title: DNMT3B supports meso-endoderm differentiation from mouse embryonic stem cells [ChIP-seq]

city: Turin

first: Andrea

last: Lauria

address: Via Accademia Albertina, 13

department: Life Sciences and Systems Biology

institute: University of Turin

summary: The correct establishment of DNA methylation patterns during mouse early development is essential for cell fate specification. However, the molecular targets as well as the mechanisms that determine the specificity of the de novo methylation machinery during differentiation are not completely elucidated. Here we show that the DNMT3B-dependent DNA methylation in epiblasts of key developmental regulatory regions provides an epigenetic priming that ensures flawless commitment at later stages. Using in vitro stem cell differentiation and loss of function experiments combined with high-throughput genome-wide bisulfite-, bulk-, and single cell RNA-sequencing, we dissected the specific role of DNMT3B in cell specification, we identified the DNMT3B-dependent regulatory elements on the genome which, in Dnmt3b knockout (3BKO), impair the differentiation into meso-endodermal (ME) progenitors and redirect epiblast-like cells (EpiLCs) towards the neuro-ectodermal lineages. Moreover, ectopic expression of DNMT3B in 3BKO re-establishes the DNA methylation of the master regulator Sox2 super-enhancer, down-modulates its expression, and restores the expression of ME markers.  Taken together, our data reveal that DNMT3B-dependent methylation at the epiblast stage is essential for the priming of the meso-endodermal lineages and provide functional characterization of the de novo DNMTs during EpiLCs lineage determination.

overall_design: ChIP-seq profiling of H3K27ac, H3K4me1 and H3K4me3 in wild-type (WT) mouse ES-derived epiblast-like cells (EpiLCs) and meso-endodermal (ME) progenitors. 10 samples, 6 ChIP and 4 Input DNA as controls

first: Guohua

last: Meng

first: Valentina

last: Proserpio

first: Stefania

last: Rapelli

first: Mara

last: Maldotti

first: Isabelle

last: Polignano

first: Francesca

last: Anselmi

first: Danny

last: Incarnato

last: Krepleova

first: Chiara

last: Levra Levron

first: Daniela

last: Donna

first: Giacomo

last: Donati

first: Ivan

last: Molineris

first: Francesco

last: Neri

first: Salvatore

last: Oliviero


title: Transcriptional profiling of melanoma-associated lymphatic endothelial cells (LECs)

status: Public on Jan 20 2023

city: New York

first: Amanda

last: Lund

state: New York

address: 522 First Ave

country: USA

institute: NYU Langone Health

type: Expression profiling by high throughput sequencing

summary:
Objective was to uncover the transcriptional changes occuring in melanoma-associated LECs relative to LECs of naïve skin.
To investigate the transcriptional changes in LECs during tumor development, RNA was extracted from LECs sorted from naïve skin and BPC (Tyr::Cre-ER, BRafV600E) murine melanomas and bulk RNA-seq performed. Naïve skin LECs were collected from 3 mice and tumor-associated LECs collected from 4 mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from LECs isolated from murine naïve skin or BPC melanomas.

middle: W

first: Maria

middle: M

last: Steele

first: Julia

last: Femel


title: in situ HiPore-C reveals higher-order 3D genome folding principles

city: Guangzhou

first: Jiayong

last: Zhong

address: Jinsui Road No.7

department: State Key Laboratory of Ophthalmology, Clinical Research Center for Ocular Disease

country: China

institute: Zhongshan Ophthalmic Centre, Sun Yat-sen University

summary:
Eukaryotic genomes are folded into three-dimensional (3D) hierarchical architectures consisting of multi-way chromatin contacts that are involved in complex gene regulation. High-throughput chromosome conformation capture (Hi-C), chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) , and methods similar to these two rely on pairwise ligation of fragments in proximity in a population of cells, thus fail to reveal multi-way chromatin interactions in single allele at single fragment resolution.  To explore higher-order chromatin interaction genome-widely, a straightforward strategy is integrating multi-fragment ligates preparation with third-generation sequencing technology. To achieve this purpose, we developed a protocol of in situ high throughput multi-way contact long read Pore-C sequencing (in situ HiPore-C)
We performed genome-wide multi-way contact profiling analysis using data obtained from in situ HiPore-C sequencing of GM12878 and K562 cell lines.

overall_design: in situ HiPore-C sequencing for GM12878 and K562 cell lines.

first: Chuanle

last: Xiao

first: Chunhui

last: Hou


title: Expression data from mid-aged decapping mutant C. elegans nematodes

city: Nicosia

first: Constantinos

last: Deltas

state: Aglantzia

address: Palaios dromos Lefkosias Lemesou No.215/6

department: Biology

country: Cyprus

institute: University of Cyprus

summary: Removal of the 5’ cap of mRNAs (decapping) is mainly catalyzed by a conserved holoenzyme, composed of the catalytic subunit DCP2 and its essential cofactor DCP1. Studies in C. elegans have shown that ageing is characterized by the accumulation of decapping factors in P-Bodies, and loss of DCAP-1/DCP1 or DCAP-2/DCP2 significantly shortens lifespan. However, the relationship between mRNA decapping and ageing remains elusive. Here we present a comparative microarray study that aims to uncover this link by identifying differentially expressed genes between wild type mid-aged worms (9 days old) and age-matched animals with reduced function of DCAP-1/DCP1.

overall_design: Three age-synchronized populations per strain were harvested independently at the 9th day of their adulthood and each was treated as an individual sample. For each population 200-300 animals were picked at the end of the last larval developmental stage (L4) and cultivated in the presence of 10μg/ml FUDR to avoid progeny hatching. In total 6 samples were analyzed by extracting total RNA, labeling with biotin and hybridization on Affymetrix GeneChip C. elegans Genome Arrays. The triplicate of wild type samples was used as reference to calculate differential expression in the triplicate of dcap-1 mutant samples.

first: Fivos

last: Borbolis

first: Dimitra

last: Ranti

first: Maria-Despoina

last: Papadopoulou

first: Sofia

last: Dimopoulou

first: Apostolos

last: Malatras

first: Ioannis

last: Michalopoulos

first: Popi

last: Syntichaki


title: A de novo transcription-dependent TAD boundary underpins critical multiway interactions during antibody class switch recombination [Micro-C]

city: Vienna

first: Maximilian

middle: Christian

last: von der Linde

state: Vienna

address: Campus-vienna-biocenter 1, IMP, Pavri GRP

country: Austria

institute: Institute of Molecular Pathology

summary: Antibody class switch recombination (CSR) requires the ligation of DNA breaks in transcribed and juxtaposed donor and acceptor switch (S) sequences (S-S synapsis) spaced 50-200 kb apart within the immunoglobulin heavy chain locus (Igh). CSR is believed to occur via the association of active S regions with the 3’ regulatory region (3’RR) super-enhancer thereby coupling transcription with S-S synapsis. Here, we map the multi-way interactome underlying CSR using Tri-C. Surprisingly, S-S synapsis is strongly associated with the 3` CTCF binding element (3`CBE), but not the 3’RR, a finding also confirmed by Micro-C measurements. Instead, the 3’RR forms a self-interacting domain independently engaging with Igh genes. Additionally, transcription at acceptor S regions creates a topological barrier that insulates S-S synapsis from loop extrusion complexes. Thus, Igh gene activation and S-S synapsis occur via distinct topological states created by the interaction between transcription and the loop extrusion machinery.

overall_design: Examination of the multi-way interactome at the Igh locus through Micro-C.

last: Costea

first: Ursula

middle: E

last: Schoeberl

first: Daniel

last: Malzl

first: Johanna

last: Fitz

first: Anton

last: Goloborodko

first: Rushad

last: Pavri


title: Single cell RNA-seq analysis for mouse activated melanocyte stem cells and mature melanocytes

status: Public on Jan 21 2023

first: Qi

last: Sun

state: NY

address: 550 1st Avenue, Smilow 410

department: Dermatology

institute: New York University

summary: We compared the transcriptomics of mouse melanocyte stem cells at the activation stage of the hair cycle (anagen onset) and mature melanocytes from the hair bulb by single cell RNAseq

overall_design: Activated melanocyte stem cells were isolated from anagen II hair follicles of the back skin of Dct-rtTA; tetO-H2B-GFP mice at 4 days after depilation, with cells from 4 independent mice combined for subsequent sequencing. Differentiated melanocytes were isolated from hair bulb of anagen VI hair follicles of the back skin of Dct-rtTA; tetO-H2B-GFP mice at 5 weeks old, with cells from 4 independent mice  combined for subsequent sequencing.

first: Mayumi

last: Ito


title: A de novo transcription-dependent TAD boundary underpins critical multiway interactions during antibody class switch recombination

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: A de novo transcription-dependent TAD boundary underpins critical multiway interactions during antibody class switch recombination [ChIP-Seq]

overall_design: Examination of the multi-way interactome at the Igh locus through Tri-C.

first: Julia


title: A Progeroid Syndrome with Severe Osteogenesis Imperfecta segregates with an Intronic TAPT1 homozygous Variant that Creates a knockout allele [RNA-seq]

city: Innsbruck

first: Univ.-Prof. Dr. Andreas

last: Mayer

address: Innrain 80/82

department: Institute for Genomics and RNomics

institute: Biocenter, Medical University Innsbruck

summary: In this study, we use transcriptomic approaches, to delineate a non-coding TAPT1 mutation (c.1237-52G>A) resulting in a protein-null allele, that segregated with a congenital recessive disease recessive consisting of Osteogenesis Imperfecta (OI) and neonatal progeria.

overall_design: RNA-seq measurements for fibroblast cells of two homzygous patients, one heterozygous mother and two unrelated wildtypes.

first: Nasrinsadat

last: Nabavizadeh

first: Annkatrin

last: Bressin

first: Poh

middle: H

last: Chia

first: Ricardo

last: Traspas

first: Nathalie

last: Escande-Beillard

first: Carine

last: Bonnard

first: Zohreh

last: Hojati

first: Scott

last: Drutman

first: Freier

last: Susanne

first: Mohammad

last: El-Khateeb

first: Rajaa

last: Fathallah

first: Jean-Laurent

last: Casanova

first: Wesam

last: Soror

first: Alaa

last: Arafat

last: Shboul

first: Andreas

first: Bruno

last: Reversade


title: A Progeroid Syndrome with Severe Osteogenesis Imperfecta segregates with an Intronic TAPT1 homozygous Variant that Creates a knockout allele [NET-seq]

first: Univ.-Prof. Dr. Andreas

last: Mayer

overall_design: SI-NET-seq measurements for fibroblast cells of two homzygous patients and one unrelated wildtype. Two replicate measurments for each proband.


title: Hepatic circadian gene expression in WT and liver specific Egr-1 knockout mice aged 2month, 6month and 12month

city: Nanjing

first: Wang

last: Haiquan

address: Hankou Road

institute: Nanjing University

summary: The circadian rhythms of older individuals are normally shifted, and the metabolic functions of these individuals are degraded. How the link between metabolism and circadian rhythms is decoupled in peripheral metabolic organs with age increased is still largely unknown. Here, we analyze hepatic transcriptome in the liver at zeitgeber time (ZT) 1, 5, 9, 13, 17, 21 from C57BL/6J aged 2month, 6month and 12month. Transcriptional changes suggest that the peripheral circadian system is shifted and that the rhythmic lipid metabolism is disrupted in the liver with aging. Furthermore, we figure out liver EGR-1 might integrate the central and peripheral rhythms and regulate metabolic homeostasis in the liver. Another hepatic transcriptome of WT and Egr-1-KO liver samples at EGR-1 highest(H) and lowest(L) zeitgeber time in 2month, 6month and 12month were analyzed. The results indicated that the rhythmic coupling of EGR-1 and CIDEA regulates age-related metabolic dysfunction in the mouse liver.

overall_design: Liver gene expression in WT and liver specific Egr-1 knockout mice aged 2month, 6month and 12month

first: Jing

last: Wu

first: Haiquan

last: Wang


title: A de novo transcription-dependent TAD boundary underpins critical multiway interactions during antibody class switch recombination [Tri-C]

first: Maximilian

last: von der Linde

first: Julia

last: Costea

first: Ursula

last: Schoeberl

first: Daniel

last: Malzl

first: Johanna

last: Fitz

first: Anton

last: Goloborodko

first: Rushad

last: Pavri


title: Characterization the crosstalk between P300 enhancers and 3D genome in murine cardiomyocyte development and maturation by H3K27ac HiChIP.

status: Public on Jan 19 2023

city: Boston

first: Pingzhu

last: Zhou

state: MA

address: 320 Longwood Ave

department: Cardiology

institute: Boston Children's Hospital

summary: We report the application of bioChIP-seq, bulk RNA-seq, Hi-C, H3K27ac HiChIP, and Massively parallel reporter assays (MPRAs) to characterize the p300-bound regulatory regions in murine cardiomyocytes (CMs). By obtaining ChIP-seq data of coactivator p300 from seven developmental stages of mouse CMs, we defined the dynamic p300 enhancers from embryonic CMs to adult CMs. We then validated the activity of dynamic p300 enhancers with AAV9-based MPRAs, we found dynamic p300 enhancers show dynamic activity from postnatal day 0 (P0) CMs to 4-week-old CMs. In addition, MRPA results suggest nuclear receptor motifs are required for the activity of some p300 late enhancers. With Hi-C and H3K27ac HiChIP data of E12.5, P0 and adult CMs, we identified chromatin structure changes such as chromatin loops, compartment switch, and new TAD boundaries are associated with dynamic p300 binding. This study provides data source of CM-selective p300 enhancers, chromatin 3D structure and gene expression during CM development and maturation.

overall_design:
Identification and characterization of p300 enhancers by CM-selective p300 bioChIP-seq, MPRAs, RNA-sq, Hi-C, and H3K27ac HiChIP.

The processed data files for GSE222160 were updated on March 10, 2023.

first: Yangpo

last: Cao

first: Yanchun

last: Zhang

first: William

middle: T

last: Pu


title: Cellular responses to long-term phosphate starvation of fission yeast: Maf1 determines fate choice between quiescence and death associated with aberrant tRNA biogenesis

first: Angad

last: Garg

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center


title: Transcriptomic analysis of pancreatic adenocarcinoma specimens obtained from Black and White patients

city: Silver Spring

first: Thomas

last: Biel

state: MD

address: 10903 New Hampshire Ave

department: OBP

institute: FDA

summary: In pancreatic cancer clinical trials, Black patients are under-represented while having higher morbidity and mortality rates as compared to other racial groups. Multiple factors, including socioeconomic and lifestyle factors may contribute to this disparity, but genomic contributions remain unclear. In an exploratory project to identify genes that may contribute to differences in survival between Black and White patients with pancreatic cancer, transcriptomic sequencing of over 24,900 genes was performed in human pancreatic tumor and non-tumor tissue obtained from Black and White patients. Over 4,400 genes were differentially expressed in tumor and non-tumor tissue, irrespective of race. Of these 4,400 genes, four (AGR2, POSTN, TFF1, and CP) met the pre-defined statistical threshold for upregulation in pancreatic tumor tissue; these findings were confirmed by quantitative PCR. Transcriptomic analysis of pancreatic tumor tissue in Black and White patients revealed differential expression in 1,200 genes. Non-tumor and tumor gene expression differences within each race were assessed, revealing over 1,500 tumor-specific differentially expressed genes in pancreatic tumor and non-tumor tissue from Black patients. We identified TSPAN8 as a potential tumor-specific gene significantly overexpressed in pancreatic tumor tissue in Black patients as compared to White patients. Using Ingenuity Pathway Analysis software to compare the race-associated gene expression profiles, over 40 canonical pathways were identified to be potentially impacted by the gene expression differences between the races. Heightened expression of TSPAN8 was associated with poor overall survival, suggesting TSPAN8 as one potential genetic factor contributing to the differential outcomes in Black patients with pancreatic cancer, supporting the potential utility of larger genomic studies to further explore the role of TSPAN8 in pancreatic cancer.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for pancreatic adenocarcinoma specimens obtained from Black and White patients.

middle: G

first: Svetlana

last: Petrovskaya

first: Francesca

last: Mascia

first: Tongzhong

last: Ju

first: Lola

last: Fashoyin-Aje

first: Kelly

last: Herremans

first: Andrea

middle: N

last: Riner

first: Patrick

last: Underwood

first: Michael

last: Gerber

first: Martha

last: Donoghue

first: Jose

last: Trevino

first: V

middle: A

last: Rao


title: Chromatin accessibility differences between alpha, beta, and delta cells identifies common and cell type-specific enhancers

city: Davis

first: Mark

middle: O.

last: Huising

state: CA

address: One Shields Ave

department: Neurobiology, Physiology and Behavior

institute: University of California, Davis

summary: High throughput sequencing has enabled the interrogation of the transcriptomic landscape of glucagon-secreting alpha cells, insulin-secreting beta cells, and somatostatin-secreting delta cells. These approaches have furthered our understanding of expression patterns that define healthy or diseased islet cell types and helped explicate some of the intricacies between major islet cell crosstalk and glucose regulation. All three endocrine cell types derive from a common pancreatic progenitor, yet alpha and beta cells have partially opposing functions, and delta cells modulate and control insulin and glucagon release. While gene signatures that define and maintain cellular identity have been widely explored, the underlying epigenetic components are incompletely characterized and understood. Chromatin accessibility and remodeling is a dynamic attribute that plays a critical role to determine and maintain cellular identity. Here, we compare and contrast the chromatin landscape between mouse alpha, beta, and delta cells using ATAC-Seq to evaluate the significant differences in chromatin accessibility. The similarities and differences in chromatin accessibility between these related islet endocrine cells help define their fate in support of their distinct functional roles. We identify patterns that suggest that both alpha and delta cells are poised, but repressed, from becoming beta-like. We also identify patterns in differentially enriched chromatin that have transcription factor motifs preferentially associated with different regions of the genome. Finally, we identify and visualize both novel and previously discovered common endocrine- and cell specific- enhancer regions across differentially enriched chromatin.

overall_design: mIns1-H2b-mCherry [1] x Rosa-LSL-YFP crossed to either Sst-Cre [44] or Gcg-Cre [45] triple transgenic mice were pooled by sex, each sample yielding a median of 20,000 cells, with islet isolation and FACS-sorting as previously described (Supplemental Fig. 1) [1, 46-48]. A minimum of two replicates were used in all analyses.

first: Alex

last: Mawla

first: Talitha

last: van der Meulen

middle: O


summary: This RNA-Seq analysis compares gene expression of fission yeast (Schizosaccharomyces pombe) strains prior to phosphate starvation (0 HR) and at various times after phosphate starvation (4, 8, 12, 24, 36, and 48 HR) contrasting to the WT fission yeast S. pombe cells grown in phosphate replete conditions (WT 0HR)

overall_design: 13 test samples and 1 control sample was processed (each sample has 3 replicate experiments)

first: Stewart

last: Shuman


title: Cellular responses to long-term phosphate starvation of fission yeast: Maf1 determines fate choice between quiescence and death associated with aberrant tRNA biogenesis (CHX experiments)

first: Angad

last: Garg

summary: This RNA-Seq analysis compares gene expression of fission yeast cells (Schizosaccharomyces pombe) at various times after phosphate starvation (2, 4, and 8 HR) either with 100 µg/ml cycloheximide or without drug contrasting to the cells grown in phosphate replete conditions (0HR) in the absence of the drug.

overall_design: 6 test samples (cycloheximide or no drug treated phosphate starved cells) were analyzed; 1  control sample (no drug, phosphate replete cells); 3 biological replicate for each sample were processed

first: Beate

last: Schwer


title: Time of Day Determines Post-Exercise Metabolism in Mouse Adipose Tissue

city: Stockholm

first: Leonidas

middle: S

last: Lundell

state: Stockholm

address: Von Eulers Väg 4a

department: Physiology and Pharmacology

country: Sweden

institute: Karolinska Institute

summary: The circadian clock is a cell-autonomous transcription-translation feedback mechanism that anticipates and adapts physiology and behavior to different phases of the day. A variety of factors including hormones, temperature, food-intake, and exercise can act on tissue-specific peripheral clocks to alter the expression of genes that influence metabolism, all in a time-of-day dependent manner. The aim of this study was to elucidate the effects of exercise timing on adipose tissue metabolism. We performed RNA sequencing on inguinal adipose tissue of mice immediately following maximal exercise or sham treatment at the early rest or early active phase. Only during the early active phase did exercise elicit an immediate increase in serum non-esterified fatty acids. Furthermore, early active phase exercise increased expression of markers of thermogenesis and mitochondrial proliferation in inguinal adipose tissue. In vitro, synchronized 3T3-L1 adipocytes showed a timing-dependent difference in Adrb2 expression, as well as a greater lipolytic activity. Thus, the response of adipose tissue to exercise is time- of-day sensitive and may be partly driven by the circadian clock. To determine the influence of feeding state on the time-of-day response to exercise, we replicated the experiment in 10- hour-fasted early rest phase mice to mimic the early active phase metabolic status. A 10-hour fast led to a similar lipolytic response as observed after active phase exercise, but did not replicate the transcriptomic response, suggesting that the observed changes in gene expression are not driven by feeding status. In conclusion, acute exercise elicits timing-specific effects on adipose tissue to maintain metabolic homeostasis.

overall_design:
For the exercise intervention, 10- to 11-week-old mice were separated into sham- or exercise- treatment at the early rest (ZT3) or early active (ZT15) phase. Exercised mice were exposed to a 1-hour exercise bout (ZT3 with lights on; ZT15 in the dark with the use of a red-light lamp) while sham-exercise counterparts were placed on an artificial treadmill for 1 hour. Following the exercise bout, mice were sacrificed under isoflurane anesthesia and samples of inguinal white adipose tissue, epididymal white adipose tissue, intrascapular brown adipose tissue, and serum were collected at 0h, 4h, 8h, 12h, 16h, and 20h (n=6 per group).

RNA concentration and purity were assessed by absorbance at 260 and 280 nm using NanoDrop One (Thermo Fisher Scientific, Waltham, MA). RNA was checked for quality using the Agilent RNA 600 nano kit and Bioanalyser instrument (Agilent Technologies, Santa Clara, CA). Aliquots of RNA (1000 ng) were analyzed using the Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold protocol (Illumina). Samples were cleaned and validated for DNA concentration using the Qubit dsDNA HS assay kit (Invitrogen) and for base pair size and purity using the Agilent High Sensitivity DNA chip and Bioanalyzer instrument. The libraries were subjected to 38-bp paired-end sequencing on a NextSeq500 (Illumina).

first: Logan

last: Pendergrast

first: Lucile

middle: C

last: Dollet

first: Juleen

middle: R

last: Zierath


title: A Progeroid Syndrome with Severe Osteogenesis Imperfecta segregates with an Intronic TAPT1 homozygous Variant that Creates a knockout allele

first: Univ.-Prof. Dr. Andreas

last: Mayer


title: ASPSCR1-TFE3 orchestrates the angiogenic program of alveolar soft part sarcoma I

city: Tokyo

first: Takuro

last: Nakamura

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

department: The Cancer Institute

country: Japan

institute: Japanese Foundation for Cancer Research

summary:
Alveolar soft part sarcoma (ASPS) is a rare soft part malignancy affecting adolescents and young adult. ASPS is characterized by its alveolar structure consisting of tumor cells and highly integrated vascular network, and its high metastatic potential indicates the importance of the prominent angiogenic activity of ASPS. Here we find that the expression of ASPSCR1-TFE3, the fusion transcription factor causatively associated with ASPS, is dispensable for in vitro tumor maintenance but required for in vivo tumor development via angiogenesis. ASPSCR1-TFE3 frequently associates with active enhancers including super-enhancers (SE) upon its DNA binding, and the loss of its expression induces dynamic modification of SE distribution related to genes belonging to the angiogenesis pathway. Using epigenomic CRISPR/dCas9 screening, we identify Pdgfb, Rab27a, Sytl2, and Vwf as critical target genes associated with reduced enhancer activities due to the ASPSCR1-TFE3 loss. ASPSCR1-TFE3 thus orchestrates higher ordered angiogenesis via enhanced intracellular trafficking of angiogenic factors.
We used microarrays to detail the global program of gene expression in mouse and human ASPS cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Murine and human ASPS cell lines expressing ASPSCR1-TFE3 were examined.

first: Miwa

last: Tanaka


title: Rat and mouse imprintomes (allele-specific DNA methylomes)

city: Kashihara

first: Hisato

last: Kobayashi

state: Nara

address: 840 Shijo-Cho

department: Department of Embryology

institute: Nara Medical University

type: Methylation profiling by high throughput sequencing

summary: The rat is a widely used model for human physiology and psychology. However, due to their longer gestation periods and husbandry costs relative to mice, as well as the availability of superior molecular techniques to manipulate the mouse genome, relatively few genome-wide studies have been conducted in the rat. As such, a comprehensive analysis of genomic imprinting, which impacts complex traits such as growth and behaviour, has yet to be conducted in the rat. Towards this end, we systematically profiled embryonic and extra-embryonic tissue gene expression and DNA methylation with allele-specific resolution. We identified 14 embryonic and 26 extra-embryonic imprinted genes in the rat. Comparative analyses with mouse revealed that orthologous imprinted gene expression and associated canonical DNA methylation imprints are conserved in the embryo proper of the Muridae family. However, only 3 paternally expressed imprinted genes in the extra-embryonic embryo are conserved in Muridae, all of which are associated with non-canonical H3K27me3 imprints. The discovery of 8 novel candidate non-canonical imprinted genes unique to the rat is consistent with more rapid evolution of extra-embryonic imprinting. Cross-species analysis of novel rat imprinted genes with mouse and human revealed multiple mechanisms by which species-specific imprinted expression may be established, including H3K27me3 deposition in the oocyte, the birth of ZFP57 binding motifs and the insertion of endogenous retroviral promoters. Thus, characterization of the rat imprintome provides insights into the conservation of imprinted gene expression and the etiology of species-specific imprinting.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Whole genome bisulfite sequencing (WGBS) of epiblasts (EBs) and ectoplacental cones (EPCs) from rat and mouse embryos.

first: Toshihiro

first: Julien

last: Albert


title: The impact of SWI/SNF and NuRD inactivation on gene expression is tightly coupled with levels of RNA Polymerase II occupancy at promoters

city: Copenhagen

first: Bo

last: Porse

address: Ole Maaløes Vej 5, 4

department: Finsen Laboratory and BRIC

country: Denmark

institute: University of Copenhagen

summary: SWI/SNF and NuRD are protein complexes that antagonistically regulate DNA accessibility. However, repression of their activities often leads to unanticipated changes in target gene expression (paradoxical), highlighting our incomplete understanding of their activities. Here we show that SWI/SNF and NuRD are in a tug-of-war to regulate PRC2 occupancy at lowly expressed and bivalent genes in mESCs. In contrast, at promoters of average or highly expressed genes, SWI/SNF and NuRD antagonistically modulate RNA Polymerase II release kinetics, arguably via modifying H3.3 and H2A.Z turnover rates at promoter-flanking nucleosomes, leading to paradoxical changes in gene expression. Owing to this mechanism, the relative activities of the two remodelers potentiate gene promoters towards Pol II-dependent open or PRC2-dependent closed chromatin states. Our results highlight RNA Polymerase II occupancy as the primary parameter determining the direction of gene expression changes in response to SWI/SNF and NuRD inactivation at gene promoters in mESCs.

overall_design:
ChIP-seq (Spike-in) of RNA Polymerase II, H2A.Z and H3.3 in WT ESC and ESCs treated with BRG1 inhibitor or CHD4 shRNA. RNA Polymerase II ChIP-seq were performed in biological triplicates. H2A.Z and H3.3 ChIP-seq were performed in biological duplicates.

Nascent RNA-Seq from mESC treated with BRG1 inhibitor (BRM014) or DMSO (control) and from mESC treated with Chd4 shRNA KD or scramble shRNA (control). RNA samples were spiked in with external reference RNA (synthetic ERCC RNA) based on cell number for sequencing read normalization. There are biological duplicates for each condition

first: Sachin

last: Pundhir

first: Jinyu

last: Su

first: Marta

last: Tapia

first: Anne

last: Hansen

first: James

last: Haile

first: Klaus


title: Characterization of dynamic p300 enhancers in murine cardiomyocyte development [HiC]

first: Pingzhu

last: Zhou

summary: We report the application of bioChIP-seq, bulk RNA-seq, Hi-C, and Massively parallel reporter assays (MPRAs) to characterize the p300-bound regulatory regions in murine cardiomyocytes (CMs). By obtaining ChIP-seq data of coactivator p300 from seven developmental stages of mouse CMs, we defined the dynamic p300 enhancers from embryonic CMs to adult CMs. We then validated the activity of dynamic p300 enhancers with AAV9-based MPRAs, we found dynamic p300 enhancers show dynamic activity from postnatal day 0 (P0) CMs to 4-week-old CMs. In addition, MRPA results suggest nuclear receptor motifs are required for the activity of some p300 late enhancers. With Hi-C data of E12.5, P0 and adult CMs, we identified chromatin structure changes such as chromatin loops, compartment switch, and new TAD boundaries are associated with dynamic p300 binding. This study provides data source of CM-selective p300 enhancers, chromatin 3D structure and gene expression during CM development and maturation.

overall_design: Identification and characterization of p300 enhancers by CM-selective p300 bioChIP-seq, MPRAs, RNA-sq, and Hi-C.

first: Nathan

middle: J

last: VANDUSEN

first: Yanchun

last: Zhang

first: William

last: Pu


title: DNMT3A-coordinated splicing governs the stem state switch toward differentiation in embryonic and hematopoietic stem cells [ChIP-seq]

city: Houston

first: Margaret

last: Goodell

state: TX

address: One Baylor Plaza, N1030

institute: Baylor College of Medicine

summary: Upon stimulation by extrinsic stimuli, stem cells initiate a program that enables differentiation or self-renewal. Disruption of the stem-state exit has catastrophic consequences for embryogenesis and can lead to cancer. While some elements of this stem-state switch are known, major regulatory mechanisms remain unclear. Here, we show this switch involves a global increase in splicing efficiency coordinated by DNMT3A, an enzyme typically involved in DNA methylation. Proper activation of murine and human embryonic and hematopoietic stem cells depends on mRNA processing influenced by DNMT3A in response to stimuli. DNMT3A coordinates splicing through recruitment of the core spliceosome protein SF3B1 to RNA polymerase and mRNA. Importantly, the DNA methylation function of DNMT3A is not required and loss of DNMT3A leads to impaired splicing during stem cell turnover. Finally, we identify the spliceosome as a potential therapeutic target in DNMT3A-mutated leukemias. Together, our results reveal a modality through which DNMT3A and the spliceosome govern exit from the stem-state towards differentiation.

overall_design:
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for flag-tagged DNMT3A in ATRA-treated mouse es cells
Lysates were harvested with 0.5% trypsin. Cells were washed and crosslinked with formaldehyde for 20 mins (final concentration of 1%). Chromatin from 30x10^6 cells was sheared to 200-500bp fragments with a Covaris M220 sonicator for 8 mins. Antibody was added into lysate and incubated overnight at 4°C. 10ul of pre-blocked Protein G dynabeads were added to each IP tube and incubated for 3 hours. After washes, DNA was eluted in Elution buffer (10ml of 1M Tris pH7.5, 10ml of 0.5M EDTA, 20ml of 5M NaCl, 100ml of 10% SDS, 1ml of Proteinase K, 859ml of Sterile Water). DNA was purified with MinElute PCR purification kit (Qiagen). Libraries were prepared using Thruplex DNA-seq kit (Takara) following manufacturer's protocol. Libraries were sequenced on an Illumina NextSeq 500 instrument (paired-end 75bp reads).

first: Raghav

last: Ramabadran

first: Jaime

last: Reyes


title: Timed Exercise and Clocks: Does a Minimally Functional Suprachiasmatic Clock Support 24h Behavioral Rhythms?

city: Manchester

first: Jean-Michel

last: Fustin

state: England

address: Faculty of Biology, Medicine and Health, , Oxford road

department: Centre for Biological Timing

country: United Kingdom

institute: University of Manchester

summary: The brain’s suprachiasmatic nucleus (SCN) is the master clock driving circadian rhythms in mammals. Vasoactive intestinal polypeptide (VIP) and its cognate receptor, VPAC2, are expressed in SCN neurons and mice with genetically targeted deletion of VPAC2 (Vipr2 -/-animals) show aberrant resetting to light, abnormal behavioral rhythms, and diminished SCN clock gene expression. Timed daily access to a running-wheel (scheduled voluntary exercise; SVE) promotes Vipr2 -/- SCN clock cell synchrony and 24h behavioral rhythms. We hypothesized that timed exercise alters the SCN transcriptome. Here, in control (Vipr2+/+) and Vipr2-/- mice under freely exercising and SVE conditions, RNAseq and qRT-PCR were used to measured gene expression of laser-dissected SCN. Compared to Vipr2+/+ mice, hundreds of genes were differentially expressed in the SCN from Vipr2-/- mice rhythmic in the freely exercising condition. Unexpectedly, SVE did not promote a Vipr2+/+-like SCN transcriptome in Vipr2-/- mice and many transcripts involved in SCN function including Avp, C1ql3, Gpr176, Prok2, Sst, Per2, and Nr1d1 remained dysregulated in the SVE condition. By contrast, circadian oscillators in the liver and lung were mostly intact in Vipr2-/- mice. This study indicates that marked molecular deficits in the SCN are sustained in behaviorally rhythmic Vipr2-/- mice, raising the possibility that a minimal functional SCN circadian clock can underpin whole animal rhythms.

overall_design: Samples of laser-microdissected SCN from four experimental groups were used to assess gene expression by bulk RNAseq analysis and included: Vipr2+/+ nSVE CT14 (n=4), Vipr2+/+ SVE ZT14/CT24 (n=4), Vipr2-/- nSVE CT14 (n=3), and Vipr2-/- SVE ZT14/CT14 (n=3). RNA extraction was carried out with ReliaPrep Kit (Promega, UK), checked with RNA 6000 Pico Kit (Agilent Technologies, USA), and amplified with with Sense Total RNA-Seq Library Prep Kit (Lexogen, USA). RNA sequencing was done by paired-end sequencing on an Illumina HiSeq 4000 NGS platform (Genomic Technologies Core Facility, University of Manchester, UK). Raw reads were uploaded to the Galaxy server at the University of Manchester (https://centaurus.itservices.manchester.ac.uk/). Reads were trimmed with Trimmomatic, aligned to the mouse genome (Version GRCm38) using HISAT2 aligner, and counts calculated using Stringtie and annotated using GENCODE. Differential gene expression was analysed using DeSeq2 was used. After obtaining the differentially expressed genes, the p-value was corrected with the Benjamini Hochberg method to obtain the False Discovery Rate.

first: Timna

last: Hitrec

first: Cheryl

last: Petit

first: Emily

last: Cryer

first: Charlotte

last: Muir

first: Natalie

last: Tal

first: Alun

last: Hughes

first: Hugh

middle: D

last: Piggins


title: TSC2 regulates tumor susceptibility to TRAIL-mediated T cell killing by orchestrating mTOR signaling

city: Amsterdam

first: Joleen

last: Traets

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

summary: Resistance to immunotherapy continues to impair common clinical benefit. Here, we uncover an important role for Tuberous Sclerosis 2 (TSC2) in tumor susceptibility to killing by cytotoxic T lymphocytes, both in in vitro and in vivo. TSC2-depleted tumor cells show disruption of mTOR regulation upon CTL attack, which was associated by enhanced cell death responses. Mechanistically, we observed induced TRAIL receptor expression in TSC2-depleted cells, causing enhanced TRAIL sensitivity of tumor cells. Corroborating these data clinically, a negative correlation between TSC2 expression and TRAIL signaling was found in TCGA patient cohorts. Moreover, a lower TSC2 immune response signature was observed in melanoma patients responding to immune checkpoint blockade. Our study reveals a critical role for TSC2 in cancer immune response by crosstalk between TSC2-mTOR and TRAIL signaling, and merits therapeutic exploration of this pathway for immuno-oncology.

overall_design: Human melanoma and lung cancer cell lines (Control or with TSC2 knock-out) were cultured in the presence of T cells or TRAIL overnight. Pure tumor cell populations were sorted for sequencing.

first: Chun-Pu

last: Lin

first: Daniel

last: Peeper


title: Rat oocyte epigenomes

first: Hisato

last: Kobayashi

overall_design: H3K4me3, K27me3, and K36me3 CUT&RUN were performed in rat fully grown (GV stage) oocytes.

first: Azusa

last: Inoue

first: Toshihiro

first: Julien

last: Albert


title: Characterization of maturational enhancer activity by massively parallel reporter assay [amplicon-Seq]

first: Pingzhu

last: Zhou

summary: The activity of enhancers with dynamic P300 binding or mutagenized nuclear receptor motifs was assessed by massively parallel reporter assay during CM maturation.

sample_organism:
Mus musculus
Adeno-associated virus 9

platform_organism:
Mus musculus
Adeno-associated virus 9

overall_design: AAV9 reporter pools were injected at P0 or P7 and tissue was harvested for measurement of enhancer activity at P0, P7, or P28 by amplicon sequencing.

first: Nathan

last: VanDusen

first: William

last: Pu


title: Rat and mouse imprintomes (allele-specific transcriptomes)

overall_design: Strand-specific RNA-seq of epiblasts (EBs) and ectoplacental cones (EPCs) from rat and mouse embryos.


title: NGS of phage antibody outputs from whole-cell panning

status: Public on Jan 18 2023

city: Jupiter

first: Henry

last: Wilson

state: FL

address: 130 Scripps Way

institute: The Scripps Research Institute

summary: We present a target-unbiased approach for antibody discovery that relies on generating mAbs against native target cell surfaces via phage display. This method combines a previously reported method for improved whole-cell phage display selections with next-generation sequencing analysis to efficiently identify mAbs with the desired target cell reactivity. This approach enabled the identification of three multiple myeloma cell surface antigens, and cognate monoclonal antibody probes.

overall_design: Rabbit phage antibody libraries were selected against human multiple myeloma cell lines, HEK293-ROR1-TetOn cells, and healthy donor-derived human PBMCs using the Fab-phage Biotinylation and Capture (FBC) method. Selected antibody outputs were subjected to NGS analysis for HCDR3 profiling.


title: Transcriptomics analysis of post-mortem substantia nigra samples from Parkinson’s disease patients and controls.

city: Belvaux

first: Enrico

last: Glaab

state: Capellen

address: 6, avenue du Swing

country: Luxembourg

institute: University of Luxembourg

summary:
Purpose: Parkinson’s disease (PD) is one of the most common neurological movement disorders. In the incidence and the clinical features of PD, significant gender differences have been observed. While males have a higher disease prevalence and are more frequently affected by muscle rigidity, females present more often with disabling tremors. The molecular mechanisms behind these disease-associated gender differences are still largely unknown, and a detailed understanding of the factors involved may open new avenues for pharmacological disease modification.
Methods: To address this gap, we have conducted a meta-analysis of disease-associated molecular gender differences in brain transcriptomics data from PD case/control studies. We studied gender-dependent expression changes in individual genes and using systems level pathway and network analyses to identify coordinated gender-related molecular alterations. In each analysis, both gender-specific changes (significant alteration in only one gender) and gender-dimorphic changes (changes in both genders, but with opposite direction) were identified.
Results: These analyses revealed significant disease-associated sex differences in immune response processes and mitochondrial pathways, and highlight regulatory factors, such as the transcription factor NR4A2, whose activity changes can explain ensuing alterations propagated through gene regulatory cascades. Overall, significant gender disparities were observed in PD-associated transcriptomic changes, resulting in coordinated modulations of molecular processes. Among the regulatory factors involved, NR4A2 has previously been reported to harbor rare mutations in familial PD and its pharmacological activation conferred neuroprotective effects in toxin-induced models of Parkinsonism. NR4A2 may therefore be of interest as a candidate target for further preclinical studies on addressing gender-related pathological features of PD.

overall_design: Transcriptomics profiles of post-mortem substantia nigra samples from 8 Parkinson’s disease patients and 8 gender-matched, non-demented controls obtained via high-throughput mRNA sequencing.

first: Léon-Charles

last: Tranchevent

first: Rashi

last: Halder


title: Epigenetic resetting in the human germline entails histone modification remodelling

city: Cambridge

first: Walfred

last: Tang

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

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

overall_design: Refer to individual Series


title: Epigenetic resetting in the human germline entails histone modification remodelling [RNA-Seq II]

summary: Epigenetic resetting in the mammalian germ line entailsacute DNA demethylation, which lays the foundation for gametogenesis, totipotency,and embryonic development. We characterize the epigenome of hypomethylated human primordial germ cells (hPGCs) to reveal mechanisms preventing the widespread derepression of genesand transposable elements (TEs). Along with the loss of DNA methylation, we show that hPGCsexhibit a profound reduction of repressive histone modifications resulting in diminished heterochromatic signaturesat most genesand TEsand the acquisition of a neutral or paused epigenetic state without transcriptional activation.Efficient maintenance of a heterochromatic state is limited to a subset of genomic loci, such asevolutionarily young TEsand some developmental genes, which require H3K9me3 and H3K27me3, respectively, forefficient transcriptional repression. Accordingly, transcriptional repression in hPGCs presentsan exemplary balanced system relying on local maintenance of heterochromatic featuresand a lack of inductive cues.

overall_design: Histone modifications ULI-NChIP-seq of human primordial germ cells gonadal somatic cells (two biological replicates for each cell type and sex)

first: Wolfram

last: Gruhn


title: Epigenetic resetting in the human germline entails histone modification remodelling [RNA-Seq I]


title: A de novo transcription-dependent TAD boundary underpins critical multiway interactions during antibody class switch recombination [PRO-seq]

first: Maximilian

last: von der Linde

address: Campus-vienna-biocenter 1, IMP, Pavri GRP

institute: Institute of Molecular Pathology

summary: Antibody class switch recombination (CSR) requires the ligation of DNA breaks in transcribed and juxtaposed donor and acceptor switch (S) sequences (S-S synapsis) spaced 50-200 kb apart within the immunoglobulin heavy chain locus (Igh). CSR is believed to occur via the association of active S regions with the 3’ regulatory region (3’RR) super-enhancer thereby coupling transcription with S-S synapsis. Here, we map the multi-way interactome underlying CSR using Tri-C. Surprisingly, S-S synapsis is strongly associated with the 3` CTCF binding element (3`CBE), but not the 3’RR, a finding also confirmed by Micro-C measurements. Instead, the 3’RR forms a self-interacting domain independently engaging with Igh genes. Additionally, transcription at acceptor S regions creates a topological barrier that insulates S-S synapsis from loop extrusion complexes. Thus, Igh gene activation and S-S synapsis occur via distinct topological states created by the interaction between transcription and the loop extrusion machinery.

overall_design: Examination of the multi-way interactome at the Igh locus through Tri-C.

first: Julia

last: Costea

first: Ursula

last: Schoeberl

last: Malzl

first: Johanna

last: Fitz

first: Anton

last: Goloborodko

first: Rushad

last: Pavri


title: Epigenetic resetting in the human germline entails histone modification remodelling [ATAC-Seq]


title: ASH2L controls ureteric bud morphogenesis via regulation of RET/GFRA1 signaling activity [RNA-seq]

city: Shanghai

first: Ziyi

last: Zhao

address: 320 Yueyang Road

institute: Shanghai jiaotong university school of medicine

summary: To elucidate the role of H3K4 methylation in metanephros development, we selectively inactivated ASH2L, core subunit of the COMPASS complex in mice UB lineage. We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different FACS-sorted UB lineage cells at E16.5 of the control and cKO mouse embryos.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for FACS-sorted UB lineage cells at E16.5 of control and Ash2l cKO mouse embryos.

first: Xuantong

last: Dai

first: Gengru

last: Jiang

first: Fujun

last: Lin


title: ASH2L controls ureteric bud morphogenesis via regulation of RET/GFRA1 signaling activity [CUT&Tag]

summary: To elucidate the role of H3K4 methylation in metanephros development, we selectively inactivated ASH2L, core subunit of the COMPASS complex in mice UB lineage. We then performed histone H3K4me3 modification landscape profiling of the control (Hoxb7Cre-GFP+,Ash2l F/+) and mutant (Hoxb7Cre-GFP+,Ash2l F/F) FACS-sorted UB lineage cells at E16.5 by CUT&Tag-seq.

overall_design: CUT&tag-seq for histoneH3K4me3 in FACS-sorted control (Hoxb7Cre-GFP+,Ash2l F/+)  and mutant (Hoxb7Cre-GFP+,Ash2l F/F) FACS-sorted UB lineage cells at E16.5.


title: ASH2L controls ureteric bud morphogenesis via regulation of RET/GFRA1 signaling activity


title: CD95/Fas ligand mRNA is toxic to cells through more than one mechanism [DISE-64]

status: Public on Jan 17 2023

city: Chicago

first: Marcus

last: Peter

state: IL

address: 303 East Superior Street, Lurie 6-123

institute: Northwestern University Feinberg School of Medicine

summary: Analysis of RISC bound short (s)RNAs in a HCT116 Drosha CD95 d.k.o. cell line expressing pLenti-CD95L and various CD95L mutant constructs.

overall_design: Argonaute protein associated short RNAs were isolated from various HCT116 knock-out single cell clones using a GW182-derived GST-FLAG-T6B peptide and analyzed by sRNA-Seq.

first: Elizabeth

last: Bartom

first: Ashley

last: Haluck-Kangas


title: CD95/Fas ligand mRNA is toxic to cells through more than one mechanism [DISE-63]

summary: Analysis of RISC bound short (s)RNAs in a HCT116 wild-type, Drosha k.o., and Ago 1/2/3 k.o. cells expressing pLenti-CD95L NP or pLenti empty vector.


title: Itaconate regulates Th17/Treg cell balance via metabolic and epigenetic reprogramming [ATAC-seq]

city: Sapporo

first: Kuniyuki

last: Aso

address: Kita 14, Nishi 5, Kita-ku

institute: Hokkaido university

summary: An imbalance of T helper (Th17) cells and regulatory T (Treg) cells contributes to the pathogenesis of autoimmune diseases. The endogenous metabolite itaconate (ITA) is a regulator of macrophages; however, its role in T cells regulation is unclear. Here, we show that ITA inhibited Th17 cell differentiation and promoted Treg cell differentiation via metabolic and epigenetic reprogramming. Mechanistically, ITA suppressed glycolysis and mitochondrial respiration in Th17 and Treg-polarizing T cells. In Th17 cells, the S-adenosyl-L-methionine/ S-adenosylhomocysteine ratio was decreased following ITA administration in vitro, subsequently altering the epigenetic status.  Further, ITA inhibited RORγt binding at the Il17a promoter, resulting in reduced IL-17A expression. In Treg cells, ITA reduced 2-hydroxyglutarate levels, which suppressed Foxp3 expression. The adoptive transfer of ITA-treated Th17-polarizing T cells ameliorated experimental autoimmune encephalomyelitis. Collectively, these results indicate that ITA serves as a crucial metabolic regulator for Th17/Treg cell balance and a potential therapeutic agent against autoimmune diseases.

overall_design: To understand the mechanisms underlying ITA-dependent modulation of T cell differentiation, we performed ATAC sequencing (ATAC-seq) using Th17 and Treg cells in the presence or abscence ITA 6 mM treatment (n=2, respectively).

first: Michihito

last: Kono

first: Masatoshi

last: Kanda

first: Yuki

last: Kudo

first: Kodai

last: Sakiyama

first: Ryo

last: hisada

first: Kohei

last: Karino

first: Yusho

last: Ueda

first: Daigo

last: Nakazawa

first: Yuichiro

last: Fujieda

first: Masaru

last: Kato

first: Olga

last: Amengual

first: Tatsuya

last: Atsumi


title: CD95/Fas ligand mRNA is toxic to cells through more than one mechanism [DISE-46]

summary: Analysis of RISC bound short (s)RNAs in a HCT116 wild-type, Drosha k.o., and Dicer k.o. cells expressing pLenti-CD95L NP or pLenti empty vector.


title: Epigenetic resetting in the human germline entails histone modification remodelling [ChIP-Seq]

first: Walfred

last: Tang

first: Wolfram

last: Gruhn


title: CD95/Fas ligand mRNA is toxic to cells through more than one mechanism [DISE-47]

first: Marcus

last: Peter

first: Elizabeth

last: Bartom


title: The impact of iron depletion on the transcriptome of Enterococcus faecalis

city: Gainesville

first: Jessica

middle: K

last: Kajfasz

address: 1395 Center Drive

department: Oral Biology

institute: University of Florida

summary: To identify the genes and pathways utilized by E. faecalis to grow under iron starvation, we used RNA deep sequencing (RNA-seq) to compare the transscriptome of the parent strain OG1RF grown to mid-log in the chemically defined FMC medium with or without the addition of FeSO4 as an iron source.

overall_design: E. faecalis OG!RF cells were grown to mid-log phase in chemically defined FMC medium with (Complete) or without (Minus Fe) supplementation with 80uM FeSO4 as a source of iron.  Total RNA was isolated and prepared for RNA-Seq analysis.

first: Debra

last: Brunson

first: Cristina

last: Colomer-Winter

first: Ling

last: Lam

first: Jose

last: Lemos


title: CD95/Fas ligand mRNA is toxic to cells through more than one mechanism


title: Synthetic regulatory genomics uncovers enhancer context dependence at the Sox2 locus

city: New York

first: Matthew

last: Maurano

address: 435 East 30th Street

department: Institute for Systems Genetics

institute: NYU Grossman School of Medicine

summary: Sequencing and coverage data produced as part of the Big-IN genome engineering sequence verification pipeline.

overall_design: (1) whole YAC/BAC (payload) sequencing data. (2) Targeted sequencing (Capture-seq) data from mouse embryonic stem cell (mESC) lines engineered to harbor landing pads (LPs) and various payloads at Sox2 locus.

first: Ran

last: Brosh

first: Camila

last: Coelho

first: André

last: Ribeiro-dos-Santos

first: Megan

last: Hogan

first: Hannah

last: Ashe

first: Gwen

last: Ellis

first: Nicolette

last: Somogyi

first: Raquel

last: Ordoñez

first: Raven

last: Luther

first: Emily

last: Huang

first: Jef

last: Boeke


title: Plasticity in airway smooth muscle differentiation during mouse lung development

city: Princeton

first: Katharine

last: Goodwin

state: NJ

address: Hoyt Laboratory, 25 William St

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

summary: Smooth muscle differentiation has been proposed to sculpt airway epithelial branches in mammalian lungs. Serum response factor (SRF) acts with its cofactor myocardin to promote the expression of contractile smooth muscle markers. However, smooth muscle cells exhibit a variety of phenotypes beyond contractile that are independent of SRF-myocardin-induced transcription. To determine whether airway smooth muscle exhibits phenotypic plasticity during embryonic development, we deleted Srf from the pulmonary mesenchyme. Srf-mutant lungs branch normally, and the mesenchyme exhibits normal cytoskeletal features and patterning. scRNA-seq revealed an Srf-null smooth muscle cluster wrapping the airways of mutant lungs that lacks contractile smooth muscle markers but retains many features of control smooth muscle. Srf-null airway smooth muscle exhibits a synthetic phenotype, compared to the contractile phenotype of wildtype airway smooth muscle. Our findings reveal plasticity in mesenchymal differentiation during lung development and demonstrate that a synthetic smooth muscle layer is sufficient for airway branching morphogenesis.

overall_design: Mouse embryos with genotypes Tbx4-rtTA;tet-O-Cre;Srf-flox/flox and littermate Srf-flox/flox controls were collected at E12.5. Lungs were dissected and dissociated in dispase. Individual cells were processed in the 10x Genomics Chromium system.

first: Celeste

last: Nelson


title: PA up-regulates the KEGG pathway ‘Lysosome’  in cultured PTECs

city: Suita

first: Jun

last: Nakamura

state: Osaka

address: Box D11, 2-2 Yamada-oka

department: Nephrology

institute: the University of Osaka Graduate School of Medicine

summary: Obesity is a major risk factor for end-stage kidney disease. We previously found that lysosomal dysfunction and impaired autophagic flux contribute to lipotoxicity in experimental and human obesity-related kidney disease. However, the transcriptional regulators involved in renal lipotoxicity is largely unknown. Here we found palmitic acid (PA) strongly promoted dephosphorylation and nuclear translocation of transcription factor EB (TFEB), which was mediated by inhibition of MTORC1 (mechanistic target of rapamycin kinase complex 1) via Rag GTPase inactivation. PA-induced TFEB nuclear translocation was, however, gradually decreased over a longer treatment. We then investigated the role of TFEB in the pathogenesis of obesity-related kidney disease. High-fat diet (HFD)-fed proximal tubular epithelial cell (PTEC)-specific Tfeb-deficient mice exhibited greater phospholipid accumulation in enlarged lysosomes, which manifested as multilamellar bodies (MLBs). Activated TFEB mediated lysosomal exocytosis of phospholipids, to help PTECs to reduce MLBs/vacuole accumulation. Furthermore, HFD-fed PTEC-specific Tfeb-deficient mice showed autophagic stagnation and exacerbated injury upon renal ischemia-reperfusion. Finally, higher BMI was associated with increased vacuolation and decreased nuclear TFEB in the proximal tubule of CKD patients and we herein proposed a new disease concept “obesity-related tubulopathy (ORT)”. In conclusion, these results indicate a critical role of TFEB-mediated lysosomal exocytosis in counteracting renal lipotoxicity.

overall_design: mRNA profiles of cultured PTECs during BSA or PA treatment for six hours

first: Takeshi

last: Yamamoto


title: Genes regulated by DEG-35, a dual degrader of IKZF2 and CK1A in AML cells

status: Public on Jan 16 2023

city: new york

first: Michael

last: Kharas

address: 417 68th street

department: Molecular Pharmacology Program

institute: Mamorial Sloan Kettering Cancer Center

summary: To investigate the genes regulated in MOLM-13 cells treated with DMSO or DEG-35, a dual degrader of IKZF2 and CK1A in AML cells

overall_design: Gene expression profiling analysis of RNA-seq data for MOLM-13 cells treated with DMSO or 50nM DEG-35 for 24hr

first: Sun

last: Park


title: Interleukin 17 B is protective in colitis by regulating colonic mononuclear phagocytes in mice [BMDM]

city: Chengdu

first: Yun

last: Shi

address: No 37, Guoxuexiang

institute: West China Hospital, Sichuan University

summary: IL17B protected mice from dextran sodium sulfate (DSS)-induced colitis since IL17B deficiency resulted in severe DSS-induced colitis with exaggerated weight loss, shorter colon length, and elevated proinflammatory cytokine production in colon. For mechanism study, we use single cell transcriptional analyses of CD45+ immune cells in colonic lamina propria to detect the effect of IL-17B on colon LP immune cells in colitis. We found increased inflammatory macrophages infiltration in colon lamina propria after colitis induction expressing inflammatory cytokines such as S100a9, S100a8, Tnf, which was confirmed by real-time PCR and flow cytometry. Reconstitute of Il17b-/- mice with recombinant IL17B alleviated the severity of DSS-induced colitis. IL17B treatment also inhibited LPS-induced inflammation in bone marrow derived macrophage and in mice. These data indicate that IL17B exerting its inhibitory role in inflammation by regulating inflammatory macrophage response. In view of the protective effect of IL17B on DSS-induced colitis and LPS-induced inflammation, IL17B might represent a novel potential therapeutic approach to treat the inflammation.

overall_design: Macrophages were derived from bone marrow with M-CSF. BMDM were stimulated with IL17B  to detect the effect of IL-17B.

first: Xiaomin

last: Zhang

first: Chuanying

last: Xiang


title: ChIP-seq analysis of Purpureocillium lavendulum H3K14 modification cultured on PDB or PDB+Ammonium Sulfate

city: Kunming

first: Lian-Ming

last: Liang

state: Yunnan

address: No.2 North Cuihu Road

institute: Yunnan University

overall_design: 1×108 fungal conidia were inoculated into PDB and PDB+(NH4)2SO4 liquid media, respectively, on 9-cm plates with 20mL medium in each plate, stationary cultured at 28°C for five days. After immunoprecipitation with H3K14ac antibody, the input and IP precipitated DNA was used for next generation sequencing on an Novaseq6000 Illumina platform.

first: Ping

last: Tang


title: COMPASS-degron cells

city: Beijing

first: Hua

last: Wang

address: 38 Xueyuan Rd

institute: Peking University


title: COVID-19 Suceptibility Florida

first: Cuong

last: Nguyen

state: Florida

address: 2015 SW 16th Ave

summary: To reveal genetic determinants of susceptibility to COVID-19 severity in the population and further explore potential immune-related factors, we performed a genome-wide association study on 284 confirmed COVID-19 patients (cases) and 95 healthy individuals (controls). We compared cases and controls of European (EUR) ancestry and African American (AFR) ancestry separately. To further exploring the linkage between HLA and COVID-19 severity, we applied fine-mapping analysis to dissect the HLA association with mild and severe cases.

overall_design: 284 confirmed COVID-19 samples were obtained from Boca Biolistics (Pompano Beach, FL) and CTSI Biorepository at the University of Florida (Gainesville, FL). The median age of the patients was 44.7 years (range: 3-94 years). Patients had positive test results for SARS-CoV-2 by RT-PCR from nasopharyngeal swabs or tracheal aspirates. 89 healthy individuals with negative PCR tests for SARS-CoV-2 viral infection were included as controls. The median age of the control group was 60 years (range: 0‐101 years). After the exclusion of samples during quality control, the final case-control data sets comprised 254 patients and 80 control participants.

first: Yiran

last: Shen

first: Bhuwan

last: Khatri

first: Santosh

last: Rananaware

first: Piyush

last: Jain

first: Christopher

last: Lessard

middle: Q


title: Interleukin 17 B is protective in colitis by regulating colonic mononuclear phagocytes in mice

overall_design: Two WT and two Il17b-/- mice were fed with 2.5% (w/v) dextran sulfate sodium (DSS) for 6 days. The colon tissue was harvested from animals at day 9 and lamina proria cells were isolated to process single cell suspension for scRNAseq on BD Rhapsody system.


title: Primary ChAdOx1 vaccination does not reactivate pre-existing, cross-reactive immunity

city: Berlin

first: Karsten

last: Jürchott

address: Luisenstraße

department: Rahel Hirsch Center

country: Germany

institute: BIH at Charité

summary: Currently available COVID-19 vaccines include inactivated virus, live attenuated virus, mRNA-based, viral vectored and adjuvanted protein-subunit-based vaccines. All of them contain the spike glycoprotein as the main immunogen and result in reduced disease severity upon SARS-CoV-2 infection. While we and others have shown that mRNA-based vaccination reactivates pre-existing, cross-reactive immunity, the effect of vector vaccines in this regard is unknown. Here, we studied cellular and humoral responses in heterologous adenovirus-vector-based ChAdOx1 nCOV-19 (AZ; Vaxzeria, AstraZeneca) and mRNA-based BNT162b2 (BNT; Comirnaty, BioNTech/Pfizer) vaccination and compared it to a homologous BNT vaccination regimen. AZ primary vaccination did not lead to measurable reactivation of cross-reactive cellular and humoral immunity compared to BNT primary vaccination. Moreover, humoral immunity induced by primary vaccination with AZ displayed differences in linear spike peptide epitope coverage and a lack of anti-S2 IgG antibodies. Contrary to primary AZ vaccination, secondary vaccination with BNT reactivated pre-existing, cross-reactive immunity, comparable to homologous primary and secondary mRNA vaccination. While induced anti-S1 IgG antibody titers were higher after heterologous vaccination, induced CD4+ T cell responses were highest in homologous vaccinated. However, the overall TCR repertoire breadth was comparable between heterologous AZ-BNT-vaccinated and homologous BNT-BNT-vaccinated individuals, matching TCR repertoire breadths after SARS-CoV-2 infection, too. The reasons why AZ and BNT primary vaccination elicits different immune response patterns to essentially the same antigen, and the associated benefits and risks, need further investigation to inform vaccine and vaccination schedule development.

overall_design: PBMC of three BNT-BNT-BNT-vaccinated, three AZ-BNT-BNT vaccinated, and three BNT-BNT-infected donors were stimulated with 1 µg/ml S-I peptide pool in the presence of purified anti-CD28 (clone CD28.2, BD Biosciences) and anti-CD40 (clone HB14, Miltenyi Biotec). CD4+ T cells were enriched by MACS (Miltenyi Biotec) and CD40L+4-1BB+ CD4+ T cells FACS sorted using an FACS Melody (BD).

first: Larissa

last: Henze

first: Lucie

last: Loyal

first: Andreas

last: Thiel


title: Effect of IL7 and/or Flt3L expression of CAR T cells on gene expression and TCR diversity in EGFRvIII heterogenous mouse glioblastoma with 0.5 Gy irradiation

city: Durham

first: Ravi

last: Bellamkonda

state: NC

address: 308 Research Dr.

department: Biomedical Engineering

institute: Duke University

summary:
We investigated the effect of intratumoral delivery of IL7 and/or Flt3L expressing CAR T cells in 50% EGFRvIII positive CT2A tumors treated with 0.5 Gy irradiation.
We performed gene expression analysis of the tumor bearing hemisphere using RNA-seq.

overall_design: Female C56BL/6 mice were given 50% CT2A-huEGFRvIII-Luc and 50% CT2A-GFP-Luc cells intracranially on day 0. On day 6, mice underwent total body irradiation and the following day 2x10^6 CAR T cells were intracranially delivered with or without poly(I:C) (pIC). Gene expression was assessed on day 14.

first: Sheridan

last: Swan


title: ASPSCR1-TFE3 orchestrates the angiogenic program of alveolar soft part sarcoma

city: Tokyo

first: Takuro

last: Nakamura

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

institute: Japanese Foundation for Cancer Research

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

overall_design: Refer to individual Series


title: An adverse tumor-protective effect of IDO1 inhibition

city: Amsterdam

first: Joleen

last: Traets

address: Plesmanlaan 121

institute: Netherlands Cancer Institute

summary: Indoleamine 2, 3-dioxygenase 1 (IDO1) is a metabolic enzyme catalyzing the conversion of the essential amino acid tryptophan to kynurenine. It is induced by IFNg and its expression is linked to poor prognosis across various cancer types. T cells are particularly sensitive to IDO1-dependent tryptophan deprivation in the tumor microenvironment, leading to tumor immune resistance. Therefore, IDO1 inhibitors, such as epacadostat, have been developed, aiming to restore T cell antitumor activity. However, a recent phase III trial assessing the clinical benefit of epacadostat with the PD-1 antibody pembrolizumab in melanoma failed. This prompted us to study the role of IDO1, and the effect of its inhibition, on tumor cells that are under IFNg treatment and T cell attack. We showed that IDO1-mediated tryptophan depletion contributes to the anti-tumor effect of CD8 T cells. Thus, while epacadostat expectedly replenished tryptophan -the desired effect-, this led to adverse protection of melanoma cells from T cell-derived IFNg. RNA sequencing and ribosome profiling of (patient-derived) melanoma cell lines revealed that IFNg caused general protein translation shut down, which was reversed by IDO1 inhibition. Impaired translation was accompanied by an amino acid deprivation-dependent stress response driving ATF4high and MITFlow transcriptomic signatures, which was also observed in melanoma patient tumors. Downregulation of MITF in tumors and PDX- derived cell lines upon treatment was strongly predictive of response to response, to  checkpoint blockade-treatment and IFNg, respectively. Conversely, MITF restoration in cultured tumor cells caused T cell resistance. These results highlight the critical role of tryptophan in the melanoma response to T cell-derived IFNg, uncovering an unexpected negative consequence of IDO1 inhibition.

overall_design: 16 low-passage (less than 30) Patient-derived cell lines were plated at day 0 and treated with recombinant human IFNg (Preprotech) at 10ng/mL at day 1 and harvested after 24 hours (day2).

first: J

last: Kenski

first: X

last: Huang

first: D

last: Peeper


title: IL-4/IL-13 Inhibitors for Atopic Dermatitis Induce Psoriatic Rash Transcriptionally Close to Pustular Psoriasis

city: Paris

first: Chloé

last: Grolleau

address: 1 avenue Claude Vellefaux

department: Hopital saint Louis

country: France

institute: INSERM U1342, eq 16

summary:
Dupilumab is an antibody targeting the IL-4/IL-13 receptors indicated for atopic dermatitis patients, but paradoxical psoriasis-like reactions have been reported under treatment.
To understand the pathogenesis of DI-Pso, we performed a gene expression profiling study using microarray on skin biopsies of dupilumab-induced psoriasis, plaque psoriasis and AD compared with healthy control skin.

overall_design: We selected paraffined-embebded skin biopsies of dupilumab-induced-psoriasis (n=7), plaque psoriasis (n=4), atopic dermatitis (n=4) and 4 healthy control skin samples for RNA extraction and hybridization on Affymetrix microarrays.

first: Hélène

last: Le-Buanec

first: Antonio

last: Alberdi


title: ASPSCR1-TFE3 orchestrates the angiogenic program of alveolar soft part sarcoma [ChIP-seq]

summary: Alveolar soft part sarcoma (ASPS) is a rare soft part malignancy affecting adolescents and young adult. ASPS is characterized by its alveolar structure consisting of tumor cells and highly integrated vascular network, and its high metastatic potential indicates the importance of the prominent angiogenic activity of ASPS. Here we find that the expression of ASPSCR1-TFE3, the fusion transcription factor causatively associated with ASPS, is dispensable for in vitro tumor maintenance but required for in vivo tumor development via angiogenesis. ASPSCR1-TFE3 frequently associates with active enhancers including super-enhancers (SE) upon its DNA binding, and the loss of its expression induces dynamic modification of SE distribution related to genes belonging to the angiogenesis pathway. Using epigenomic CRISPR/dCas9 screening, we identify Pdgfb, Rab27a, Sytl2, and Vwf as critical target genes associated with reduced enhancer activities due to the ASPSCR1-TFE3 loss. ASPSCR1-TFE3 thus orchestrates higher ordered angiogenesis via enhanced intracellular trafficking of angiogenic factors.

overall_design: Mouse ASPS was induced by expressing ASPSCR1-TFE3 in embryonic mesenchymal cells followed by subcutaneous transplantation into nude mice. Subcutaneous tumors were subjected to cell culture. Human ASPS cell lines were used for gene knockdown experiments.

first: Miwa

last: Tanaka


title: A truncated and catalytically inactive isoform of KDM5B histone demethylase accumulates in breast cancer cells and regulates H3K4 tri-methylation and gene expression

status: Public on Jan 15 2023

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

summary: KDM5B histone demethylase is overexpressed in many cancers and plays an ambivalent role in oncogenesis, depending on the specific context. This ambivalence could be explained by the expression of KDM5B protein isoforms with diverse functional roles, which could be present at different levels in various cancer cell lines. We show here that one of these isoforms, namely KDM5B-NTT, accumulates in breast cancer cell lines due to remarkable protein stability relative to the canonical PLU-1 isoform, which shows a much faster turnover. This isoform is the truncated and catalytically inactive product of an mRNA with a transcription start site downstream of the PLU-1 isoform, and the consequent usage of an alternative ATG for translation initiation. It also differs from the PLU-1 transcript in the inclusion of an additional exon (exon-6), previously attributed to other putative isoforms. Overexpression of this isoform in MCF7 cells leads to an increase in bulk H3K4 methylation and induces derepression of a gene cluster, including the tumor suppressor Cav1 and several genes involved in the interferon-alpha and -gamma response. We discuss the relevance of this finding considering the hypothesis that KDM5B may possess regulatory roles independent of its catalytic activity.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MCF7 and MDA-MB-231 cells over-expressing the KDM5B-NTT vs control samples.

first: Elena

last: Di Nisio

first: Rodolfo

last: Negri


title: MNRR1 is a driver of ovarian cancer progression

city: Detroit

first: Gil

middle: G.

last: Mor

state: Michigan

address: 275 E. Hancock

department: C.S. Mott Center for Human Growth and Development

institute: Wayne State University School of Medicine

summary: This study was conducted to investigate the role of MNRR1 in regulating the extracellular matrix and focal adhesion modulating ovarian cancer metastasis

overall_design: Gene expression profiles were compared between MNRR1-knockout (KO) versus Wild Type (WT) Triple Knockout (TKO) mouse ovarian cancer cell lines

first: Hussein

last: Chehade

first: Neeraja

last: Purandare

first: Alexandra

last: Fox

first: Nicholas

last: Adzibolosu

first: Shawn

last: Jayee

first: Aryan

last: Singh

first: Roslyn

last: Tedja

first: Radhika

last: Gogoi

first: Siddesh

last: Aras

first: Lawrence

middle: I

last: Grossman

first: Ayesha

middle: B

last: Alvero


title: Igh and Igk loci use different folding principles for V gene recombination due to distinct chromosomal architectures of pro-B and pre-B cells

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

institute: IMP

summary: Extended loop extrusion across the immunoglobulin heavy-chain (Igh) locus facilitates VH-DJH recombination in pro-B cells by aligning the VH and DJH segments for RAG-mediated cleavage. This cohesin-mediated process, resulting in global changes of the chromosome architecture in pro-B cells, depends on a 3-fold downregulation of the cohesin-release factor Wapl by Pax5-induced repression of the Wapl promoter. Here, we demonstrate that chromatin looping and VK-JK recombination at the Igk locus was insensitive to a 3-fold Wapl increase in pre-B cells. Given the equally low Wapl mRNA levels in pro-B and pre-B cells, the Wapl protein was unexpectedly expressed at a 2.2-fold higher level in pre-B cells compared to pro-B cells, which resulted in a distinct chromosomal architecture with normalized loop sizes in pre-B cells. High-resolution analysis of the Igk locus identified multiple internal loops, which likely juxtapose VK and JK elements to facilitate VK-JK recombination. The higher Wapl expression in Igm-transgenic pre-B cells prevented extended loop extrusion at the Igh locus, leading to recombination of only the 6 most 3’ proximal VH genes and to allelic exclusion of all other VH genes in pre-B cells. Hence, the different chromosomal architectures in pro-B and pre-B cells forced the Igh and Igk loci to assume distinct folding principles to undergo V gene recombination.

overall_design:
VDJ-Seq: Comparison of VDJ arrangements in the Igk and Igh loci. The comparison is done between wildtype (Wapl(+/+)) and mutant (Wapl(deltaP1,2/deltaP1,2) for pro-B and pre-B samples, Immature B cells (Igh locus) samples are not used for a direct comparison. Hi-C-Seq:  Comparison of wildtype (Wapl(+/+) and mutant (Wapl(deltaP1,2/deltaP1,2)) samples, the Igh(B1.8hi/+) Rag2(-/-) is not used for a direct comparison. MicroC-Seq: Comparison of wildtype (Rag2(-/-)) with mutant (Igh(B1.8hi/+) Rag2(-/-)) samples. ChIP-Seq: this sample is used as phasing data for the Eigen value decomposition of Micro-C data.

Please note that the GSM6427700 records have been updated with additional processed data file on Mar 28, 2023.

first: Louisa

last: Hill

first: Markus

last: Jaritz

first: Gordana

last: Wutz

first: Hiromi

last: Tagoh

first: Lesly

last: Calderon

first: Jan-Michael

last: Peters

first: Anton

last: Goloborodko

first: Meinrad

last: Busslinger


title: The transcriptional co-activator Yap1 promotes adult hippocampal neural stem cell activation

city: Biberach an der Riss

first: Gregorio

last: Alanis-Lobato

address: Birkendorfer Str 65

department: Global Computational Biology and Digital Sciences

institute: Boehringer Ingelheim Pharma

summary: Adult radial glia-like cells (RGLs) residing in the subgranular zone (SGZ) of the dentate gyrus (DG) are finely regulated to control the generation of new neurons. Quiescence is essential for the long-term maintenance of the RGL pool. Intrinsic factors as well as extrinsic niche signals orchestrate the balance between RGL quiescence and activation, but the mechanisms are still not completely understood.   Yap1, a core factor of Hippo signaling, is very important for the proliferation of stem cells of various organs and species, such as intestinal stem cells of the mouse and neural stem cells in Drosophila brain. Here I addressed the role of Yap1 in adult hippocampal neurogenesis by gain- and loss-of-function studies. I found that the expression of Yap1 was enriched in adult RGLs, but was undetectable in other cell types such as neurons and cells of the oligodendroglial lineage. Through the analysis of conditional knock-out of Yap1 in adult RGLs and their lineage, I found that fewer RGLs became activated while a significantly higher proportion of RGLs remained in the quiescent state. Conversely, overexpression of constitutively active mutant variant of Yap1 (Yap1 5SA) induced the proliferation of quiescent RGLs in vitro and in vivo. This effect was dependent on functional interaction with the TEA Domain Transcription Factor (TEAD). Pharmacological blocking the interaction between endogenous Yap1 and TEAD by verteporfin reduced the rate of proliferation of neural progenitors in vitro, which indicates a physiological role of Yap1-TEAD interaction in regulating the transition between quiescence and activation. Interestingly, constitutive expression of Yap1 5SA in RGLs blocked adult neurogenesis and retained the cells in a progenitor-like (Sox2+) state. To further explore the molecular mechanisms of Yap1 in regulating the activation of quiescent RGLs, single-cell RNA sequencing analysis was performed at 3 and 7 days following Yap1 5SA overexpression. Yap1 5SA overexpressing cells exhibited increased signature of active NSCs but also displayed distinct features such as epithelial-to-mesenchymal transition (EMT). Importantly, we found that Catenin Beta 1 (CTNNB1) was upregulated suggesting a potential involvement of Wnt signaling in the proliferative effect of Yap1 5SA overexpression in adult NSCs. In sum, this work  provides compelling evidence for regulation of the balance between activation and quiescence of adult hippocampal RGLs by Yap1.

overall_design: Examination of role of Yap1 in adult neural stem cells at 3 days and 7 days after Yap1 overexpression

first: Wenqiang

last: Fan


title: A DLG1-ARHGAP31-CDC42 axis regulates the Wnt response in intestinal stem cells

city: San Francisco

first: Tomas

last: Wald

address: 513 Parnassus Ave

institute: UCSF

summary: A central factor in maintenance of tissue integrity is the response of stem cells to variations in the levels of niche signals. In the gut, intestinal stem cells (ISCs) depend on Wnt ligands for self-renewal and proliferation. Transient increases in Wnt signaling promote regeneration after injury or in inflammatory bowel diseases, whereas constitutive activation of this pathway leads to colorectal cancer. Here, we report that Discs large 1 (Dlg1) is dispensable for polarity and cellular turnover during intestinal homeostasis; however, Dlg1 is required for ISC survival in the context of increased Wnt signaling. RNA sequencing (RNAseq) and genetic mouse models demonstrated that DLG1 regulates the cellular response to increased canonical Wnt signaling. This occurs via transcriptional regulation of Arhgap31, a GTPase-activating protein that deactivates CDC42, an effector of the non-canonical Wnt pathway. These findings reveal a DLG1-ARHGAP31-CDC42 axis that is essential for the ISC response to fluctuating niche Wnt signaling.

overall_design: Identification of differentially expressed genes in Dlg1 conditional knock out intestinal stem cells compared to wildtype controls at two days and 14 days after tamoxifen injection.

first: David

last: Castillo-Azofeifa

first: Walter

last: Eckalbar

first: Ophir

last: Klein


title: Itaconate regulates Th17/Treg cell balance via metabolic and epigenetic reprogramming

city: Sapporo

first: Kuniyuki

last: Aso

address: Kita 14, Nishi 5, Kita-ku

institute: Hokkaido university

summary: An imbalance of T helper (Th17) cells and regulatory T (Treg) cells contributes to the pathogenesis of autoimmune diseases. The endogenous metabolite itaconate (ITA) is a regulator of macrophages; however, its role in T cells regulation is unclear. Here, we show that ITA inhibited Th17 cell differentiation and promoted Treg cell differentiation via metabolic and epigenetic reprogramming. Mechanistically, ITA suppressed glycolysis and mitochondrial respiration in Th17 and Treg-polarizing T cells. In Th17 cells, the S-adenosyl-L-methionine/ S-adenosylhomocysteine ratio was decreased following ITA administration in vitro, subsequently altering the epigenetic status. Further, ITA inhibited RORγt binding at the Il17a promoter, resulting in reduced IL-17A expression. In Treg cells, ITA reduced 2-hydroxyglutarate levels, which suppressed Foxp3 expression. The adoptive transfer of ITA-treated Th17-polarizing T cells ameliorated experimental autoimmune encephalomyelitis. Collectively, these results indicate that ITA serves as a crucial metabolic regulator for Th17/Treg cell balance and a potential therapeutic agent against autoimmune diseases.

overall_design: To understand the mechanisms underlying ITA-dependent modulation of T cell differentiation, we performed RNA sequencing (RNA-seq) using Th0, Th17, and Treg cells in the presence or abscence ITA treatment (n=3, respectively).

first: Michihito

last: Kono

first: Masatoshi

last: Kanda

first: Yuki

last: Kudo

first: Kodai

last: Sakiyama

first: Ryo

last: Hisada

first: Kohei

last: Karino

first: Yusho

last: Ueda

first: Daigo

last: Nakazawa

first: Yuichiro

last: Fujieda

first: Masaru

last: Kato

first: Olga

last: Amengual

first: Tatsuya

last: Atsumi


title: TGFbR signaling in squamous epithelial cells plays a fundamental role in controlling tissue specific allergic inflammation

city: Bethesda

first: Karen

last: Laky

address: 9000 Rockville Pike

department: NIAID

institute: NIH

summary: Allergic diseases are becoming a global health crisis. Individuals harboring loss-of-function variants in transforming growth factor beta receptor (TGFbR) have an increased prevalence of allergic disease, but the mechanisms responsible are poorly understood. We demonstrate that mice harboring a variant identified in patients spontaneously develop disease that clinically, immunologically, histologically, and transcriptionally recapitulates eosinophilic esophagitis, a condition characterized by allergic inflammation in the esophagus. Diminished TGFbR signaling impairs epithelial cell maturation, resulting in local expression of inflammatory mediators that drive accumulation and activation of eosinophils, mast cells, T cells, and innate lymphoid cells. Our work reveals a fundamental, non-redundant, cell-intrinsic role for TGFbR signaling in epithelial cells needed to maintain immune homeostasis and prevent allergic inflammation, independent of barrier function or adaptive immune tolerance. Moreover, we demonstrate that epithelial dysfunction alone is sufficient to initiate and perpetuate allergic inflammation, which has implications for the prevention and treatment of allergic diseases.

overall_design: 18 total samples were mRNA sequenced, with 9 WT, and 9 TGFBR1M318R mutant mice.

first: Jessica

middle: L

last: Kinard

first: Jenny

last: Li

first: Ian

last: Moore

first: Justin

last: Lack

first: Elizabeth

last: Fischer

first: Jurai

last: Kabat

first: Mahnaz

last: Minai

first: Rachel

last: Latanich

first: Nicholas

last: Zachos

first: Ajinkya

last: Limkar

first: Helene

middle: F

last: Rosenberg

first: Robert

middle: W

last: Thompson

first: Thomas

last: Wynn

first: Harry

last: Dietz

first: Anthony

last: Guerrerio

first: Pamela

last: Frischmeyer-Guerrerio


title: CTLA-4 inhibition facilitates follicular T-B cell interaction and the production of tumor-specific antibodies

status: Public on Jan 14 2023

city: Seoul

first: AREUM

last: JO

address: 222, Banpo-daero, Seocho-gu

country: South Korea

institute: The Catholic University of KOREA

summary: Immune checkpoint inhibitors (ICIs) induce activation and expansion of cytotoxic T cells. To depict a comprehensive immune cell landscape reshaped by the CTLA-4 checkpoint inhibitor, we performed single-cell RNA sequencing in a mouse syngeneic tumor transplant model. After CTLA-4 inhibition, tumor regression was accompanied by massive immune cell expansion, especially in T and B cells. We found that B cells in tumor transplant represented follicular, germinal center, and plasma B cells, some of which shared identical B cell receptor clonotypes and possessed tumor reactivity. Furthermore, the posttreatment tumor contained a tertiary lymphoid structure with intermingled T and B cells. These data suggest germinal center formation within the tumor mass and in situ differentiation of tumor-specific plasma cells. Taken together, our data provide a panoramic view of the immune microenvironment after CTLA-4 inhibition and suggest a role for tumor-specific B cells in anti-tumor immunity.

overall_design: BALB/c mice were inoculated subcutaneously with 2 × 105 CT26 cells. Mice were injected intraperitoneally with 100㎍ anti-CTLA-4(9H10) or phosphate-buffered solution (PBS) on days 5, 8, and 11 after tumor inoculation. Mice were sacrificed 13 days after tumor inoculation. Tissue specimens were analyzed by immunofluorescence tissue staining, scRNAseq(10x genemics).

first: Hae-Ock

last: Lee

first: Areum

last: Jo


title: Dysregulation of the chromatin environment leads to differential alternative splicing as a mechanism of disease in a human model of autism spectrum disorder

city: Providence

first: Calvin

last: Leung

state: RI

address: 70 Ship Street

department: MCB

institute: Brown University

summary: Autism spectrum disorder (ASD) affects 1 in 44 children. Chromatin regulatory proteins are overrepresented among genes that contain high risk variants in ASD. Disruption of the chromatin environment leads to widespread dysregulation of gene expression, which is traditionally thought of as a mechanism of disease pathogenesis associated with ASD. Alternatively, alterations in chromatin dynamics could also lead to dysregulation of alternative splicing, which is understudied as a mechanism of ASD pathogenesis. The anticonvulsant valproic acid (VPA) is a well-known environmental risk factor for ASD that acts as a class I histone deacetylase (HDAC) inhibitor. However, the precise molecular mechanisms underlying defects in human neuronal development associated with exposure to VPA are understudied. To dissect how VPA exposure and subsequent chromatin hyperacetylation influence molecular signatures involved in ASD pathogenesis, we conducted RNA sequencing (RNA-seq) in human cortical neurons that were treated with VPA. We observed that differentially expressed genes (DEGs) were enriched for mRNA splicing, mRNA processing, histone modification, and metabolism related gene sets. Furthermore, we observed widespread increase in the number and the type of alternative splicing events. Analysis of differential transcript usage (DTU) showed that exposure to VPA induces extensive alterations in transcript isoform usage across neurodevelopmentally important genes. Finally, we find that DEGs and genes that display DTU overlap with known ASD-risk genes. Together, these findings suggest that, in addition to differential gene expression, changes in alternative splicing correlated with alterations in the chromatin environment could act as an additional mechanism of disease in ASD.

overall_design: Bulk RNA-sequencing of human iPSC-derived neurons treated with valproic acid (VPA).

first: Shoshana

last: Rosenzweig

first: Brian

last: Yoon

middle: A

last: Marinelli

first: Ethan

last: Hollingsworth

first: Abbie

last: Maguire

first: Mara

middle: H

last: Cowen

first: Michael

last: Schmidt

first: Jaime

last: Imitola

first: Ece

last: Gamsiz Uzun

first: Sofia

last: Lizarraga


title: GM-free immortalization and high yield production of cultured chicken [RNA-seq]

city: Jerusalem

first: Avner

last: Ehrlich

address: Silberman 3-512, Edmond J. Safra Campus (Givat Ram)

department: Bioengineering

country: Israel

institute: The Hebrew University of Jerusalem

summary: Global demand for animal protein is expected to double by 2050 at a time when resource-intensive livestock production is reaching peak capacity. Cellular agriculture offers an opportunity to meet the increasing demand for animal products, but the technology is currently limited by the genetic stability of immortalized cells, low culture yields, and high production costs. Here we demonstrate the spontaneous immortalization and long-term genetic stability of fibroblasts derived from the indigenous Israeli Baladi and the commercial Broiler Ross chicken breeds. Cells were adapted for growth as single-cell suspensions in animal-component free culture medium reaching cell densities of over 100x10^6 cells/mL in ATF perfusion presenting a production yield of over 33% w/v. We show that soy phosphatidylcholine, a major component of lecithin, activates PPAR, driving adipogenesis in immortalized chicken fibroblasts. Harvesting cultured adipocytes and blending them with high moisture extruded soy protein formed cultured chicken strips in which mouth feel and texture were supported by a blend of animal and plant proteins while aroma and flavor were driven by cultured animal fat. Visual and sensory analysis graded the product 4.5 out of 5.0, with over 85% percent of the study group said they are extremely likely to replace their food choice with this cultured meat product. The ability to create immortalized lines without genetic modification and the high yield process for cultured meat production presents an important steppingstone in the market realization of cultured meat.

overall_design: 3 biological replicates of primary and immortalized chicken fibroblasts from 2 different species (Broiler Ross 308; Israeli Baladi)

first: Yaakov

last: Nahmias

first: Merav

last: Cohen

first: Laura

last: Pasitka


title: Coordinated histone variant H2A.Z eviction and H3.3 deposition control plant thermomorphogenesis [RNA-seq III]

status: Public on Jan 13 2023

first: Fengyue

last: Zhao

address: No. 1 West Beichen Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology Chinese Academy of Sciences

summary: Plants can sense temperature changes and adjust their development and morphology accordingly in a process called thermomorphogenesis. This phenotypic plasticity implies complex mechanisms regulating gene expression reprogramming in response to environmental alteration. Histone variants contribute to the chromatin dynamics and transcriptional control, yet how their deposition/eviction modulates transcriptional changes induced by environmental cues remains elusive. In Arabidopsis thaliana, temperature elevation-induced transcriptional activation at thermo-responsive genes entails the chromatin eviction of a histone variant H2A.Z by INO80, which is recruited to these loci via interacting with a key thermomorphogenesis regulator PHYTOCHROME-INTERACTING FACTOR 4 (PIF4). Here, we show that both INO80 and the deposition chaperones of another histone variant H3.3 associate with EARLY FLOWERING7 (ELF7), a critical component of the transcription elongation factor polymerase-associated factor 1 complex (PAF1c). H3.3 promotes thermomorphogenesis and the high temperature-enhanced RNA Pol II transcription at PIF4 targets, and it is broadly required for the H2A.Z removal-induced gene activation. Reciprocally, INO80 and ELF7 regulate H3.3 deposition, and are necessary for the high temperature-induced H3.3 enrichment at PIF4 targets. Our findings demonstrate close coordination between H2A.Z eviction and H3.3 deposition in gene activation induced by high temperature, and pinpoint the importance of histone variants dynamics in transcriptional regulation.

overall_design: Transcriptome profiles were examined by RNA-seq in WT (Col), h3.3kd, h2a.z and h3.3kd;h2a.z at 27°C

first: Danhua

last: Jiang


title: Dual-omics reveals the different roles of α1 and β-adrenergic receptors in acute sympathetic stress-induced cardiac inflammation

first: Di

last: Zhang

address: No.5 YiHeYuan Road, Haidian District

institute: Peking University

summary: Sympathetic overactivation under strong acute stresses triggers acute cardiovascular events including myocardial infarction (MI), sudden cardiac death, and stress cardiomyopathy. α1-ARs and β-ARs, two dominant subtypes of adrenergic receptors in the heart, play a significant role in the physiological and pathologic regulation of these processes. However, little is known about the functional similarities and differences between α1- and β-ARs activated temporal responses in stress-induced cardiac pathology. In this work, we systematically compared the cardiac temporal genome-wide profiles of acute α1-AR and β-AR activation in the mice model by integrating transcriptome and proteome. We found that α1- and β-AR activations induced sustained and transient inflammatory gene expression, respectively. Particularly, the overactivation of α1-AR but not β-AR led to neutrophil infiltration at 1 day, which was closely associated with the up-regulation of chemokines, activation of NF-κB pathway, and sustained inflammatory response. Furthermore, there are more metabolic disorders under α1-AR overactivation compared with β-AR overactivation. These findings provide a new therapeutic strategy that besides using β-blocker as soon as possible, blocking α1-AR within one day should also be considered in the treatment of acute stress associated cardiovascular diseases.

overall_design: RNA-seq of Mouse heart tissue under α1- and β-AR overactivations.

first: Jimin

last: Wu

first: Mingming

first: Rui

last: Wang

first: Gang

last: Xue

first: Jiqi

last: Shao

first: Youyi

first: Erdan

last: Dong

first: Zhiyuan

last: Li

first: Han

last: Xiao


title: Assessment of the impact of the IL23R R381Q variant in terms of IL-23-sensitive transcript induction

first: Gaspard

last: Kerner

address: 25-28 rue du docteur roux

institute: Institut Pasteur

summary: We stimulated T-cell blasts from IL23R R381Q homozygotes (n = 2), healthy controls homozygous for the ancestral allele (n = 9), homozygous individuals for TYK2 P1104A (n = 2) that selectively impairs responses to IL-23, and one patient each with autosomal recessive, complete TYK2 or IL-12Rb1 deficiency with IL-12, IL-23, IL-1b, and IL-1b plus IL-23 for 6 hours and performed RNA-sequencing. We used IL-1b as an IL-23-sensitizing agent as previously reported. We found that while T-cell blasts from IL23R R381Q homozygotes respond normally to IL-12 and IL-1b, their response to IL-23 and to IL-23 plus IL-1b is impaired

overall_design: Comparative gene expression profiling analysis of RNA-seq data for T-cell blasts of individuals with the IL23R R381Q derived allele and its ancestral complementary allele at the same genomic position

first: Philippot

last: Quentin

first: Bohlen

last: Jonathan


title: Distinct reward processing by subregions of the nucleus accumbens

city: Guangzhou

first: Jincan

last: Ke

state: Guangdong

address: 190 KaiYuan Road, Huangpu District

department: Center for Cell Lineage and Development

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

summary: The nucleus accumbens (NAc) plays an important role in motivation and reward processing. Recent studies suggest that different NAc subnuclei differentially contribute to reward-related behaviors. However, how reward is encoded in individual NAc neurons remains unclear. Using in vivo single-cell resolution calcium imaging, we discovered diverse patterns of reward encoding in the medial and lateral shell subdivision of the NAc (NAcMed and NAcLat, respectively). Reward consumption increases NAcLat activity but decreases NAcMed activity, albeit with high variability among neurons. The heterogeneity in reward encoding could be attributed to differences in their synaptic inputs and transcriptional profiles. Specific optogenetic activation of Nts-positive neurons in the NAcLat promotes positive reinforcement, while activation of Cartpt-positive neurons in the NAcMed induces behaviour aversion. Collectively, our study reveals organizational and transcriptional differences in NAc subregions, and provides a framework for future dissection of NAc subregions in physiological and pathological conditions.

overall_design: Expression profiling by high throughput sequencing

first: Gaowei

last: Chen

first: ShiShi

last: Lai

first: Guo

last: Bao

first: Xiaogao

last: Meng

first: Shanshan

last: Lu

first: Xiaocong

first: Hua

last: Xu

first: Fengyi

first: Yu

first: Fang

first: Guoqiang

last: Bi

first: Guangdun

last: Peng

first: Kuikui

last: Zhou

first: Yingjie

last: Zhu


title: Coordinated histone variant H2A.Z eviction and H3.3 deposition control plant thermomorphogenesis [HTR5-GFP ChIP-seq]

city: Beijing

first: Fengyue

last: Zhao

overall_design: HTR5-GFP enrichment was examined by ChIP-seq in WT (Col), elf7-3 and ino80-5 at 21°C

first: Danhua

last: Jiang


title: Coordinated histone variant H2A.Z eviction and H3.3 deposition control plant thermomorphogenesis [RNA-seq II]

overall_design: Transcriptome profiles were examined by RNA-seq in WT (Col), h3.3kd, h2a.z and h3.3kd;h2a.z at 21°C