title: The small and large intestine contain transcriptionally related mesenchymal stromal cell subsets that derive from embryonic Gli1+ mesothelial cells [adult bulk RNA-Seq]

city: Lyngby

first: Line

last: Wulff

address: Kemitorvet, Building 204

department: Health Technology

country: Denmark

institute: Technical University of Denmark

summary: Sorted populations of stroma cells from the small and large intestinal lamina propria. Each population has 3 replicates per tissue and were individually subjected to RNA-seq.

overall_design: Gating strategy of each MSC population is described in the paper. For small intestine; pericytes, SMCs, subepithelial FBs and two interstitial FB subsets (one including a mix of interstitial and adventitial). For LI; pericytes, subepithelial FBs, adventitial FBs and two interstitial FB subsets.

first: Simone

last: Pærregaard

first: Sophie

last: Schussek

first: Kristoffer

last: Niss

first: Urs

last: Mörbe

first: Johan

last: Jendholm

first: Kerstin

last: Wendland

first: Anna

middle: T

last: Andrusaite

first: Kevin

middle: F

last: Brulois

first: Robert

last: Nibbs

first: Katarzyna

last: Sitnik

first: Eugene

last: C. Butcher

first: Allan

last: Mowat

first: Søren

last: Brunak

first: William

middle: W

last: Agace


title: The small and large intestine contain transcriptionally related mesenchymal stromal cell subsets that derive from embryonic Gli1+ mesothelial cells [scRNA-Seq]

status: Public on Mar 17 2023

type: Expression profiling by high throughput sequencing

summary: One round of grafted SI and LI presorted YFP+ mesenchymal stromal cells were subjected to scRNA-seq.

overall_design: Embryonic small and large intestines from EYFP mice were grafted under the kidney capsules of adult WT mice. 4weeks later grafts were dissected out, made into single cell suspensions and sorted (Live, CD45-, Ter119-, BP3-, CD31-, EpCAM-, L1CAM-, Itgb1+, YFP+) MSCs sorted for scRNA-seq

middle: I

middle: J

last: C Butcher

middle: M


title: The small and large intestine contain transcriptionally related mesenchymal stromal cell subsets that derive from embryonic Gli1+ mesothelial cells [adult scRNA-Seq]

summary: Two rounds of small and large intestinal lamina propria pre-sorted intestinal mesenchymal stromal cells were subjected for scRNA-seq.

overall_design: The adult presorted stroma data consists of two replicates from both small and large intestinal lamina propria.

middle: C

last: Butcher


title: The inability to disassemble Rad51 nucleoprotein filaments   leads to aberrant mitosis and cell death

status: Public on Mar 16 2023

city: Edinburgh

first: Tadas

last: Andriuskevicius

address: Alexander Crum Brown Road

department: Institute of Cell Biology, School of Biological Sciences

country: United Kingdom

institute: The University of Edinburgh

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The proper maintenance of genetic material is essential for the survival of living organisms. One of the main safeguards of genome stability is homologous recombination involved in the faithful repair of DNA double-strand breaks, the restoration of collapsed replication forks, and the bypass of replication barriers. Homologous recombination relies on the formation of Rad51 nucleofilaments which are responsible for the homology-based interactions between DNA strands. Here we demonstrate that without the regulation of these filaments by Srs2 and Rad54, which are known to remove Rad51 from single-stranded and double-stranded DNA respectively, the filaments strongly inhibit damage-associated DNA synthesis during DNA repair. Furthermore, this regulation is essential for cell survival under normal growth conditions as in the srs2Δ rad54Δ mutants unregulated Rad51 nucleofilaments cause activation of the DNA damage checkpoint, formation of mitotic bridges and loss of genetic material. These genome instability features may stem from the problems at stalled replication forks as the lack of Srs2 and Rad54 in the presence of Rad51 nucleofilaments impedes cell recovery from replication stress. This study demonstrates that the timely and efficient disassembly of recombination machinery is essential for genome maintenance and cell survival.

overall_design: Rad51-specific ChIP-seq. The locus specific accumulation of Rad51 in induced PGAL1-RAD55 srs2Δ rad54Δ cells was tested (two biological repeats). PGAL1-RAD55 strains were used as controls (two biological repeats). A strain with an HO-inducible unrepairable double-strand break was also included as a control for the ChIP-seq protocol.

first: Anton

last: Dubenko

first: Svetlana

last: Makovets


title: The small and large intestine contain transcriptionally related mesenchymal stromal cell subsets that derive from embryonic Gli1+ mesothelial cells [E12.5 scRNA-Seq]

first: Line

last: Wulff

summary: Two rounds of embryonic (E12.5) small and large intestinal pre-sorted intestinal mesenchymal stromal cells were subjected for scRNA-seq.

overall_design: The embryonic presorted SI and LI stroma consist of two replicates from both small and large intestine (including cecum).

first: Simone

last: Pærregaard

last: Schussek

last: Niss


title: Dexamethasone effect on gene expression in human pancreatic islets and human pancreatic EndoC-βH1 cells

city: Malmö

first: Lena

last: Eliasson

address: Jan Waldenströms gata 35

country: Sweden

institute: Lund University Diabetes Centre

summary: To investigate the glucocorticoid-mediated transcriptomic changes in human pancreatic islets and the human insulin-secreting EndoC-βH1 cells in order to uncover genes and molecular pathways involved in β-cell steroid stress-response processes.

overall_design: Comparative gene expression profiling analysis of human pancreatic islets (n=4 donors) and EndoC-βH1 cells (n=4 biological replicates) after high-dose dexamethasone treatment (2 μΜ)

first: Alexandros

last: Karagiannopoulos


title: Strength of CAR signaling determines T cell versus ILC differentiation from pluripotent stem cells

city: LOS ANGELES

first: Suwen

last: Li

state: CA

address: 610 Charles E Young Dr E, Room 3031

country: USA

institute: UCLA

summary: Generation of chimeric antigen receptor (CAR) T cells from pluripotent stem cells (PSCs) will enable advances in cancer immunotherapy. A detailed understanding of the effects of CARs on T cell differentiation from PSCs is important to this effort. The recently described artificial thymic organoid (ATO) system supports in vitro differentiation of PSCs to T cells. Unexpectedly, PSCs transduced with a CD19-targeted CAR resulted in diversion of T cell differentiation to the ILC2 lineage in ATOs. T cells and ILC2s are closely related lymphoid lineages which share certain developmental and transcriptional programs. Mechanistically, we show that antigen-independent CAR signaling during early lymphoid development was evident in ILC2-primed lymphoid precursors. We applied this understanding to rationally modulate CAR signaling strength through changes to CAR expression level, structure, or expression of cognate antigen and demonstrate that the T-versus-ILC lineage decision can be controlled in either direction, providing a framework for achieving normal CAR-T cell development from PSCs.

overall_design: The goal of this project was to analyze and compare transcriptome of lymphoid progenitors generated in early stage ATOs at single cell level between H1 and H1-CAR ATOs

first: Chloe

middle: S

last: Wang

first: Amélie

last: Montel-Hagen

first: Ho-Chung

last: Chen

first: Shawn

last: Lopez

first: Olivia

last: Zhou

first: Kristy

last: Dai

first: Steven

last: Tsai

last: Satyadi

first: Carlos

last: Botero

first: Claudia

last: Wong

first: David

last: Casero

first: Gay

last: Crooks

first: Christopher

last: Seet


title: Effect of long-term ethanol treatment in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs)

city: Atlanta

first: Hyun

last: Hwang

state: Georgia

address: 2015 Uppergate Dr

department: Pediatric Cardiology

institute: Emory University School of Medicine

summary: We treated our iPSC-CMs with EtOH for 30+ days to investigate changes in gene expression

overall_design: Comparative gene expression profiling analysis of RNA-seq data for iPSC-CMs with and without EtOH exposure.

first: Chunhui

last: Xu


title: Effect of afpb gene disruption in the expression profile of P. digitatum PHI26 strain (CECT 20796)

city: Paterna (Valencia)

first: Carolina

last: Ropero-Pérez

state: Comunidad Valenciana

address: Carrer del Catedràtic Agustín Escardino Benlloch, 7

department: Biotechnology

country: Spain

institute: Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC)

summary: The potential biological function of PdAfpB antifungal protein in the producer fungus is still unknown. The goal of this study was to evaluate the transcriptomic changes in P. digitatum PHI26 strain (CECT 20796) when the afpb codifying gene is disrupted. For this we have conducted an RNA-Seq analysis to compare the differentially expressed genes between the wild-type strain and the afpb null mutant PDMG122

overall_design: Comparative gene expression profiling of RNA-seq data for PHI26 parental strain (wild-type) and the afpb null strain PDMG122 (four biological replicates per strain)

first: Begoña

last: Bolós

first: Moisés

last: Giner-Llorca

first: Antonella

last: Locascio

first: Sandra

last: Garrigues

first: Mónica

last: Gandía

first: Paloma

last: Manzanares

first: Jose

last: Marcos


title: Effect of PdAfpB antifungal protein in the expression profile of P. digitatum PHI26 strain (CECT 20796)

summary: Transcriptomic study to characterize the functional role of AfpB and its interaction with the producer fungus P. digitatum. For this, the transcriptome of P. digitatum PHI26 strain (CECT 20796) was compared with samples treated with AfpB and an AfpB overproducing strain.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PHI26 parental strain under several PdAfpB treatments and comparison with an AfpB overproducing strain (three replicates per sample)


title: Single substitution in H3.3G34 alters DNMT3A recruitment to cause progressive neurodegeneration [multiome]

city: Montréal

middle: L

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

country: Canada

institute: Lady Davis Institute for Medical Research

summary: Germline histone H3.3 amino acid substitutions, including H3.3G34R/V, cause severe neurodevelopmental syndromes. To understand how these mutations impact brain development, we generated H3.3G34R/V/W knock-in mice and identified strikingly distinct developmental defects for each mutation. H3.3G34R-mutants uniquely exhibited progressive microcephaly and neurodegeneration, with abnormal accumulation of disease-associated microglia and concurrent neuronal depletion. G34R severely decreased H3K36me2 on the mutant H3.3 tail, impairing recruitment of DNA methyltransferase DNMT3A. Redistribution of DNMT3A on chromatin promoted sustained expression of complement and other innate immune genes through loss of non-CG (CH) methylation, and silencing of neuronal gene promoters through aberrant CG methylation. Persistent complement expression in G34R neurons led to neuroinflammation possibly accounting for progressive neurodegeneration. Our study reveals that H3.3G34-substitutions have differential impact on the epigenome, which underlie the diverse phenotypes observed, and uncovers unappreciated roles for H3K36me2 and DNMT3A-dependent CH-methylation in modulating synaptic pruning and neuroinflammation in post-natal brains.

overall_design: 6 multiome samples (expression and ATAC-seq). Comparison of mutant (H3f3a +/G34R, n = 3) and wild type (WT, n = 3) murine cortex

first: Sima

last: Khazaei

first: Carol

last: Chen

first: Augusto

last: Andrade

first: Nisha

last: Kabir

first: Pariya

last: Azarafshar

first: Shahir

last: Morcos

first: Josiane

middle: A

last: França

first: Mariana

last: Lopes

first: Peder

last: Lund

first: Geoffroy

last: Danieau

first: Lata

last: Adnani

first: Nadine

last: Nzirorera

first: Xiao

first: Gayathri

last: Yogarajah

first: Caterina

last: Russo

first: Michele

last: Zeinieh

first: Cassandra

first: Laura

last: Bryant

last: Hébert

first: Bethany

last: Tong

first: Tianna

last: Sihota

first: Damien

last: Faury

first: Evan

last: Puligandla

first: Wajih

last: Jawhar

first: Veronica

last: Sandy

first: Mitra

last: Cowan

first: Emily

last: Nakada

first: Loydie

last: Jerome-Majewska

first: Benjamin

last: Ellezam

last: Cavalieri Gomes

first: Jonas

last: Denecke

first: Davor

last: Lessel

first: Marie

last: McDonald

first: Carolyn

middle: E

last: Pizoli

first: Kathryn

last: Taylor

last: Cocanougher

first: Elizabeth

last: Bhoj

first: Anne-Claude

last: Gingras


title: A shade-induced long non-coding RNA promotes shade response through repressing the transcriptional induction of PHYTOCHROME A

city: Shanghai

first: Tongdan

last: Zhu

address: 2005 Songhu Road, Yangpu District, Shanghai

country: China

institute: Fudan university

summary: A high-depth strand-specific RNA sequencing (ssRNA-seq) using 5-day-old white-light grown Col-0 and pif7-1 seedlings with additional 1 hr shade or white light treatment.

overall_design: 5-day-white-light grown seedlings were treated 1 hr shade or white light before harvesting for RNA extraction.

first: Lin

last: Li


title: N-acetylcysteine overcomes NF1-loss driven resistance to PI3K alpha inhibition in breast cancer [T47D RNA-seq]

city: Basel

first: Mohamed

last: Bentires-Alj

address: Hebelstrasse 20

department: DBM

country: Switzerland

institute: University Hospital Basel

summary: The aim of our study was to investigate PIK3CA collaborative mutations that result in resistance to BYL719, a PI3Kα selective inhibitor. One of the tumor suppressor genes discovered was neurofibromin 1 (NF1). Using shRNA-mediated knockdown and CRISPR/Cas9-mediated knockout of NF1 in murine and human PIK3CAH1047R cell lines and a patient derived xenograft organoid model, we found that NF1 loss reduces sensitivity to PI3Kα inhibition. By looking at differentially expressed genes we wanted to investigate the effect of NF1 KO in T47D cells and if they respond differentially to BYL719 compared to the T47D CTRL cells.

overall_design: Comparative gene expression profiling of T47D CTRL and NF1 cells at baseline and after 48 h of treatment with BYL719 or DMSO. Total RNA of 3 experimental replicates was collected.

first: Priska

last: Auf der Maur

first: Atul

last: Sethi

first: Michal

last: Kloc


title: N-acetylcysteine overcomes NF1-loss driven resistance to PI3K alpha inhibition in breast cancer [RNAseq_WAP]

overall_design: Comparative gene expression profiling of WAP-Cre/PIK3CA-H1047R mammary tumors treated with vehicle or BYL719. In the BYL719 treated group tumors were separated in "Responding" and "Stable" tumors. Total RNA of 7  tumors in each group was collected.

first: Pedro

last: Ramos

first: Cedric

last: Leroy


title: Single substitution in H3.3G34 alters DNMT3A recruitment to cause progressive neurodegeneration [RNA-seq]

first: Claudia

last: Kleinman

summary: De novo germline histone H3.3 amino acid substitutions, including H3.3G34R/V, cause severe neurodevelopmental syndromes. To understand how these mutations impact brain development, we generated heterozygous H3.3G34R/V/W direct knock-in mutant mice and identified strikingly distinct developmental defects for each amino acid substitution. H3.3G34R-mutant mice uniquely exhibited progressive microcephaly and neurodegeneration, associated with abnormal accumulation of damage-associated microglia and astrocytes, and concurrent neuronal depletion in postnatal brains. On the mutant H3.3 tail, G34R severely decreased H3K36me2, impairing recruitment of DNA methyltransferase DNMT3A and promoting its redistribution on chromatin. This results in loss of CH methylation at complement and other innate immune genes promoting their sustained expression, and, aberrant CG methylation at neuronal gene promoters and undue silencing. Persistent complement expression in G34R neurons led to excessive synaptic pruning, neuroinflammation, and neuronal damage accounting for progressive neurodegeneration. Our study reveals H3.3G34-substitutions have differential impact on chromatin, which underlie the diverse phenotypes observed. Notably, we uncover unappreciated roles for H3K36me2 and DNMT3A-dependent CH-methylation in modulating pruning and neuroinflammation in post-natal brains.

overall_design: 23 RNA-seq samples of mouse cortex at 7 days or 10 weeks with H3f3a G34R/V/W histone substitutions.

first: Sima

last: Khazaei

first: Carol

last: Chen

first: Nisha

last: Kabir

first: Pariya

last: Azarafshar

first: Augusto

last: Andrade

first: Shahir

last: Morcos

first: Josiane

last: França

first: Mariana

last: Lopes

first: Peder

last: Lund

first: Lata

last: Adnani

first: Xiao

first: Gayathri

last: Yogarajah

first: Caterina

last: Russo

first: Michele

last: Zeinieh

first: Cassandra

last: Wong

first: Laura

last: Bryant

first: Steven

last: Hébert

first: Bethany

last: Tong

first: Tianna

last: Sihota

first: Veronica

last: Sandy

first: Mitra

last: Cowan

first: Emily

last: Nakada

first: Loydie

last: Jerome-Majewska

first: Carolina

last: Gomes

last: Garcia

first: Chao

last: Lu

first: Eric

last: Campos

first: Livia

last: Garzia


title: Single substitution in H3.3G34 alters DNMT3A recruitment to cause progressive neurodegeneration [ChIP-seq]

first: Claudia

last: Kleinman

overall_design: ChIP-seq (23 samples) of mouse cortex at 7 days or 10 weeks with H3f3a G34R/V/W histone substitutions.

first: Sima

last: Khazaei

first: Carol

last: Chen

first: Nisha

last: Kabir

first: Pariya

last: Azarafshar

first: Augusto

last: Andrade

first: Shahir

last: Morcos

first: Josiane

last: França

first: Mariana

last: Lopes

first: Peder

last: Lund

first: Lata

last: Adnani

first: Xiao

last: Yogarajah

first: Jonas

last: Denecke

first: Davor

last: Lessel

first: Marie

last: McDonald

first: Carolyn

last: Pizoli

first: Kathryn

last: Taylor

first: Benjamin

last: Cocanougher

first: Elizabeth

last: Bhoj

first: Anne-Claude

last: Gingras


title: Single substitution in H3.3G34 alters DNMT3A recruitment to cause progressive neurodegeneration [WGBS]

first: Claudia

last: Kleinman

type: Methylation profiling by high throughput sequencing

overall_design: WGBS (4 samples) of mouse cortex at 7 days or 10 weeks with H3f3a G34R/V/W histone substitutions.

first: Sima

last: Khazaei

first: Carol

last: Chen

first: Nisha

last: Kabir

first: Gayathri

first: Caterina

last: Russo

first: Michele

last: Zeinieh

first: Cassandra

last: Wong

first: Laura

last: Bryant

first: Steven

last: Hébert

first: Bethany

last: Tong

first: Tianna

last: Sihota

first: Veronica

last: Sandy

first: Mitra

last: Cowan

first: Emily

last: Nakada

first: Loydie

last: Jerome-Majewska

first: Carolina

last: Gomes

last: Garcia

first: Chao

last: Lu

first: Eric

last: Campos

first: Livia

last: Garzia


title: Single substitution in H3.3G34 alters DNMT3A recruitment to cause progressive neurodegeneration

first: Claudia

last: Kleinman

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

overall_design: RNA-seq (23 samples), WGBS (4 samples), ChIP-seq (23 samples) and single-cell multiome (6 samples) of mouse cortex at 7 days or 10 weeks with H3f3a G34R/V/W histone substitutions.


title: Mutating DDM1 in Physcomitrella patens disrupts DNA methylation with a minute effect on transposon regulation and development [RNA-seq]

city: Tel Aviv

first: Ofir

last: Griess

address: Haim Levanon 31

department: Plant Sciences and Food Security

country: Israel

institute: Tel Aviv University

summary: We mutated PpDDM1 and the early land plant. Using BS-seq and RNA-seq, we here show that though DNA methylation is disrupted in all contexts development isn't and TE and gene differential expression are minute

overall_design: mRNA-sequencing of P. patens wild type and ddm1

first: Aviva

last: Katz

first: Katherine

last: Domb

first: Keith

middle: D

last: Harris

first: Karina

middle: G

last: Heskiau

first: Nir

last: Ohad

first: Assaf

last: Zemach


title: N-acetylcysteine overcomes NF1-loss driven resistance to PI3K alpha inhibition in breast cancer [ATAC-seq]

first: Mohamed

last: Bentires-Alj

overall_design: Overall genomic DNA from 51 resistant and 94 untreated tumors was isolated and processed by splinkerette PCR for NGS-based transposon integration mapping

first: Priska

last: Auf der Maur

first: Pedro

last: Ramos

first: Michael

last: Stadler

first: Atul

last: Sethi

first: Michal

last: Kloc


title: Mutating DDM1 in Physcomitrella patens disrupts DNA methylation with a minute effect on transposon regulation and development

overall_design: Refer to individual Series


title: Tumor Suppressor Role of INPP4B in Chemoresistant Retinoblastoma

status: Public on Mar 15 2023

city: Essen

first: Bettina

last: Budeus

address: Virchowstrasse 173

department: Institute for Cell Biology

country: Germany

institute: University Hospital Essen

summary: Chemotherapy of retinoblastoma (RB), a malignant ocular childhood disease, is often limited by the development of resistances against commonly used drugs. We identified inositol polyphosphate 4-phosphatase type II (INPP4B) as a differentially regulated gene in etoposide resistant RB cell lines, potentially involved in the development of RB resistances. INPP4B is controversially discussed as a tumor suppressor and an oncogenic driver in various cancers, but its role in retinoblastoma in general and chemoresistant RB in particular is yet unknown. In the study presented, we investigated the expression of INPP4B in RB cell lines and patients and analyzed the effect of INPP4B overexpression on etoposide resistant RB cell growth in vitro and in vivo. INPP4B mRNA levels were significantly downregulated in RB cells lines compared to the healthy human retina, with even lower expression levels in etoposide resistant compared to the sensitive cell lines. Besides, a significant increase in INPP4B expression was observed in chemotherapy treated RB tumor patient samples compared to untreated tumors. INPP4B overexpression in etoposide resistant RB cells resulted in a significant reduction in cell viability with reduced growth, proliferation, anchorage-independent growth, and in ovo tumor formation. Caspase-3/7 mediated apoptosis was concomitantly increased, suggesting a tumor suppressive role of INPP4B in chemoresistant RB cells. No changes in AKT signalling were discernible, but p-SGK3 levels increased following INPP4B overexpression, indicating a potential regulation of SGK3 signalling in etoposide-resistant RB cells. RNAseq analysis of INPP4B overexpressing, etoposide resistant RB cell lines revealed differentially regulated genes involved in cancer progression, mirroring observed in vitro and in vivo effects of INPP4B overexpression and strengthening INPP4B`s importance for cell growth control and tumorigenicity.

overall_design: Two cell lines Y79_Etop and RB355_Etop. Three biological replicates (n=3). INPP4B lentiviral overexpression (INPP4B) versus control (K).

first: Natalia

last: Miroschnikov

first: Oliver

last: Dräger

first: Dario

last: Van Meenen

first: Nicole

last: Dünker

first: Maike

last: Busch

first: Klaus

last: Metz


title: The adjuvant combination of dmLT and MPL-A activates the canonical, non-pyroptotic NLRP3 inflammasome in dendritic cells

city: New Orleans

first: James

last: McLachlan

state: Louisiana

address: 1430 Tulane Ave.

department: Microbiology & Immunology

institute: Tulane School of Medicine

summary: The purpose if this experiment was to determine how a 24 hour treatment with dmLT, MPL-A, and the combination thereof induced gene expression in dendritic cells when compared to LPS and ATP treatment. The knowledge gained from this study would allow us to identify mechanistic pathways that are unique to each adjuvant, which would allow us to further explore their function in DCs.

overall_design: We compared bone marrow derived dendritic cell RNA expression when treated with either the adjuvants dmLT, MPL-A, or the combination of the two adjuvants for 24 hours to determine differences in gene expression between these groups

first: David

last: Bauer


title: Genome-wide identification of chromosomal translocations induced by estradiol in breast cancer

city: Boston

first: Roberto

last: Chiarle

state: Massachusetts

address: 300 Longwood Avenue

department: Department of Pathology

institute: Children’s Hospital Boston and Harvard Medical School

summary: Focal copy-number amplification is an oncogenic event in many cancers. Although several studies showed the complex structure of amplified oncogens and the evolution of amplicons after their formation, the origin of the initial amplicons remains poorly understood. To understand the mechanisms, we generated genome-wide chromosomal translocation maps with/out beta-estradiol in estrogen receptor (ER) positive breast cancer cells when a DNA double strand breark occurs in SHANK2 or RARA. We found that estrogen treatment induces DNA double strand breaks in the estrogen receptor target regions that are repaired by translocations, suggesting the role of estrogen in generating the original translocations initiating amplication.

overall_design: We applied high-throughput genome-wide chromosomal translocation sequencing (HTGTS) to compare translocation patternes with/out estradiol treatment in MCF7 and T-47D breast cancer cells with DNA double strand breaks in either SHANK2 or RARA.

first: Taek-Chin

last: Cheong

first: Qi

last: Wang


title: Mutating DDM1 in Physcomitrella patens disrupts DNA methylation with a minute effect on transposon regulation and development [Bisulfite-seq]

first: Ofir

last: Griess

overall_design: Whole-genome bisulfite sequencing of P. patens Wild-type and ddm1

first: Aviva

last: Katz

first: Katherine

last: Domb

first: Keith

last: Harris

first: Karina

last: Heskiau

first: Nir

last: Ohad

first: Assaf

last: Zemach


title: RBBP4 is an epigenetic barrier for inducing pluripotent stem cells to totipotent 2C-like cells [scRNA-seq]

city: Guangzhou

first: Wang

middle: Fang

last: Ping

state: Guangdong

address: 190 Kaiyuan Avenue

department: Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

summary: Cellular totipotency is critical for generating a whole organism, yet how to establish totipotency is still poorly illustrated. Unlike pluripotent stem cells, abundant transposable elements (TEs) are activated in the totipotent cells. Here, we show that histone chaperone RBBP4 but not its homologous RBBP7 is indispensable in maintaining the identity of mouse embryonic stem cells (mESCs). Auxin-induced degradation of RBBP4, but not RBBP7, reprograms pluripotent state to a totipotent-like (also known as 2C-like) state. Mechanistically, RBBP4 could recruit G9a and KAP1 to bind on retrotransposons, especially endogenous retroviruses. RBBP4 degradation reduces the binding of G9a-mediated H3K9me2 on ERVL (particularly MERVL) and KAP1-mediated H3K9me3 on ERV1/ERVK, respectively. Moreover, RBBP4 facilitates nucleosome occupancy through chromatin remodeler CHD4 and RBBP4 depletion leads to attenuation of CHD4 binding and nucleosome occupancy on TEs. Together, our study reveals the important roles of RBBP4 in heterochromatin assembly and its loss activates TEs in mESCs, opening a new way to obtain totipotent cells in vitro.

overall_design: Gene expression profile at single cell level with or without RBBP4 depletion in mESCs.


title: RBBP4 is an epigenetic barrier for inducing pluripotent stem cells to totipotent 2C-like cells [RNA-seq]

overall_design: Gene expression profiling of overexpression of Biotin alone, Biotin-Rbbp4 and Biotin-Rbbp7, respectively.


title: scRNAseq of islets extracted from NOD-SCID mice shows no evidence for non-endocrine origin of regenerated beta cells

city: Haifa

first: Nadav

last: Sharon

address: Technion, Israel Institute of Technology

department: Faculty of biology

summary: Single cell RNA sequencing was performed on adult NOD-SCID mice to identify the various cell types in the pancreatic islets of Langerhans

overall_design: Islets were extracted from NOD-SCID pancreata, dissociated into single cells and processed for single cell RNA sequencing using 10x Genomics. Data includes three biological replicates, each represents islets from a single female.

first: Nadv


title: The transcriptome-wide mapping of 2-methylthio-N6-isopentenyladenosine at single-base resolution by ReACT-seq

city: Wuhan

first: Ziang

last: Lu

address: Wuhan University, No.299, Bayi Road, Wuchang District

institute: Wuhan University

summary: Through chemoselective methylthio group bioconjugation, we introduce a new approach (redox activated chemical tagging sequencing, ReACT-seq) to detect ms2i6A transcriptome-wide at single-base resolution.

overall_design:
Comparative enrichment data analysis of ReACT-seq for ReACT strategy treated and no treated E. coli total RNA.
For samples E.coli-RTase_SS, E.coli-RTase_HIV-RT, and E.coli-RTase_MMuLV, the protocols used were almost same, expect the choice of reverse transcriptase in library construction. To assess whether diverse reverse transcriptases have influence on the reverse transcription stop rate, Superscript III, HIV reverse transcriptase and MMuLV were used in sample E.coli-RTase_SS, E.coli-RTase_HIV-RT, and E.coli-RTase_MMuLV, respectively. ReACT label strategy were used in all three samples but not DBCO-s-s-Biotin enrichment method. Other protocols were the same for all samples.

first: Zhentian

last: Fang

first: Xiang

last: Zhou


title: RBBP4 regulates pluripotent-to-2C-like state transition through modulating heterochromatin assembly (CUT&Tag)

overall_design: Examination the binding sites of H3K9me2 in Rbbp4-AID mES cells with or without auxin-induced degradation of RBBP4.


title: RBBP4 regulates pluripotent-to-2C-like state transition through modulating heterochromatin assembly (CUT&RUN)

overall_design: Examination the binding sites of H3K9me3, KAP1, G9a and CHD4 in Rbbp4-AID mES cells with or without auxin-induced degradation of RBBP4.


title: RBBP4 regulates pluripotent-to-2C-like state transition through modulating heterochromatin assembly (Mnase-Seq)

overall_design: Examination nucleosome occupancy in Rbbp4-AID mES cells with or without auxin-induced degradation of RBBP4.


title: Detection of Ψ in RNA oligonucleotides and in tRNAs from S. cerevisiae strains by reverse transcription using RT-KTq I614Y

city: Konstanz

first: Luisa

middle: Barbara

last: Huber

state: Baden-Württemberg

address: Universitätsstraße 10

department: Department of Chemistry

institute: Universität Konstanz

summary: We have engineered an RT-active DNA polymerase variant called RT-KTq I614Y that produces error RT‑signatures specific for pseudouridine (Ψ) without prior chemical treatment of the RNA samples. These signatures are amplified during DNA amplicon library preparation and are detected by NGS. This method was applied to distinguish U from Ψ in RNA oligonucleotides (modified or unmodified) used in the previous polymerase screening and oligonucleotides which are designed from the human 18S rRNA at the position around 1445. Finally, RT-KTq I614Y was used to detect Ψ55 in tRNAGly(GCC) from Saccharomyces cerevisiae wildtype compared to data from tRNAGly(GCC) from S. cerevisiae pus4Δ.

sample_organism:
Saccharomyces cerevisiae
synthetic construct

overall_design: RNA oligonucleotides (modified or unmodified) used in the enzyme screening and oligonucleotides (modified or unmodified) designed from the human 18S rRNA were reverse transcribed by RT-KTq I614Y. Respective cDNA was used to prepare DNA amplicon libraries which were analyzed by NGS. Furthermore, purified total tRNA fractions from S. cerevisiae wt and pus4Δ deletion strain were employed to detect Ψ55.

middle: B

first: Andreas

last: Marx

first: Yuri

last: Motorin

first: Virginie

last: Marchand


title: RBBP4 regulates pluripotent-to-2C-like state transition through modulating heterochromatin assembly (ChIP-Seq)

overall_design: Examination of RBBP4 and RBBP7 binding sites.


title: Detection of Q-modification in RNAs from S. pombe and S. flexneri via reverse transcription using RT-KTq I614Y (Q-MaP-Seq)

city: Berlin

first: Ann

middle: E.

last: Ehrenhofer-Murray

address: Philippstr. 13

department: Institut für Biologie

institute: Humboldt-Universität zu Berlin

summary: In most eukaryotes and bacteria, queuosine (Q) replaces the guanosine at the wobble position of tRNAs harboring a GUN anticodon. To faithfully detect Q-modification in RNAs from Schizosaccharomyces pombe and Shigella flexneri, Q-MaP-Seq was established and applied to tRNAs from S. pombe WT (AEP1) cells and Shigella flexneri WT cells and tgt∆ cells. Q-modification of in vitro-transcribed RNAs and RNAs isolated from S. pombe and S. flexneri followed by reverse transcription using the RT-active DNA polymerase variant RT-KTq I614Y and sequencing of unmodified compared to modified RNAs allowed identification of Q-sites within tRNAs.

sample_organism:
Shigella flexneri
Schizosaccharomyces pombe

overall_design: in vitro-trasncribed tRNAs Asn and Asp were modified with queuine. Furthermore, RNA from S. pombe cells and S. flexneri cells were Q-modified in vivo. RNA from cells was extracted, and reverse transcribed using the RT-KTq I614Y; tRNAs were amplified and subjected to HTS. HTS reads were analyzed for error RT-signatures in Q-modified compared to unmodified tRNAs.

first: Navpreet

last: Kaur


title: RBBP4 regulates pluripotent-to-2C-like state transition through modulating heterochromatin assembly (RNA-Seq)

overall_design: Gene expression profiling of auxin-induced degradation of RBBP4 and RBBP7 at different time points (0h,4h,12h and 24h), respectively.


title: Transcriptomic characterization of FLC-mutant engineered human hepatocyte organoids

city: Utrecht

first: Delilah

last: Hendriks

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: We engineered human hepatocyte organoids to study the effect of different fibrolamellar carcinoma mutations. To study the effects and differences between the different mutations, we performed bulk RNA-sequencing to understand the transcriptomic changes.

overall_design: Multiple clonal lines per genotype (DNAJB1-PRKACAfus, BAP1KO, PRKAR2AKO and double BAP1KO;PRKAR2AKO) were generated and replicates of parental wild type organoids are included, all were cultured in hepatocyte medium. For wild type organoids and double mutant BAP1KO;PRKAR2AKO organoids samples were also analyzed when cultured in ductal medium.

first: Benedetta

last: Artegiani


title: RNA sequencing of LSKs in the bone marrow from WT and MC5R-null mice

city: Chongqing

first: Naicheng

last: Chen

state: Chongqing

address: Gaotanyan Street 30

department: College of Preventive Medicine

institute: Third Military Medical University

summary: LSKs(lineage-, Sca-1+, c-kit+ cells) in bone marrow from wild type (WT) and MC5R-knockout (KO) mice after after irradiation were isolated to explore the differentially expressed genes by RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for LSKs in the bone marrow from WT and MC5R-null mice after irradiation.

first: Mengjia

last: Hu


title: ATAC-seq profiling of human Tregs and conventional CD4+ cells that were transduced with a non-tonic signaling (CD19) or a tonic signaling (HA) CAR

city: Vancouver

first: Megan

middle: K

last: Levings

address: 950 West 28th Ave

institute: University of British Columbia

summary: Whether or not human Tregs are susceptible to exhaustion, and if so, if this would limit their therapeutic effect, was unknown. We studied how a tonic-signaling CAR, which induce Tconv exhaustion, affect human Tregs. We thus sorted naïve Tregs and naïve conventional CD4s and transduced them with a non-TS CAR (CD19) or a TS-CAR (HA).

overall_design: Human naive Tregs or naive conventional CD4s were flow-sorted from 3 independent donors (2 independent experiments) and were kept untransduced (UT) or were retrovirally transduced with a non-tonic signaling C AR (CD19) or a TS CAR (HA) at day 2 and 3. They were than cultured for another 4 days and live CAR positive cells (or live CD4s for UT) were flow sorted. They were then expanded for another 5 days using CD3/28 beads with 300U il-2.

first: Caroline

last: Lamarche

first: Andrew

last: Brown

first: Kirsten

last: Ward-Hartstonge


title: Effect of Gsdma1and Gsdma3 epithelial knockout on gene expression of mouse dorsal skin keratinocytes after olive oil/acetonr treatment to induce epidermal barrier disruption

city: Zhunan Town

first: Liang-Tung

last: Yang

state: Miaoli County

address: No. 35, Keyan Road

country: Taiwan

institute: National Health Research Institutes

summary: To investigate the biological fundtion regualted by Gsdma1/a3 during epidermal barrier formation, we perform acetone/olive oil vs. water treatment on the dorsal skin of control and Gsdma1/Gsdma3 epithelial knowckout (GsdA1A3eKO) mice. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 water-treated and 3 aceton/olive oil treated for each genotype (wild type vs. GsdmA1A3eKO samples).

overall_design: Comparative gene expression profiling analysis on RNA-seq data of mouse back skin keratinocytes from control and Gsdma1/a3 epitheial knockout mice after topical olive oil/acetone (AOO) or water on dorsal skin


title: Contribution of Poly-unsaturated Fatty Acids on Cerebral Neurobiology: An Integrated Omics Approach with Epigenomic Focus [Agilent]

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

summary: Fish oil or its major constituent, namely omega-3 poly-unsaturated fatty acid (n3-PUFA), are popular diets to improve neurogenesis, neuroprotection, and overall brain functions. A growing number of studies advocate for the balanced dietary supplements of n3- and n6-PUFA to maximize the brain functions. Our objective was to probe the implication of PUFA to ameliorate social stress (SS). Mice were fed a customized n-3 PUFA-enriched diet (ERD, n3:n6= 7:1), a balanced diet (BLD, n3:n6= 1:1) or a standard lab diet (STD, n3:n6= 1:6). Past reports linked these diets to brain transcriptomic regulations; hence, we aimed to investigate the effects of these diets on mice exposed to Aggressor-exposed SS (Agg-E SS) model. Mice randomly encountered life-threatening trauma from conspecific aggressor for 10 consecutive days. Stressed mice on STD showed multiple behavioral deficits that lingered even 6 weeks post-Agg-E SS. In comparison, ERD and BLD elevated bodyweights but potentially triggered behavioral resilience to SS. Comprehensive mapping of the behavioral traits projected a diet-specific variance, which was mirrored by the brain transcriptomic readouts. We focused on those brain transcriptomic networks that were exclusively perturbed by the cumulative effects of Diet, Stress and Time. STD adversely affected the gene networks associated with the cell mortality, energy homeostasis and neurodevelopment disorder; however, BLD showed long-term benefits in regulating these gene networks. Further titration of PUFA supplements in daily diets can reduce the adverse effects caused by unbalanced supplement of PUFA without compromising their health benefits.

overall_design: A N-3 PUFA-enriched diet (ERD, n3:n6= 7:1) and a balanced diet (BLD, n3:n6= 1:1) were customized to contain equivalent caloric content as that of the standard lab diet (STD, n3:n6= 1:6). These diets were administered to three groups of C57BL/6j male mice from their weaning age until late adolescence. Left hemibrains were analyzed for differential transcripts, DNA methylation and microRNAs.

first: Nabarun

last: Chakraborty

first: Seid

last: Muhie

first: Stacy-Ann

last: Miller

first: James

last: Meyerhoff

first: Marti

last: Jett

first: Rasha

last: Hammamieh


title: Hematopoietic somatic mosaicism is associated with an increased risk of postoperative atrial fibrillation

city: Lille

first: Vance

last: Gao

address: 1 Rue du Professeur Calmette

country: France

institute: Institut Pasteur de Lille

summary:
Background: On-pump cardiac surgery triggers sterile inflammation and postoperative complications such as postoperative atrial fibrillation (POAF). Hematopoietic somatic mosaicism (HSM) is a recently identified risk factor for cardiovascular diseases and results in a shift toward a chronic proinflammatory monocyte transcriptome and phenotype.

Objectives: The aim of this study was to assess the prevalence, characteristics, and impact of HSM on preoperative blood and myocardial myeloid cells as well as on outcomes after cardiac surgery.

Methods: Blood DNA from 104 patients referred for surgical aortic valve replacement (AVR) was genotyped using the HemePACT panel (576 genes). Four screening methods were applied to assess HSM, and postoperative outcomes were explored. In-depth blood and myocardial leukocyte phenotyping was performed in selected patients using mass cytometry and preoperative and postoperative RNA sequencing analysis of classical monocytes.

Results: The prevalence of HSM in the patient cohort ranged from 29%, when considering the conventional HSM panel (97 genes) with variant allelic frequencies ≥2%, to 60% when considering the full HemePACT panel and variant allelic frequencies ≥1%. Three of 4 explored HSM definitions were significantly associated with higher risk for POAF. On the basis of the most inclusive definition, HSM carriers exhibited a 3.5-fold higher risk for POAF (age-adjusted OR: 3.5; 95% CI: 1.52-8.03; P = 0.003) and an exaggerated inflammatory response following AVR. HSM carriers presented higher levels of activated CD64+CD14+CD16- circulating monocytes and inflammatory monocyte-derived macrophages in presurgery myocardium.

Conclusions: HSM is frequent in candidates for AVR, is associated with an enrichment of proinflammatory cardiac monocyte-derived macrophages, and predisposes to a higher incidence of POAF. HSM assessment may be useful in the personalized management of patients in the perioperative period.

overall_design: RNA-seq profiling of 33 cardiopulmonary bypass surgery patients, 20 of which had mutations associated with hematopoietic somatic mosaicism/clonal hematopoieisis

first: Sandro

last: Ninni

first: Tanya

last: Kuznetsova

first: Rocio

last: Vicario

first: Joel

last: Haas

first: Eloise

last: Woitrain

first: Olivier

last: Melendi-Coste

first: Augustin

last: Coisne

first: Annette

last: Neele

first: Koen

last: Prange

first: Lisa

last: Willemsen

first: Samy

last: Aghezzaf

first: Stamatina

last: Frakogianni

first: Caitlin

last: Stewart

first: Luiz

last: Diaz Jr.

first: Victor

last: Fourdinier

first: Laurent

last: Pineau

middle: R

last: White

first: Jérôme

last: Eeckhoute

first: Mohammed

last: Koussa

first: Henri

last: Dubrelle

first: Francis

last: Juthier

last: Soquet

first: André

last: Vincentelli

first: Jean-Louis

last: Edme

first: Menno

last: de Winter

first: Frederic

last: Geissmann

first: David

last: Dombrowicz

first: Bart

last: Staels

last: Montaigne


title: A genome-scale CRISPR-Cas9 loss-of-function screen in ALCL cells treated with crizotinib

first: Roberto

last: Chiarle

summary: We used a CRISPR-Cas9-based genome-wide guide RNA (sgRNA) library to identify genes responsible for driving drug resistance in ALK+ ALCL cells under crizotinib treatment.We screened 4 diffrerent ALK+ ALCL cell lines, TS, SU-DHL1, COST and KARPAS299. Every cell line was transduced with GeCKO A and GeCKO B sgRNA libraries separately. After puromycin selection, cells were splitted into 3 groups: Day 0  (baseline time point), crizotinib treated group (treated for 14 days) and DMSO treated group (treated for 14 days). TS and SU-DHL1 cells were treated with 40nM criztonib for 14 days and at the end of this period crizotinib concentration was increased to 80nM. COST cells received 50nM crizotinib for 14 days. KARPAS299 cells first received 50nM crizotinib for 14 days and at the end of this period crizotinib concentration was increased to 100nM. Crizotinib concentrations were determined based on their sensitivity for crizotinib for each cell line. The screening was repeated twice for TS and SU-DHL1 ALK+ ALCL cells. DNA isolotation was performed from all groups and each sgRNA sequence served as a barcode for Next Generation Illumina-based DNA sequencing. We compared enriched sgRNA sequences between Day 0 and DMSO conditions. We found that while PTPN2 was a top hit for all 4 ALK+ ALCL cells, PTPN1 was a top hit for TS and SU-DHL1 cells. We subsequently validated roles of PTPN1 and PTPN2 in crizotinib resistance separately. We demonstrated that both PTPN1 and PTPN2 can drive crizotinib resistance in ALK+ ALCL cells. In this study, we found two phosphatases, PTPN1 and PTPN2, involved in drug resitance in ALK+ ALCL using a CRSIPR Cas9-based screening approach. These two phosphatases regulate ALK phospharylation and therefore affect downstream signalling pathways involved in tumor growth and proliferation.

overall_design: Identify drug resistance mechanisms in ALK+ ALCL

first: Elif

last: Karaca-Atabay

first: Qi

last: Wang


title: Astrocytes deficient in circadian clock gene Bmal1 show enhanced activation responses to amyloid-beta pathology without changing plaque burden

status: Public on Mar 14 2023

city: Worcester

first: Patrick

last: Sheehan

state: MA

address: 364 Plantation Ave.

department: Neurobiology

institute: University of Massachusetts Medical School

summary: An emerging link between circadian clock function and neurodegeneration has indicated a critical role for the molecular clock in brain health. We previously reported that deletion of the core circadian clock gene Bmal1 abrogates clock function and induces cell-autonomous astrocyte activation. Regulation of astrocyte activation has important implications for protein aggregation, inflammation, and neuronal survival in neurodegenerative conditions such as Alzheimer's disease (AD). Here, we investigated how astrocyte activation induced by Bmal1 deletion regulates astrocyte gene expression, amyloid-beta (Aβ) plaque-associated activation, and plaque deposition. To address these questions, we crossed astrocyte-specific Bmal1 knockout mice (Aldh1l1-CreERT2;Bmal1(fl/fl), termed BMAL1 aKO), to the APP/PS1-21 and the APP(NL-G-F) models of Aβ accumulation. Transcriptomic profiling showed that BMAL1 aKO induced a unique transcriptional profile affecting genes involved in both the generation and elimination of Aβ. BMAL1 aKO mice showed exacerbated astrocyte activation around Aβ plaques and altered gene expression. However, this astrogliosis did not affect plaque accumulation or neuronal dystrophy in either model. Our results demonstrate that the striking astrocyte activation induced by Bmal1 knockout does not influence Aβ deposition, which indicates that the effect of astrocyte activation on plaque pathology in general is highly dependent on the molecular mechanism of activation.

overall_design: Assessed cortical gene expression of 4 month old Aldh1l1-Cre;Bmal1(f/f) mice.

first: Sheehan

middle: W

last: Patrick

first: McKee

last: Celia

first: Musiek

last: Erik


title: RNA-seq profiling of human Tregs and conventional CD4+ cells that were left untransduced or transduced with a non-tonic signaling (CD19) or a tonic signaling (HA) CAR

first: Megan

last: Levings

summary: Whether or not human Tregs are susceptible to exhaustion, and if so, if this would limit their therapeutic effect, was unknown. We studied how a tonic-signaling CAR, which induce Tconv exhaustion, affect human Tregs. We thus sorted naïve Tregs and naïve conventional CD4s and either left them untransduced (UT) or transduced them with a non-TS CAR (CD19) or a TS-CAR (HA). After 12 days in culture, we isolated their RNA and did RNA sequencing.

first: Caroline

last: Lamarche


title: High baseline tumor burden-associated macrophages promote an immunosuppressive microenvironment and reduce the efficacy of immune checkpoint inhibitors through the IGFBP2-STAT3-PD-L1 pathway

city: guangzhou

first: wen

middle: zhao

last: wei

address: No. 1838, Guangzhou Avenue North, Baiyun District, Guangzhou

department: Department of Oncology,

institute: Nanfang Hospital, Southern Medical University

summary: In order to study the difference between high tumor burden and low tumor burden, we established MC38 tumor-bearing mice. We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells at two time points.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for HTB and LTB.
*** Submitter declares that the raw data are no longer available. ***

first: Zhaowei

last: Wen


title: EZH2 inhibition remodels the inflammatory senescence-associated secretory phenotype to potentiate pancreatic cancer immune surveillance [RNA-seq2]

first: Marcus

last: Ruscetti

address: 364 Plantation Street, LRB-613, LRB-613

department: MCCB

institute: Umass Chan Medical School

summary: Immunotherapies that produce durable responses in some malignancies have failed in pancreatic ductal adenocarcinoma (PDAC) due to rampant immune suppression and poor tumor immunogenicity. We and others have demonstrated that induction of the senescence-associated secretory phenotype (SASP) can be an effective approach to activate anti-tumor Natural Killer (NK) and T cell immunity. Here we found the pancreas tumor microenvironment (TME) suppresses NK and T cell surveillance following therapy-induced senescence through EZH2-mediated epigenetic repression of pro-inflammatory SASP genes. EZH2 blockade stimulated production of SASP chemokines CCL2 and CXCL9/10, leading to enhanced NK and T cell infiltration and PDAC eradication in mouse models. EZH2 activity was also associated with suppression of chemokine signaling and cytotoxic lymphocytes and reduced survival in PDAC patients. These results demonstrate that EZH2 represses of the pro-inflammatory SASP, and that EZH2 inhibition combined with senescence-inducing therapy could be a powerful means to achieve immune-mediated tumor control in PDAC.

overall_design: RNA-seq analysis was performed on FACS sorted GFP+ PDAC tumor cells from KPC1 orthotopic PDAC tumors transplanted in the pancreas of C57BL/6 female mice following 2 week treatment with vehicle (V), combined trametinib (1 mg/kg body weight) and palbociclib (100 mg/kg) (T/P), and/or ganciclovir (50 mg/kg body weight).

first: Loretah

last: Chibaya

first: Katherine

last: Murphy

first: Kelly

last: DeMarco

first: Sneha

last: Gopalan

first: Haibo

last: Liu

first: Chaitanya

middle: N

last: Parikh

first: Yvette

last: Lopez-Diaz

first: Melissa

last: Faulkner

first: Junhui

last: Li

first: John

last: Morris IV

first: Yu-jui

last: Ho

first: Sachliv

last: K Chana

first: Janelle

last: Simon

first: Wei

last: Luan

first: Amanda

last: Kulick

first: Elisa

last: de Stanchina

first: Karl

last: Simin

first: Lihua

middle: J

last: Zhu

first: Thomas

last: Fazzio

first: Scott

last: Lowe


title: COMMD10 is essential for neural plate development during embryogenesis

city: Oklahoma City

first: Alla

last: Tsytsykova

state: OK

address: 1122 NE 13th Street

department: Neurosurgery

institute: OUHSC

summary: The COMMD (Copper metabolism MURR1 domain containing) family includes ten structurally conserved proteins (COMMD1 to COMMD10) in eukaryotic multicellular organisms which are involved in a diverse array of cellular and physiological processes, including endosomal trafficking, copper homeostasis, and cholesterol metabolism, among others. To understand the role of COMMD10 in embryonic development, we used Commd10Tg(Vav1-icre)A2Kio/J mice, where the Vav1-cre transgene is integrated into an intron of the Commd10 gene, creating a functional knockout of Commd10 in homozygous mice.  Breeding of heterozygous mice produced no COMMD10-deficient (Commd10Null) offspring, suggesting that COMMD10 is required for embryogenesis. Analysis of Commd10Null embryos demonstrated that they display stalled development by embryonic day 8.5 (E8.5). Transcriptome analysis revealed that numerous neural crest-specific gene markers had lower expression in mutant versus wild-type (WT) embryos. Specifically, Commd10Null embryos displayed significantly lower expression levels of a number of transcription factors, including a major regulator of the neural crest, Sox10. Moreover, several cytokines/growth factors involved in early embryonic neurogenesis were also lower in mutant embryos. On the other hand, Commd10Null embryos demonstrated higher expression of genes involved in tissue remodeling and regression processes. Taken together, our findings show that Commd10Null embryos die by day E8.5 due to COMMD10-dependent neural crest failure, revealing a new and critical role of COMMD10 in neural development.

overall_design: RNA-seq analysis of COMMD_Null vs. WT mouse embryo during different stages of embryogenesis: day 8.5 (E8.5), E9.5, and E10.5

first: Khanh

middle: P

last: Phan

first: Panayiotis

last: Pelargos

first: Erdyni

last: Tsitsikov

first: Graham

last: Wiley

first: Chuang

last: Bebak

first: Ian

middle: F

last: Dunn


title: Transcriptome profiling of colorectal cancer cells on BZW2 knockdown.

city: Birmingham

first: Upender

last: Manne

state: AL

address: 1824 6th Ave South

department: Pathology

institute: The University of Alabama at Birmingham

summary: Basic leucine zipper and W2 domains 2 (BZW2), also known as translation initiation regulator eIF5-mimic protein 1 (5MP1), is a member of the basic‐region leucine zipper (bZIP) superfamily of transcription factors. BZW2 has partial homology with eIF5 and can function as a competitive inhibitor of eIF5. In human Colorectal cancers, high mRNA and protein expression levels of BZW2 were associated with tumor progression. BZW2-knockdown reduced malignant phenotypes, including cell proliferation, invasion, and spheroid and colony formation. BZW2-knockdown also reduced tumor growth and metastasis  In summary, our study characterizes the expression BZW2 in colorectal cancer and explore its regulation mechanism. Future studies are needed to decipher the biological significance of these findings.

overall_design: RNA from corectal cancer cell lines (HCT116, HT29 and SW480) treated with BZW2 shRNA and non-targeting shRNA were sequenced. RNA-seq experiment is intended to identify genes and pathways altered on BZW2 knockdown.

first: Sumit

last: Agarwal


title: EZH2 inhibition remodels the inflammatory senescence-associated secretory phenotype to potentiate pancreatic cancer immune surveillance [CUT&Tag sequencing for H3K27me3]

first: Marcus

last: Ruscetti

overall_design: CUT&TAG analysis to assess H3K27me3 expression was performed on KPC1 PDAC tumor cells treated with vehicle or trametinib (25 nM) and palbociclib (500 nM) for 8 days in vitro, or on FACS sorted GFP+ KPC1 PDAC tumor cells isolated from orthotopic transplant PDAC tumors following 2 week treatment  with vehicle or trametinib (1 mg/kg body weight) and palbociclib (100 mg/kg body weight) (T/P) per os for 4 consecutive days followed by 3 days off treatment.

first: Loretah

last: Chibaya

first: Katherine

middle: C

last: Murphy

first: Kelly

last: DeMarco

first: Sneha

last: Gopalan

first: Haibo

last: Liu

first: Chaitanya

last: Parikh

first: Yvette

last: Lopez-Diaz

first: Melissa

last: Faulkner

first: Junhui

last: Li

first: John

last: Morris IV

first: Yu-jui

last: Ho

first: Sachliv

last: K Chana

first: Janelle

last: Simon


title: Single cell transcriptomes of neurally differentiated wildtype and ASCL1-KO human iPSCs, in the presence of NOTCH inhibitor DAPT [scRNA-seq]

city: London

first: Cristina

last: Dias

address: 1 Midland Road

institute: The Francis Crick Institute

summary: The roles of neurogenic pioneer transcription factors and chromatin remodelers have been characterized in that process in developing animal models and cancers. However how these factors interact with each other to regulate cell state transitions in human neurogenesis remains unclear. Here we investigated the activity of the pioneer proneural factor ASCL1 in an in vitro model of human neurogenesis. We found that ASCL1 expression characterizes a transitional state from cycling neural progenitor to post-mitotic neuron, and ASCL1 knockout impedes progenitor neuronal differentiation. ASCL1 binds to genomic targets to regulate loci promoting differentiation by different mechanisms. Acting as a classical pioneer transcription factor, its binding to compacted chromatin is required to induce transcriptional activity. At other loci, it acts as a non-pioneer chromatin remodeler, accessing permissive chromatin to further increase chromatin accessibility. We show that ASCL1 interacts with ATPase-active BAF mSWI/SNF chromatin remodelers at cis-regulatory elements, altering the chromatin regulatory landscape at a subset of target genes. This cooperative function is predominant at sites of non-pioneer chromatin remodeler function where ASCL1 requires mSWI/SNF for DNA binding while ASCL1 classical pioneer activity does not involve significant mSWI/SNF binding. Our work establishes novel roles for ASCL1 and for an interaction with mSWI/SNF in regulating epigenetic states in human neurogenesis.

overall_design: KOLF2 human induced pluripotent stem cells were differentiated into neurons using a dual-SMAD inhibition protocol and collected for scRNAseq 24hrs following treatment with the NOTCH inhibitor DAPT. Untreated samples were also collected at the same timepoint. KOLF2 iPSCs with ASCL1 knocked out by CRISPR-cas9 were also similarly differentiated and collected following DAPT treatment. Each condition was done in triplicate, and differentiations done in parallel to minimize batch effects.

first: Francois

last: Guillemot

first: Oana

last: Paun

first: Yu

middle: X

last: Tan

first: Avinash

last: Ghanate

first: Stephanie

last: Strohbuecker


title: Identifying the transcriptional output associated with distal regulatory elements where ASCL1 interacts with mSWI/SNF remodelers to regulate neural differentiation [RNA-seq]

summary: We interfeered with the ASCL1-mSWI/SNF interaction: to abolish ASCL1 function, we knocked out ASCL1 in human iPSCs, while  we used the BRM014 inhibitor to block the mSWI/SNF ATPase activity. We then collected RNA from WT, ASCL1 KO and BRM014-treated cells at DIV24, when ASCL1 expression is highest during neural differentiation.

overall_design: Differential gene expression analysis between WT and ASCL1 KO and WT and BRM014-treated cells. Overlap between the identified changes in gene expression observed in the two conditions.

first: Lina

last: Gerontogianni

first: Harshil

last: Patel


title: Pioneer factor ASCL1 cooperates with the mSWI/SNF complex at distal regulatory elements to regulate human neural differentiation

summary:
This SuperSeries is composed of the SubSeries listed below.
Pioneer transcription factors are thought to play pivotal roles in developmental processes by binding nucleosomal DNA to activate gene expression, though mechanisms through which pioneer transcription factors remodel chromatin remain unclear. Here, using single-cell transcriptomics, we show that endogenous expression of neurogenic transcription factor ASCL1, considered a classical pioneer factor, defines a transient population of progenitors in human neural differentiation. Testing ASCL1’s pioneer function using a knockout model to define the unbound state, we found that endogenous expression of ASCL1 drives progenitor differentiation by cis-regulation both as a classical pioneer factor and as a nonpioneer remodeler, where ASCL1 binds permissive chromatin to induce chromatin conformation changes. ASCL1 interacts with BAF SWI/SNF chromatin remodeling complexes, primarily at targets where it acts as a nonpioneer factor, and we provide evidence for codependent DNA binding and remodeling at a subset of ASCL1 and SWI/SNF cotargets. Our findings provide new insights into ASCL1 function regulating activation of long-range regulatory elements in human neurogenesis and uncover a novel mechanism of its chromatin remodeling function codependent on partner ATPase activity.

overall_design: Refer to individual Series


title: Single-cell RNA-sequencing of stria vascularis cells in the adult Slc26a4-/- mouse

city: Baltimore

first: Jin-Young

last: Koh

state: Maryland

address: 670 W Baltimore St

department: Otorhinolaryngology-Head & Neck Surgery

institute: University of Maryland, Baltimore

summary: The primary pathological alternations of SLC26A4-related hearing loss are endolymphatic pH acidification and luminal enlargement of the inner ear. However, the molecular cell type-specific influences remain poorly characterized. In this study, we confirmed a method of isolating single cells in the cochlea's stria vascularis (SV) from wild-type (WT) animals. We then applied it to characterize the distinct transcriptomes from mutant (Slc26a4+/- and Slc26a4-/-) samples. Single-cell RNA-sequencing (scRNA-seq) identified transcriptional profiles in Slc26a4-expressing (spindle) cells and Kcnj10-expressing (intermediate) cells of the SV. By Gene Set Enrichment Analysis (GSEA), we found that spindle cells contain extrinsic cellular components, a factor that enables cell-to-cell communication. In addition, the gene expression profile informed signaling pathways associated with pH regulation in spindle cells. Compared to WT control, the transcriptional profiles in the SV cells of Slc26a4-/- mice showed downregulation of extracellular exosome-related genes in spindle cells and GPI-anchor-related genes in the intermediate cells. Immunofluorescence studies in spindle cells of Slc26a4-/- mice validated the increased expression of the clathrin-mediated endocytosis-related protein. Overall, cell isolation of SV from WT and mutant (Slc26a4+/- and Slc26a4-/-) samples combined with cell type-specific transcriptomic analyses revealed pH-dependent alternations in spindle cells and intermediate cells, inspiring further studies into the dysfunctional role of SV cells in SLC26A4-related hearing loss.

overall_design: Stria vascularis cells of the the129S6 WT mice and mutant (Slc26a4+/- and Slc26a4-/-) mice were isolated and analyzed using scRNAseq.

first: Richard

last: Smith


title: EZH2 inhibition remodels the inflammatory senescence-associated secretory phenotype to potentiate pancreatic cancer immune surveillance

first: Marcus

last: Ruscetti

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


title: EZH2 inhibition remodels the inflammatory senescence-associated secretory phenotype to potentiate pancreatic cancer immune surveillance [CUT&Tag]

overall_design: CUT&TAG analysis was performed on KPC1 PDAC tumor cells harboring Renilla (Ren) or Ezh2 shRNAs treated with vehicle or trametinib (25 nM) and palbociclib (500 nM) for 8 days.

first: Loretah

last: Chibaya

first: Katherine

last: Murphy

first: Kelly

last: DeMarco

first: Sneha

last: Gopalan

first: Haibo

last: Liu

first: Chaitanya

last: Parikh

first: Yvette

last: Lopez-Diaz

first: Melissa

last: Faulkner

first: Wei

last: Luan

first: Amanda

last: Kulick

first: Elisa

last: de Stanchina

first: Karl

last: Simin

first: Lihua

last: Zhu

first: Thomas

last: Fazzio

first: Scott

last: Lowe


title: Transcriptome analysis of human hairy melanocytic nevi

city: Irvine

first: Maksim

middle: V

last: Plikus

state: California

address: 845 Health Sciences Road

department: Developmental and Cell Biology

institute: University of California, Irvine

summary: RNA-seq data was obtained from three individual patients. The whole skin samples were collected for RNA extraction using TRIZOL.

overall_design: Transcriptome profiling of normal versus nevus skin from the facial region of human subjects

first: Xiaojie

last: Wang


title: Identifying the genomic regions where ASCL1 and mSWI/SNF remodelers are both required to regulate chromatin accessibility during neural differentiation [ATAC-seq]

first: Cristina

last: Dias

summary: We interfeered with the ASCL1-mSWI/SNF interaction: to abolish ASCL1 function, we knocked out ASCL1 in human iPSCs, while  we used the BRM014 inhibitor to block the mSWI/SNF ATPase activity. We performed ATACseq in WT, ASCL1 KO, and BRM014-treated cells at DIV24, when ASCL1 expression is highest during neural differentiation.

overall_design: We performed differential accessibility analysis between WT and ASCL1 KO cells to identify the sites where ASCL1 regulates chromatin accessibility. We then investigated the accessibility level at those sites when cells were treated with BRM014 inhibitor and thus identified the regions where the ASCL1-mSWI/SNF interaction is required to shape the accessibility landscape.

first: Francois

last: Guillemot

first: Oana

last: Paun

first: Stephanie

last: Strohbuecker

first: Miriam

middle: L

last: Sopena

first: Harshil

last: Patel


title: Identifying the genomic regions co-bound by ASCL1 and mSWI/SNF remodelers during neural differentiation [ChIP-seq]

summary: We interfeered with the ASCL1-mSWI/SNF interaction: to abolish ASCL1 function, we knocked out ASCL1 in human iPSCs, while  we used the BRM014 inhibitor to block the mSWI/SNF ATPase activity. We then performed ASCL1 ChIPseq in DIV24 WT and BRM014-treated neural cultures, and SMARCB1 ChIPseq in DIV24 WT and ASCL1 KO neural cultures, when ASCL1 expression is highest.

overall_design: We first identified the ASCL1 and SMARCB1 binding sites in DIV24 WT cultures, and then overlaped them to identify the ASCL1-SMARCB1 co-bound genomic regions. By comparing the ASCL1 binding profile in WT versus BRM014-treated cell, as well as the SMARCB1 binding profile in WT versus ASCL1 KO cells at the ASCL1-SMARCB1 co-bound regions, we were able to investigate the recruitment dynamics between ASCL1 and mSWI/SNF remodellers.


title: GMP-MoPs display mixed gene expression profiles of both neutrophil and monocyte progenitors [RNAseq mouse]

status: Public on Mar 13 2023

city: Hachioji

first: Kenichi

last: Asano

state: Tokyo

address: 1432-1 Horinouchi

department: Life Sciences

country: Japan

institute: Tokyo University of Pharmacy and Life Sciences

summary:
This analysis was performed to visualize the distinction between GMP-MoPs and other monocyte and neutrophil progenitors.
Transcription factors differentially expressed between GMP-MoPs and cMoPs were selected.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MDPs, cMoPs, GMP, proNeu1, proNeu2, and GMP-MoPs.

first: Naoki

last: Ikeda


title: The chromatin structures of GMP-MoPs are shifted toward ones that favors an aberrant differentiation pathway generating GMP-MoPs from proNeu1 [ATAC-seq]

summary: To assess the chromatin structure of GMP-MoPs, we performed assay for transposase-accessible chromatin sequencing (ATAC-seq) analysis of MDP, cMoP, GMP, proNeu1, proNeu2, and GMP-MoP of mouse BM. The PCA of ATAC-seq positioned GMP-MoPs between proNeu1 and cMoPs.

overall_design: Profilings of chromatin configuration by ATAC-seq.

first: Akira

last: Nishiyama


title: EZH2 inhibition remodels the inflammatory senescence-associated secretory phenotype to potentiate pancreatic cancer immune surveillance [RNA-seq]

first: Marcus

last: Ruscetti

overall_design: RNA-seq analysis was performed on FACS sorted GFP+ KPC1 PDAC tumor cells harboring Renilla (Ren) or Ezh2 shRNA from KPC1 orthotopic PDAC tumors transplanted in the pancreas of C57BL/6 female mice following 2 week treatment with vehicle (V) or combined trametinib (1 mg/kg body weight) and palbociclib (100 mg/kg) (T/P).

first: Loretah

last: Chibaya

first: Katherine

last: Murphy

first: Kelly

last: DeMarco

first: Sneha

last: Gopalan

first: Haibo

last: Liu

first: Chaitanya

last: Parikh

first: Yvette

last: Lopez-Diaz

first: Melissa

last: Faulkner

first: Junhui

last: Li

first: John

last: Morris IV

first: Yu-jui

last: Ho

first: Sachliv

last: K Chana

first: Janelle

last: Simon

first: Wei

last: Luan

first: Amanda

last: Kulick

middle: G


title: Epigenetic dysregulation from chromosomal transit in micronuclei [MMCT ATAC-seq]

city: New York

first: Albert

middle: S

last: Agustinus

state: New York

address: 408 East 69th Street, Room 419-G

institute: Memorial Sloan Kettering Cancer Center

summary: Chromosomal instability (CIN) and epigenetic reprograming are characteristic of advanced and metastatic human cancers, yet whether they are mechanistically linked is unknown. Here we show that missegregation of mitotic chromosomes, their sequestration in micronuclei, and subsequent micronuclear envelope rupture significantly disrupt normal histone post-translational modifications, a phenomenon conserved across humans and mice as well as cancer and non-transformed cells. Mislocalization of missegregating chromosomes during anaphase promotes loss of Histone H2B ubiquitination enrichment of histone H3 trimethylation, whereas micronuclear rupture engenders loss of histone H3 acetylation and histone H2A ubiquitination. Using fluorescence lifetime imaging, ATAC-see, and ATAC-seq we show that micronuclei exhibit profound differences in chromatin accessibility. Additionally, chromosomes that are reincorporated into the primary nucleus after transient encapsulation in micronuclei exhibit durable epigenetic dysregulation. Thus, in addition to genomic copy number alterations, CIN can serve as a vehicle for stochastic epigenetic reprogramming and heterogeneity in cancer.

overall_design: ATAC-Seq on MMCT HCT116 cells from Kneissig M, et al. 2019 (clones and their parental control)

first: Bhargavi

last: Dameracharla

first: Kristina

last: Keuper

first: Zuzana

last: Storchova


title: Single-cell transcriptome analysis of cells in mouse hairy melanocytic nevi

first: Maksim

last: Plikus

summary: Single cell RNA-seq data was obtained from different skin cell types at days P30 or P56, when WT hair follicles are in active state (aka anagen) or resting state (aka telogen), respectively. Cell types include: Bulge stem cells, melanocytes, and myeloid cells. All cells were FACS sorted and only live single cells were collected for RNA extraction.

overall_design: Whole transcriptome profiling of different skin cell types in normal versus hairy nevus mouse model skin

first: Xiaojie

last: Wang


title: Epigenetic dysregulation from chromosomal transit in micronuclei [ATAC-Seq]

overall_design: ATAC Seq on 4T1 cells overexpressing either dnMCAK (increased chromosomal instability) or KIF2C (decreased chromosomal instability) in triplicates

first: Ramya

last: Raviram


title: Transcriptome analysis of cells in mouse hairy melanocytic nevi

summary: RNA-seq data was obtained from different skin cell types at two time points: postnatal day P30, when WT dorsal hair follicles are in actively growing state (aka anagen) and P56, when WT hair follicles are in resting state (aka telogen). Cell types include: Bulge stem cells (B), dermal papilla fibroblasts (DP), secondary hair germ cells (HG), melanocytes (Melan), myeloid cells (Myel) and CD45-positive immune cells (I). All cell were FACS sorted and only live single cells were collected for RNA extraction.

overall_design: Whole transcriptome profiling of different skin and hair follicle cell types in normal versus hairy nevus mouse model skin


title: Epigenetic dysregulation from chromosomal transit in micronuclei [Chr4 ATAC-seq]

overall_design: ATAC-Seq on RPE-1 p53KO cells that missegregates chromosome 4 during mitosis, and their control. Experiment was done in triplicates

first: Duaa

last: Al-Rawi


title: GMP-MoPs can be classified as an independent cell type that differentiate from GMPs through proNeu1 without going through the MDP-cMoP pathway [scRNA-seq]

first: Kenichi

last: Asano

summary: This analysis was performed to track the bifurcation of differentiation path of neutrophil lineage at the proNeu1 stage, giving rise to either prNeu2 or GMP-MoPs.

overall_design: A single cell RNA-seq analysis of cKit+Lin- bone marrow progenitor cells and GMP-MoPs from one naïve mouse and one LPS-injected mouse, cMoPs from one naïve mouse.

first: Naoki

last: Ikeda

first: Shigeyuki

last: Shichino

first: Takao

last: Seki


title: Epigenetic dysregulation from chromosomal transit in micronuclei [MN CUT&RUN]

overall_design: CUT&RUN using antibodies for H3K4me3, H3K9me3 and H3K27me3 in isolated intact and ruptured micronuclei (MN) and primary nuclei (PN) samples from 4T1 cells


title: Epigenetic dysregulation from chromosomal transit in micronuclei [RPE-1 CUT&RUN]

overall_design: CUR&RUN using H3K4me3, H3K27me3 and H3K27ac antibodies on RPE-1 cells p53KO or p53KO LMB2 OE, treated with either reversine or DMSO (vehicle control) long term

first: Epi

last: Cypher


title: miRNA-483-3p overexpression unleashes invasive growth of metastatic colorectal cancer via NDRG1 downregulation and ensuing activation of the ERBB3/AKT axis

city: Naples

first: Gennaro

last: Gambardella

address: Via Campi Flegrei 34,

country: Italy

institute: Telethon Institute of Genetics and Medicine (TIGEM)

summary: Colorectal cancer is a prevalent disease that is the third most common cause of cancer-associated death globally. The genetic mechanisms underlying tumor aggressiveness in colorectal cancer require further elucidation. Taking advantage of a large panel of human metastatic colorectal cancer xenografts and matched stem-like cell cultures (m-colospheres), we show here that overexpression of miRNA-483-3p, encoded by a frequently amplified gene locus encompassing IGF2, confers an aggressive phenotype. Following ectopic overexpression of miRNA-483-3p, m-colospheres displayed (i) increased proliferative response to exogenous EGFR family ligands EGF and neuregulin 1; (ii) increased spontaneous and growth factor-induced invasiveness and epithelial-mesenchymal transition (EMT); and (iii) enhanced stem-cell frequency and resistance to differentiation. Transcriptomic analyses and functional validation found that miRNA-483-3p directly targets NDRG1, a known metastasis suppressor responsible for downregulation of the EGFR family. As a result, induced or endogenous miRNA-483-3p overexpression associated with stimulation of the signaling pathway triggered by ERBB3, including AKT and GSK3β, which is responsible for EMT transcription factor activation. Consistently, treatment of miRNA-483-3p-overexpressing m-colospheres with selective ERBB3 antibodies counteracted their proliferative and invasive phenotype. The pro-malignant role of miRNA-483-3p was further corroborated by analysis of human colorectal tumors, where miRNA-483-3p expression levels directly correlated with expression of EMT transcription factors and poor prognosis, and downregulation of miRNA-483-3p, which prevented invasion of tumors formed by m-colosphere transplantation. These results unveil a previously unrecognized link between miRNA-483-3p, NDRG1, and ERBB3-AKT signaling, which can directly support colorectal cancer invasion and is amenable to therapeutic targeting.

overall_design: Gene expression profiling analysis (RNA-seq) of colospheres CRC264 and CRC327, each compared with its derivative transduced with miR-483-3p  (CRC364miR and CRC327miR, respectively).

first: Carla

last: Boccaccio

first: Ermes

last: Candiello

first: Federica

last: Verginelli


title: EZH2 inhibition remodels the inflammatory senescence-associated secretory phenotype to potentiate pancreatic cancer immune surveillance

first: Yu-Jui

last: Ho

address: 417 E 68th St

department: Cancer Biology & Genetics Program

summary: Immunotherapies that produce durable responses in some malignancies have failed in pancreatic ductal adenocarcinoma (PDAC) due to rampant immune suppression and poor tumor immunogenicity. We and others have demonstrated that induction of the senescence-associated secretory phenotype (SASP) can be an effective approach to activate anti-tumor Natural Killer (NK) and T cell immunity. Here we found the pancreas tumor microenvironment (TME) suppresses NK and T cell surveillance following therapy-induced senescence through EZH2-mediated epigenetic repression of pro-inflammatory SASP genes. EZH2 blockade stimulated production of SASP chemokines CCL2 and CXCL9/10, leading to enhanced NK and T cell infiltration and PDAC eradication in mouse models. EZH2 activity was also associated with suppression of chemokine signaling and cytotoxic lymphocytes and reduced survival in PDAC patients. These results demonstrate that EZH2 represses of the pro-inflammatory SASP, and that EZH2 inhibition combined with senescence-inducing therapy could be a powerful means to achieve immune-mediated tumor control in PDAC.

overall_design: For RNA-seq analysis of PIP, PIL, LIL, and LIP tumor samples, GFP+ tumor cells were FACS sorted on a FACSAria (BD Biosciences) from the lungs or pancreas of tumor-bearing mice following 2-week treatment with vehicle or combined trametinib (1 mg/kg body weight) and palbociclib (100 mg/kg). Total RNA was extracted from tumor cells using the RNeasy Mini Kit (Qiagen). Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation. For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate condition. RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic, version 0.36, aligning sequencing data to GRCm38 (Ensembl, version 101) with STAR, version 2.5.3a, and genome wide transcript counting using featureCounts, version 1.6.3 to generate a RPKM matrix of transcript counts. Genes were identified as differentially expressed using R package DESeq2, version 1.28.1 with a cutoff of absolute log2FoldChange ≥ 1 and adjusted p-value <0.05 between experimental conditions. Heatmaps were generated using pheatmap, version 1.0.12. Over-representation analysis of differentially expressed genes (DEGs) against KEGG Pathways was performed using clusterProfiler, version 4.0.5.

first: Loretah

last: Chibaya

first: Katherine

last: Murphy

first: Kelly

middle: D

last: DeMarco

first: Sneha

last: Gopalan

first: Haibo

last: Liu

first: Chaitanya

last: Parikh

first: Yvette

last: Lopez-Diaz

first: Melissa

last: Faulkner

first: Junhui

last: Li

first: John

last: Morris IV

first: Sachliv

last: Chana

first: Janelle

last: Simon

first: Wei

last: Luan

first: Amanda

last: Kulick

first: Elisa

last: de Stanchina

first: Karl

last: Simin

first: Lihua

last: Zhu

first: Thomas

last: Fazzio

first: Scott

last: Lowe

first: Marcus

last: Ruscetti


title: Next Generation Sequencing Facilitates analysis of IL17 EGFP positive and negative  cells from small intestine (SI) lamina propia (lp) genes expression

city: Boston

first: jinzhi

last: duan

address: 6th Floor, Room 641, NRB, 77 Louis Pasteur Avenue

institute: Brigham and Women' hospital

summary: We performed the bulk RNA seq on IL17 EGFP positive and negative  cells from small intestine (SI) lamina propia (lp) of antibiotic treated XBP1ΔIEC mice and found the different genes expression in the setting of IEC ER stress induced Th17 positive and negative cells

overall_design: Two hundred Il17a-egfp positive (CD45+TCRβ+CD4+ Il17a-egfp+) or negative T cells (CD45+TCRβ+CD4+ Il17a-egfp-) of antibiotic treated Xbp1Two hundred Il17a-egfp positive (CD45+TCRβ+CD4+ Il17a-egfp+) or negative T cells (CD45+TCRβ+CD4+ Il17a-egfp-) of antibiotic treated Xbp1ΔIEC mice were sorted by flow cytometry and used as input material. The RNA extraction and cDNA was generated following the smart-seq2 protocol as previous described(Picelli, Faridani et al; Nat Protoc ;2014). The library preparation and sequencing were performed at the Biopolymers Facility at the Harvard Medical School on Illumina NextSeq 500 sequencer to generate 75-bp paired-end reads.

first: Jinzhi

last: Duan


title: Droplet-based single-cell RNA-sequencing  facilitates transcription analysis of  small intestine epithelial cells from  SubAA273IEC and  littermate control

summary: We performed theDroplet-based single-cell RNA-sequencing on small intestine epithelial cells from  SubAA273IEC and littermate control and found  the effect of ER stress in epithelia cells on epithelial cells.

overall_design: SI epithelial  (CD45-EpCAM+) living epithelial cells from  SubAA273IEC and littermate control were FACS-sorted for sequencing. The sorted live cells were separated into a single droplet using the Chromium Single Cell 3' v3 kit according to the manufacturer’s instruction (10x Genomics). The libraries were sequenced on NovaSeq 6000 S2 platform.

first: Xi

last: Lin


title: Dissecting the interface between ARID1A and mRNA translation in bladder cancer

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

overall_design: Refer to individual Series


title: Dissecting the interface between ARID1A and mRNA translation in bladder cancer (CUT&Tag)

summary: Chromatin remodeling and protein synthesis are tightly regulated processes that impact gene expression and cellular phenotypes. However, it is unknown if these two regulatory mechanisms are linked or exert independent effects in normal epithelial physiology and disease states. We have uncovered a new functional relationship between the chromatin remodeler ARID1A and mRNA translation elongation that is involved in maintaining cellular fitness in the context of bladder carcinogenesis. Loss of ARID1A triggers inhibition of the translation elongation factor eEF2 and ribosome accumulation, which results in a reduction in protein synthesis. In the setting of ARID1A deficiency the bladder carcinogen BBN induces DNA damage and cell death without impacting cancer initiation. As such, ARID1A is necessary for tumorigenesis. Remarkably, restoration of translation elongation through eEF2 is sufficient to initiate transformation in the context of ARID1A loss. However, dependence on ARID1A for transformation appears to be context specific, as loss of ARID1A after tumor establishment is sufficient for cancer progression.

overall_design: CUT&Tag  data from 3 biological replicates each for wild-type (WT) and ARID1A knockout (KO) cells

first: Sujata

last: Jana

first: Sandipan

last: Brahma

first: Andrew

last: Hsieh


title: Epigenetic dysregulation from chromosomal transit in micronuclei [DLD-1 ATAC-seq]

first: Albert

last: Agustinus

summary: Chromosomal instability (CIN) and epigenetic reprograming are characteristic of advanced and metastatic human cancers, yet whether they are mechanistically linked is unknown. Here we show that missegregation of mitotic chromosomes, their sequestration in micronuclei, and subsequent micronuclear envelope rupture significantly disrupt normal histone post-translational modifications, a phenomenon conserved across humans and mice as well as cancer and non-transformed cells. Mislocalization of missegregating chromosomes during anaphase promotes loss of Histone H2B ubiquitination  enrichment of histone H3 trimethylation, whereas micronuclear rupture engenders loss of histone H3 acetylation and histone H2A ubiquitination. Using fluorescence lifetime imaging, ATAC-see, and ATAC-seq we show that micronuclei exhibit profound differences in chromatin accessibility. Additionally, chromosomes that are reincorporated into the primary nucleus after transient encapsulation in micronuclei exhibit durable epigenetic dysregulation. Thus, in addition to genomic copy number alterations, CIN can serve as a vehicle for stochastic epigenetic reprogramming and heterogeneity in cancer.

overall_design: ATAC-Seq of single cell clones DLD-1 cells that mis-segregates only the Y-chromosomes and their parental control The colones obtained from CEN-SELECT strategy from Ly et al., Nat. Genet. 2019

first: Bhargavi

last: Dameracharla

first: Peter

last: Ly


title: Epigenetic dysregulation from chromosomal transit in micronuclei [RPE-1 RNA-Seq]

overall_design: RNA-Seq of p53KO or LMB2 over expressing RPE-1 cells that are either treated with vehicle control (DMSO) or reversine long term.

first: Mathieu

last: Bakhoum


title: Transcripts identified by microarray analysis that were deregulated in GFP positive cells of E11.5 Tbx18(GFP/GFP) and Tbx18(cre/+);HPRT(Tbx18VP16) kidney rudiments.

city: Hannover

first: Mark-Oliver

last: Trowe

address: Carl-Neuberg-Str. 1

department: Molekularbiologie

institute: Medizinische Hochschule Hannover

summary: Evaluation of the transcriptional changes in E11.5 ureter mesenchyme cells upon loss of Tbx18 or overexpression of an activator version of Tbx18, respectively.

overall_design: GFP positive cells extracted from kidney rudiments of E11.5 Tbx18(GFP/+) (as control), Tbx18(GFP/GFP) and Tbx18(cre/+);Hprt(CAG:Tbx18VP16-GFP) embryos were sorted based on endogeneous GFP expression and analyzed by microarray analysis.

first: Andreas

last: Kispert

first: Marc-Jens

last: Kleppa


title: Epigenetic dysregulation from chromosomal transit in micronuclei [4T1 MN ATAC-Seq]

overall_design: ATAC-Seq of intact micronuclei, ruptured micronuclei, and primary nuclei from 4T1 breast cancer cells


title: Epigenetic dysregulation from chromosomal transit in micronuclei [RPE-1 ATAC-Seq]

overall_design: ATAC-Seq of p53KO or LMB2 over expressing RPE-1 cells that are either treated with vehicle control (DMSO) or reversine long term.

first: Ramya

last: Raviram


title: Dissecting the interface between ARID1A and mRNA translation in bladder cancer (Polysome)

summary: Chromatin remodeling and protein synthesis are tightly regulated processes that impact gene expression and cellular phenotypes. However, it is unknown if these two regulatory mechanisms are linked or exert independent effects in normal epithelial physiology and disease states. We have uncovered a new functional relationship between the chromatin remodeler ARID1A and mRNA translation elongation that is involved in cancer initiation and progression.

overall_design: Polysome to Subpolysome Profiling and RNASeq of samples


title: Droplet-based single-cell RNA-sequencing  facilitates trancritption analysis of  small intestine CD4 cells from Germline free Xbp1ΔIEC and Xbp1fl/fl

summary: We performed theDroplet-based single-cell RNA-sequencing on small intestine CD4 cells from Germline free(GF) Xbp1ΔIEC and Xbp1fl/fl mice and found  the effect of ER stress in epithelia cells on CD4 cells.

overall_design: SI LP CD4 (CD45+CD4+TCRβ+) living cells from Germline free Xbp1ΔIEC and Xbp1fl/fl were FACS-sorted for sequencing. The sorted live cells were separated into a single droplet using the Chromium Single Cell 3' v3 kit according to the manufacturer’s instruction (10x Genomics). The libraries were sequenced on NovaSeq 6000 S2 platform.

first: Conner

last: Lambden


title: Next Generation Sequencing Facilitates analysis of MODE-K SubAa272 and control cells genes expression

summary: We performed the bulk RNA seq on the MODE-K SubAa272 and Control stable cell line and found the different genes expression in the setting of SubAa272 caused ER stress.

overall_design: The RNA were extracted from 1x10^6  MODE-K SubAa272 and Control stable cells by RNeasy Plus Mini Kit(Qiagen,74134). Then Library preparation and transcriptome sequencing on an Illumina HiSeq X Ten platform were performed by Novogene Bioinformatics Technology Co., Ltd. to generate 150-bp paired-end reads.


title: The transcriptional and regulatory identity of erythropoietin producing cells

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

institute: Weizmann Institute of Science

summary: Erythropoietin (Epo) is the master regulator of erythropoiesis and oxygen homeostasis. Despite its physiological importance, the molecular and genomic contexts of the cells responsible for renal Epo production have not yet been resolved, limiting effective cell-based therapies for anemia. Here, we performed single-cell profiling of an Epo reporter mouse to molecularly identify Epo-producing cells under hypoxic conditions. We report that a distinct and homogeneous population of kidney stromal cells, which we name Norn cells, are the sole source of Epo production in vivo. Extensive characterization of the Norn epigenetic and transcriptional landscapes revealed Norn-specific markers, pathways, and transcription factor circuits conserved from mice to humans. These findings open new avenues to functionally dissect EPO gene regulation in human evolution and disease, and pave the way for the next generation of genetic and cell-based approaches for EPO therapies.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Wild type C57BL/6 and Epo-tdTomato reporter mice were subjected to hypoxic conditions for 4 hours to extract renal cells responsible for Epo expression and secretion. Epo-CreERT2-tdTomato were first subjected to Epo-tdTomato induction by 5 consecutive gavages of tamoxifen. Different gating scheme were used to enrich for Epo-producing Norn cells. Non-tumour kidney samples were obtained from partial or radical nephrectomies with renal cell carcinoma indication under the Helsinki protocols 6370-19-SMC (Sheba-Telhashomer medical center), 0417-20-TLV (Ichilov hospital), and 0297-22-HMO (Hadassah medical center) with local IRB approval from Weizmann Institute of Science (1568-1).

first: Bjørt

last: Kragesteen

first: Amir

last: Giladi

first: Eyal

last: David

first: Laufey

last: Geirsdóttir

first: Baoguo

last: Li

middle: M

last: Bapst

first: Sophie

last: Dahl

first: Hadas

last: Keren-Shaul

first: Merav

last: Kedmi

first: Thorfinn

last: Korneliussen

first: Josef

middle: T

last: Prchal

first: Barak

last: Rosenzweig

first: Fernando

last: Racimo

first: Roland

middle: H

last: Wenger

first: Eske

last: Willerslev


title: Profiling the lncRNA-miRNA-mRNA interaction network in diabetes submandibular gland

city: Beijing

first: Jinghua

last: Yang

address: 32 North Third Ring Road West, Haidian District, Beijing

institute: Beijing Zhiyun data technology co. LTD

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Dysfunction of salivary glands is one of the common symptoms of diabetes. Although the long non-coding RNA has recently been identified to play a role in the pathogenesis of diabetes, it is still unclear about the role of lncRNA in diabetes salivary glands. This work was aimed to explore the lncRNA-miRNA-mRNA expression profiles and functional network in diabetes submandibular gland

overall_design: LncRNA and mRNA expressional profiles were analyzed by microarray technology from the SMG of db/db mice and db/m mice (n=4). Differentially expressed (DE) lncRNAs were confirmed by qRT-PCR. We constructed a CNC and ceRNA network to reveal the core genes in hyposalivation.   Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed to explicit the biological functions.

first: Ruo-Lan

last: Xiang

first: Xi-Jin

last: Shi

first: Li

first: Yan

last: Zhang

first: Xin

last: Cong

first: Li-ling

last: Wu


title: Epigenetic dysregulation from chromosomal transit in micronuclei

first: Albert

last: Agustinus

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


title: Genetics of Myocardial Interstitial Fibrosis in the Human Heart and Association with Disease

status: Public on Mar 11 2023

city: Cambridge

first: Matthew

last: Hill

address: 75 Aimes Street

institute: Broad Institute of MIT and Harvard

summary: Myocardial interstitial fibrosis is a common thread in multiple cardiovascular diseases including heart failure, atrial fibrillation, conduction disease and sudden cardiac death. To investigate the biologic pathways that underlie interstitial fibrosis in the human heart, we developed a machine learning model to measure myocardial T1 time, a marker of myocardial interstitial fibrosis, in 41,505 UK Biobank participants. Greater T1 time was associated with diabetes mellitus, renal disease, aortic stenosis, cardiomyopathy, heart failure, atrial fibrillation, conduction disease and rheumatoid arthritis. Mendelian randomization analysis supported a potential causal role for diabetes mellitus type 1 in myocardial interstitial fibrosis. In genome-wide association analysis, we identified 11 independent loci associated with native myocardial T1 time. The identified loci implicated genes involved in glucose transport (SLC2A12), iron homeostasis (HFE, TMPRSS6), tissue repair (ADAMTSL1, VEGFC), oxidative stress (SOD2), cardiac hypertrophy (MYH7B) and calcium signaling (CAMK2D). Transcriptome-wide association studies highlighted the role of expression of ADAMTSL1 and SLC2A12 in human cardiac tissue in modulating myocardial interstitial fibrosis. Using a TGFβ1-mediated cardiac fibroblast activation assay, we found that 9 out of the 11 genome-wide significant loci comprised genes that exhibited temporal changes in expression and/or open chromatin conformation supporting the biological relevance of these loci to myocardial fibrosis and myofibroblast cell state acquisition. Harnessing machine learning to perform large-scale phenotyping of interstitial fibrosis in the human heart, our results yield novel insights into biologically relevant pathways to myocardial fibrosis and prioritize a number of pathways for further investigation.

overall_design: Comparative differential expression and chromatin accessibility in primary human cardiac fibroblasts treated with or without human TGFB1.

first: Patrick

last: Ellinor

first: Victor

last: Nauffal

first: Steven

middle: A

last: Lubitz


title: Systematic characterization of Ustilago maydis sirtuins shows Sir2 as a modulator of pathogenic gene expression

status: Public on Mar 10 2023

city: Seville

first: Blanca

last: Navarrete

state: Seville

address: Ctra. de Utrera, Km 1

department: Genetic

institute: Pablo de Olavide University (UPO)

summary:
To investigate the role of Sir2 controlling gene expression during U. maydis pathogenesis, sir2 was deleted and overexpressed with Ppit2 promoter.
RNA-Seq analysis were performed during axenic growth or filament formation in PD-Charcoal plates comparing Δsir2 mutan and wild type strains. Additionally RNA-Seq analysis were performed at 3 days post infection comparing Ppit2:sir2 >1c overexpression mutant and wild type strains.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for U. maydis cells and its Sir2 mutants (Δsir2 and Ppit2:sir2 >1c).

first: José

middle: I

last: Ibeas

first: Ramón

middle: R

last: Barrales


title: Liver in humanized-liver mice: Control vs ortho-toluidine treatment

city: Osaka

first: Shugo

last: Suzuki

state: Osaka

address: 1-4-3 Asahi-machi, Abeno-ku

department: Molecular Pathology

institute: Osaka Metropolitan University Graduate School of Medicine

summary: The gene expression profiling between Control and ortho-toluidine exposure for 4 weeks in liver of NOG-TKm30 female mice transplanted with commercially available human hepatocytes.

overall_design: Female 6- or 7-week-old NOG mice expressing HSVtk mutant clone 30 cDNA under the control of mouse transthyretin gene enhancer/promoter (NOG-TKm30 mice) were transplanted with commercially available human hepatocytes. After 9 or 8 weeks (16-week-old), mice were treated with 0 or 0.6% ortho-toluidine (OTD) for 1 week and 0 or 0.3% OTD for 3 weeks (totally 4 weeks treatment). After treatment, mice were sacrificed, and removed livers. Control and OTD treatment: 2 control female mice, 3 OTD-treated female mice, respectively. Mixed 2 or 3 samples from each group for each RNA-seq.


title: Specific gene expression signatures of low grade meningiomas

first: Alla

last: Tsytsykova

address: 1122 NE 13th Street

summary:
Meningiomas, named for their cell of origin, are the most common intracranial tumors in adults, representing 39% of all primary adult central nervous system tumors. These tumors originate in the meninges, which are the outer three layers of tissue between the skull and the brain that cover and protect the brain just under the skull. Most meningioma tumors (85-90 percent) are categorized as benign, with the remaining 10-15 percent being atypical meningioma or malignant meningioma (cancerous). The word “benign” can be misleading for meningiomas. Depending on location and growth rate, a benign meningioma brain tumor may impinge on vital nerves or compress the brain, causing disability. They may even become life threatening. We describe transcriptional signatures of four most common groups of benign meningiomas. Each subgroup of meningiomas displayed a unique gene expression program identifying signaling pathways potentially implicated in the tumorigenesis. These findings will improve our understanding of meningioma tumorigenesis.
Objective: To define gene expression signatures of the most common subtypes of meningiomas to better understand cellular processes and signaling pathways specific for each tumor genotype.

overall_design: RNA-seq was performed to determine whole transcriptome profiles of twenty meningiomas with genomic alterations including NF2 inactivation, loss of chr1p and missense mutations in TRAF7, AKT1 and KLF4.

first: Erdyni

last: Tsitsikov

first: Sherwin

last: Tavakol

first: Tressie

last: Stephens

first: Sanaa

last: Hameed

first: Lori

last: Garman

first: Wenya

last: Bi

first: Ian

last: Dunn