertile beef heifers at weaning

status: Public on Jul 17 2023

city: Auburn

first: Paul

last: Dyce

state: Alabama

address: 559 Devall Dr,

department: Animal Science

institute: Auburn University

type: Non-coding RNA profiling by high throughput sequencing

summary: The miRNA profiles were measured using small-RNA sequencing in beef heifers sampled at weaning that was retrospectively classified as fertile or subfertile following the breeding protocol. To accomplish this, the miRNA profiles were generated from the blood samples (10 mL) collected from crossbred heifers (Angus-Simmental) at the time of weaning (~238 days after birth). Peripheral white blood cells (PWBC) were extracted from the blood samples and stored at -80°C until further processing. During the breeding season, all the heifers followed the same breeding protocol, estrus synchronization, and fixed-time artificial insemination (AI). Fourteen days following the fixed-time AI, the non-pregnant heifers were exposed to fertile bulls for 60 days. Depending on the presence or absence of conceptus at 75 days following AI, heifers were classified as fertile for those who were pregnant through artificial insemination, pregnant to natural breeding (P-NB), or subfertile for those who were not pregnant. Heifers from fertile (n = 7) and subfertile (n = 7) groups were considered for the study. Total RNA was extracted from the PWBC of 14 samples and was subjected to small RNA library preparation and sequencing. After quality control, adapter trimming, and alignment, mature miRNAs were used for differential expression analysis. The read counts were transformed to counts per million (CPM), and raw counts with CPM < 1 in 50% of the samples were filtered out. The filtered raw counts were analyzed using DESeq2 v 1.26.0 to identify differentially expressed miRNAs (DEMIs). The DEMIs identified with a p-value < 0.05 and absolute (log2 fold change) > 0.5 were considered significant. With the subfertile heifers as the reference group, we identified 16 DEMIs between fertile and subfertile groups. To determine the genes targeting the DEMIs, we downloaded the target genes for each DEMI and retained only those genes expressed in the PWBCs. For the miRNA-gene correlation, we used the partial correlation and information theory (PCIT) approach to identify the significant gene-miRNA correlated pairs. The significant genes correlated with the miRNAs identified pathways including MAPK, ErbB, HIF-1, FoxO, p53, mTOR, T-cell receptor, insulin and GnRH signaling, apoptosis, and pathways regulating pluripotency of stem cells in the fertile group while cell cycle, p53 signaling pathway and apoptosis pathways in the subfertile group.

overall_design: Peripheral white blood cell miRNA profiles from 14 Angus-Simmental crossbred heifers (fertile = 7; subfertile = 7) were generated with the Illumina Next-Seq 500 platform using the single-end 50 bp chemistry.

first: Priyanka

last: Banerjee

first: Wellison

last: Diniz

first: Soren

last: Rodning


title: Langerhans cells shape postnatal oral homeostasis in a mechanical force-dependent but microbiota and IL17-independent manner

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

summary: The postnatal microbiota-immune axis establishes lifelong homeostasis at mucosal epithelial barriers. However, whether barrier-specific physiological activities regulate this process remains ill-defined. During weaning, the oral epithelium, which is monitored by Langerhans cells (LCs), is challenged by the development of a microbial plaque and the initiation of masticatory forces capable of damaging the epithelium. We demonstrate that microbial colonization following birth facilitates the differentiation of oral LCs, setting the stage for the weaning period, where adaptive immunity develops. Despite the presence of the challenging microbial plaque, LCs mainly respond to masticatory mechanical forces, inducing adaptive immunity to maintain epithelial integrity that is also associated with bone loss. Unlike adult life, this bone loss is IL-17-independent, suggesting that the establishment and maintenance of oral mucosal homeostasis involve distinct mechanisms. Moreover, barrier-specific features play a fundamental role in this early-life process.

overall_design: the samples are mice gingival epithelium samples taken from Langerin-DTR mice that were injected with either PBS or Diphtheria toxin, and therefore are either depleted (DT) or non depleted (PBS) of Langerhans cells. The samples include 5 replicates of PBS samples and 6 replicates of DT samples.

first: Yasmin

last: Jaber

first: Avi-Hai

last: Hovav


title: Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD

city: New York

first: Stella

last: Dracheva

address: 1 Gustave L. Levy Pl

department: Psychiatry

institute: Icahn School Of Medicine at Mount Sinai

overall_design: Refer to individual Series


title: Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snRNA-seq)

summary: Neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are strongly influenced by inherited genetic variation, but environmental and epigenetic factors also play key roles in the course of these diseases. A hexanucleotide repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of ALS and FTD. To determine the cellular alterations associated with the C9 repeat expansion, we performed single nucleus transcriptomics (snRNA-seq) and epigenomics (snATAC-seq) in postmortem samples of motor and frontal cortices from C9-ALS and C9-FTD donors. We found pervasive alterations of  gene expression across multiple cortical cell types in C9-ALS, with the largest number of affected genes in astrocytes and excitatory neurons. Astrocytes increased expression of markers of activation and pathways associated with structural remodeling. Excitatory neurons in upper and deep layers increased expression of genes related to proteostasis, metabolism, and protein expression, and decreased expression of genes related to neuronal function. Epigenetic analyses revealed concordant changes in chromatin accessibility, histone modifications, and gene expression in specific cell types. C9-FTD patients had a distinct pattern of changes, including loss of neurons in frontal cortex and altered expression of thousands of genes in astrocytes and oligodendrocyte-lineage cells. Overall, these findings demonstrate a context-dependent molecular disruption in C9-ALS and C9-FTD, resulting in distinct effects across cell types, brain regions, and disease phenotypes.

overall_design: Single nucleus RNA sequencing (snRNA-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snRNA-seq was performed using 10X Genomics platform.

first: Junhao

last: Li

first: Manoj

middle: K

last: Jaiswal

first: Jo-Fan

last: Chien

first: Alexey

last: Kozlenkov

first: Ping

last: Zhou

first: Veronique

middle: V

last: Belzil

first: Eran

middle: A

last: Mukamel


title: Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (bulk RNA-seq)

overall_design: RNA sequencing (RNA-seq) of the three major brain cell populations (neurons, oligodendrocytes, and other glia) from adult human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. The populations were isolated using fluorescence-activated nuclei sorting.


title: Induction of neurons from mouse ESC by the bHLH factors Ascl1 and Ngn2 shows distinct genetic dependencies, pluripotency exit, and cell cycle shutdown. [RNA-Seq]

city: Vienna

first: Gintautas

last: Vainorius

address: Dr. Bohr-Gasse 3

country: Austria

institute: Institute of Molecular Biotechnology

summary: Two closely related proneural bHLH transcription factors, Ascl1 and Ngn2, both can induce mouse embryonic stem cells to differentiate into induced neurons. Although Ascl1 and Ngn2 induced transcriptional programs partially overlap, it is not known whether the differences translate into the distinct mechanisms. We found that both transcription factors induce mutually exclusive side populations by binding and inducing different lineage drivers. Furthermore, Ascl1 rapidly dismantles the pluripotency network and installs neuronal and trophoblast cell fates, while Ngn2 generates a neural stem cell-like intermediate supported by incomplete shutdown of the pluripotency network. Using CRISPR-Cas9 knockout screening, we revealed differential genetic dependencies between Ascl1 and Ngn2. Specifically, Ascl1 is more dependent on factors including Tcf7l1, that regulate pluripotency and cell cycle. In the absence of the pluripotency network repressor Tcf7l1 Ascl1 is still able to repress the core pluripotency genes, however failed to exit cell cycle. Overexpression of Cdkn1c induced cell cycle exit and restored the generation of neurons. This study illuminates two different mechanistic approaches to convert ESC to induced neurons: rapid shutdown of the initial state while installing a terminal cell identity versus repurposing the initial gene regulatory network to allow generation of neurons via intermediate states. Understanding the precise mechanism and the variety of cell states induced is essential to design efficient cell replacement therapeutic applications or precise tools for disease modelling.

overall_design: RNA-Seq

first: Ulrich

last: Elling


title: Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (snATAC-seq)

overall_design: Single nucleus ATAC sequencing (snATAC-seq) of nuclei isolated from the adult autopsied human motor and frontal cortices of C9orf72(C9)-ALS, C9-FTD, and control donors. snATAC-seq was performed using 10X Genomics platform.


title: Induction of neurons from mouse ESC by the bHLH factors Ascl1 and Ngn2 shows distinct genetic dependencies, pluripotency exit, and cell cycle shutdown. [ChIP-Seq]

overall_design: ChIP-seq for FLAG-Ascl1 or FLAG-Ngn2 at day 1 post induction in mouse embryonic stem cells .


title: The master energy homeostasis regulator PGC-1α exhibits a novel mRNA nuclear export function [RNA-Seq]

city: London

first: Simeon

last: Mihaylov

overall_design: Comparative gene expression analysis using RNA-seq data from 12 samples from stable inducible Flp-In T-REx 293 cell lines. We used whole-cell (total; WCT) RNA and cytoplasmic fraction (CyT) RNA for each cell line. The cells lines included (i) PGC-1α WT-res - a cell line with endogenous depletion of PGC-1α and replacement with wild-type cDNA; (ii) PGC-1α ΔRS-res - a cell line with endogenous depletion of PGC-1α and replacement with deletion construct of PGC-1α lacking amino acids 595-633. For each group, cells from three consecutive passages were used.

first: Lydia

middle: M

last: Castelli

first: Guillaume

last: Hautbergue


title: Induction of neurons from mouse ESC by the bHLH factors Ascl1 and Ngn2 shows distinct genetic dependencies, pluripotency exit, and cell cycle shutdown. [Ascl1_Ngn2_RNAseq_timecourse]

overall_design: Ascl1 or Ngn2 overexpression in mouse embryonic stem cells over period of 6 days and sorted for Mapt-Venus positive (neurons) or negative cells (non-neurons)


title: RNA-Seq of chondrocyte with or without CircRREB1 knockdown

first: shuying

last: shen

address: 3 East Qingchun Road

department: Department of Orthopaedic Surgery

institute: Sir Run Run Shaw Hospital

summary: Purpose: RNA-Seq was used to detect the dwonstream genes after CircRREB1 knockdow. Method: Three chondrocyte total RNA profiles of Si-NC samples and Si-CircRREB1  samples were analyzed.

overall_design: We collected three human knee joint samples and primary chondrocytes were cultured.  Then, chondrocytes were transfected with CircRREB1 SiRNA or negetive SiRNA. After transfections, RNAs were collected and RNA-seq were performed

first: Shuying

last: Shen


title: Induction of neurons from mouse ESC by the bHLH factors Ascl1 and Ngn2 shows distinct genetic dependencies, pluripotency exit, and cell cycle shutdown. [CRISPR-UMI]

sample_organism:
Escherichia coli
Mus musculus

platform_organism:
Escherichia coli
Mus musculus

overall_design: CRISPR-UMI


title: Novel human pluripotent stem cell-derived hypothalamus organoids demonstrate cellular diversity

status: Public on Jul 16 2023

city: Darlinghurst

first: Drew

last: Neavin

state: New South Wales

address: 384 Victoria St

department: Cellular Science

country: Australia

institute: Garvan Institute of Medical Research

summary: The hypothalamus is a region of the brain that plays an important role in regulating body functions and behaviors. There is a growing interest in human pluripotent stem cells (hPSCs) for modeling diseases that affect the hypothalamus. Here, we established an hPSC-derived hypothalamus organoid differentiation protocol to model the cellular diversity of this brain region. Using an hPSC line with a tyrosine hydroxylase (TH)-TdTomato reporter for dopaminergic neurons (DNs) and other TH-expressing cells, we interrogated DN-specific pathways and functions in electrophysiologically active hypothalamus organoids. Single-cell RNA sequencing (scRNA-seq) revealed diverse neuronal and non-neuronal cell types in mature hypothalamus organoids. We identified several molecularly distinct hypothalamic DN subtypes which demonstrated different developmental maturities. Our in vitro 3D hypothalamus differentiation protocol can be used to study the development of this critical brain structure and can be applied to disease modeling to generate novel therapeutic approaches for disorders centered around the hypothalamus.

overall_design: Tyrosine hydroxylase(TH) high and low samples were sorted using FACS in triplicate. Each replicate was tagged with an antibody-oligo hashtag before pooling the three TH high and TH low samples and capturing ~15k cells for each group in a separate 10x reaction well using 3'


title: Transcriptome sequencing of K562 cells stably expressing SUMO negative MYB

city: Oslo

first: Roza Berhanu

last: Lemma

address: Blindernveien 31

department: Department of Biosciences

country: Norway

institute: University of Oslo

summary: We expanded our previously reported transcriptome profiling of K-562 cells (GSE85187) by analyzing the global transcriptional change upon rescue of endogenous MYB knock down (KD) with SUMO-conjugation deficient mutant of MYB (2KR-MYB) and SUMO-binding deficient mutant of MYB (ANAA-MYB) in comparison with K-562 cells treated with siGENOME non-targeting siRNA (GSE85187) , endogenous MYB KD treated with si2992 (GSE85187), rescue of endogenous MYB KD with wild-type MYB (GSE85187) and rescue of endogenous MYB KD with D152V mutant of MYB (GSE85187).

overall_design: Cells were tranfected with siRNA and 24 hours after transfection total RNA was extracted. Three biological replicates were used for RNA sequencing, where 150 bp PE-reads were obtained using Illumina Hiseq 4000 sequencer

first: Odd

middle: S

last: Gabrielsen

first: Roza

middle: B


title: Induction of neurons from mouse ESC by the bHLH factors Ascl1 and Ngn2 shows distinct genetic dependencies, pluripotency exit, and cell cycle shutdown.


title: Pathogenesis and outcome of VA1 astrovirus infection in the human brain are defined by disruption of neural functions and imbalanced host immune responses.

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: Infections of the central nervous system (CNS) in humans are on the rise due to changing environmental conditions and increase in vulnerable populations comprised of immunocompromised subjects with primary (genetic) or secondary (acquired) immunodeficiency. Many viruses take the opportunity to invade the CNS by capitalizing on impaired immunity of the host. Here we investigate neuropathogenesis of a rare CNS infection in immunocompromised patients caused by the astrovirus and show that it shares many features with another opportunistic infection of the CNS associated with human immunodeficiency virus. We show that astrovirus infects CNS neurons with a major impact on the brainstem. This leads to disrupted synaptic integrity loss of afferent innervation related to infected neurons and global impairment of both excitatory and inhibitory neurotransmission. In the settings of impaired peripheral adaptive immunity host responses to astrovirus infection are dominated by the microglia-macrophage-phagocytosis axis which may be a common compensatory defense mechanism employed by the CNS against opportunistic infections.

overall_design: tissue sample comparisons

first: Olga

last: Maximova

first: Melody

middle: L

last: Weller

first: Tammy

last: Krogmann

first: Craig

last: Sauter

first: Daniel

last: Martens

first: Kurt

last: Wollenberg

first: W

last: Lipkin

first: Marc

last: Eloit

first: Mahnaz

last: Minai

first: Ian

middle: N

last: Moore

first: Stefano

last: Marenco

first: Avindra

last: Nath

first: Jeffrey

last: Cohen


title: Divergent impacts of C9orf72 repeat expansion on neurons and glia in ALS and FTD (bulk H3K27ac ChIP-seq)

first: Stella

last: Dracheva

overall_design: H3K27ac chromatin immunoprecipitation sequencing (ChIP-seq) of four major brain cell populations (neurons, oligodendrocytes, microglia and astrocytes) from adult human motor and frontal cortices of C9orf72(C9)-ALS and control donors. The populations were isolated using fluorescence-activated nuclei sorting.

first: Junhao

last: Li

first: Manoj

last: Jaiswal

first: Jo-Fan

last: Chien

first: Alexey

last: Kozlenkov

first: Ping

last: Zhou

first: Veronique

last: Belzil

first: Eran

last: Mukamel


title: RNA-Seq of chondrocyte with or without FASN knockdown

status: Public on Jul 14 2023

first: shuying

last: shen

summary: Purpose: RNA-Seq was used to detect the dwonstream genes after FASN knockdow. Method: Three chondrocyte total RNA profiles of Si-NC samples and Si-FASN  samples were analyzed.

overall_design: We collected three human knee joint samples and primary chondrocytes were cultured.  Then, chondrocytes were transfected with FASN SiRNA or negetive SiRNA. After transfections, RNAs were collected and RNA-seq were performed

first: Shuying

last: Shen


title: Metabolic reprogramming from fatty acid oxidation to glycolysis in a patient mutation knock-in mouse model of Barth Syndrome.

status: Public on Jul 15 2023

city: Göttingen

first: André

last: Fischer

state: Niedersachsen

address: Von-Siebold-Str. 3a

department: Epigenetics and Systems Medicine in Neurodegenerative Diseases

country: Germany

institute: Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE)


title: Metabolic reprogramming from fatty acid oxidation to glycolysis in a patient mutation knock-in mouse model of Barth Syndrome. [human]

summary: Mitochondria are central for cellular metabolism and energy supply. Barth Syndrome (BTHS) is a severe disorder due to dysfunction of the mitochondrial cardiolipin acyl transferase tafazzin. Altered cardiolipin remodeling affects mitochondrial inner membrane organization and function of membrane proteins such as transporters and the oxidative phosphorylation (OXPHOS) system. Here, we describe a mouse model that carries a G197V exchange in tafazzin, corresponding to BTHS patient. TAZG197V mice recapitulate disease-specific pathology including cardiac dysfunction and reduced oxidative phosphorylation. We show that mutant mitochondria display defective fatty acid driven oxidative phosphorylation due to reduced levels of carnitine palmitoyl transferases. A metabolic switch in ATP production from OXPHOS to glycolysis is apparent in mouse heart and patient iPS cell-derived cardiomyocytes. An increase in glycolytic ATP production inactivates AMPK causing altered metabolic signaling in TAZG197V. Treatment of mutant cells with AMPK activator reestablishes fatty acid driven OXPHOS and protects mice against cardiac failure.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human iPS cell-derived cardiomyocytes from healthy donors and Barth Syndrome patients with a pathological missense mutation in TAZ.

first: Arpita

last: Chowdhury

first: Angela

last: Boshnakovska

first: Abhishek

last: Aich

first: Aditi

last: Methi

first: Ana

last: Vergel Leon

first: Ivan

last: Silbern

first: Lukas

last: Cyganek

first: Jiri

last: Lindovsky

first: Dominic

last: Wachs

first: Zuzana

last: Nichtova

first: Dagmar

last: Zudova

first: Gizela

last: Koubkova

first: Henning

last: Urlaub

first: Britta

last: Brügger

first: Dörthe

last: Katschinski

first: Jan

last: Dudek

first: Peter

last: Rehling


title: Metabolic reprogramming from fatty acid oxidation to glycolysis in a patient mutation knock-in mouse model of Barth Syndrome.[mouse]

first: André

last: Fischer

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and TAZG197V mouse hearts.

first: Arpita

last: Chowdhury


title: Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects [Joint-snhmC-seq: snmCseq2.split]

city: Philadelphia

first: Hao

last: Wu

address: 415 Curie Boulevard

department: Genetics

institute: University of Pennsylvania

summary: Oxidative modification of 5-methylcytosine (5mC) by TET DNA dioxygenases generates 5-hydroxymethylcytosine (5hmC), the most abundant form of oxidized 5mC. Existing single-cell bisulfite sequencing methods cannot resolve  5mC and 5hmC, leaving the cell-type-specific regulatory mechanisms of TET and 5hmC largely unknown. Here we present Joint single-nucleus (hydroxy)methylcytosine sequencing (Joint-snhmC-seq), a scalable and quantitative approach that simultaneously profiles 5hmC and true 5mC in single cells by harnessing differential deaminase activity of APOBEC3A towards 5mC and chemically protected 5hmC. Joint-snhmC-seq profiling of single nuclei from the mouse brains reveals an unprecedented level of epigenetic heterogeneity of both 5hmC and true 5mC at single-cell resolution. We show that cell-type-specific profiles of 5hmC or true 5mC improve multi-modal single-cell data integration, enable accurate identification of neuronal subtypes, and uncover context-specific regulatory effects of cell-type-specific genes by TET enzymes.

overall_design: Joint single-nucleus (hydroxy)methylcytosine sequencing (Joint-snhmC-seq) analysis of adult mouse cortex

first: Emily

last: Fabyanic

first: Peng

last: Hu

first: Qi

last: Qiu


title: Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects [Joint-snhmC-seq: snhmCseq2.split]


title: Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects [snRNAseq]

overall_design: Single-nucleus RNA-seq (snRNA-seq or sNucDrop-seq) analysis of adult mouse cortex


title: Daam2 phosphorylation by CK2α negatively regulates Wnt activity during white matter development and injury

status: Public on Jul 13 2023

city: Tainan

first: Chih-Yen Wang

last: Wang

address: No.1, University Rd

department: Biotechnology and Bioindustry Sciences

institute: National Cheng Kung University

summary: Wnt signaling plays an essential role in developmental and regenerative myelination in the CNS. The Wnt signaling pathway is comprised of multiple regulatory layers; thus, how these processes are coordinated to orchestrate oligodendrocyte development remains unclear. Here we show CK2α, a Wnt/β-catenin signaling Ser/Thr kinase, phosphorylates Daam2, inhibiting its function and Wnt-activity during oligodendrocyte development. Intriguingly, we found Daam2 phosphorylation differentially impacts distinct stages of oligodendrocyte development, accelerating early differentiation followed by decelerating maturation and myelination. Application towards white matter injury revealed CK2α-mediated Daam2 phosphorylation plays a protective role for developmental and behavioral recovery after neonatal hypoxia, while promoting myelin repair following adult demyelination. Together, our findings identify a novel regulatory node in the Wnt pathway that regulates oligodendrocyte development via protein phosphorylation-induced signaling complex instability and highlights a new biological mechanism for myelin restoration.

overall_design: P21 mouse cortical tissues from WT and the E-mutant containing corpus callosum (3 animals combined per group).

first: Chih

middle: Y

first: Hyun

last: Lee


title: Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects [snhmCseq]

overall_design: Single-nucleus 5-hydroxymethylcytosine sequencing (snhmC-seq) analysis of adult mouse cortex


title: Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation [IV]

city: Copenhagen N

first: Laura

middle: Maarit

last: Pikkupeura

address: Ole Maaloes vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

summary: During intestinal organogenesis, equipotent epithelial progenitors mature into phenotypically distinct stem cells that are responsible for life-long maintenance of the tissue. While the morphological changes associated with the transition are well-characterized, the molecular mechanisms underpinning the maturation process are not fully understood. Here, we leverage intestinal organoid cultures to profile transcriptional, chromatin accessibility, DNA methylation and 3D chromatin conformation landscapes in fetal and adult epithelial cells. We observed prominent differences in gene expression and enhancer activity, which are accompanied by local changes in 3D organization,  DNA accessibility and methylation, between the two cellular states. Using integrative analyses, we identified sustained YAP transcriptional activity as a major gatekeeper of the immature fetal state. We found the YAP-associated transcriptional network to be regulated at various levels of chromatin organization, and likely to be coordinated by changes in extracellular matrix composition. Altogether, our work highlights the value of unbiased profiling of regulatory landscapes for the identification of key mechanisms underlying tissue maturation.

overall_design: Profiling of transcription and chromatin accessibility and organisation in E16.5 fetal and adult small intestinal epithelial organoids with CAGE, ATAC-Seq, WGBS, and Hi-C, gene expression profiling of adult crypt proximal small intestinal epithelium, and comparative gene expression profiling of adult intestinal organoid cultures from an inducible TetON-hYAP/H2B-mCherry mouse strain with or without doxycyclin (DOX) induced expression of a constitutively active (S127A mutant) YAP transgene.

first: Raul

last: Bressan

first: Jordi

last: Guiu

first: Yun

last: Chen

first: Martti

last: Maimets

first: Daniela

last: Mayer

first: Pawel

middle: J

last: Schweiger

first: Stine

last: Hansen

first: Grzegorz

last: Maciag

first: Hjalte

last: Larsen

first: Kadi

last: Lõhmussaar

first: Marianne

last: Terndrup Pedersen

first: Joji

last: Yap Teves

first: Jette

last: Bornholdt

first: Vladimir

last: Benes

first: Albin

last: Sandelin

first: Kim

last: Jensen


title: Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation

first: Laura

last: Pikkupeura


title: Dot1l cooperates with Npm1 to repress endogenous retrovirus MERVL in embryonic stem cells

first: Haiyang

last: Sun

summary: Dot1l is a histone methyltransferase without a SET domain and is responsible for H3K79 methylation, which marks active transcription. In contradiction, Dot1l also participates in silencing gene expression. The target regions and mechanism of Dot1l in repressing transcription remain enigmatic. Here, we examined the possibility for Dot1l as an repressor of MERVL, which is a marker of 2-cell-like cells. Mechanistically, Dot1l interacted with and colocalized with Npm1 on MERVL, and depletion of Npm1 similarly augmented MERVL expression.

overall_design: We knocked out Dot1l in E14 by CRISPR/Cas9 System. We performed RNA-seq analysis in order to exam the transcriptome after Dot1l KO, performed ChIP-seq analysis in order to exam the DNA binding sites of DOT1L and NPM1.


title: RNA-seq analysis of Lrig1+ and Lrig1- CD4+ T cells in mouse spleen

city: Seoul

first: Chun-Chang

last: Ho

address: 189 Seongam-ro

country: South Korea

institute: Good T cells.,Inc.

summary:
Regulatory T cell (Treg) is the immune-suppressive T cell subset and the crucial component for preventing autoimmunity. The molecules defining the suppressive population of T cells phenotypically and functionally remain to be discovered.
In this study, we report that Lrig1 is highly expressed in suppressive CD4+ T cell populations. We performed RNA-seq analysis of CD4+Lrig1+ and CD4+Lrig1- T cells from mouse splenocytes to analyze the genes involeved in the suppressive function of T cells.

overall_design: To investigate the transcriptional difference between Lrig1+ and Lrig1- CD4+ T cells, we isolated Lrig1+ and Lrig1- CD4+ T cells from spleen of 7 weeks of age female C57BL/6 mice using flow cytometry.

first: Sang-Kyou

last: Lee

first: Jae-Seung

last: Moon

first: Su-Hyeon


title: Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation [III]

summary: During intestinal organogenesis, equipotent epithelial progenitors mature into phenotypically distinct stem cells that are responsible for life-long maintenance of the tissue. While the morphological changes associated with the transition are well-characterized, the molecular mechanisms underpinning the maturation process are not fully understood. Here, we leverage intestinal organoid cultures to profile transcriptional, chromatin accessibility, DNA methylation and 3D chromatin conformation landscapes defining fetal and adult epithelial cells. We observed prominent differences in gene expression and enhancer activity, accompanied by changes in 3D organization and local changes in DNA accessibility and methylation, between the two cellular states. Using integrative analyses, we identified sustained YAP transcriptional activity as a major gatekeeper of the immature fetal state. We found the YAP-associated transcriptional network to be regulated at various levels of chromatin organization, and likely to be coordinated by changes in extracellular matrix composition. Altogether, our work highlights the value of unbiased profiling of regulatory landscapes for the identification of key mechanisms underlying tissue maturation.

first: Raul

last: Bressan

first: Jordi

last: Guiu

first: Yun

last: Chen

first: Martti

last: Maimets

first: Daniela

last: Mayer

first: Pawel


title: The effects of broflanilide on developing zebrafish

city: Gainesville

first: Christopher

last: Martyniuk

state: FL

address: 8891 SW 79th Avenue

institute: University of Florida

summary: For RNA-seq experiments, 20 embryos were placed into 5 mL final volume of sterile ERM. Each treatment group were exposed within a 10-minute window. (N=5 beakers per treatment). On 7 days post fertilization (dpf), fish were transferred to a labeled and pre-weighed 1.7 mL tube. The tube was then immediately flash frozen in liquid nitrogen prior to RNA-seq analysis.

overall_design: Exposure groups included 3 treatments:  DMSO control (n=5), 1 ug/L broflanilide (n=4), and 10 ug/L broflanilide (n=3).

first: Chris

first: Sarah

last: Patuel

first: Isaac

last: Konig

last: Souders II

first: Cole

last: English

first: Emma

last: Ivantsova

first: Victoria

last: Lopez-Scarim


title: An organoid-based CRISPR/Cas9 screen for regulators of intestinal epithelial maturation

first: Laura

last: Pikkupeura

summary: Generation of functionally mature organs requires exquisite control of transcriptional programs governing cell state transitions during development. Despite advances in understanding the behavior of adult intestinal stem cells and their progeny, the transcriptional regulators that control the emergence of the mature intestinal phenotype remain largely unknown. Using mouse fetal and adult small intestinal organoids, we uncover transcriptional differences between the fetal and adult state and identify rare adult-like cells present in fetal organoids. This suggests that fetal organoids possess an inherent potential to mature, which is locked by a regulatory program. By implementing a CRISPR/Cas9 screen targeting transcriptional regulators expressed in fetal organoids, we establish Smarca4 and Smarcc1 as important factors safeguarding the immature progenitor state. Our approach demonstrates the utility of organoid models in the identification of factors regulating cell fate and state transitions during tissue maturation and reveal that Smarca4 and Smarcc1 prevent precocious differentiation during intestinal development.

overall_design: CRISPR screen of transcriptional regulators in mouse intestinal organoids analysed by sgRNA-sequencing and subsequent scRNA-seq, RNA-seq, and ATAC-seq profiling of mutant organoid lines.

first: Stine

last: Hansen

first: Hjalte

last: Larsen

first: Grzegorz

last: Maciag

first: Iris

last: Müller

first: Christina

last: Mueller

first: Ditte

last: Clement

first: Jens

last: Vilstrup Johansen

first: Kristian

last: Helin

first: Mads

last: Lerdrup

first: Kim

last: Jensen


title: Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation [II]

first: Raul

last: Bressan

first: Jordi

last: Guiu

first: Yun

last: Chen

first: Martti

last: Maimets

first: Daniela

last: Mayer

first: Pawel

last: Schweiger

first: Kadi

last: Lõhmussaar

first: Marianne

last: Terndrup Pedersen

first: Joji

last: Yap Teves

first: Jette

last: Bornholdt

first: Vladimir

last: Benes

first: Albin

last: Sandelin


title: Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects

first: Hao

last: Wu

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

overall_design: Refer to individual Series


title: Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation [I]

first: Laura

last: Pikkupeura

first: Stine

last: Hansen

first: Grzegorz

last: Maciag

first: Hjalte

last: Larsen


title: Microglial REV-ERBα regulates inflammation and lipid droplet formation to drive tauopathy

status: Public on Jul 12 2023

city: St. Louis

first: Eric

last: Tycksen

state: Missouri

address: 4444 Forest Park Avenue

department: McDonnell Genome Institute

institute: Washington University in St. Louis School of Medicine

summary: Alzheimer’s disease is associated with disrupted circadian rhythms and clock gene expression. REV-ERBα (Nr1d1) is a circadian transcriptional repressor involved in the regulation of lipid metabolism and macrophage function. While global REV-ERBα deletion increases microglial activation and mitigates amyloid plaque formation, the cell-autonomous effects of microglial REV-ERBα on tau pathology are unexplored. Here, we show that microglial REV-ERBα deletion enhances inflammatory signaling, disrupts lipid metabolic processes, and causes lipid droplet (LD) accumulation specifically in male microglia. Inflammation and LD accumulation combine to inhibit microglial tau phagocytosis, which can be partially rescued by blockage of lipid droplet formation. Microglial REV-ERBα deletion exacerbates tau aggregation and neuroinflammation in P301S and AAV-P301L tauopathy models in male, but not female mice. These data demonstrate the importance of microglial lipid droplets in tau accumulation and reveal REV-ERBα as a therapeutically accessible, sex-dependent regulator of microglial inflammatory signaling, lipid metabolism, and tauopathy.

overall_design: To analyze the different genes between normal mouse cultured microglia and Rev-erbα KO microglia. Control (Cre-) and REV-ERBα KO (Cre+) microglia from CAG::CreERT2; Nr1d1fl/fl P1-3 pups, treated with 4-hydroxy-tamoxifen for 2 days, and analyzed them by bulk RNA-sequencing.

first: Jiyeon

last: Lee

first: Erik

last: Musiek


title: Pbrm1 regulates interferon signaling in mouse AML [RNA-seq Mouse]

city: Boston

first: Bin

middle: E

last: Li

state: Massachusetts

address: 1 Blackfan Circle Karp Research Building Boston Children's Hospital Boston MA 02115

department: Hematology/Oncology

institute: Boston Children's Hospital

summary: CRISPR/Cas9 screening approaches are powerful tools to identify in vivo cancer dependencies. Hematopoietic malignancies are genetically complex disorders in which sequential acquisition of somatic mutations generates clonal diversity. With time, additional cooperating mutations may drive disease progression. Using an in vivo pooled gene editing screen of epigenetic factors in primary murine hematopoietic stem and progenitor cells (HSPCs), we sought to uncover unrecognized genes that contribute to leukemia progression. We first modeled myeloid leukemia in mice by functionally abrogating both Tet2 and Tet3 in HSPCs followed by transplantation. We then performed pooled CRISPR/Cas9 editing of genes encoding epigenetic factors and identified Pbrm1/Baf180, a subunit of polybromo BRG1/BRM-associated factor (PBAF) SWI/SNF chromatin remodeling complex, as a negative driver of disease progression. We found that Pbrm1 loss promoted leukemogenesis with significantly shortened latency. Pbrm1-deficient leukemia cells were less immunogenic, and characterized by attenuated interferon signaling and reduced MHC II expression. We explored potential relevance to human leukemia by assessing the involvement of PBRM1 in control of interferon pathway components and found that PBRM1 binds at promoters of a subset of these genes, and most notably at IRF1, which in turn regulates MHC II expression. Our findings revealed a novel role of Pbrm1 in leukemia progression. More generally, CRISPR/Cas9 screening, coupled with phenotypic readouts in vivo, has identified a pathway by which transcriptional control of interferon signaling influences leukemia cell interactions with the immune system.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for in vivo generated mouse AML cells by targeting Tet2/Tet3 and its knockout derivatives (Tet2/Tet3/Pbrm1 knockout).

first: Stuart

middle: H

last: Orkin


title: Recapitulation of pathophysiological features of AD in SARS-CoV-2 infected subjects

status: Public on Jul 11 2023

first: Molly

last: Estill

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

summary: Infection with the etiological agent of COVID-19, SARS-CoV-2, appears capable of impacting cognition, which some patients with Post-acute Sequelae of SARS-CoV-2 (PASC). To evaluate neuro-pathophysiological consequences of SARS-CoV-2 infection, we examine transcriptional and cellular signatures in the Broadman area 9 (BA9) of the frontal cortex and the hippocampal formation (HF) in SARS-CoV-2, Alzheimer’s disease (AD) and SARS-CoV-2 infected AD individuals, compared to age- and gender-matched neurological cases. Here we show similar alterations of neuroinflammation and blood-brain barrier integrity in SARS-CoV-2, AD, and SARS-CoV-2 infected AD individuals. Distribution of microglial changes reflected by the increase of Iba-1 reveal nodular morphological alterations in SARS-CoV-2 infected AD individuals. Similarly, HIF-1α is significantly upregulated in the context of SARS-CoV-2 infection in the same brain regions regardless of AD status. The finding may help to inform decision-making regarding therapeutic treatments in patients with neuro-PASC, especially those at increased risk of developing AD.

overall_design: Brain tissue was collected from the cortical BA9 and HF of four COVID_ADneg cases, four CONTROL ADpos and four COVID_ADpos and four CONTROL_ADneg autopsies. Tissue was collected in accordance with IRB-approved guidelines and regulations by the Brain Bank at Mount Sinai, and clinical data  including cardiovascular and neurological conditions were collected by the Department of Neurology. Samples collected and homogenized  to collect total RNA and generation of cDNA libraries for RNA sequencing study.

first: Elizabeth

last: Griggs

first: Kyle

last: Trageser

first: Sean

last: Naughton

first: Eun-Jeong

last: Yang

first: Brian

last: Mathew

first: Grace

last: Van Hyfte

first: Linh

last: Hellmers

first: Nathalie

last: Jette

first: Li

last: Shen

first: Tracy

last: Fischer

first: Giulio

last: Pasinetti


title: A biallelic multiple nucleotide length polymorphism explains functional causality at the 5p15.33 prostate cancer risk locus [ATAC-Seq]

city: Budapest

first: Andras

last: Furedi

state: HU

address: Magyar tudosok krt 2

department: Molecular Life Sciences

country: Hungary

institute: HUN-REN RCNS

summary: To date, single-nucleotide polymorphisms (SNPs) have been the most intensively investigated class of polymorphisms in genome wide associations studies (GWAS), however, other classes such as insertion-deletion or multiple nucleotide length polymorphism (MNLPs) may also confer disease risk. Multiple reports have shown that the 5p15.33 prostate cancer (PCa) risk region is a particularly strong expression quantitative trait locus (eQTL) for IRX4 transcripts. Here, we demonstrate using epigenome and genome editing that a biallelic (47bp/21bp) MNLP is the causal variant regulating IRX4 transcript levels. In LNCaP PCa cells (homozygous for the short allele), a single copy knock-in of the long allele potently alters the chromatin state, enabling de novo functional binding of the androgen receptor (AR) associated with increased chromatin accessibility, H3K27 acetylation, and ~3-fold upregulation of IRX4 expression. We further show that an MNLP is amongst the strongest candidate susceptibility variants at two additional PCa risk loci. We estimated that at least 5% of PCa risk loci could be explained by functional non-SNP causal variants, which may have broader implications for other cancers GWAS. More generally, our results underscore the importance of investigating other classes of inherited variation as causal mediators of human traits.

overall_design: ATA-seq LNCaP_clones  H3K27ac and LNCaP_parental

first: Matthew

last: Freedman

first: Sandor

last: Spisak


title: Am80 activates cardiomyocytes cell cycle via retinoic acid receptor for efficient transplantation

city: Kyoto

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

institute: Kyoto University

summary: Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-cardiomyocytes) are promising sources for the regenerative therapy to treat heart failure. To realize this therapy, the engraftment potential of hiPSC-cardiomyocytes following the injection into the host heart should be improved. Here, we established the efficient method to analyze the cell cycle activity of hiPSC-cardiomyocytes using Fluorescence Ubiquitination-based Cell Cycle Indicator (FUCCI) system. High-throughput screening analysis using FUCCI-expressing hiPSC-cardiomyocytes identified a retinoic acid receptor (RAR) agonist, Am80, as an effective cell cycle activator in hiPSC-cardiomyocytes. The transplantation of hiPSC-cardiomyocytes treated by Am80 prior to the injection significantly enhanced the engraftment into the damaged mouse heart for 6 months. RNA sequencing analysis in Am80-treated iPSC-cardiomyocytes revealed that both RARA and RARB played important roles in the Am80-mediated cell cycle activation in hiPSC-cardiomyocytes. Collectively, this study highlights the effectiveness of FUCCI system to easily analyze the cell cycle status in hiPSC-cardiomyocytes and the cell cycle activation by Am80 is the possible strategy to increase the graft size following the cell transplantation into the damaged heart.

overall_design: Fluorescent Ubiqutination-based Cell Cycle Indicator (FUCCI) reporter human induced pluripotent stem cells (201B7) were differentiated into cardiomyocytes (CMs). All cardiomyocytes were isolated from lineage (CD31, CD90, CD49a, CD140b) negative and SIRPA (CD172a/b) positive population by fluorescence activated cell sorting (FACS). Three FUCCI subpopulations (Red:Kusabira-Orange(+) and Azami-Green(-), White:Kusabira-Orange(-) and Azami-Green(-), Green:Kusabira-Orange(-) and Azami-Green(+)) were collected on day 20 (N=2). For Am80/DMSO treated samples, Am80 and DMSO were administered to embryonic bodies in culture medium from day 18 and CMs were purified on day 20 (N=3). For knockdown experiments,  purified CMs were transfected with siRNA for negative control (siNC), RARA (siRARA), RARB (siRARB) and  seeded onto fibronectin coated plates on day 17. Am80 and DMSO were administered from day 18 and RNA was collected on day 20 (N=3).

first: Manabu

last: Kasamoto

first: Chikako

last: Okubo

first: Narita

last: Megumi


title: A biallelic multiple nucleotide length polymorphism explains functional causality at 5p15.33 prostate cancer risk locus [RNA-Seq]

overall_design: Comparative gene expression profiling analysis of RNA-seq data.


title: A biallelic multiple nucleotide length polymorphism explains functional causality at the 5p15.33 prostate cancer risk locus [ChIP-Seq]

overall_design: ChIP-seq LNCaP_clones, H3K27ac and LNCaP_parental


title: SNORD90 induces glutamatergic signaling following treatment with monoaminergic antidepressants

city: Montreal

first: Gustavo

last: Turecki

state: Quebec

address: 6875 Boulevard LaSalle

country: Canada

institute: McGill University

summary: To investigate the role of small nucleolar RNAs in the context of antidepressant response and major depressive disorder

overall_design: We ustilized small RNA-seq to investigate the expression profiles of snoRNAs. Small RNA-seq was performed on human blood samples collected from individuals with depression and subsiquently treated with antidepressants for eight weeks.

first: Rixing

last: Lin

first: Aron

last: Kos

first: Juan

last: Lopez

first: Julien

last: Dine

first: Laura

last: Fiori

first: Jennie

first: Yair

last: Ben-Efraim

first: Zahia

last: Aouabed

first: Pascal

last: Ibrahim

first: Haruka

last: Mitsuhashi

first: Tak

last: Wong

first: El

middle: C

first: Catherine

last: Belzung

first: Pierre

last: Blier

first: Faranak

last: Farzan

first: Benicio

last: Frey

first: Raymond

middle: W

last: Lam

first: Roumen

last: Milev

first: Daniel

last: Muller

first: Sagar

last: Parikh

first: Claudio

last: Soares

first: Rudolf

last: Uher

first: Corina

last: Nagy

first: Naguib

last: Mechawar

first: Jane

last: Foster

first: Sidney

last: Kennedy

first: Alon

last: Chen


title: Pbrm1 regulates interferon signaling in mouse AML [ChIP-seq HAP1]

first: Bin

last: Li

summary: CRISPR/Cas9 screening approaches are powerful tools to identify in vivo cancer dependencies. Hematopoietic malignancies are genetically complex disorders in which sequential acquisition of somatic mutations generates clonal diversity. With time, additional cooperating mutations may drive disease progression. Using an in vivo pooled genetic mutagenesis screen of epigenetic factors in primary murine HSPCs, we sought to uncover unrecognized genes that contribute to leukemia progression. We first modeled myeloid leukemia in mice by functionally abrogating both Tet2 and Tet3 in HSPCs followed by transplantation. We then performed pooled mutagenesis of genes encoding epigenetic factors and identified Pbrm1/Baf180, a subunit of polybromo (PBAF) SWI/SNF chromatin remodeling complex, as a negative driver of disease progression. We found that Pbrm1 loss promoted leukemogenesis with significantly shortened latency. Pbrm1-deficient AML cells were less immunogenic, and characterized by attenuated interferon signaling and reduced MHC II expression. We explored potential relevance to human leukemia by assessing the involvement of Pbrm1 in control of interferon pathway components and found that Pbrm1 binds at promoters of a subset of these genes, and most notably at IRF1, which in turn regulates in MHC II expression. Our findings revealed a novel role of Pbrm1 in leukemia progression. More generally, CRISPR/Cas9 screening, coupled with phenotypic readouts in vivo, has revealed a pathway by which transcriptional control of interferon signaling influences leukemia cell interactions with the immune system.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for epigenetic factor Pbrm1/Baf180 in HAP1 cells without or with IFN-γ treatment.

first: Stuart

last: Orkin


title: Metabolic Programs of T Cell Tissue Residency Empower Tumor Immunity [scRNA-seq]

status: Public on Jul 10 2023

city: La Jolla

first: Miguel

last: Reina-Campos

state: California

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

summary: Tissue-resident memory CD8 T cells (TRM) offer fast, robust, and long-term protection at sites of re-infection1. Tumor-infiltrating lymphocytes (TIL) with characteristics of TRM maintain enhanced effector functions, predict responses to immunotherapy, and accompany better prognoses2,3. Thus, an improved understanding of the metabolic strategies that enable tissue residency could inform new approaches to empower T cell responses in tissues and solid tumors. To systematically define the basis for the metabolic reprogramming supporting TRM differentiation, survival, and function, we leveraged in vivo functional genomics, untargeted metabolomics, and transcriptomics of virus-specific memory CD8 T cell populations. We found that memory CD8 T cells deployed a range of adaptations to tissue residency, including a marked reliance on non-steroidal products of the mevalonate/cholesterol pathway, such as Coenzyme Q (CoQ), driven by increased activity of the transcription factor Srebp2. This metabolic adaptation was most pronounced in the small intestine (SI), where TRM interface with dietary cholesterol and maintain a heightened state of activation4, and was shared by functional TIL in diverse tumor types in mice and humans. Enforcing CoQ synthesis through Fdft1 deletion or Pdss2 overexpression promoted mitochondrial respiration, memory formation upon viral infection, and enhanced antitumor immunity. In sum, through a systematic exploration of TRM metabolism, we reveal how these programs can be leveraged to empower CD8 T cell memory formation in the context of acute infections and enhance antitumor immunity.

overall_design: RNAseq of sorted P14 CD8 T cells from mice at day 7 after infection with LCMV. P14 CD8 T cells were isolated from the spleen, liver, kidney and small intestine. All samples but spleen were gated on intravascular-associated negative cells based on in vivo CD8a stain prior to analysis. Every replicate has cells pooled from two mice.

first: Ananda

last: W Goldrath


title: Short-term mucosal disruption enables colibactin-producing E. coli to cause long-term perturbation of colonic homeostasis

city: Berlin

first: Michael

last: Sigal

address: Augustenburger Platz 1

department: Dept. Hepatology and Gastroenterology

institute: Charité Universitätsmedizin

summary: Colibactin, a bacterial genotoxin produced by E. coli harboring the pks genomic island, induces cytopathic effects such as DNA breaks, cell cycle arrest and apoptosis. Patients with a colonic dysfunction due to inflammatory bowel disease such as ulcerative colitis have an elevated likelihood of carrying pks+ E. coli in their colon microbiota but it is not clear whether and how they contribute to the pathogenesis of colitis. Using a gnotobiotic mouse model, we show that pks+ E. coli do not affect colonic integrity under homeostatic conditions, with the microbiota remaining separated from the epithelium by a mucus barrier. However, upon chemical disruption of this barrier by DSS, the microbes gain direct access to the epithelium, causing severe epithelial injury, and development of colitis, while mice colonized with an isogenic ΔclbR mutant incapable of producing colibactin suffer significantly less pronounced effects. While ΔclbR-colonized animals show efficient recovery of the mucus barrier and crypt homeostasis, recovery in WT-colonized mice is impaired. Instead, the mucosa remains in a chronic regenerative state characterized by high proliferation and impaired differentiation of enterocytes and goblet cells, preventing the re-establishment of a functional barrier. In turn, pks+ E. coli remain in direct contact with the epithelium, perpetuating the process and triggering chronic mucosal inflammation that morphologically and transcriptionally resembles human ulcerative colitis. It is characterized by high levels of stromal R-spondin 3. Genetic overexpression of R-spondin 3 in colon myofibroblasts is sufficient to mimic this chronic regenerative state, resulting in barrier disruption and expansion of E. coli. Together, our data reveal that pks+ E. coli are pathobionts that upon contact with the epithelium promote severe injury and interfere with recovery, initiating chronic tissue dysfunction and inflammation.

overall_design: To study how colibactin-producing E. coli affect the colon epithelium, gnotobiotic E. coli-free mice, originally colonized by the Charles River altered Schaedler flora (CRASF®) were used, kindly provided by Till Strowig. These mice were used to establish in-house colonies of Enterobacteriaceae free C57BL/6, Axin2CreErt2/Rosa26-tdTomato and Krt20CreErt2/Rosa26-tdTomato mice Mice were treated for 48 h with 2 mg/ml streptomycin in drinking water. Streptomycin was replaced by drinking water 24 h before infection. Mice were infected with 1x 109 CFU of M1/5 E. coli, a pks+ E.coli strain and its isogenic Δ clbR mutant via oral gavage. At 5 days post-infection, mice were treated with 2% (Axin2CreErt2/Rosa26-tdTomato and Krt20CreErt2/Rosa26-tdTomato mice) or 2.5% DSS (C57BL/6) provided as drinking water for 7 days. After DSS treatment, mice were changed to normal drinking water and allowed to recover.  Microarray experiments were performed as independent dual-color dye-reversal color-swap hybridizations using two biological replicates per group for the infected mice.  on Agilent whole mouse catalog 4x44K (Agilent-014868) arrays. To compensate for dye-specific effects, a dye-reversal color-swap was applied.

first: Christine

last: Harnack

first: Thomas

middle: F

last: Meyer

first: Hans

last: Mollenkopf

first: Hilmar

last: Berger


title: TMBIM6 deficiency leads to bone loss by accelerating osteoclastogenesis

city: Cheongju

first: Kyunghwan

last: Kim

address: Rm #202a, Bldg. S1-5, 1 chungdae-ro

institute: Chungbuk National University

summary: To screen for altered gene expression during osteoclastogenesis,  BMM cells depleted of TMBIM6 with or without RANKL were subjected to gene expression profiling.

overall_design: Transcriptome profiles of RANKL-treated BMMs, which were depleted of TMBIM6, were generated in duplicate using Hiseq2500.


title: Metabolic Programs of T Cell Tissue Residency Empower Tumor Immunity


title: Pbrm1 regulates interferon signaling in mouse AML


title: Pbrm1 regulates interferon signaling in mouse AML [RNA-seq HAP1]

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wild-type HAP1 and Pbrm1-deficient HAP1 cells, with or without IFNγ treatment.


title: A CSF-1R-blocking antibody/IL-10 fusion protein increases anti-tumor immunity by effectuating tumor-resident CD8+ T cells

status: Public on Jul 09 2023

city: Taipei

first: JuPei

address: No. 155, Sec. 2, Linong St. Beitou Dist.

institute: National Yang Ming Chiao Tung University

summary: To investigate the in vivo effect of the fusion protein and its subcomponents on T cell function, CD8 T cells of the indicated treament were isolated from tumor, spleen and lympho nodes (LN) for T cell receptor sequencing assay.

overall_design:
Total RNAs were extracted form CD8 T cells form tumor, spleen and LN, follwed by constructing RNA sequencing libraries with the same amount RNA (100ng, RIN >8) using QIAseq mouse TCR Sequencing kit (#333705)
TCR libraries were sequenced using an Illumina NextSeq 550 system for CDR3 region. The TCR repertoire analysis were processed by QIAseq Immune Repertoire RNA Library Kit Data Analysis Portal.
Each sequencing sampele was mixed sample from same treatment (N=3); Total 12 samples from 4 treatment groups and 3 different tissues

first: YaoWen

last: Chang

first: Muh-Hwa

last: Yang

first: Tze-Tze

last: Liu


title: Genomewide profiling of H3K27ac following HDAC1/2 inhibition with romidepsin and evaluation of co-regulated mechanisms by HDAC2 and SMAD3 in BTSC genome.

city: Calgary

first: Ravinder

last: Bahia

state: Alberta

address: 3330 Hospital drive NW

department: Cell Biology and Anatomy

institute: University of Calgary

summary: To investigate the impact on global H3K27ac patterns following HDAC1/2 inhibition with romidepsin, we performed using ChIP-seq using formaldehyde crosslinked BT67 romidepsin treated versus vehicle treated cells.

overall_design: To explore the cooperative mechanisms regulated by HDAC2 and SMAD3 in  BTSC, we performed ChIP-seq using dual crosslinked BT67 cells.

first: Xiaoguang

last: Hao

first: Rozina

last: Hassam

first: Orsolya

last: Cseh

first: Danielle

last: Bozek

first: H

last: Luchman

first: Samuel

last: Weiss