title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [BICCN-11H_200730]

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

type: Methylation profiling by high throughput sequencing

summary: Illustrating the cellular architecture of the mammalian brain is critical to understanding its diverse functions and complex animal behaviors. With support from NIMH and NINDS as part of the BRAIN Initiative Cell Census Network (BICCN), the Center for Epigenomics of the Mouse Brain Atlas (CEMBA) applied single nucleus methylation sequencing in 117 brain funtional regions across the whole adult male P56 C57BL/6J mouse brain. In each major brain regions, we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster. We integrate the single cell methylome with single cell gene expression and chromatin accessibility profiles from the same brain region to further identify potential enhancers and their corresponding genes for several neuronal cell types. By brain region spacial comparisons, we found spatial specificity among excitatory neuronal clusters within the same cortical layer. We identify brain-region-specific transcription factors that may regulate cortical region development of excitatory neurons. These data define the landscape of cell type and spatial heterogeneity in the mouse brain and the underlining regulatory epigenomic basis.

overall_design: Apply snmC-seq3 to 117 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (11H).

first: Hanqing

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

first: Julia

last: Osteen

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Rosa

last: Castanon

last: Nery

first: Peter

last: Berube

first: Huaming

last: Chen

first: Michael

last: Nunn

first: Jesse

last: Dixon

first: M

last: Behrens


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [BICCN-11H_200813]

status: Public on Apr 26 2023

middle: R

state: CA

country: USA

last: Liu

middle: K

middle: G

middle: M


title: Cyclic GMP-AMP synthase and interferon activation diminish MEF2C-mediated cognitive resilience II

city: New York

first: Li

last: Gan

state: NY

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

type: Expression profiling by high throughput sequencing

summary: Here we report that activation of cyclic GMP-AMP synthase (cGAS) diminishes cognitive resilience by decreasing the neuronal transcriptional network of myocyte enhancer factor 2c (MEF2C) through type I interferon (IFN-I) signaling. Pathogenic tau activates cGAS and IFN-I responses in microglia, in part mediated by cytosolic leakage of mitochondrial DNA. Genetic ablation of cGAS in tauopathy mice diminished microglial IFN-I response, preserved synapse integrity and plasticity, and protected against cognitive impairment without affecting the pathogenic tau load.  cGAS ablation enhanced, while activation of IFN-I downregulated, neuronal MEF2C expression network linked with cognitive resilience in AD.

overall_design: Droplet-based single nuclear RNA sequencing of mouse hippocampus of WT, cgas+/- and cgas-/- with and without the presence of P301S Tau.

first: Joe

middle: C

last: Udeochu

first: Sadaf

last: Amin

first: Yige

last: Huang

last: Fan

first: Eileen

last: Torres

first: Gillian

last: Carling

first: Bangyan

first: Hugo

last: McGurran

first: Guillermo

last: Coronas-Samano

first: Grant

last: Kauwe

first: Gergey

middle: A

last: Mousa

first: Man

middle: Y

last: Wong

first: Pearly

last: Ye

first: Ravi

last: Nagiri

first: Iris

last: Lo

last: Holtzman

first: Carlo

last: Corona

first: Allan

last: Yarahmady

first: Sue-Ann

last: Mok

middle: T

last: Gill

first: Ravikiran

last: Raju

first: Shiaoching

last: Gong

first: Wenjie

last: Luo

first: Mingrui

last: Zhao

first: Tara

middle: E

last: Tracy

first: Rajiv

last: Ratan

first: Li-Huei

last: Tsai

first: Subhash

last: Sinha


title: Cyclic GMP-AMP synthase and interferon activation diminish MEF2C-mediated cognitive resilience I

first: Li

last: Gan

summary: Analysis of differentially expressed genes (DEGs) revealed a striking upregulation of interferon genes in P301S, compared to non-transgenic hippocampi, and enrichment of transcription factor motifs of interferon-response factors (IRFs) and interferon-sensitive response elements (ISREs). Cgas deletion reduced the induction of a subset of tau-stimulated inflammatory and cytokine expression including interferon stimulated genes such as Stat1, Ddx60, Isg20, Rnf213, Parp12, Ifi35, and Sp100. Thus, microglial cGAS promotes IFN-I expression in response to tau.

overall_design: To characterize gene expression changes associated with tauopathy, we performed bulk RNA sequencing of P301S tau transgenic and non-transgenic hippocampi (8–9 months) . To determine if cGAS mediates tau-induced interferon responses, we treated Cgas-/- and Cgas+/+ primary microglia with tau fibrils or herring testis DNA (HT-DNA) and performed RNA sequencing.

first: Joe

last: Udeochu

first: Sadaf

last: Amin

first: Yige

last: Huang

last: Fan

first: Eileen

last: Torres

first: Gillian

last: Carling

first: Bangyan

last: Liu

first: Hugo

last: McGurran

first: Guillermo

last: Coronas-Samano

first: Grant

last: Kauwe

last: Mousa

last: Wong

first: Julia

first: Michael


title: Synthetic TLR7/8 agonist bottlebrush prodrugs enable tumor-selective immune stimulation following systemic administration

city: Cambridge

first: Yuzhou

middle: Evelyn

last: Tong

state: MA

address: 77 Massachusetts Ave

institute: Massachusetts Institute of Technology

summary: We used single cell RNA sequencing to understand how the tumor microenvironment changes with TLR7/8 agonist bottlebrush

overall_design: MC38 tumors were dissociated for scRNA-seq

first: Sachin

last: Bhagchandani

first: Michelle

middle: L

last: Ramseier

first: Alex

last: Shalek


title: Global analysis of binding sites of SF3B1 by CLIP-seq

city: Seoul

first: Young-Soo

last: Kwon

address: Nungdongro 209, Gwangjingu

department: Department of Bioscience and Biotechnology

country: South Korea

institute: Sejong University

summary: SF3B1 is one of shared components of U2 and U12 snRNPs that are required for splicing of U2-type and U12-type introns, respectively. Interestingly, recurrent somatic mutations have been identified in the spliceosome components in human cancer. By using CLIP-seq for SF3B1, binding sites in human embryonic stem cells were determined. The most prominent binidng sites were at 3' splice sites on pre-mRNA. Interestingly, 5' and 3' ends of introns spliced out  were enriched by CLIP.

overall_design: CLIP-seq of endogenous SF3B1 by using anti-SF3B1-antibody (Bethyl, Catalog # A300-996A) and a rabbit IgG control.


title: Open chromatin, HIF binding and mRNA expression analysis in podocytes (ChIP-Seq).

city: Aachen

first: René

last: Krüger

address: Pauwelsstraße 20

department: Institute for Stem Cell Biology

country: Germany

institute: RWTH Aachen University Medical School

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The course of Apolipoprotein 1 (APOL1) nephropathy is extremely heterogeneous and shaped by systemic factors such as the interferon response. However, additional environmental factors operating in a second-hit model have been less well defined. We identified an active regulatory DNA-element upstream of APOL1 that interacted with Hypoxia inducible factors (HIF). ATAC-seq, ChIP-seq and RNA-seq analysis were performed in podocytes to analyse the effect of HIF stabilization on the expression of pathogenic APOL1 variants. This study links the regulation of the kidney-disease gene APOL1 with the HIF-pathway in podocytes and renal tubular cells.

overall_design: This study consists of ATAC-seq, ChIP-seq and RNA-seq samples from a podocytes cell line (M. Saleem) in biological duplicates (n=2).

first: Johannes

last: Schödel

first: Steffen

last: Grampp


title: Open chromatin, HIF binding and mRNA expression analysis in podocytes (ATAC-Seq).


title: Mechanisms of Action of Fu Fang Gang Liu Liquid in Treating Condyloma Acuminatum by Network Pharmacology and Experimental Validation

city: Beijing

first: zhu

last: fan

state: State...

address: No.5, Beixiange, Xicheng District, Beijing,

country: China

institute: China Academy of Chinese Medical Sciences Guang'anmen Hospital

summary: Condyloma acuminatum is a sexually transmitted disease characterized by the anomalous proliferation of keratinocytes caused by human papillomavirus (HPV) infection. Fu Fang Gang Liu liquid (FFGL) is an effective external prescription to treat condyloma acuminatum, but its potential molecular mechanism is still unclear. This study aimed to identify the major active ingredients and prospective targets of FFGL by using network pharmacology, molecular docking, and transcriptomics, and validating it experimentally. Network pharmacology analysis found that FFGL contains a total of 78 active compounds, from which 610 compound-related targets were screened. Among them, 59 compound-related targets overlapped with CA targets and were considered as targets with potential therapeutic effects. Protein-protein network analysis showed that AKT serine/threonine kinase 1 was the potential therapeutic target. To further confirm this result we performed RNA-seq assays on HPV18+ cells after FFGL intervention, and conducted enrichment analyses on the screened differentially expressed genes. Enrichment analyses results indicated that the phosphatidylinositol 3-kinase/protein kinase B (PI3K/Akt) pathway may be a key pathway for FFGL to function. Further in vitro experiments revealed that FFGL significantly inhibited the activity of HPV18+ cells and reduced PI3K and Akt protein levels. Rescue experiment indicated that the reduction in cell viability caused by FFGL was partially restored after the use of activators of the PI3K/Akt pathway. We further explored the active components of FFCL for the treatment of condyloma acuminatum and screened two active compounds, periplogenin and periplocymarin. Molecular docking showed that these two compounds have good binding activity to AKT1.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from Fu Fang Gang Liu Liquid-treated HeLa cells

first: Fan

last: Zhu

first: Wang

last: Shuxin

first: Xu

last: Chenchen

first: Yang

last: Jiao

first: Cui

last: Bingnan


title: CXCR4/miR-1910-5p/MMRN2 Axis is Involved in Corneal Neovascularization by Affecting Vascular Permeability

city: Guangzhou

first: Keming

last: Yu

address: No.7 Jinsui Road

institute: State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University

type: Non-coding RNA profiling by high throughput sequencing

summary: To further investigate the molecular functions of CXCR4 in angiogenesis, we knocked out CXCR4 in HCE-T-cell lines, which were further undergo hypoxic treatment, using the CRISPR‒Cas9 system.

overall_design: We then performed miRNA expression profiling analysis using data obtained from miRNA-seq of 2 different cells (wild-type cells and CXCR4-KO cells).

first: Xiao

last: Wang

first: Zedu

last: Cui

first: Xi

last: Chen

first: Qian

last: Luo

first: Jing

last: Zhuang


title: Open chromatin, HIF binding and mRNA expression analysis in podocytes

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

overall_design: Refer to individual Series


title: MicroRNAs in Peripheral Blood Cell in Nonallergic Childhood Asthma

city: Taipei

first: Jyh-Hong

last: Lee

address: 8 Chung-Shan South Road

country: Taiwan

institute: National Taiwan University Hospital

summary: We aimed to apply microRNA to explore the underlying mechanism of nonallergic childhood asthma

overall_design: Comprehensive miRNA sequencing (RNA-seq) was performed using peripheral blood from 11 nonallergic (NA) and 11 allergic (AA) patients,respectively.


title: Comparison of EVs isolation methods for miRNAs sequencing

city: Madrid

first: Celia

last: Perales

address: C. Darwin, 3

country: Spain

institute: Centro Nacional de Biotecnología

summary: Background & aims:  MicroRNAs (miRNAs) encapsulated in EVs are potential diagnostic and prognostic biomarkers. However, discrepancies on miRNA patterns and their validation are still frequent due to differences in sample origin, EVs isolation, miRNA extraction and sequencing methods. Selecting appropriate EVs isolation methods is therefore a critical step for miRNA-based biomarker discovery. The aim of the present study is to find the most suitable EVs isolation method for miRNAs sequencing adequate for clinical application.  Material & Methods EVs were isolated by Size Exclusion Chromatography (SEC), iodixanol gradients (GRAD) and the combination of both (SEC+GRAD), using the same plasma sample, in triplicate isolation assays. Isolated EVs were characterized and RNA was extracted. Three different protocols for miRNA library preparation were compared (NEBNext, NEXTFlex and SMARTer smRNA-seq) and miRNAs encapsulated on EVs were sequenced using NextSeq 500 system (Illumina). Finally, the yield, abundance and diversity of miRNAs using the three different EVs isolation protocols were analyzed and compared between them.  Results The majority of lipoproteins, total cholesterol and plasma proteins were removed from the EVs-containing fractions by using SEC, GRAD, and SEC+GRAD. SEC method recovered a larger amount of EVs followed by GRAD and SEC+GRAD, while GRAD and SEC+GRAD yielded the purest vesicles. NEBNext was the library preparation kit that showed the highest reproducibility among replicas, higher number of reads corresponding to miRNAs and more different miRNAs, followed by NEXTFlex and SMARTer smRNA-seq. GRAD method showed the highest reproducibility among replicas, a higher number of reads corresponding to miRNAs and more different miRNAs, followed by SEC and SEC+GRAD methods.   Conclusions These results render the GRAD method to isolate EVs as one of the most appropriate to detect miRNAs from Evs.

overall_design: Comparative miRNA abundance of 3 different miRNA preparation kits (NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England BioLabs, Ipswich, MA, USA), NEXTFlex Small RNA-Seq Kit v3 (PerkinElmer, Waltham, MA, USA), and SMARTer smRNA-seq kit (Clontech Laboratories, CA, USA)) and 3 different extracellular vesicles protocols (Size exclusion chromatography (SEC), Isopycnic ultracentrifugation using iodixanol gradients (GRAD), and Combination of SEC and GRAD (SEC+GRAD))

first: Meritxell

last: Llorens-Revull

first: Brenda

last: Martínez-González

first: Josep

last: Quer

first: Juan

middle: I

last: Esteban

first: Gonzalo

last: Núñez-Moreno

first: Pablo

last: Minguez

first: Idoia

last: Burgui

first: Ricardo

last: Ramos-Ruiz

first: María

last: Soria

first: Angie

last: Rico

first: Mar

last: Riveiro

first: Silvia

last: Sauleda

first: Maria

last: Piron

first: Francesc

last: Borràs

first: Francisco-Rodríguez

last: Frías

first: Ariadna

last: Rando

first: Clara

last: Ramírez

last: Camós

first: Esteban

last: Domingo

first: Marta

last: Bes

last: Costafreda


title: Polypropylene microplastics promote metastatic features in human breast cancer

first: Jung-Woong

last: Kim

address: 84 Heuksuk-ro Dongjak-ku

department: Life Science

institute: Chung-Ang University

summary:
we studied the effect that 16.4 µm fragment type polypropylene (PP) MPs, which have an irregular shape and sharp edges and form naturally in the environment, had on breast cancer
PPMP incubation for 24 hours in the MDA-MB-231 cells significantly altered the level of cell cycle-related transcripts in an RNA-seq analysis

overall_design: LM vs LMMP

first: Sungguan

last: Hong

first: Hyun

middle: J

last: Lee


title: Highly efficient and rapid generation of human pluripotent stem cells by chemical reprogramming (WGBS)

first: Yulin

last: Lyu

address: No.5 Yiheyuan Road Haidian District

department: School of Life Sciences

institute: Peking University

summary: We recently demonstrated the chemical reprogramming of human somatic cells to pluripotent stem cells, which provides a fundamentally new approach for cell fate manipulation. However, the utility of this chemical approach is currently hampered by the slow kinetics. Here, by screening for new small-molecule boosters and systematically optimizing the original chemical reprogramming condition, we have established a robust, chemically defined protocol. With this new protocol, the entire chemical reprogramming process is remarkably accelerated, reducing the time needed from ~50 days to a minimum of 16 days. Moreover, this new protocol enables highly reproducible and efficient generation of human pluripotent stem cells from all 17 tested donors with a reprogramming efficiency of up to 31%. Our method provides a unique and powerful strategy for human cell fate manipulation and pluripotent stem cell manufacturing for cell-based therapeutic applications.

overall_design: To characterize human chemically induced pluripotent stem cells (hCiPSCs), hCiPSCs were analyzed and compared to human somatic cells and human embryonic stem cells (hES) by WGBS.

first: Shijia

last: Liuyang

first: Guan

last: Wang

first: Yanglu

first: Huanjing

last: He

first: Jinlin

first: Hongkui

last: Deng


title: 3D spheroid culture to examine adaptive therapy response in invading tumor cells

city: Nijmegen

first: Peter

last: Friedl

address: Geert Groteplein 28

department: Cell Biology

country: Netherlands

institute: RIMLS, Radboudumc

summary: 3D in vitro culture models of cancer cells in extracellular matrix (ECM) have been developed to investigate drug targeting and resistance or, alternatively, mechanisms of invasion, however models allowing analysis of shared pathways mediating invasion and therapy resistance are lacking. To evaluate therapy response associated with cancer cell invasion, we here used 3D invasion culture of tumor spheroids in 3D fibrillar collagen and applied Ethanol-Ethyl cinnamate (EtOH-ECi) based optical clearing to detect both spheroid core and invasion zone by subcellular-resolved 3D microscopy. When subjected to a single dose of irradiation (4 Gy), we detected preferential cell survival in the invasion zone, compared to the spheroid core. By physical separation of core and invasion zone we identified differentially regulated genes between preferentially engaged in invading cells controlling cell division, repair and survival. This imaging-based 3D invasion culture may be useful for analysis of complex therapy-response patterns in cancer cells in drug discovery and invasion-associated resistance development.

overall_design: 50,000 MV3 H2B-GFP spheroids were embedded in collagen I for 3D invasion. Two days after embedding cells from core and invasion zone were enriched by punch biopsy and RNA was isolated for RNAseq.

first: Felix

last: Weiss

first: Cornelia

last: Veelken-Hulsbergen

first: Vince

last: van Reijmersdal

first: Nader

last: Atlasy

first: Henk

last: Stunnenberg


title: Open chromatin, HIF binding and mRNA expression analysis in podocytes (RNA-Seq).

first: René

last: Krüger

first: Johannes

last: Schödel

first: Steffen

last: Grampp


title: Effect of depletion of RBM4 on gene expression of esophageal squamous cell carcinoma cell KYSE150

city: Dalian

first: Wang

last: Yang

address: 9 Lvshun South Rd West Section, Lüshunkou District, Dalian, Liaoning, China

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

summary:
To explore the role of RBM4 in esophageal squamous cell carcinoma cell,we performed high-throughput mRNA sequencing (mRNA-seq) in KYSE150  with stable knockdown of RBM4 by shRNA .
We then performed gene expression profiling analysis using data obtained from RNA-seq of KYSE150 cells,three replicates were sequenced.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from KYSE150 cells infected with lentivirus  pLKO.1-RBM4 sh or with pLKO.1-CTL.

first: Lei

last: Chen

first: Yang


title: Highly efficient and rapid generation of human pluripotent stem cells by chemical reprogramming (RNA-Seq)

first: Yulin

overall_design: To characterize human chemically induced pluripotent stem cells (hCiPSCs), hCiPSCs, human somatic cells and human embryonic stem cells (hES) were analyzed by RNA-seq.

first: Shijia

first: Guan


title: dSLAM-seq of MCMV

city: Wuerzburg

first: Florian

last: Erhard

address: Versbacher Straße 7

institute: Institute of Virology and Immunobiology, University of Wuerzburg

summary: Swiss murine embryonic fibroblasts (NIH-3T3) were infected with wild-type Smith strain mouse cytomegalovirus (MCMV) at a multiplicity of infection (MOI) of 10. Metabolic RNA labelling was performed using 400µM 4sU for one hour prior to cell lysis. Total RNA was isolated using the Trizol protocol and U-to-C conversions were induced by IAA treatment according to the SLAM-seq protocol (Herzog et al., Nature Methods 2017). Sequencing libraries were prepared using the dRNA-seq protocol from the indicated time points of infection as described by Whisnant A.W. et al, Nat. Commun (2020).

overall_design:
MCMV infection was conducted on NIH-3T3 cells at an MOI of 10. Nascent RNA was labelled with 400µM 4sU one hour prior to RNA harvesting. 4sU labelled RNA was subject to alkylation to mediate U to C conversions to track newly synthesized RNA through GRAND-SLAM. Sequencing was conducted for total purified RNA obtained . Two biological replicates were performed for each of the time points: 0,1,2,4,6,12,18,24, 36, 48, 72 hpi. One biological replicate utilised phosphonoacetic acid and cycloheximide pre-treatment
Please note that MCMV_tss.tar.gz contains a list of transcription start sites which are determined based on both dSLAM-seq and cRNA-seq datasets.

first: Manivel

last: Lodha

first: Ihsan

last: Muchsin

first: Christopher

last: Jürges

first: Vanda

last: Lisnic

first: Anne

last: L'hernault

first: Andrzej

last: Rutkowski

first: Bhupesh

last: Prusty

first: Arnhild

last: Grothey

first: Thomas

last: Hennig

first: Andrea

last: Milic

first: Stipan

last: Jonjic

first: Caroline

last: Friedel

first: Lars

last: Dölken


title: cRNA-seq of MCMV

summary: Swiss murine embryonic fibroblasts (NIH-3T3) were infected with wild-type Smith strain mouse cytomegalovirus (MCMV) at a multiplicity of infection (MOI) of 10. Sequencing libraries were prepared using the cRNA-seq protocol from the indicated time points of infection as described by Whisnant A.W. et al, Nat. Commun (2020)

overall_design:
MCMV infection was conducted on NIH-3T3 cells at an MOI of 10. Total RNA was isolated for sequencing using the Trizol protocol. Circularization of RNA was performed as described in Whisnant et al., Nature commun. 2020. This results in a strong enrichment of reads at transcription start sites.  Two biological replicates were performed for each of the time points: 0, 2, 6, 12, 24 and 48 hpi
Please note that MCMV_tss.tar.gz contains a list of transcription start sites which are determined based on both dSLAM-seq and cRNA-seq datasets.


title: RNA helicase DDX5-induced circPHF14 promotes gastric cancer cell progression

city: Changzhi

first: Jia

last: Wang

state: Shanxi

address: Jiefang East Street

department: Immunology

institute: Changzhi Medical College

summary: To identify whether the expression of DDX5 was linked to circular RNAs splicing processes, we transfected AGS cell with FLAG-DDX5 or FLAG-tagged empty vector (negative control, NC), and analyzed the differentially expressed circRNAs

overall_design: Analyzed the differentially expressed circRNAs for transfecting AGS cell with FLAG-DDX5 and FLAG-tagged empty vector (negative control, NC)

first: Qiu

last: Peng


title: Decoding murine cytomegalovirus


title: Single-cell transcriptome of commissural and non-commissural dentate gyrus granule cells

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zurich

summary: Dentate granule cells (GCs) have been characterized as unilaterally projecting neurons within each hippocampus. Using anterograde and retrograde labeling, we identified a unique class, the commissural GCs, which atypically project to the contralateral hippocampus in mice. This data set includes single-cell mRNA sequencing reads from retrogradely-labeled (commmissural) and -non-labeled (non-commissural) GCs from control mice and from mice treated with unilateral intrahippocampal kainic acid microinjections (70 nl, 5 mM; cells were collected two weeks after microinjection); control mice were treated with unilateral intrahippocampal saline microinjections (equal amount to kainic acid; cells were collected two weeks after microinjection). These experiments were performed in adult (2.5-3.5 months old) Rbp4-Cre transgenic mice.

overall_design:
To label contralateral hippocampus-projecting GCs, we injected retroAAV-EGFP into the right (contralateral) ventral hippocampus, and saline or kainic acid together with AAV.cDIO-mCherry (mCherry is to be expressed in GCs in a Cre-dependent manner to visualize the injection site) into the left (ipsilateral) hippocampus of Rbp4-Cre transgenic mice with symmetrical injection coordinates. Two weeks later, patch-RNA-seq was used to sample EGFP-expressing (EGFP+) and EGFP-non-expressing (EGFP-) GCs in the ipsilateral hippocampus, irrespective of their mCherry expression.
Partitioning of the data is as follows (number of sequenced cells / number of cells that passed quality control / number of mice from the cells were collected): (1) saline, EGFP+ cells: 7 / 5 / 3, (2) saline, EGFP- cells: 62 / 57 / 3, (3) kainic acid, EGFP+ cells: 30 / 27 / 9, (4) kainic acid, EGFP- cells: 39 / 36 / 3.

first: Matteo

last: Egger

first: Wenshu

last: Luo

first: David

last: Lukacsovich


title: Modeling cross-talk of RNA modification enzymes reveals tumor microenvironment associated clinical significance and immunotherapy prediction in hepatobiliary malignancy

city: Urumqi

first: Zhang

middle: Qing

last: hua

state: Xinjiang

address: Liudao Bay Street

institute: The Second Affiliated Hospital of Xinjiang Medical University

summary: The purpose of this study is to analysis 41 RNA modification enzymes in 1659 HBM samples from 10 public datasets, and 100 HCC samples from  Zhongshan Hospital of Fudan University (Shanghai, China). we designed an RH score model to predict the clinical prognosis, response to molecular targeted drugs and immunotherapy and transcriptional and posttranscriptional events, thereby providing a novel panel of next-generation sequencing for clinical translation.

overall_design: Transcriptome sequencing,were used to obtain the characteristics of samples.RH_Score was involved in transcriptional regulation and post-transcriptional events in HBM.

first: Feng

last: Qi

last: Li

first: Zhuoran

first: Bin

last: Zhou

first: Biwei

last: Yang

first: Wenxing

last: Qin

first: Jun

last: Zhang


title: 4sU-seq of MCMV

first: Florian

last: Erhard

summary: Swiss murine embryonic fibroblasts (NIH-3T3) were infected with wild-type Smith strain mouse cytomegalovirus (MCMV) at a multiplicity of infection (MOI) of 10. Sequencing libraries were prepared using the 4sU-seq protocol (Dölken et al., RNA 2008 and Rutkowski et al.) from the indicated time points of infection as described in Rutkowski, A.J. et al, Nat. Commun (2015)

overall_design: MCMV infection was conducted on NIH-3T3 cells at an MOI of 10. Nascent RNA was labelled with 200µM 4sU one hour prior to RNA harvesting. 4sU labelled RNA was biotinylated and separated from 'old' RNA using streptavidin-coated magnetic beads (Miltenyi). Sequencing was conducted for both new and total RNA. While rRNA was depleted from total RNA, no rRNA depletion was performed for all 4sU-RNA samples. Two biological replicates were performed for each of the time points: 0,1,2,4,6,12,18,24,48 hpi

first: Manivel

last: Lodha

first: Ihsan

last: Muchsin

first: Christopher

last: Jürges

first: Vanda

last: Lisnic

first: Anne

last: L'hernault

first: Andrzej

last: Rutkowski

first: Bhupesh

last: Prusty

first: Arnhild

last: Grothey

first: Thomas

last: Hennig

first: Andrea

last: Milic


title: Ribosome profiling of MCMV

summary: Swiss murine embryonic fibroblasts (NIH-3T3) were infected with wild-type Smith strain mouse cytomegalovirus (MCMV) at a multiplicity of infection (MOI) of 10. Ribosome profiling was performed at various times during infection with minor modification to the protocol described in Stern-Ginossar N et al., Science 2012. The detailed protocol is described in Rutkowski et al, Nature commun 2015, and Whisnant et al., Nature commun. 2020. Translation start site profiling was performed by culturing cells in presence of Harringtonin or Lactimidomycin for 30 min prior to cell harvest.

overall_design: Ribosome profiling was performed a 0, 2, 6, 12, 24 and 48 h post infection. Translation start site profiling was performed using Harringtonin (2µg/ml for for 30 min) or Lactimidomycin (50µM for 30 min) prior to cell lysis. Two biological replicates were analysed.

first: Stipan

last: Jonjic

first: Caroline

last: Friedel

first: Lars

last: Dölken


title: Activation of immediate early response genes initiates a restorative gene expression program during each arousal from torpor in hibernating 13-lined ground squirrels

city: Aurora

first: Austin

last: Gillen

state: CO

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

summary: RNA-seq libraries were prepared from replicate samples (n=5-6) from six physiolocial groups to capture key changes in circannual hibernation.

overall_design: RNA-seq libraries were prepared from replicate samples (n=5-6) in the adrenal gland from six physiological groups to capture key changes in circannual hibernation.

first: Sandra

last: Martin


title: CBP and Gcn5 drive zygotic genome activation in the Drosophila embryo

city: Freiburg in Breisgau

first: Nicola

last: Iovino

address: Stübeweg 51

institute: MPI of Immunobiology and Epigenetics


title: Effect of depletion of histone acetyltransferases and histone deacetylases on gene expression in Drosophila embryos

summary:
To understand the impact of histone acetyltransferases and histone deacetylases during ZGA (stage 5) and before ZGA (stage 2), maternally deposited mRNAs were specifically targeted and transcriptomes were interrogated in their absence
We then performed  similar experiments in stage 5 embryos upon Gcn5 and Nejire KD, rescued with either a wild type or a catalytic dead version of the HAT

overall_design: RNA-seq

first: Filippo

last: Ciabrelli

first: Leily

last: Rabbani

first: Francesco

last: Cardamone

first: Fides

last: Zenk


title: CBP and Gcn5 drive zygotic genome activation in the Drosophila embryo [CUT&Tag]

summary:
Mapping H3K9ac, H3K18ac and H3K27ac during Drosophila zygotic genome activation
Mapping Gcn5 and Nejire in catalytic wild-type or catalytic dead rescue of Gcn5KD and NejireKD during Drosophila zygotic genome activation

overall_design:
CUT&Tag for the H3K9ac, H3K18ac and H3K27ac marks in control, NejireKD, Gcn5KD and in catalytic wild-type or catalytic dead rescues during Drosophila zygotic genome activation (stage 5, nuclear cycle 14)
CUT&Tag for Gcn5 and Neijere-HA in catalytic wild-type or catalytic dead rescues of Gcn5KD and NejireKD during Drosophila zygotic genome activation (stage 5, nuclear cycle 14)


title: Transcriptome of myelin oligodendrocyte glycoprotein (MOG)-reactive CD4 T cells and control CD4 T cells from draining lymp nodes and spleens of mice during experimental autoimmune encephalomyelitis (EAE)

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

country: France

institute: INRA

summary: MOG-reactive CD4 T cells were isolated from draining lymph nodes (dLN) and spleen of C57BL6/N female mice on day 10 after subcutaneous immunization with MOG(35-55) emulsified in Complete Freund’s adjuvant (CFA). Some mice received the CpG-B-1826 (50 microg; TCCATgACgTTCCTgACgTT; TIB MOLBIOL Syntheselabor GmbH), which was added to the MOG(35-55)/CFA mixture before emulsification. To isolate MOG-reactive CD4 T cells, dLN and spleens were harvested from mice on day 10 post-immunization, and single cell suspensions were re-stimulated for 5 hours using a mixture of MOG(35-55) (20 microg/ml), anti-CD40, anti-CD28, and anti-CD40L-PE (all from a commercial kit – Miltenyi Biotec – cat number 130-093-129). After 5 hours, CD4-positive cells were enriched magnetically by MACS using anti-CD4 microbeads (Miltenyi Biotec GmbH, cat. 130-049-201, clone L3T4), and subsequently subjected to FACS sorting to isolate CD4+CD40L+ and CD4+CD40L- cells after staining with anti-CD4 (clone RM4-5, conjugated to Pacific Blue), including a bin channel for CD8-positive cells (clone 53-6.7) and a marker for staining dead cells (NHPO). Sorted CD4+CD40L+ and CD4+CD40L- cells were then quickly checked for purity and directly lysed in 350 microlitre RLT buffer containing 1% beta-mercaptoethanol (Invitrogen). Purity was >95%. Mice were 6-10 weeks of age at the time of immunization. The goal was to identify genes differentially expressed between MOG-reactive CD4 T cells in mice treated or not with CpG-B, and to characterize the transcriptome of autoreactive CD4 T cells in draining lymph nodes and spleen on day 10 after immunization.

overall_design: The experiments include a total of 15 arrays, each corresponding to a distinct biological sample. There are 3 arrays (3 samples) for CD4+CD40L+ cells from the dLN of control EAE mice. There are 3 arrays (3 samples) for CD4+CD40L+ cells from the dLN of CpG-treated EAE mice. There are 3 arrays (3 samples) for CD4+CD40L+ cells from the spleen of control EAE mice. There are 3 arrays (3 samples) for CD4+CD40L+ cells from the spleen of CpG-treated EAE mice. There are 3 arrays (3 samples) for CD4+CD40L- cells from the dLN of control EAE mice.

first: Simon

last: Fillatreau

first: Ping

last: Shen

first: Luc

last: Jouneau


title: Transcriptome of cells from draining lymph nodes of mice during experimental autoimmune encephalomyelitis (EAE)

summary: Cells were prepared from draining lymph nodes (dLN) from naïve C57BL6/N female mice, as well as from C57BL6/N female mice at day 1 and day 3 after subcutaneous immunization with MOG(35-55) emulsified in Complete Freund’s adjuvant (CFA). Some mice received the CpG-B-1826 (50 microg; TCCATgACgTTCCTgACgTT; TIB MOLBIOL Syntheselabor GmbH), which was added to the MOG(35-55)/CFA mixture before emulsification. Cells from dLN were directly lysed in 350 microlitres RLT buffer containing 1% beta-mercaptoethanol (Invitrogen). Mice were 6-10 weeks of age at the time of immunization. The goal was to identify genes differentially expressed between dLN cells from mice immunized with the classical EAE protocol versus mice immunized with the addition of CpG-B-1826 to the immunization cocktail in order to gain some insights into the immune-modulatory effect of this treatment using an unbiased approach.

overall_design: The experiments include a total of 15 arrays, each corresponding to a distinct biological sample. There are 3 arrays (3 samples) for dLN cells from naïve mice. There are 3 arrays (3 samples) for dLN cells taken from mice on day 1 post-immunization using the classical “control” protocol. There are 3 arrays (3 samples) for dLN cells taken from mice on day 3 post-immunization using the classical “control” protocol. There are 3 arrays (3 samples) for dLN cells taken from mice on day 1 post-immunization using the protocol supplemented by the addition of CpG-B-1826 to the immunization cocktail. There are 3 arrays (3 samples) for dLN cells taken from mice on day 3 post-immunization using the protocol supplemented by the addition of CpG-B-1826 to the immunization cocktail.


title: The RNA demethylase FTO controls m6A marking on SARS-CoV-2 and classifies COVID-19 severity in patients

city: Bruxelles

first: Margot

last: CELERIER

address: 808 Route de Lennik

country: Belgium

institute: ULB

summary: The RNA modification N6-methyladenosine (m6A) plays a key role in the life cycles of several RNA viruses. Whether this applies to SARS-CoV-2 and whether m6A affects the outcome of COVID-19 disease is still poorly explored. Here we report that the RNA demethylase FTO strongly affects both m6A marking of SARS-CoV-2 and COVID-19 severity. By m6A profiling of SARS-CoV-2, we confirmed in infected cultured cells and showed for the first time in vivo in hamsters that the regions encoding TRS_L and the nucleocapsid protein are multiply marked by m6A, preferentially within RRACH motifs that are specific to β-coronaviruses and well conserved across SARS-CoV-2 variants. In cells, downregulation of the m6A demethylase FTO, occurring upon SARS-CoV-2 infection, increased m6A marking of SARS-CoV-2 RNA and slightly promoted viral replication. In COVID-19 patients, a negative correlation was found between FTO expression and both SARS-CoV-2 expression and disease severity. FTO emerged as a classifier of disease severity and hence a potential stratifier of COVID-19 patients.

overall_design: Identification of m6A RNA marks in SARSCOV2 infected Vero76 cell line FTO-depleted through shRNA or controls (scrambled shRNA) using m6A RNA immunoprecipitation and Input controls

first: Lionel

last: Malbec

last: Célérier

first: Martin

last: Bizet

first: Emilie

last: Calonne

first: Pascale

last: Putmans

first: Bouchra

last: Hassabi

first: Rachel

last: Deplus

first: Heike

last: Hofmann-Winkle

first: Leen

last: Delan

first: Bram

last: Boeck

first: Diether

last: Lambrechts

first: Stefan

last: Pöhlmann

first: Jana

last: Jeschke

first: François

last: Fuks


title: Transcriptomics study on HepG2 cells treated with different doses of caffeine for 24 h.

first: Yuan

last: Li

address: 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing

department: Post-translational modification

institute: Beijing Proteome Research Center

summary: With the general adoption of new approach methodologies, the omic-based technologies are of particular importance for chemical hazard characterization owning to the premise that any apical endpoint change indicative of impaired health must be underpinned by some alterations at the omic level. In this work we studied cellular response to caffeine by measuring transcriptomics experiments. The HepG2 cells were treated with 6 doses of caffeine for 24 h. 1 control group was set (0 uM of coumarin). Each group has 3 biological replicates.

overall_design: The HepG2 cells were treated with 6 doses of caffeine for 24 h. 1 control group was set (0 uM of caffeine). Each group has 3 biological replicates (21 samples in total).

last: Xu

first: Kukic

last: Predrag

first: Tao

last: Zuo


title: Transcriptomics study on HepG2 cells treated with different doses of caffeine for 6 h

summary: With the general adoption of new approach methodologies, the omic-based technologies are of particular importance for chemical hazard characterization owning to the premise that any apical endpoint change indicative of impaired health must be underpinned by some alterations at the omic level. In this work we studied cellular response to caffeine by measuring transcriptomics experiments. The HepG2 cells were treated with 6 doses of caffeine for 6 h. 1 control group was set (0 uM of coumarin). Each group has 3 biological replicates.

overall_design: The HepG2 cells were treated with 6 doses of caffeine for 6 h. 1 control group was set (0 uM of coumarin). Each group has 3 biological replicates (21 samples in total).

first: Ping


title: PAT1-type GRAS-domain proteins control regeneration following wounding by transcriptional activation of DOF3.4 driving cell proliferation

city: Ghent

first: Bert

last: De Rybel

address: Technologiepark 71

department: Center for Plant Systems Biology

institute: VIB

summary: Plant roots possess a remarkable regenerative potential owing to the presence of stem cells that constantly generate new tissues. Key molecular mechanisms have been linked to this potential, among which the ETHYLENE RESPONSE FACTOR 115 (ERF115) that plays a predominant role in the activation of regenerative cell divisions. However, the downstream operating molecular machinery driving wound-activated cell divisions is largely unknown. Here, we biochemically and genetically identified the GRAS-domain transcription factor protein SCARECROW-LIKE 5 (SCL5) as an interaction partner of ERF115. Although being non-essential under control growth conditions, SCL5 drives redundantly with the related PAT1 and SCL21 transcription factors the expression of the DNA-BINDING ONE FINGER 3.4 (DOF3;4) transcription factor gene. DOF3.4 expression is wound inducible and ERF115 dependent, and in turn activates D3-type cyclin expression. Accordingly, ectopic DOF3.4 expression drives periclinal cell division, whereas its downstream D3-type cyclins are essential for regeneration. The data highlight the importance of the PAT1-branch of GRAS-domain transcription factors for wound activated regeneration processes and pinpoint the DOF3.4 transcription factor as a key element driving regenerative cell divisions.

overall_design: Three biological replicates of root tips of Col-0 or of the triple mutant scl5 scl21 pat1 treated with 0.5ug/ml bleomycin for 24h were compared with three biological replicates of root tips of Col-0 or of the triple mutant scl5 scl21 pat1 under control conditions.

first: Anchal

last: Bisht

first: Thomas

last: Eekhout

first: Lieven

last: De Veylder


title: Effect of depletion of intestinal TLR4 on gene expression of small intestine

city: 松江区

first: Mei

last: Qixiang

state: 上海市

address: 新松江路650号上海市第一人民医院

institute: 上海市第一人民医院

summary:
To investigate the effect of altered intestinal TLR4 expression on acute pancreatitis, we established intestines‐specific TLR4 KO mice in which TLR4 gene has been knocked down by CRISPR-Cas9
We then performed gene expression profiling analysis using data obtained from RNA-seq of gut of wide type mice（n=3） and TLR4ΔIEC mice（n=3）

overall_design: Comparative gene expression profiling analysis of RNA-seq data for gut of wide type mice (n=3) and TLR4ΔIEC mice (n=3)

first: QiXiang

last: Mei

first: Yang

last: Fu

first: Zehua

last: Huang

first: Yue

last: Zeng


title: ACE2 activator diminazene modulates astrocyte-mediated neuroinflammation via miR-224-5p/NLRP3 pathway and offers neuroprotection in a transgenic mouse model of Alzheimer’s disease

city: Nanjing

first: Rui

last: Duan

address: No.68 Changle road

institute: Nanjing first hospital

summary:
Objective: The protective components ACE2/Ang(1-7)/MasR of the renin-angiotensin system has been verified to play a role in Alzheimer's disease (AD). Our previous study revealed that enhancement of brain ACE2 activity, an important effector of RAS, by diminazene aceturate (DIZE) ameliorated Alzheimer's disease-like neuropathology and attenuated neuroinflammation in the brain of SAMP8 mice. However, the potential molecular mechanisms by which DIZE modulates neuroinflammation in AD remain unclear.
Materials and Methods: APP/PS1 mice were injected intraperitoneally with DIZE (once a day for 30 consecutive days). Cognitive functions, neuronal and synaptic integrity, and inflammation-related markers were assessed by Morris water maze, Nissl staining, Western blot and ELISA, respectively. Since astrocytes played a crucial role in AD-related neuroinflammation whilst miRNAs were reported to participate in modulating inflammatory responses, astrocytes of APP/PS1 mice were then isolated for high-throughput miRNAs sequencing to identify the most differentially expressed miRNA following DIZE treatment. Afterward, the downstream pathway of this miRNA in the anti-inflammatory action of DIZE was investigated using primary astrocytes.
Results: The results showed that DIZE alleviated cognitive impairment and neuronal and synaptic damage in APP/PS1 mice. Simultaneously, DIZE suppressed the secretion of pro-inflammatory cytokines and the expression of NLRP3 inflammasome. Importantly, miR-224-5p was significantly up-regulated in the astrocytes of APP/PS1 mice treated by DIZE, and NLRP3 is one of the targets of miR-224-5p. Upregulation of miR-224-5p inhibited the expression of NLRP3 in Aβ1–42-stimulated cells, whereas miR-224-5p downregulation reversed this effect. Furthermore, the inhibition of miR-224-5p could reverse the inhibitory effect of DIZE on astrocytic NLRP3 inflammasome.
Conclusion: These results firstly suggested that DIZE inhibits astrocyte-mediated neuroinflammation via miR-224-5p/NLRP3 pathway. Moreover, these results reveal the underlying mechanisms by which DIZE inhibits neuroinflammation under AD condition and uncovers the potential of DIZE in AD treatment.

overall_design: Astrocytes miRNA profiles of 8 months old APP/PS1 mice and APP/PS1 mice were treated with DIZE

first: Ying-Dong

last: Zhang

first: Xiao-Jin

last: Sun

last: Deng


title: Alternative splicing and gene expression defects in motorneurons derived from DM1 hiPSCs and MBNL knockouts hiPSCs generated by CRISPR/Cas9.

city: Corbeil-Essonnes

first: MARGOT

last: JARRIGE

address: 28, Rue Henri Desbruères

institute: I-Stem/INSERM U861

summary: Myotonic dystrophy type I (DM1) is the most frequent neuromuscular disease (NMD) in adults and only symptomatic treatments have been proposed to patients. DM1 has long been defined by muscular defects but several studies suggested the involvement of the neuromuscular junction (NMJ). In this aim, our purpose raised the question about the pathological contribution of the motoneurons (MNs) in DM1 physiopathology. By using a micropatterned 96-well plate as a co-culture platform, we generated a functional humanized system in 11 days which associates hiPS-derived MNs and human primary skeletal muscle cells. To focus only on DM1 motoneurons-dependent phenotypes, we generated hybrid systems using wild-type skeletal muscle cells combined with mutated hiPS-derived MNs. In this context, we have identified several alterations affecting synaptic vesicular trafficking, AChR clustering and communication between pre- and post-synaptic compartments. More interestingly, hiPS-derived MNs depleted for MBNL1 and MBNL2 reproduced alterations at the pre- and post-synaptic levels. These experiments suggested that the functional defects associated to MNs can be directly attributed to the MBNL family proteins.  These findings may be clinically relevant to open new therapeutic approaches taking into account the alterations affecting DM1 motoneurons.

overall_design: 12 samples were analyzed with 3 replicates per condition: 3 WT hiPSC-derived motorneurones (control), 3 Myotonic Dystrophy type 1 (DM1) hiPSC-derived motorneurones, 3 MBNL2(-/-) hiPSC-derived motorneurones and 3 MBNL1(-/-); MBNL2(-/-) (DKO) hiPSC-derived motorneurones.

first: Julie

last: Tahraoui-Bories

first: Cécile

last: Martinat

first: Antoine

last: Mérien

first: Margot

last: Jarrige

first: Hélène

last: Polvèche


title: Microarray expression profiling of the spiral ganglion of hearing and deafened rats

city: Iowa City

first: Steven

middle: Haym

last: Green

state: Iowa

address: 143 Biology Building

department: Biology

institute: University of Iowa

summary:
Gene expression profiling of apical and basal halves of the spiral ganglion of hearing and kanamycin-deafened rats at P32 and P60 was performed using microarray analysis.
The data are further described in Rahman MT, Bailey EM, Gansemer BM, Pieper AA, Manak JR, and Green SH. Anti-inflammatory compounds improve spiral ganglion neuron survival after aminoglycoside-induced hair cell loss in rats.

overall_design: Rats were deafened with kanamycin from P8-P16. Cochleae were collected at P32 or P60 and the spiral ganglia isolated and hemisected into apical and basal halves. Gene expression was analyzed by microarray profiling.

first: Muhammad

last: Rahman

first: Erin

last: Bailey

first: Benjamin

last: Gansemer

first: Andrew

last: Pieper

first: John

last: Manak

middle: H


title: LMD-RNAseq of resting chondrocytes and proliferative chondrocytes

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

summary: We investigated the molecular mechanisms that regulate the self-renewal and differentiation of chondroprogenitors by comparing the transcriptome profiles between resting chondrocytes and proliferative chondrocytes

overall_design: Cells in resting and proliferative zones in mouse grwoth plate were captured by LMD. Four biological replicates for each zone were sequenced.

first: Takeshi

last: Oichi

last: Kawasawa

first: Satoru

last: Otsuru

first: Motomi

last: Enomoto-Iwamoto


title: Batf stabilizes Th17 cell development via limiting STAT5 signaling pathway

city: Birmingham

first: Min

last: Gao

state: AL

address: 1900 University Blvd, THT Building Suite #130G

institute: University of Alabama at Birmingham

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

overall_design: Refer to individual Series


title: Batf stabilizes Th17 cell development via limiting STAT5 signaling pathway (RNA-Seq)

summary: Th17 cells secrete IL-17A, IL-17F, IL-21, and IL-22 cytokines that are critical in mediating inflammation and protecting the host from microorganisms infection. The basic leucine zipper transcription factor ATF-like (Batf) contributes to the transcriptional programming of multiple effector T cells, and is required for Th17 cell development. Here, we have interrogated mechanisms by which Batf promotes and stabilizes Th17 cell phenotype. We have shown that in vitro differentiated Th17 cells have increased expression of Th1 and Treg signature genes in the absence of Batf. In addition, Citrobacter rodentium infected Batf-deficient (Batf KO) mice fail to clear the infection, and that is correlated with diminished IL-17A and IL-22 cytokine production and increased Foxp3 and Ifng expression compared to WT mice. We find that Batf sustains Th17 phenotype in long-term culture conditions by suppressing Th1- and Treg-specific gene expression. Mechanistically, we reveal that Batf negatively regulates IL-2-STAT5 signaling and modulates STAT5 binding at the Ifng and Foxp3 gene loci thus suppressing Th1-Treg phenotype in Th17 cell development. Inhibition of STAT5 DNA binding activity in Batf KO Th17 cells was able to repress Ifng and Foxp3 expression compared to control-treated cells. Moreover, STAT5 cooperates with transcription factors Ets1 and Runx1 to mediate epigenetic modification and regulate gene expression. Thus, our study has revealed an essential function of Batf in modulating the IL-2-STAT5 signaling to promote and stabilize Th17 cell development.

overall_design: Naïve CD4+ T cells isolated from spleen/lymph nodes WT and Batf KO mice were actiated under Th17 culture conditions. Cells were rested or re-activated with anti-CD3 for 6 h and used for RNA-seq experiments.

first: Duy

last: Pham

first: Robin

last: Hatton

first: Casey

last: Weaver


title: Expression data from human mesenchymal stem cells (hMSCs) [miRNA]

city: Beijing

first: Yan

last: Zheng

address: 22 Zhongguancun South Avenue, Haidian District

institute: School and Hospital of Stomatology, Peking University

summary:
Mesenchymal stem cells derived from human bone marrow have multi-directional differentiation potential.There are differences in expression of related genes in the process of osteogenesis induction.
We used microarrays to detail the global programme of gene expression underlying osteogenesis and identified distinct classes of up-regulated genes or down-regulated genes during this process.

overall_design: Samples from human mesenchymal stem cells on the 0,7 days of osteogenic induction were for RNA extraction and hybridization on Affymetrix microarrays.


title: Expression data from human mesenchymal stem cells (hMSCs)


title: Batf stabilizes Th17 cell development via limiting STAT5 signaling pathway (ChIP-Seq)

overall_design: Naïve CD4+ T cells isolated from spleen/lymph nodes WT and Batf KO mice were actiated under Th17 culture conditions. Cells were harvested on day 5 and used for ChIP-seq experiments


title: Methylation Diet and Lifestyle

city: Montreal

first: David

last: Cheishvili

state: Quebec

address: 3655 Sir William Osler

country: Canada

institute: McGill

type: Methylation profiling by genome tiling array

summary: Epigenome analysis of 18 subjects and 20 controls, before, midpoint, and after a change in diet, exercise, and other lifestyle modifications

overall_design: Bisulphite converted DNA from the 38 samples were hybridized to the Illumina Epic 850K Human Methylation Beadchip

first: Kara

last: Fitzgerald

first: Ryan

last: Bradley


title: Expression data from human mesenchymal stem cells (hMSCs) [circRNA]

overall_design:
Samples from human mesenchymal stem cells on the 0,7 days of osteogenic induction were for RNA extraction and hybridization on Affymetrix microarrays.
The  human mesenchymal stem cells were obtained from Cyagen Biosciences Inc., and the catalog number is HUXMA-01001.


title: FOXD1 is associated with poor outcome and maintains tumor-promoting enhancer-gene programs in basal-like breast cancer [RNA-seq]

status: Public on Apr 25 2023

city: Tokyo

first: Kohei

last: Kumegawa

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

country: Japan

institute: Japanese Foundation for Cancer Research

summary: Breast cancer biology varies markedly among patients. Basal-like breast cancer is one of the most challenging subtypes to treat because it lacks effective therapeutic targets. Despite numerous studies on potential targetable molecules in this subtype, few targets have shown promise. However, the present study revealed that FOXD1, a transcription factor that functions in both normal development and malignancy, is associated with poor prognosis in basal-like breast cancer. We analyzed publicly available RNA sequencing data and conducted FOXD1-knockdown experiments, finding that FOXD1 maintains gene expression programs that contribute to tumor progression. We first conducted survival analysis of patients grouped via a Gaussian mixture model based on gene expression in basal-like tumors, finding that FOXD1 is a prognostic factor specific to this subtype. Furthermore, our RNA sequencing and chromatin immunoprecipitation sequencing experiments on the basal-like breast cancer cell lines BT549 and Hs578T with FOXD1 knockdown revealed that FOXD1 regulates enhancer-gene programs related to tumor progression. These findings suggest that FOXD1 plays an important role in basal-like breast cancer progression and may represent a promising therapeutic target.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BT549 and Hs578T and their KD derivatives (siFOXD1).

first: Liying

last: Yang

first: Kenichi

last: Miyata

first: Reo

last: Maruyama


title: RIG-I is an intracellular checkpoint that limits CD8+ T-cell antitumor immunity

city: zhuhai

first: zhang

last: yuncong

state: guangdong

address: 79 kangning road

institute: Jinan University

summary: RIG-I is a pattern recognition receptor involved in innate immunity, but its role in adaptive immunity remains unclear. Here, we demonstrate that RIG-I is upregulated in tumor infiltrating CD8+ T cells, where it functions as an intracellular checkpoint to negatively regulate CD8+ T cell function and limit antitumor immunity. Mechanically, up-regulation of RIG-I in CD8+ T cells is induced by retinoic acid (RA), a metabolite of vitamin A in TME, and direct inhibits the AKT/glycolysis signaling pathway. In addition, deletion of RIG-I enhances the efficacy of adoptively transferred T cells against solid tumors and inhibition of RIG-I enhances the response to PD-1 blockade. Our findings identify RIG-I as an intracellular checkpoint and a potential target for alleviating inhibitory constraints on T cells in cancer immunotherapy, either alone or in combination with immune checkpoint blockade.

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

first: Xiaobing

last: Duan

first: Jiali

last: Hu

first: Yuncong

last: Zhang

first: Xian-Yang

last: Li

first: Ligong

last: Lu


title: Development and validation of a genomic nomogram based on a ceRNA network for comprehensive analysis of obstructive sleep apnea

city: Zhanjiang

first: Junfen

last: Chen

address: NO.12,Minyou Road

institute: The Second Affiliated Hospital of Guangdong Medical University

summary: Some ceRNA associated with lncRNA have been considered as possible diagnostic and therapeutic biomarkers for obstructive sleep apnea (OSA). We intend to identify the potential hub genes for the development of OSA, which will provide a foundation for the study of the molecular mechanism underlying OSA and for the diagnosis and treatment of OSA.We collected plasma samples from OSA patients and healthy controls for the detection of ceRNA using a chip. Based on the differential expression of lncRNA, we identified the target genes of miRNA that bind to lncRNAs. We then constructed lncRNA-related ceRNA networks, performed functional enrichment analysis and protein-protein interaction analysis, and performed internal and external validation of the expression levels of stable hub genes. Then, we conducted LASSO regression analysis on the stable hub genes, selected relatively significant genes to construct a simple and easy-to-use nomogram, validated the nomogram, and constructed the core ceRNA sub-network of key genes.We successfully identified 282 DElncRNAs and 380 DEmRNAs through differential analysis, and we constructed an OSA-related ceRNA network consisting of 292 miRNA-lncRNAs and 41 miRNA-mRNAs. Through PPI and hub gene selection, we obtained 7 additional robust hub genes, CCND2, WT1, E2F2, IRF1, BAZ2A, LAMC1, and DAB2. Using LASSO regression analysis, we created a nomogram with four predictors (CCND2, WT1, E2F2, and IRF1), and its area under the curve (AUC) is 1. Finally, we constructed a core ceRNA sub-network composed of 74 miRNA-lncRNA and 7 miRNA-mRNA nodes.Our study provides a new foundation for elucidating the molecular mechanism of lncRNA in OSA and for diagnosing and treating OSA.

overall_design: In our study, we included 6 OSA patients and 3 healthy subjects, with 3 of them serving as the normal group , 3 obese OSA patients serving as the training cohort, and 3 non-obese OSA patients serving as the internal validation cohort.

first: Wang

last: Liu

first: Xishi

last: Sun

first: Wei

last: Lei

last: Cheng


title: Genomic DNA copy number alterations of radiation-induced lung adenocarcinomas in mice

city: Chiba

first: Kazuhiro

last: DAINO

address: 4-9-1 Anagawa, Inage-ku

institute: National Institutes for Quantum and Radiological Science and Technology

type: Genome variation profiling by genome tiling array

summary: To investigate DNA copy number changes in mouse lung cancers induced by ionizing radiation.

overall_design: DNA copy number changes in radiation-induced mouse lung adenocarcinomas were analyzed using array-CGH microarray.

first: Kenshi

last: Suzuki

first: Shunsuke

last: Yamazaki

first: Ken-Ichi

last: Iwata

last: Daino

first: Shizuko

last: Kakinuma


title: Effect of adenosine treatment on HAP1 cells with a knockout of MTHFD1

city: Vienna

first: Stefan

last: Kubicek

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary: Folate metabolism provides the building blocks of many classes of biomolecules including purine nucleotides, thymidylate, serine and methionine and is an important target of antimetabolite drugs. A central enzyme in the pathway is the trifunctional MTHFD1, that catalyzes the interconversion of folates by its formyltetrahydrofolate synthetase and methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase domains. Here, we employ large-scale chemical and genome-wide genetic screens to investigate the chemical and genetic dependencies caused by MTHFD1 loss-of-function and uncover a central role of the enzyme in balancing the response to extracellular adenosine. We show that adenosine is essential in MTHFD1KO cells, where adenine-containing compounds counter AMPK activation and increase proliferation in a PARP8, ATF7 and PML-dependent manner. In contrast, adenosine supplementation causes strong toxicity in patient-derived MTHFD1-derived cells harboring dehydrogenase/cyclohydrolase domain mutations. This response, mediated by replication stress and activation of the DNA damage response, is dependent on the nucleotide salvage enzyme HRPT1 and on NUDT5, an enzyme involved in nuclear ATP generation. Our findings suggest an evolutionary rationale for integrating three distinct enzymatic activities within the single MTHFD1 protein and propose the application of dehydrogenase/cyclohydrolase inhibitors in tumors located in an adenosine-rich microenvironment.

overall_design: RNAseq samples were performed in at least duplicates. All experiments contain respective control samples.

first: Jung

last: Lin

first: Luna

middle: D

last: di Durazzo

first: Pisanu

last: Buphamalai

first: Marton

last: Siklos

first: Jakob

middle: W

last: Genger

first: Gerald

last: Hofstaetter

first: Anna

last: Koren

first: Kathrin

last: Runggatscher

first: Bettina

last: Guertl

first: D

middle: S

last: Froese

first: David

last: Rosenblatt

first: J

last: Hannich

first: Kristaps

last: Klavins

first: Andreas

last: Bregthaler

first: Joerg

last: Menche

first: Sara

last: Sdelci


title: Exceptionally rare IDH1-mutant adult medulloblastoma with concurrent GNAS mutation revealed by in vivo magnetic resonance spectroscopy and deep sequencing

city: Rome

first: Evelina

last: Miele

address: Piazza di Sant'Onofrio 4

department: Oncoematologia

country: Italy

institute: Ospedale Pediatrico Bambino Gesù

summary: Medulloblastoma (MB) is the most common malignant brain tumor occurring in childhood and rarely found in adult. Based on transcriptome profile MB are currently classified into four major molecular groups reflecting a considerable biological heterogeneity: WNT-activated, SHH-activated, group 3 and group 4. Recently, DNA methylation profiling allowed the identification of additional subgroups within the four major molecular groups associated with different clinic-pathological and molecular features. Isocitrate Dehydrogenase-1 (IDH1) mutations have been described in several tumours, including gliomas, while in MB are exceptionally reported and not routinely investigated. By mean of magnetic resonance spectroscopy (MRS) we unequivocally assessed the presence the oncometabolite D-2-Hydroxyglutarate (2HG), a marker of IDH1 and IDH2 mutation, in a case of adult MB. Immunophenotypical work-up and methylation profiling assigned the diagnosis of MB, subclass SHH-A, and molecular testing revealed the presence of the non-canonical somatic IDH1(p.R132C) mutation and an additional GNAS mutation, also exceptionally described in MB. To our knowledge this is the first reported case of MB harboring both mutations together. Of note, tumour exhibited a heterogeneous phenotype with a tumour component displaying glial differentiation, with robust GFAP expression, and a component with conventional MB features and selective presence of GNAS mutation, suggesting coexistence of two different major tumour clones. These findings draw attention to the need of a deeper genetic characterization of MB in order to get insights into their biology and improve stratification and clinical management of the patients. Moreover, reported data underling the importance of performing MRS for the identification of IDH mutations in non-glial tumours. The use of throughput molecular profiling analysis and advanced medical imaging technology will certainly increase the frequency with which rare tumour entities will be identified. Whether they have any particular therapeutic implications or prognostic relevance requires further investigations.

overall_design: Tumor case report


title: E2F transcription factor-1 modulatesglutamine metabolism in transformed cells

city: Lausanne

first: Lluis

last: Fajas

address: UNIL Sorge

institute: UNIL

summary:
To investigate the impact of E2F1 loss on glutamine metabolism we isolated mouse embryonic fibroblasts from E2f1-wildtype (wt) and E2f1-knockout (ko) mice
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different treatment conditions (standard growth media vs media containing glutamine but depleted of glucose ).

overall_design: Primary mouse embryonic fibroblasts (MEFs) were previously derived from E2f1-wt and E2f1-ko mice (B6;129S4- E2f1tm1 Meg/J) and SV40-immortalized. MEFs were cultivated with DMEM without glucose, glutamine, phenol red, and sodium pyruvate (A14430-01, Thermo Fisher Scientific) supplemented with 10% dialyzed and filtered FBS (26-400-044, Thermo Fisher Scientific), and either 25 mM glucose (G8769, Sigma-Aldrich) and 4 mM glutamine (25030-024, Thermo Fisher Scientific) or only 4 mM glutamine for 16 hours.

first: Katharina

last: Huber

first: René

last: Dreos

first: Viviane

last: Praz

first: Julien

last: Marquis

first: Johann

last: Weber

first: Hannes

last: Richter


title: Transcriptional signatures of heroin intake and relapse throughout the brain reward circuitry in male mice

city: New York

first: Molly

last: Estill

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

summary: Identifying changes in gene expression throughout the brain reward system induced across various conditions of heroin self-administration in mice as a model of opioid use disorder

overall_design:
Comparative gene expression profiling using bulk RNA-seq from brain tissue following experimental procedures:
S24: 15d saline intravenous self-administration, 24h withdrawal
H24: 15d heroin intravenous self-administration, 24h withdrawal
SS: 15d saline intravenous self-administration, 30d withdrawal, saline challenge + 2h drug-seeking test
SH: 15d saline intravenous self-administration, 30d withdrawal, heroin challenge + 2h drug-seeking test
HS: 15d heroin intravenous self-administration, 30d withdrawal, saline challenge + 2h drug-seeking test
HH: 15d heroin intravenous self-administration, 30d withdrawal, heroin challenge + 2h drug-seeking test

first: Caleb

last: Browne

first: Rita

last: Futamura

first: Angélica

last: Minier-Toribio

first: Emily

last: Hicks

first: Aarthi

last: Ramakrishnan

first: Freddyson

last: Martínez-Rivera

first: Arthur

last: Godino

first: Eric

last: Parise

last: Torres-Berrío

first: Ashley

last: Cunningham

first: Peter

last: Hamilton

first: Deena

last: Walker

first: Laura

last: Huckins

first: Yasmin

last: Hurd

first: Li

last: Shen

last: Nestler


title: Guadecitabine increases response to combined anti-CTLA-4 and anti-PD-1 treatment in mouse melanoma in vivo by controlling the responses of T-cells, myeloid derived suppressor cells and NK cells

city: Bari

first: Fabio

last: Sallustio

state: Bari

address: Piazza G. Cesare N°11

institute: University of Bari

summary: The combination of PD-1 and CTLA-4 blockade has determined an improved overall survival (OS) rate for malignant melanoma at 3 years of 58% as compared to ipilimumab alone. Immune checkpoint blockers (ICB) limit the tumor’s immune escape yet only for approximately a third of all tumors and, in most cases, for a limited amount of time. Several approaches to overcome resistance to ICB are being investigated among which the addition of epigenetic drugs that are expected to act on both immune and tumor cells. Guadecitabine, a dinucleotide prodrug of a decitabine linked via phosphodiester bond to a guanosine, showed promising results in the phase-1 clinical trial, NIBIT-M4 (NCT02608437). We used the syngeneic B16F10 murine melanoma model to study the effects of immune checkpoint blocking antibodies against CTLA-4 and PD-1 in combination, with and without the addition of Guadecitabine. We comprehensively characterized the tumor’s and the host’s responses under different treatments by flow cytometry, immunohistochemistry (MANTRA), gene methylation and scRNA sequencing. Guadecitabine in combination with ICBs significantly reduced tumor growth compared to ICB and Guadecitabine treatment. The demethylating drug led to a general DNA-demethylation and transcriptional modification of gene expression. In particular, Guadecitabine greatly enhanced the efficacy of combined ICBs by increasing effector memory CD8+ T cells, inducing effector NK cells in the spleen and reducing tumor infiltrating regulatory T cells and MDSC cells, in the TME. These results indicate Guadecitabine as a promising epigenetic drug to be added to ICB therapy.

overall_design: Bisulphite converted DNA from mice tumoral tissue was hybridised to the Illumina Infinium MouseMethylation array  BeadChip

first: Ulrich

last: Pfeffer


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [12B_190325]

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

summary: Illustrating the cellular architecture of the mammalian brain is critical to understanding its diverse functions and complex animal behaviors. With support from NIMH and NINDS as part of the BRAIN Initiative Cell Census Network (BICCN), the Center for Epigenomics of the Mouse Brain Atlas (CEMBA) applied single nucleus methylation sequencing in 117 brain funtional regions across the whole adult male P56 C57BL/6J mouse brain. In each major brain regions, we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster. We integrate the single cell methylome with single cell gene expression and chromatin accessibility profiles from the same brain region to further identify potential enhancers and their corresponding genes for several neuronal cell types. By brain region spacial comparisons, we found spatial specificity among excitatory neuronal clusters within the same cortical layer. We identify brain-region-specific transcription factors that may regulate cortical region development of excitatory neurons. These data define the landscape of cell type and spatial heterogeneity in the mouse brain and the underlining regulatory epigenomic basis.

overall_design: Apply snmC-seq2 to 117 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (12B).

first: Hanqing

last: Liu

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

first: Julia

middle: K

last: Osteen

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Rosa

middle: G

last: Castanon

last: Nery

last: Berube

first: Huaming

last: Chen

first: Michael

last: Nunn

first: Jesse

last: Dixon

first: M

last: Behrens


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [11J_210128]

overall_design: Apply snmC-seq3 to 117 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (11J).

first: Peter

middle: M


title: Time-course transcriptome of developing brown adipose tissue

city: Tsukuba

first: Yutaro

last: Kumagai

state: Ibaraki

address: Central 5-41, Higashi 1-1-1

department: BRD

institute: AIST

summary: Transriptome of brown adipose tissues from E18, 4 and 10 days old, and 4 and 8 weeks old C57BL6/N mice were examined to describe the development of the tissue.

overall_design: Whole brown adipose tissues from E18, 4 and 10 days old, and 4 and 8 weeks old C57BL6/N mice were subjected to microarray analysis

first: Yasuyuki

last: Kida


title: Use of DNA-alkylating pyrrole-imidazole polyamides for anti-cancer drug sensitivity screening in PDAC

first: Jason

last: Lin

state: Chiba

address: 666-2 Nitona-cho, Chuo-ku

institute: Chiba Cancer Center Research Institute

summary: Activating mutations of the KRAS gene are found in >90% of pancreatic ductal adenocarcinoma (PDAC) cases. However, direct pharmacological targeting of the activated KRAS protein has been challenging. We previously reported that KR12, a DNA-alkylating pyrrole-imidazole polyamide designed to recognize the KRAS G12D/V mutation, showed an anti-tumor effect in colorectal cancer. In this study, we evaluated the anti-tumor effect of KR12 in PDAC. We found that KR12 inhibited tumor growth in a spontaneous PDAC mouse model, although the anti-tumor activity appeared to be limited in a human PDAC xenograft model. We developed a pyrrole-imidazole polyamide screening process based on the hypothesis that genetic elements otherwise unaffected by KR12 could exert attenuating effects on KRAS-suppression-resistant PDAC. We identified RAD51 as a potential therapeutic target in human PDAC cells. A RAD51 inhibitor showed an inhibitory effect on cell growth and affected the cytotoxic activity of KR12 in PDAC cells. These data suggested that the simultaneous inhibition of RAD51 and mutant KRAS blockage would be an important therapeutic strategy for PDAC.

overall_design: KP-4 cells were plated overnight prior to the administration of polyamide (100 nM) for 12 h. DMSO (0.01%) was used as control. According to the instructions provided by the manufacturer, cells were lysed for RNA extraction using the RNeasy Plus Mini Kit (Qiagen), and sample replicates were labeled with the RNA Spike-In Kit to be analyzed by SurePrint G3 Human GE 8x60K V2 expression microarrays (Agilent). Differential expression analyses were performed with our previously developed custom R workflow (Lin et al PLoS ONE 14:e0215247, 2019).

first: Akiko

last: Tsujimoto

first: Atsushi

last: Takatori

first: Hiroki

last: Nagase


title: Bidirectional changes in postmitotic H3K27me3 distributions underlie cerebellar granule neuron maturation dynamics [RNA-Seq]

city: Durham

first: Anne

last: West

state: NC

address: 311 Research Dr

department: Neurobiology

institute: Duke University

summary: The functional and transcriptional maturation of neurons is a prolonged process that extends well beyond mitotic exit and terminal fate commitment of progenitors. The differentiation of cerebellar granule neurons (CGNs) in the postnatal mouse cerebellum provides a useful model to identify chromatin mechanisms that orchestrate temporal changes in transcription as postmitotic CGNs mature. Here we report that CGN maturation is associated with dynamic changes in the genomic distribution of histone H3 lysine 27 trimethylation (H3K27me3), a modification best known for its role in repressing alternative fates during cell specification. H3K27me3 is gained rapidly in newly postmitotic CGNs at progenitor-expressed genes that are repressed in neurons. H3K27me3 is lost more gradually at the promoters of a subset of neuronal genes that are transcriptionally induced upon CGN maturation. The loss of H3K27me3 is facilitated by the lysine demethylase KDM6B, and genes that are induced in maturing CGNs show impaired expression in the cerebellum of conditional KDM6B knockout mice. Genes that lose H3K27me3 gain H3K27 acetylation and binding of the pro-maturation ZIC1/2 transcription factors, suggesting that developmental loss of H3K27me3 may be required to permit the onset of transcriptional maturation. Interestingly, pharmacological inhibition of the H3K27 methyltransferase EZH2 in early postmitotic CGNs not only blocked the repression of progenitor genes but also impaired the induction of mature CGN genes. These data show that regulation of H3K27me3 functions in developing postmitotic neurons beyond the period of cell fate commitment to regulate the dynamics of gene expression programs that underlie functional neuronal maturation.

overall_design: Vijyendra Ramesh

first: Fang

last: Liu

first: Melyssa

last: Minto

first: Urann

last: Chan


title: Spatiotemporal multi-omics decoding of the developing human spinal cord II

city: Solna

first: Paulo

last: Czarnewski

address: Tomtebodavägen 23b

country: Sweden

institute: KTH

summary: The human spinal cord contains diverse cell types, governed by a series of spatiotemporal events for tissue assembly and functions. However, the regulation of cell fate specification in the human developing spinal cord remains largely unknown.  By performing single-cell and spatial multi-omics methods, we integrated the datasets and created a comprehensive human developmental atlas of the first trimester spinal cord. Unexpectedly, we discovered unique events in human spinal cord development, including early loss of active neural stem cells, simultaneous occurrence of neurogenesis and gliogenesis, and distinct spatiotemporal genetic regulations of fate choices. We also identified distinct regulations of cancer stem cells in ependymomas from our atlas. Thus, we demonstrate spatiotemporal genetic regulation of human spinal cord development and its potential to understand novel disease mechanisms.

overall_design:
The human embryos and fetuses were transported immediately from the clinics to the dissection lab in Hibernation medium (Gibco A13706-01). After staging, spinal cords were removed from the intact tissue in ice cold saline (Fresenius Kabi, B306443/01). W5-7 spinal cords were kept as one piece, and W8-12 spinal cords were dissected into cervical, thoracic, and lumbar regions. Spinal cords were then kept in ice cold hibrination medium or snap frozen in OCT for scRNA-seq immediately, or cryosectioning in the future respectively.
--------------------------
Authors state "However, raw reads from our cohort are considered sensitive and protected by GDPR regulations, and will therefore be uploaded to Swedish federated EGA."

first: Xiaofei

last: Li

first: Erik

last: Sundström


title: A primary cell-based in vitro model of the human small intestine reveals the induction of OLFM4 expression as host cell response during Salmonella Typhimurium infection

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

summary: Infection research largely relies on classical cell culture or mouse studies; both having limitations in translating mechanistic principles to human pathologies. Alternatives can be derived from modern Tissue Engineering approaches, allowing the reconstruction of functional tissue models. As the replication of biological and physico-chemical properties of the host tissue is of high importance in this context, we combined a biological extracellular matrix with primary tissue-derived enteroids to establish an in vitro model of the human small intestinal epithelium exhibiting in vivo-like characteristics. Further, using the foodborne pathogen Salmonella enterica serovar Typhimurium, we demonstrated the applicability of our generated model for modern infection research in the human context. Infection assays coupled to spatio-temporal readouts provided evidence that the key steps of epithelial infection by the pathogen could be reconstructed in our model. Interestingly, we detected the upregulation of Olfactomedin-4 in infected cells, a previously unknown host cell response upon Salmonella infection.

overall_design: Analysis of two replicates of the human intestinal tissue model via 10x Genomics 3'Gene expression. Multiplexing via Biolegend TotalSeqA Hashtags. Hashtag1 = Replicate1; Hashtag2 = Replicate2

first: Thomas

last: Däullary

first: Fabian

last: Imdahl

first: Oliver

last: Dietrich

first: Laura

last: Hepp

first: Tobias

last: Krammer

first: Christina

last: Fey

first: Winfired

last: Neuhaus

first: Marco

last: Metzger

first: Jörg

last: Vogel

first: Alexander

last: Westemann

first: Daniela

last: Zdzieblo


title: Spatiotemporal multi-omics decoding of the developing human spinal cord

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

overall_design:
Refer to individual Series

Authors state "However, raw reads from our cohort are considered sensitive and protected by GDPR regulations, and will therefore be uploaded to Swedish federated EGA."


title: RT-qPCR analysis of apoptosis related genes in patient-derived xenografts of small intestine neuroendocrine tumors in Balb/c NM after administration of Lu-177-octreotate, Lu-177-octreotate + A1M and A1M

city: Gothenburg

first: Nishte

last: Rassol

address: Gula stråket 2b

institute: University of Gothenburg

summary: This work aimed to examine the regulation of apoptosis-related genes in GOT1 tumors one and seven days after administration of 177Lu-octreotate with and without A1M and of A1M alone. At study start, 22 adult female Balb/c GOT1 tumor-bearing mice were divided into four groups of six animals that received 30 MBq 177Lu-octreotate or 5 mg/kg A1M, or co-treatment with both 177Lu-octreotate and A1M by i.v. injection. Also, a control group was sham-treated with saline. Half of the animals in each treatment and control group were terminated by cardiac puncture one-day post-injection (1 dpi), and the remaining animals were terminated at 7dpi. Tumor tissues were dissected at the time of termination, snap-frozen in liquid nitrogen and stored at -80°C.

overall_design: Three biological replicated were included in each test group at both 1 dpi and 7dpi, and two biological replicates were included in corresponding controls. An equal amount of total RNA (40 µg) was extracted from all samples, and 200 ng of total RNA was reversed transcribed into cDNA per sample.

first: N

first: C

last: Andersson

first: D

last: Pettersson

first: A

last: Al-awar

first: E

last: Shubbar

first: B

last: Åkerström

first: M

last: Gram

first: K

last: Helou

last: Forssell-Aronsson


title: RNA degradome analysis reveals substrates of NYN-domain containing DNE1 endoribonuclease in Arabidopsis

city: Newark

first: Pamela

last: Green

state: DE

address: 15 Innovation Way

department: Plant and Soil Sciences

institute: Delaware Biotechnology Institute

summary: To gain insight into the functional role of DNE1 in cytoplasmic mRNA decay, we performed Parallel Analysis of RNA Ends (PARE) and Global Mapping of Uncapped and Cleaved Transcripts (GMUCT) analysis to identify DNE1-dependent cleavage sites based on their sensitivity to XRN4 within the Arabidopsis transcriptome

overall_design:
RNA degradome analysis (ATH1036-41; ATH1082-87): Comparing the RNA decay profiles allowed for the detection of abundant monophosphorylated 5' ends (5'P) within transcripts in xrn4 that were absent in dne1xrn4. Thereby, we identified a number of 5'P sites that were dependent on DNE1 activity.
RNA-seq analysis (ATH1046-57): For comparing full-length transcript abundances between xrn4 and dne1xrn4.

first: Vinay

last: Nagarajan


title: Excessive transcription-replication conflicts are a vulnerability of BRCA1-mutant cancers

city: Toronto

first: Razq

last: Hakem

state: Ontario

address: TMDT, 101 College Street. Rm13-310

department: Princess Margaret Cancer Centre

institute: University Health Network

summary: BRCA1 primarily functions to maintain genomic integrity; therefore, mutations in BRCA1 are associated with increased risk of developing breast (≥70%) and ovarian (≥40%) cancers. Additionally, tumors arising from BRCA1 mutations are typically high grade and recurrent in nature. Thus, there is an urgent need to identify novel optimal therapeutic options for the majority of these patients. Herein, we performed a targeted CRISPR-Cas9 dropout screen and identified Methylphosphate Capping Enzyme, MEPCE, as a potential synthetic lethal interactor of BRCA1. Mechanistically, depletion of MEPCE in a BRCA1-deficient setting results in increased RNA polymerase II redistribution, R-loop accumulation, as well as replication stress, concomitantly contributing to transcription-replication collision events. These factors compromise genomic integrity, thereby resulting in loss of viability of BRCA1-deficient tumor cells. We also identified RNA polymerase II-associated factor I, PAF1, as a synthetic lethal interactor of BRCA1. Similar to MEPCE depletion, loss of PAF1 in a BRCA1-deficient setting results in R-loop accumulation, transcription-replication conflicts, and cell death. Our study highlights the dependence of BRCA1-defective tumors on factors such as MEPCE and PAF1 that suppress transcription-replication conflicts through RNAPII pausing and release regulation to maintain genomic stability. This highlights the untapped potential of factors such as MEPCE as novel therapeutic targets for the treatment of cancers associated with BRCA1 mutations.

overall_design:
ChIP-seq of RNA polymerase II and RNA polymerase II phospho-Serine2 in WT and MEPCE depleted MDA MB 436 cells
DRIP-seq in WT and MEPCE depleted MDA MB 436 cells

first: Arash

last: Algouneh

first: Parasvi

last: Patel

first: Anne

first: Kevin

last: Nixon


title: β-catenin programs a tissue-specific epigenetic vulnerability in aggressive adrenocortical carcinoma

city: Ann Arbor

first: Antonio

middle: Marcondes

last: Lerario

state: MI

address: 109 Zina Pitcher Place, 1528 BSRB

department: MEND

institute: University of Michigan

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: Refer to individual Series


title: The transcription factor Cdx2 regulates inflammasome activity through expression of the NLRP3 suppressor TRIM31 to maintain intestinal homeostasis

city: Ottawa

first: Sanzida

last: Jahan

state: ON

address: 451 Smyth Road

department: Cellular and Molecular Medicine

institute: University of Ottawa

summary: We report differentially expressed genes due to Cdx loss in mouse large intestinal tissue using RNA-seq. We report Cdx2 binding sites and chromatin accessibilty for target genes occupied by Cdx2 in mouse large intestinal tissue using ChIP-seq and ATAC-seq.

overall_design: Identification Cdx2 binding sites, changes in chromatin accessibility and changes in expression of Cdx2 target genes.

first: Bradley

last: Hess

first: Stephanie

last: Hajjar

first: Subash

last: Sad

first: David

last: Lohnes


title: Comparative 3D Genome Architectures of Adipose Tissues Provide Insight into Human-specific Regulation of Metabolic Homeostasis

city: Chengdu

first: jin

last: long

address: Hui ming

institute: Sichuan Agricultural University

summary: Elucidating the regulatory mechanisms of human adipose tissue (AT) evolution is essential for understanding human metabolic homeostasis. In this study, we compared the chromatin architectures of anatomically distinct ATs from humans and six representative mammalian models. We recognized evolutionarily conserved and human-specific chromatin conformation at multiple scales, including compartmentalization, topologically associating domain (TAD), and promoter-enhancer interactions (PEI). We found PEIs are more evolutionarily dynamic with respect to compartmentalization and TAD. Human-specific chromatin structure-related genes were involved in multiple biological processes, including energy metabolism and maintenance of metabolic homeostasis. The genes regulated by human-specific PEIs were depleted for diabetic variations, implying a beneficial role in metabolic homeostasis. Additionally, numerous human-specific chromatin structures were observed among subcutaneous and visceral ATs, indicating the diversified functions of ATs during evolution. Collectively, the presented data highlight the value of comparative 3D genome analyses in dissecting the regulatory mechanisms of different ATs and evolution.

sample_organism:
Ovis aries
Mus musculus

platform_organism:
Ovis aries
Mus musculus

overall_design: To interrogate 3D genome organization of ATs in an evolutionary framework, we profiled the chromatin architectures through in situ high-throughput chromatin conformation capture (Hi-C) and profiled the transcriptome through rRNA-depleted RNA-seq for SATs collected from human and other six mammalian models (2-3 biological replicates for each mammal), including rodents (mouse and rat), lagomorphs (rabbit), carnivores (dog) and artiodactylids (pig and sheep), and three representative VATs (i.e., greater omentum [GOM], mesenteric adipose [MAD] and retroperitoneal adipose [RAD]) from human, pig and sheep (3 biological replicates for each VAT of each mammal).

first: Pengliang

last: Liu

first: Jiaman

last: Zhang

first: Diyan

last: Li

first: Mingzhou


title: Elevated enhancer-oncogene contacts and higher oncogene expression levels by recurrent CTCF inactivating mutations in acute T cell leukemia [HiC]

status: Public on Apr 29 2023

city: Utrecht

first: Rico

last: Hagelaar

address: Heidelberglaan 25

institute: Princess Maxima Center

summary: CCCTC-binding factor (CTCF) regulates the 3D chromatin architecture by facilitating chromosomal loops. In addition to insulation of euchromatin from heterochromatin, CTCF is an important transcription factor and regulator of antigen receptor and T cell receptor recombination events. CTCF inactivating events have been found in human cancer, resulting in deregulation of global gene expression by altered methylated genomic states. In contrast to these studies, we here describe that inactivation of CTCF can drives subtle and local genomic effects that elevates oncogene expression levels from driving chromosomal rearrangements. For T cell acute lymphoblastic leukemia (T-ALL), heterozygous CTCF deletions or inactivating mutations are predominantly found in nearly 50 percent of t(5;14)(q35;q32.2) rearranged patients that couples the TLX3 oncogene in the vicinity of the BCL11B enhancer. This unique entity has been associated with γδ-lineage development. Functional CTCF loss results in diminished expression of the αβ-lineage commitment factor BCL11B from the non-rearranged allele, but unexpectedly drives higher levels of the TLX3 oncogene from the translocated allele. In line, Ctcf conditional knockout mice have reduced numbers of αβ T cells but increased numbers of γδ T cells, a phenotype identical to that of Bcl11b knockout mice and implying that CTCF is directly involved in the regulation of the BCL11B enhancer. We demonstrate that most TLX3-rearranged patients with heterozygous CTCF aberrations preserved single intervening CTCF bindings sites in the translocation breakpoint areas located in between the BCL11B enhancer and the TLX3 oncogene. These intervening CTCF sites insulate TLX3 from the enhancer by forming competitive loops with TLX3 regulatory sequences. Using reverse genetics, we provide evidence that heterozygous inactivation of CTCF diminishes competitive loop formation in favor of high-affinity TLX3 promoter loops to BCL11B enhancer sequences formed among multiple convergent CTCF binding sites. This boosts oncogene expression levels and leukemia burden in T-ALL patients.

overall_design: HiC to detect global genomic interactions. CTCF wild type, mutant CTCF and CTCF deleted patients are used to investigate whether there are global differences

first: Jules

middle: P

last: Meijerink

first: Willem

last: Smits

first: Carlo

last: Vermeulen


title: Differentially expressed genes after transfection of miRNA in a human cancer cell line

status: Public on Apr 24 2023

city: Kagoshima

first: Yuya

last: Tomioka

institute: Kagoshima University

summary: To identify differentially expressed genes by miRNAs transfection in human cancer, lung adenocarcinoma cells were subjected to agilent whole genome microarrays

overall_design: Human lung adenocarcinoma cells (A549) were treated with miRNAs (miR-486-5p and miR-486-3p)

first: Naohiko

last: Seki


title: c-Kit signaling potentiates CAR T-cell efficacy in solid tumors by CD28- and IL-2–independent costimulation

first: Navin

last: Chintala

state: NY

address: 417 E 68th Street, 4th Flr, Room 427D

department: Surgery

institute: MSKCC

summary: The limited efficacy of chimeric antigen receptor (CAR) T-cell therapy for solid tumors necessitates engineering strategies that promote functional persistence in an immunosuppressive environment. Herein, we exploit c-Kit signaling, a physiological pathway associated with stemness in hematopoietic progenitor cells (T cells lose expression of c-Kit during differentiation). CAR T cells with intracellular expression—but no cell-surface receptor expression—of the c-Kit D816V mutation (KITv) have upregulated STAT phosphorylation, antigen-activation-dependent proliferation, CD28- and IL-2–independent and IFN-γ–mediated costimulation, augmenting the cytotoxicity of first-generation CAR T cells. This translates to enhanced survival, including in TGF-β–rich and low-antigen-expressing solid tumor models. KITv CAR T cells have equivalent or better in vivo efficacy than second-generation CAR T cells and are susceptible to tyrosine kinase inhibitors (safety switch). When combined with CD28 costimulation, KITv costimulation functions as a third signal, enhancing efficacy and providing a potent approach to treat solid tumors.

overall_design: Mesothelin-specific CAR T cells either Unstimulated or Stimulated with Mesothelin-expressing target cells were flow stained and CD8+ cells were sorted for RNA extraction and gene expression analysis.

first: Yuquan

last: Xiong

first: Prasad

last: Adusumilli


title: GABA, glucose and insulin orchestrate CD4+ T cells effector functions

city: Uppsala

first: Bryndis

last: Birnir

address: Husargatan 3

department: Department of Medical Cell Biology

institute: Uppsala University

summary: This study investigated the transcriptome profiling of in vitro activated CD4+ T cells from normal  individuals

overall_design: Study gene expression profiling analysis of RNA-seq data for in vitro activated CD4+ T cells for 66-72 hours from 6 normal individuals

first: Hayma

last: Hammoud

first: Zhe

last: Jin


title: Effect of ONWAY on gene expression in bone marrow of mice after 4T1 cancer surgery

first: Yang

last: Fuming

address: 汉口路22号南园21舍

institute: 南京大学

summary: To explore the RNA effects of Onway on bone marrow cells after TNBC surgery, we performed gene sequencing of bone marrow cells from mice treated with and without Onway.

overall_design: After tumor resection, 4T1 female Balbc mice were treated with Onway by gavage for 2 weeks, while the Control mice were not. Bone marrow cells of the mice were havested after treatment. We then performed gene expression profiling analysis using data obtained from RNA-seq of bone marrow cells .

first: Fuming

last: Yang


title: Identification of a novel gene signature for neuroblastoma differentiation using a Boolean implication network

first: Debashis

last: Sahoo

state: California

address: 9500 Gillman Drive

department: Pediatrics

institute: UCSD

summary: In this dataset, we report the analysis by RNA-sequencing (RNA-seq) of the transcriptional profile of neuroblastoma cell lines at baseline and after treatment with 13-cis-retinoic acid. Data from this study validated Boolean Implication Network derived differentiation signature in neuroblastoma. Our differentiation signature included a cluster of genes involved in intracellular signaling and growth factor receptor trafficking pathways that is strongly associated with neuroblastoma differentiation, and we validated the associations of UBE4B, a gene within this cluster, with neuroblastoma cell and tumor differentiation. Our findings demonstrate that Boolean network analyses of symmetric and asymmetric gene expression relationships can identify novel genes and pathways relevant for neuroblastoma tumor differentiation that could represent potential therapeutic targets.

overall_design: Neuroblastoma cell lines were treated with 5μM 13-cis-retinoic acid for 48 hours, while control plates were left untreated.

first: Peter

last: Zage


title: Aberrant cortical layer development of brain organoids developed from Noonan syndrome-iPSCs

city: Daejeon

first: Jong-Eun

last: Park

address: 291, Daehak-ro, Yuseong-gu

institute: Korea Advanced Institute of Science and Technology

summary: Noonan syndrome (NS) is a genetic disorder mainly caused by gain-of-function mutations of SHP2. Although diverse neurological manifestations are commonly diagnosed in NS patients, mechanisms on how the SHP2 mutation induces the neurodevelopmental defects remain elusive. Here, we report that cortical organoids (NS-COs) derived from NS-induced pluripotent stem cells (iPSCs) exhibit developmental abnormalities, especially in excitatory neurons (ENs). Although NS-COs normally develop in appearance, single-cell transcriptomic analysis represented increment of EN population and overexpression of cortical layer markers in NS-COs. Surprisingly, EN subpopulation co-expressing upper layer marker SATB2 and deep layer maker CTIP2 was enriched in NS-COs during the cortical development. In parallel with the developmental disruptions, NS-COs also exhibited reduced synaptic connectivity. Collectively, our findings suggest that perturbed cortical layer identity and impeded neuronal connectivity account for the neurological manifestations of NS.

overall_design: COs were obtained at week 8, 16, and 24 during the differentiation of WT-iPSCs, NS-iPSCs, and gene-corrected isogenic control cell line of NS-iPSCs (NS-Cor-iPSCs)

first: Bumsoo

last: Kim

first: Yongjun

last: Koh

first: Yong-Mahn

last: Han


title: Bulk-RNA-sequencing from chamber specific heart tissue and isolated cardiomyocytes

city: London

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

country: United Kingdom

institute: The Francis Crick Institute

summary: Healthy hearts from warm cadavers not usable for heart transplants were identified and tissues were isolated from these. From ventricle tissues, cardiomyocytes were further isolated. Bulk-RNA-sequencing was performed.

overall_design: Bulk-RNA-sequencing from 3 different donors (tissue) and 3 other donors (isolated CMs)

first: Andreia

last: Bernardo

first: Nicola

last: Dark