title: RNA immunoprecipitation sequencing (RIP-seq) of BUD31 in ovarian cancer cells

city: Jinan

first: Zixiang

last: Wang

state: Shandong

address: No.44 Wenhuaxi Road

department: Cheeloo College of Medicine

institute: Shandong University

summary: Mis-regulation of splicing factors are thought to activate cancer specific splicing programs that contribute to cancer development and progression. However, it remains a major challenge to identify the key splicing variants caused by aberrant expression of splicing factors in cancer. Here we report that splicing factor BUD31 is commonly overexpressed in high-grade serous ovarian carcinoma (HGSOC) and high level of BUD31 is associated with poor prognosis. RNA-seq analysis reveals that BUD31 inhibition predominantly results in alternation of exon skipping and intron retention.  RNA immunoprecipitation sequencing (RIP-seq)  was used to analysis the interaction between BUD31 and the target RNA. Our data indicate that BUD31 is a critical oncogenic splicing factor in ovarian cancer and might act as a potential therapeutic target.

overall_design: RNA immunoprecipitation sequencing (RIP-seq)  was performed in HEY cells with BUD31 antibody . HEY cells were collected for the RIP assay, which was performed using the EZ-Nuclear RIP Kit (17-701, Merck Millipore) following the manufacturer's instructions. In brief, cells were collected and lysed in RIP lysis buffer. Lysates were incubated with magnetic beads coated with anti-BUD31 antibody (Proteintech, 11798-1-AP) at 4 °C overnight. The beads combined with immunocomplexes were washed with RIP wash buffer for 6 times and digested by protease K. RNA was extracted with Phenol/Chloroform/Isoamyl Alcohol (125:24:1 Mixture).

first: Zhaojian

last: Liu


title: Hormonal Therapies Upregulate MANF and Overcome Female Susceptibility to Immune Checkpoint Inhibitor-Myocarditis

status: Public on Sep 18 2022

city: Houston

first: Haoqiang

last: Ying

state: Texas

address: 1515 Holcombe Blvd

country: USA

institute: M. D. Anderson Cancer Center

type: Expression profiling by high throughput sequencing

summary: Immune checkpoint inhibitors (ICIs) have been increasingly used in combination for cancer treatment, but are particularly associated with myocarditis. Here, we report that tumor-bearing mice exhibited response to treatment with combinatorial anti-PD-1 (programmed cell death 1) and anti-CTLA-4 (Cytotoxic T-lymphocyte Antigen-4) antibodies but also presented with cardiovascular toxicities observed clinically with ICI therapy, including myocarditis and arrhythmia. Female mice were preferentially affected with myocarditis compared to male mice, consistent with a previously described genetic model of ICI-myocarditis as well as emerging clinical data. Mechanistically, myocardial tissue from ICI-treated mice, the genetic mouse model, and human heart tissue from affected patients with ICI-myocarditis all exhibited downregulation of MANF (Mesencephalic Astrocyte Derived Neurotrophic Factor) and HSPA5 (Heat Shock 70kDa Protein 5) in the heart; this downregulation was particularly striking in female mice. ICI-myocarditis was amplified by heart-specific genetic deletion of mouse Manf and was attenuated by administration of recombinant MANF protein, suggesting a causal role. Ironically, both MANF and HSPA5 were transcriptionally induced by liganded estrogen receptor-βbeta and inhibited by androgen receptor. However, ICI treatment reduced serum estradiol concentration to a greater extent in female compared to male mice. Treatment with an estrogen receptor β-specific agonist as well as androgen depletion therapy attenuated ICI-associated cardiac effects. Taken together, our data suggest that ICI treatment inhibits the estradiol-dependent expression of MANF/HSPA5 in the heart, curtailing the cardiomyocyte response to immune injury. This endocrine-cardiac-immune pathway offers new insights into the mechanisms of sex differences in cardiac disease and may offer treatment strategies for ICI-myocarditis.

overall_design: Murine melanoma cancer model B16F10 was used. Tumors were treated with vehicle (PBS) or recombinant MANF. Heart tissues were collected for RNA extraction and sequencing.

first: Yaohua

last: Zhang

first: Chengcao

last: Sun

first: Yajuan

last: Li

first: Juan

last: Qin

first: Kaushik

last: Amancherla

first: Ying

last: Jing

first: Qingsong

last: Hu

first: Ke

last: Liang

first: Zhao

first: Youqiong

last: Ye

first: Lisa

middle: A

last: Huang

first: Tina

middle: K

last: Nguyen

first: Sergey

middle: D

last: Egranov

first: Zilong

last: Zhao

first: Andrew

last: Wu

first: Yutao

last: Xi

first: Jun

last: Yao

first: Mien

middle: C

last: Hung

first: George

last: Calin

first: Jie

last: Cheng

first: Bora

last: Lim

first: Lorenz

middle: H

last: Lehmann

first: Joe

middle: E

last: Salem

first: Douglas

middle: B

last: Johnson

first: Michael

last: Curran

first: Dihua

last: Yu

first: Leng

last: Han

first: Radbod

last: Darabi

first: Liuqing

last: Yang

first: Javid

middle: J

last: Moslehi

first: Chunru

last: Lin


title: The histone variant macroH2A modulates inflammatory response in cancer [xenograft]

status: Public on Sep 20 2022

city: Badalona

first: Roberto

last: Malinverni

state: Barcelona

address: Josep Carreras Building, Ctra de Can Ruti,

country: Spain

institute: Josep Carreras Leukaemia Research Institute

summary: MacroH2A histone variants have a major role in nuclear organization and large-scale 3D chromatin architecture. How these alterations impinge on the behaviour of cancer cells is not known. Here, we describe the analysis of the total macroH2A loss of function phenotype in a model of hepatoblastoma, the main childhood liver cancer. Performing transcriptomic analyses in xenografts and cell cultures, we find that macroH2A modulated the response of cancer cells to paracrine inflammatory signalling. Specifically, ablation of macroH2A ablation neutralized the induction of a large subset of genes by TNFα and led to the hyperactivation of another subset of genes. Among the top macroH2A-sensitive genes we find the cancer-related gene DKK1 . Depletion of macroH2A rendered the DKK1 gene hypersensitive to TNFα signalling boosting the secretion of DKK1 protein. On the gene regulation level, this was mediated by an alteration of the local chromatin structure and facilitated activation of distal enhancer elements. The study of human samples of hepatoblastoma showed that DKK1 is strongly upregulated in tumors and associated with poor patient outcome. Taken together our results suggest that the regulation of 3D chromatin architecture by macroH2A histone variants has a central role in the response and regulation of paracrine signalling that might be relevant for the interaction of cancers with immune cells and other cells in their microenvironment.

overall_design: Transcriptomic profiling of xenografts grown in immunosupressed NOD/SCID mice from HepG2 cell lines stably expressing either control shRNAs (CTL) or shRNAs targeting macroH2A1 and macroH2A2 (DKD), 5 different tumors per condition

first: David

last: Corujo

first: Juan

last: Carrillo-Reixach

first: Arce

last: Garcia-Jaraquemada

first: Vanesa

last: Valero

first: Ainhoa

last: Pérez

first: Laura

last: Royo

first: Josep

last: Manyé

first: Carolina

last: Armengol

first: Marcus

last: Buschbeck


title: Titration of 124 antibodies using CITE-Seq on human PBMCs

city: La Jolla

first: Klaus

last: Ley

state: California

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

summary: Single-cell RNA-sequencing (scRNA-Seq) is widely used to characterize immune cell populations. However, mRNA levels correlate poorly with expression of surface proteins, which are well established to define immune cell types. CITE-Seq (cellular indexing of transcriptomes and epitopes by sequencing) utilizes oligonucleotide-tagged antibodies to simultaneously analyze surface phenotypes and transcriptomes. Considering the high costs of adding surface phenotyping to scRNA-Seq, we aimed to determine which of 188 tested CITE-Seq antibodies can detect their antigens on human peripheral blood mononuclear cells (PBMCs), a commonly interrogated cell population in immunology, and find the optimal concentration for staining. The recommended concentration was optimal for 76 antibodies, whereas staining quality of 7 antibodies improved when the concentration was doubled. 33 and 8 antibodies still worked well when the concentration was reduced to 1/5 or 1/25, respectively. 64 antigens were not detected at any antibody concentration. Optimizing the antibody panel by removing antibodies not able to detect their target antigens and adjusting concentrations of the remaining antibodies could enable a cost reduction of almost 50%. In conclusion, our data are a resource for building an informative and cost-effective panel of CITE-Seq antibodies and use them at their optimal concentrations in future CITE-seq experiments on human PBMCs.

overall_design: CITE-seq on PBMCs antibody dilutions of 2x, 1x, 0.2x, 0.04x

first: Felix

middle: S

last: Nettersheim

first: Sujit

last: Suthahar


title: Spalt and Disco define the Dorsal-Ventral Neuroepithelial Compartments of the Developing Drosophila Medulla

status: Public on Sep 19 2022

city: Mississauga

first: Priscilla

last: Valentino

state: ON

address: 3359 Mississauga Rd

country: Canada

institute: University of Toronto

summary: Spatial patterning of neural stem cell populations is a powerful mechanism by which to generate neuronal diversity. In the developing Drosophila medulla, the symmetrically dividing stem cells of the outer proliferation center (OPC) crescent are spatially patterned by the non-overlapping expression of three transcription factors: Vsx1 in the center, Optix in the adjacent arms and Rx in the tips. These spatial genes compartmentalize the OPC and, together with the temporal patterning of the neuroblasts derived from the OPC, act to diversify medulla neuronal fates. The observation that the dorsal and ventral halves of the OPC grow as distinct compartments, together with the fact that a subset of neuronal types are generated from only one half of the crescent, suggests that additional transcription factors spatially pattern the OPC along the D-V axis. Here, we identify the spalt (salm and salr) and disco (disco and disco-r) genes as the D-V patterning transcription factors of the OPC. Spalt and Disco are differentially expressed in the dorsal and ventral OPC from the embryo through to the third instar larva, where they cross-repress each other to form a sharp dorsal-ventral boundary. We show that hedgehog is necessary for disco expression in the embryonic optic placode and that disco is subsequently required for the development of the ventral OPC and its neuronal progeny. We further demonstrate that this D-V patterning axis acts independently of Vsx1-Optix-Rx and thus propose that Spalt and Disco represent a third OPC patterning axis that may act to further diversify medulla fates.

overall_design: bulk RNA-seq of dorsal and ventral Drosohpila OPC neuroepithelial cells

first: Ted

last: Erclik


title: ATF4-dependent fructolysis fuels brain tumorigenesis

city: Beijing

first: Chao

last: Chen

address: Datun

department: CAS Key Laboratory of Infection and Immunity

country: China

institute: Institute of Biophysics, Chinese Academy of Sciences

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The goals of ChIP-seq analysis using an anti-ATF4 antibody  in GBM cells to obtain ATF4 target genes under glucose deprivation.

overall_design: Sequencing libraries were prepared using the NEBNext DNA Library Prep Master Mix Set (Illumina) according to the manufacturer’s instructions. The libraries were single-end sequenced on an Illumina NovaSeq 6000 (Annoroad Gene Technology Beijing Co. Ltd.).

first: Xinjian

last: Li


title: Effect of depletion of NHR-114/HNF4, and maternal B12 treatment on gene expression of  C. elegans in Larva 4 stage.

city: Hangzhou

first: Shenlu

last: Qin

state: Zhejiang

address: No. 600 Dunyu Road

institute: Westlake University

summary:
Vitamin B12 (B12) deficiency is a critical problem worldwide. Such deficiency in infants has long been known to increase the propensity to develop obesity and diabetes later in life through unclear mechanisms. Here, we establish a  ∆nhr-114 animal as a Caenorhabditis elegans model to study how early-life B12 impacts adult health. We find that early-life B12 deficiency causes increased lipogenesis and lipid peroxidation in adult worms, which in turn induces germline defects through ferroptosis.
In order to further identify genes that respond to early-life B12, we carried out an RNA sequencing (RNA-seq) assay to analyze the gene expression profiles of WT and ∆nhr-114 animals maternally supplied with 8 μM B12 or not.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT, ∆nhr-114 animals (Larva 4 stage) with or without maternal B12 treatment (8 μM).

first: Lianfeng

last: Wu


title: A molecular pathway for transcriptional regulation of daily sleep need in mice

city: Chongqing

first: dapeng

last: ju

address: 1 Yixueyuan Road, Yuzhong District

institute: Department of Anesthesiology The Second Affiliated Hospital,,Chongqing Medical University ,

summary: Different mammalian species vary greatly in their daily sleep quota, ranging from 2-4 hours in giraffes to 20-22 hours in koalas and bats. In humans, the sleep quantity and quality of individuals are governed by genetic factors and exhibit age-dependent variations. However, the molecular pathways and effector mechanisms that regulate daily sleep need in mammals remain unknown. Here, using an adult brain chimeric (ABC)-expression/knockout (KO) system for somatic genetics analysis of sleep in adult mice, we report that gain-of-function of histone deacetylases HDAC4/5 significantly reduces, whereas loss-of-function of HDAC4/5 increases daily non-rapid eye movement sleep (NREMS) amount and delta power–two key indicators of sleep need. Similarly, ABC-expression of cAMP-response element binding protein (CREB) or A-CREB, an inhibitor of transcriptional activity of CREB, decreases or increases NREMS amount and delta power, respectively. A combination of genetic and transcriptomic analysis reveals that HDAC4 functions in tandem with CREB in both transcriptional and sleep regulation. Consistent with their functions downstream of LKB1-SIK3 kinase cascade, ABC-expression of HDAC4/5CA or CREB rescues hypersomnia of Sik3E13∆/+ mice, whereas ABC-expression of SIK3/SLP-ST221E or HDAC(4+5)VP16 rescues insomnia of ABC-Lkb1KO mice. Taken together, these results identify LKB1-SIK3-HDAC4/5-CREB as the first major molecular pathway for transcriptional regulation of daily sleep need in mammals.

overall_design: 1. CREB bound genomic DNA. 2. HDAC4CA bound genomic DNA. 3.IgG ChIP as negative control.

first: Rui

last: Zhou

first: Dapeng

last: Ju

first: Meimei

last: Liao

first: Qinghua

last: Liu


title: snRNA-Seq data of human iPSC-midbrain organoids without and with microglia

city: Belvaux

first: Jens

middle: Christian

last: Schwamborn

address: 6, Avenue du Swing

country: Luxembourg

institute: LCSB

summary: The human brain is a complex, three-dimensional structure. To better recapitulate the brain complexity, recent efforts focused on the development of human specific midbrain organoids. Midbrain organoids consist of differentiated and functional neurons, which contain active synapses, as well as astroglia and oligodendrocytes. However, the absence of microglia, with their ability to phagocyte apoptotic cells and debris represents a major disadvantage for the midbrain organoid system. Additionally, neuro-inflammation-related disease modeling is not possible in the absence of microglia. So far, no studies about the effects of iPSC-derived microglia in brain organoid neural cells have been published. Here we describe an approach to derive microglia from human iPSCs and integrate them into midbrain organoids. Using single nuclear RNA sequencing in collaboration with the RIKEN institute we provide a detailed characterization of the microglia in brain organoids as well as of the influence their presence has on the other cells of the organoids.

overall_design: We generated human midbrain organoids from a wild-type (WT) iPSC line. At day 15 of differentiation, we co-cultured them with human iPSC-macrophage precursors generated from three different WT lines and promoted microglia differentiation in 3D. After 20 days of co-culture, we snap-froze the organoids and proceeded to single nuclei RNA seq to see differences in gene expression coming from the presence or absence of microglia in the system.

first: Sonia

last: Sabate-Soler

first: Sarah

last: Nickels

first: Lan

middle: Y

last: Jun


title: Siponimod ameliorates metabolic injury via the sphingosine1 phospohate receptor 5

status: Public on Sep 17 2022

city: Aachen

first: Tim

last: Clarner

state: Germany

address: Wendlingweg 2

country: Germany

institute: Neuroanatomie

summary: we followed the hypothesis that Siponimod, a sphingosine-1 phosphate receptor modulator exerts protective effects by a direct modulation of glia cell function

overall_design: To this end, we used the toxin-mediated, nonautoimmune MS animal model of cuprizone intoxication. NGS experiments were performed with mixed corpus callosum/neocortical tissues isolated from control (n=5), 3 weeks cuprizone intoxicated mice (Cup3wks-Veh; n=5) and Cuprizone 3 weeks plus siponimod 3.125mg/kg (Cup3wks-Sipo; n=5)

first: Newshan

last: Behrangi

first: Linda

last: Frintrop

first: Athanassios

last: Fragoulis

first: Markus

last: Kipp

first: Lin

last: Gan

first: Ali

last: Abdallah


title: Analysis of enhancer activity in response to microgravity in C2C12 mouse myotubes

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

country: Japan

institute: Chiba University

summary: We analyzed the change of H3K27Ac globally in response to microgravity in C2C12 mouse myotubes.

overall_design: ChIP-seq profiling of effects of microgravity in C2C12 myotubes.

first: Oishi

last: Yumiko

first: Manabe

last: Ichiro


title: Transcriptional profiling of interneurons in the mouse prefrontal cortex

status: Public on Sep 16 2022

city: New York

first: Ines

last: Ibanez-Tallon

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in neurons in the prefrontal cortex of adult Crh-IRES-Cre mice (Jackson 012704).  This work was supported by the Howard Hughes Medical Institute (N.H) and NIDA UG3-UH3 DA048385

overall_design: TRAP-Seq of neurons in the prefrontal cortex of adult Crh-IRES-Cre mice (Jackson 012704)

first: Michael

last: Riad


title: b1-integrin regulates marginal zone B cell differentiation

city: Freiburg

first: Senthilkumar

last: Ramamoorthy

address: Stübeweg 51

department: Cellular & Molecular Immunology

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Integrin b1-deficient mice have a defect in the differentiation of MZ B cells and plasma cells.We performed a genome-wide   transcriptome analysis of ex vivo-sorted Fo B, transitional B and MZ B cells of in Integrin b1 KO and Integrin b1 WT mice. We also performed invitro culture of CD93+ (AA4.1+) transitional B cells to study the role of PI3 Kinase signalling.

overall_design: The ex-vivo sorted Follicular (CD19+CD93-CD23+CD21-), Transitional (CD19+CD93+) and Marginal zone (CD19+CD93-CD23-CD21+) B cells from b1WT and b1KO mice were used for expression analysis. The invitro culture of CD93+ (AA4.1+) transitional B cells that were incubated with DMSO or PI3K inhibitor.

first: Virginia

last: Andreani

first: Reinhard

last: Fässler

first: Rudolf

last: Grosschedl


title: Insight into the pulmonary molecular toxicity of heated tobacco products using human bronchial and alveolar mucosa models at air-liquid interface

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary: Heated tobacco products (HTP) are novel nicotine delivery products with limited toxicological data. HTP uses heating instead of combustion to generate aerosol (HTP-smoke). Physiologically relevant human bronchial and alveolar lung mucosa models developed at air-liquid interface were exposed to HTP-smoke to assess broad toxicological response (n=6-7; ISO puffing regimen; compared to sham; non-parametric statistical analysis; significance: p<0.05). Elevated levels of total cellular reactive oxygen species, stress responsive nuclear factor kappa-B, and DNA damage markers [8-hydroxy-2΄-deoxyguanosine, phosphorylated histone H2AX, cleaved poly-(ADP-Ribose) polymerase] were detected in HTP-smoke exposed bronchial and/ or alveolar models. RNA sequencing detected differential regulation of 724 genes in the bronchial- and 121 genes in the alveolar model following HTP-smoke exposure (cut off: p≤0.01; fold change: ≥2). Common enriched pathways included estrogen biosynthesis, ferroptosis, superoxide radical degradation, xenobiotics, and α-tocopherol degradation. Secreted levels of interleukin (IL)1ꞵ and IL8 increased in the bronchial model whereas in the alveolar model, interferon-γ and IL4 increased and IL13 decreased following HTP-smoke exposure. Increased lipid peroxidation was detected in HTP-smoke exposed bronchial and alveolar models which was inhibited by ferrostatin-1. The findings form a basis to perform independent risk assessment studies on different flavours of HTP using different puffing topography and corresponding chemical characterization.

overall_design: Human bronchial and alveolar lung mucosa models cultured at air-liquid interface were treated with heated tobacco products or controls

first: Mizanur

last: Rahman

first: Martin

last: Irmler

first: Micol

last: Introna

first: Lena

last: Palmberg

first: Gunnar

last: Johanson

first: Swapna

last: Upadhyay

first: Koustav

last: Ganguly


title: Methylation data from nine tissues from GTEx samples profiled with Infinium HumanMethylationEPIC BeadChip

city: Chicago

first: Meritxell

last: Oliva

state: Illinois

address: 5841 S. Maryland Ave

department: Public Health Sciences

institute: University of Chicago

summary: Genome wide DNA methylation profiling of tissue samples from GTEx donors. The Infinium HumanMethylationEPIC BeadChip was used to obtain DNA methylation profiles across approximately 850,000 CpGs sites from 1000 tissue samples.

overall_design:
Epigenome-wide DNAm was derived from 1,000 tissue samples from 9 unique tissue types - breast mammary tissue, colon transverse, kidney cortex, lung, muscle skeletal, ovary, prostate, testis and whole blood - obtained from 424 GTEx subjects, mostly (~83%) from European ancestry given available genotype data and the majority self-identified as white. DNA samples were extracted from GTEx tissue samples using Qiagen Gentra Puregene method at GTEx Laboratory Data, Analysis and Coordinating Center (LDACC), and sent to the Institute for Population and Precision Health Laboratory on 96-well plates. Tissue types were not batched by plate. Bisulfite conversion was applied to 500 ng of DNA using EZ-96 DNA methylation kit (Zymo Research, Irvine, CA, USA). All samples were then prepared and analyzed in accordance with the manufacturer guidelines and protocol for the Infinium MethylationEPIC array (Illumina, San Diego, CA, USA); which was utilized to measure DNAm levels for 866,895 (867K) genomic locations, encompassing primarily CpG dinucleotides but also non-CpG sites.

>>>Submitter states: the IDAT files are currently available at AnVIL/dbGaP (phs000424.v9).  By GTEx consortium policy, IDAT files cannot be made publicly available as they could be used to re-identify GTEx samples <<<

first: Brandon

middle: L

last: Pierce

first: Muhammad

middle: G

last: Kibriya

first: Kristin

last: Ardlie

first: Kathryn

last: Demanelis


title: Generation of human iPS cell-derived mesenchymal cells capable of forming alveolar organoids [bulkRNA-Seq]

city: Kyoto

first: Shimpei

last: Gotoh

address: 53 Kawaharacho, Shogoin, Sakyo-ku

department: Center for iPS cell Research and Application

institute: Kyoto University

summary: We developed a method of generating human induced pluripotent stem cell (iPSC)-derived mesenchymal cells (iMES) that were able to induce AT1 and AT2 epithelial lineage cells in organoids. Transcriptomic analysis of human fetal lung fibroblasts (HFLF), human dermal fibroblasts (HDF), and their corresponding iMES revealed that iMES harbor characteristics of lung distal tip mesenchyme.

overall_design: We stepwise differentiated SFTPC-GFP reporter iPSCs into lung progenitor cells and they were co-cultured with HFLF, HDF or their corresponding iMES in the organoid differentiation system. Each mesenchyme in pre-3D culture condition was collected and total RNA was extracted, respectively. In addition, each mesenchyme in post-3D culture condition was isolated by fluorescence-activated cell sorting (FACS) after gating for EPCAM negative cells derived from the alveolar organoids at P0 and total RNA was extracted as well. The transcriptomes of these cells were sequenced with paired-end reads (100-bp) on an Illumina Novaseq 6000 instrument.

first: Koji

last: Tamai


title: Generation of human iPS cell-derived mesenchymal cells capable of forming alveolar organoids [scRNA-Seq]

summary: We have developed a method to generate human induced pluripotent stem cell (iPSC)-derived mesenchymal cells (iMES) that were able to induce AT1 and AT2 epithelial cells within their organoids (iMES-AO). Single-cell transcriptome analysis comparing iMES-AO with our previously reported alveolar organoids using human fetal lung fibroblasts delineated not only differences in composition of epithelial lineages but also distinctive mesenchymal lineages.

overall_design: Lung progenitors differentiated from SFTPC-GFP reporter iPSC were co-cultured with human fetal lung fibroblasts (HFLF) or iMES differentiated from its parental iPSC (201B7)  to form alveolar organoids in matrigel (P0). Then, SFTPC-GFP positive cells were recovered by fluorescence-activated cell sorting (FACS) and passaged for generating alveolar organoids with newly differentiated iMES or HFLF (P1). The passage was repeated again to form alveolar organoids (P2). Single-cell RNA sequencing (scRNA-seq) of alveolar organoids at P0 and P2 was performed. Single-cell RNA libraries were prepared by using a 10x genomics Chromium device according to the manufacturer’s protocol (Single Cell 3′ Reagent Kits v3.1 or Single Cell 3′ Reagent Kits v3.1(Dual Index)). Alveolar organoids with iMES (iMES-AO) at P0, Alveolar organoids with HFLF at P0 and P2 were prepared using Dual Index Kit TT Set A. iMES-AO at P2 was prepared using Single Index Kit T Set A. The libraries were sequenced using NovaSeq 6000 (Illumina).


title: LCK-mediated RIPK3 Activation Controls Double-Positive Thymocyte Proliferation and Restrains Thymic Lymphoma by Regulating the PP2A-ERK Axis

city: Seoul

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

country: South Korea

institute: Yonsei University

summary: Receptor-interacting protein kinase 3 (RIPK3) is the primary regulator of necroptotic cell death. RIPK3 expression is often silenced in various cancer cells, which suggests that it may have tumor suppressor properties. However, the exact mechanism by which RIPK3 negatively regulates cancer development and progression remains unclear. This report indicates that RIPK3 acts as a potent regulator of homeostatic proliferation of CD4+CD8+ double-positive (DP) thymocytes. Abnormal proliferation of RIPK3-deficient DP thymocytes occurs independently of the well-known role for RIPK3 in necroptosis (upstream of MLKL activation), and is associated with an incidental thymic mass, likely thymic hyperplasia. In addition, Ripk3-null mice developed increased thymic tumor formation accompanied by reduced host survival in the context of a N-ethyl-N-nitrosourea (ENU)-induced tumor model. Moreover, RIPK3 deficiency in p53-null mice promoted thymic lymphoma development via upregulated ERK signaling, which correlated with markedly reduced survival rates. Mechanistically, lymphocyte-specific protein tyrosine kinase (LCK) activates RIPK3, which in turn leads to increases in the phosphatase activity of protein phosphatase 2 (PP2A), thereby suppressing hyper-activation of ERK in DP thymocytes. Overall, these findings suggest that a RIPK3-PP2A-ERK signaling axis regulates DP thymocyte homeostasis and may provide a potential therapeutic target to improve thymic lymphoma therapies.

overall_design: RNA-seq of thymus with p53 or Ripk3 KO

first: Jae-Seok

first: Hwa-Ryeon

last: Kim


title: Generation of human iPS cell-derived mesenchymal cells capable of forming alveolar organoids

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

overall_design: Refer to individual Series


title: ERK signalling orchestrates neural differentiation by promoting the polycomb repressive complex.

city: Dundee

first: Kate

last: Storey

address: Dow Street

department: School of Life Sciences

country: United Kingdom

institute: University of Dundee


title: ERK signalling orchestrates neural differentiation by promoting the polycomb repressive complex [dataset 3]

summary: mRNAseq was examined in human embryonic stem cells (H9) and neuromesodermal progenitors differentiated from these cells in vitro

overall_design: mRNAseq from triplicate samples from human embryonic stem cells (H9) and neuromesodermal progenitors differentiated from these cells in vitro

first: Claudia

middle: I

last: Semprich

first: Vicki

last: Metzis

first: Harshil

last: Patel

first: James

last: Briscoe


title: BAF complex maintains glioma stem cells in pediatric H3K27M-glioma [ChIP-seq]

status: Public on Sep 15 2022

city: Boston

first: Joana

middle: Graca

last: Marques

state: MA

address: 360 Longwood Avenue

institute: Dana-Farber Cancer Institute

summary: Diffuse midline gliomas (DMGs) are uniformly fatal pediatric central nervous system cancers, refractory to standard of care therapeutic modalities. The primary genetic drivers are a set of recurrent amino acid substitutions in genes encoding histone H3 (H3.3 and H3.1, K27M), which are currently undruggable. These H3K27M oncohistones perturb normal chromatin architecture, resulting in an aberrant epigenetic landscape, which we interrogated here for epigenetic dependencies using a CRISPR screen in patient-derived H3K27M-glioma neurospheres. We show that H3K27M-glioma cells are dependent on core components of the mammalian SWI/SNF (BAF) chromatin remodeling complex for maintaining glioma stem cells in a cycling, oligodendrocyte precursor cell (OPC)-like state. Genetic perturbation of the BAF catalytic subunit SMARCA4 (BRG1), as well as pharmacological suppression opposes proliferation, promotes differentiation, and improves overall survival of patient-derived xenograft (PDX) models. In summary, we demonstrate that therapeutic inhibition of BAF complex has translational potential for children with H3K27M-gliomas.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the histone modifications H3K27ac and H3K27me3 as well as for BRG1 in BT869 cells (H3K27M diffuse midline glioma).

first: Eshini

last: Panditharatna

first: Li

last: Jiang

first: Mariella

last: Filbin


title: A signaling pathway for transcriptional regulation of sleep amount in mice

first: Rui

last: Zhou

address: NIBS

institute: NIBS

summary: In mice and humans, sleep quantity of individuals are governed by genetic factors and exhibit age-dependent variations. However, the core molecular pathways and effector mechanisms that regulate sleep time in mammals remain unclear. Here, we characterize a major signaling pathway for transcriptional regulation of sleep quantity in mice by adeno-associated virus-mediated somatic genetics analysis. Adult brain chimeric-knockout of LKB1 kinase, an activator of AMPK-related protein kinase SIK3/SLEEPY, markedly reduces non-rapid eye movement sleep (NREMS) amount and delta power–a measure of sleep depth. Downstream of LKB1-SIK3 pathway, gain or loss-of-function of histone deacetylases HDAC4/5 in adult brain neurons causes bidirectional changes of NREMS amount and delta power. Phosphorylation of HDAC4/5 is regulated in relation to sleep need, and HDAC4 specifically regulates sleep amount in posterior hypothalamus. Genetic and transcriptomic studies reveal that HDAC4 cooperates with CREB in both transcriptional and sleep regulation. These findings introduce the concept of signaling pathways targeting transcription modulators to regulate daily sleep amount and demonstrate utility of somatic genetics in mouse sleep research.

overall_design: 1. Differential expression analysis between ABC-HDAC4CA and mCherry mouse cortex, hypothalamus and thalamus.   2. Differential expression analysis between ABC-CREB and mCherry mouse cortex, hypothalamus and thalamus.  3. Differential expression analysis between Sik3E13∆/+ and WT mouse cortex, hypothalamus and thalamus at ZT0.5 or ZT12.5.  4. Differential expression analysis between HDAC4CA and eGFP expressed Sik3E13∆/+ mouse cortex, hypothalamus and thalamus at ZT0.5 or ZT12.5.  5. Differential expression analysis between CREB and eGFP expressed Sik3E13∆/+ mouse cortex, hypothalamus and thalamus at ZT12.5.  Four biological replicates were prepared for mRNA profiles.

first: Guodong

last: Wang

first: Qi

last: Li

first: Junjie

last: Xu

first: Jiawen

first: Tao

last: Cai

first: Qinghua

last: Liu


title: BAF complex maintains glioma stem cells in pediatric H3K27M-glioma [RNA-seq]

overall_design: Gene expression profiling by bulk RNAseq of BT869 cells upon SMARCA4 knockout or treatment with BAF complex antagonists.


title: The DEAD box RNA helicase DDX42 is an intrinsic inhibitor of positive-strand RNA viruses

city: Evry-Courcouronnes

first: Emmanuel

last: Labaronne

address: Genopôle Campus  4 rue Pierre Fontaine - Pépinière du Génopôle

country: France

institute: ADLIN science

summary: To investigate the impact of DDX42 depletion on the cellular transcriptome, we silenced DDX42 by transfecting siRNAs in U87-MG and A549-ACE2 cells. DDX42-depleted cells were used to perform RNA-seq analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for U87-MG/CD4/CXCR4 and A549-ACE2 cells depleted or not for DDX42. The analysis includes three or two DDX42-targeting siRNAs (for U87-MG/CD4/CXCR4 cells and A549-ACE2 cells, respectively)  and a non-targeting siRNA as control. The analysis was perfomed in three biological replicates

first: Boris

last: Bonaventure

first: Emiliano

last: Ricci

first: Caroline

last: Goujon


title: BAF complex maintains glioma stem cells in pediatric H3K27M-glioma


title: ERK signalling orchestrates neural differentiation by promoting the polycomb repressive complex [dataset 2]

first: Kate

last: Storey

summary: In this experiment, Ring1b occupancy was examined in human neuromesodermal progenitors derived from embryonic stem cells (H9)

overall_design: In this experiment we compared Ring1b ChIP-seq in human embryonic stem cells (H9) and NMP-Ls. Experiments wer done in biological triplicate.

first: Claudia

last: Semprich

first: Vicki

last: Metzis

first: Harshil


title: Cross-lineage Potential of Ascl1 Uncovered by Comparing Diverse Reprogramming Regulatomes [MA Timepoint RNA-seq]

city: Chapel Hill

first: LI

last: QIAN

address: 111 Mason Farm Road, MBRB

department: Department of pathology

institute: UNC

summary: Direct reprogramming has revolutionized the fields of stem cell biology and regenerative medicine. Direct reprogramming makes it possible to interconvert somatic cell fates without intermediary pluripotency. Although studies have identified different transcription factor (TF) cocktails that can reprogram fibroblasts into different cell types, the common mechanisms governing how reprogramming cells undergo transcriptome and epigenome remodeling (i.e. regulatome remodeling) have not been investigated. Here, by characterizing early changes in the regulatome of three different types of direct reprogramming – induced neurons, induced hepatocytes, and induce cardiomyocytes – we identified two non-cocktail TFs, Tead4 and Atf7, that co-operate with reprogramming TFs to regulate target cell-type specific gene expression. Additionally, by identifying shared pro-cardiac features of iN and iCM reprogramming, we demonstrate Ascl1’s cross-lineage potential to induce highly efficient iCM reprogramming in a two-factor cocktail with Mef2c (A+M). Single-cell multi-omics showed that A+M reprogramming terminates in a more mature iCM phenotype than MGT. Finally, through ChIP-seq and RNA-seq, we find that Mef2c drives the shift in Ascl1 binding away from neuronal genes towards cardiac gene, guiding their co-operative epigenetic and transcription activities. These findings demonstrate the existence of common regulators of different direct reprogramming process and argue against the premise that TFs are lineage specific – the basic premise used to develop direct reprogramming approaches.

overall_design: RNA-seq libraries of A+M reprogrammed cells using the Roche KAPA Stranded mRNA-Seq kit

first: Haofei

first: Ben

last: Keepers

first: Jianodng

first: Li

last: Qian


title: Age- and stage-dependent degeneration of Huntington’s disease neurons is linked to declining autophagy mediated by mir-29b-3p

city: Saint Louis

first: Youngmi

last: Oh

state: MO

address: 660 S. Euclid Avenue

department: Development department

institute: Washington University in St. Louis


title: Deletion of adipocyte prohibitin 1 exacerbates high-fat diet-induced steatosis but not liver inflammation and fibrosis

city: Rockville

first: Bin

last: Gao

state: MD

address: 5625 Fishers Lane, Room 2S-33

institute: NIAAA

summary: Adipose tissue dysfunction is closely associated with the development and progression of nonalcoholic fatty liver disease (NAFLD). Recent studies have implied an important role of prohibitin-1 (PHB1) in adipose tissue function. In the current study, we aimed to explore the function of adipocyte PHB1 in the development and progression of NAFLD. The PHB1 protein levels in adipose tissues were markedly decreased in mice fed a high-fat diet (HFD) compared to those fed a chow diet. To explore the function of adipocyte PHB1 in the progression of NAFLD, mice with adipocyte-specific (adipo) deletion of Phb1 (Phb1adipo-/- mice) were generated. Notably, Phb1adipo-/- mice did not develop obesity but displayed severe liver steatosis under HFD feeding. Compared to HFD-fed wild-type (WT) mice, HFD-fed Phb1adipo-/- mice displayed dramatically lower fat mass with significantly decreased levels of total adipose tissue inflammation, including macrophage and neutrophil number as well as the expression of inflammatory mediators. To our surprise, although liver steatosis in Phb1adipo-/- mice was much more severe, liver inflammation and fibrosis were similar to WT mice after HFD feeding. RNA sequencing analyses revealed that the interferon pathway was markedly suppressed while the bone morphogenetic protein 2 pathway was significantly up-regulated in the liver of HFD-fed Phb1adipo-/- mice compared with HFD-fed WT mice. Conclusion: HFD-fed Phb1adipo-/- mice display a subtype of the lean NAFLD phenotype with severe hepatic steatosis despite low adipose mass. This subtype of the lean NAFLD phenotype has similar inflammation and fibrosis as obese NAFLD in HFD-fed WT mice; this is partially due to reduced total adipose tissue inflammation and the hepatic interferon pathway.

overall_design: Phb1adipo-/- and WT mice (male, 7–8 weeks of age) were fed an HFD (60 kcal% fat; D12492; Research Diets, New Brunswick, NJ) for 3 months and sacrificed for analyses.

first: Yukun

last: Guan

first: Xiaolin


title: Age- and stage-dependent degeneration of Huntington’s disease neurons is linked to declining autophagy mediated by mir-29b-3p (Figure 5, 7 and S4)

summary: Direct neuronal conversion of fibroblasts from Huntington’s disease (HD) patients to striatal medium spiny neurons (MSNs) has been shown to recapitulate neurodegenerative pathology of HD. Here, we carried out comparative analyses between reprogrammed MSNs from patients at different disease stages to investigate age-associated molecular processes driving neurodegeneration. We found that neuronal death was manifested in reprogrammed MSNs from symptomatic HD patients (HD-MSNs) compared to MSNs derived from younger, pre-symptomatic patients (pre-HD-MSNs) and healthy controls. Dissecting the differential cellular state between HD-MSNs and pre-HD-MSNs by transcriptome and chromatin accessibility analyses identified miR-29b-3p, whose age-associated upregulation impairs autophagic function via human-specific targeting of STAT3. Reducing miR-29b-3p or treating with G2-115, a glibenclamide analog, increased the resilience of HD-MSNs against neurodegeneration by promoting autophagy, demonstrating that the autophagic decline during aging in HD underlies MSN degeneration and pointing to potential approaches for enhancing autophagy and resilience of MSNs against degeneration in HD.

overall_design: To delineate cellular events underlying HD-MSN degeneration, we compared the transcriptomes of pre-HD-MSNs (six independent patients), HD-MSNs (six independent patients), young-Ctrl-MSNs (six independent samples), and old-Ctrl-MSNs (six independent samples) by RNA-seq (all with triple biological replicates, 72 samples total).

first: Young

middle: M

first: Seong

middle: W

last: Lee

first: Woo

last: Kim

first: Andrew

last: Yoo


title: Age-related Huntington's disease progression modeled in directly reprogrammed patient-derived striatal neurons highlights impaired autophagy (Figure 2 and S2)

first: Tiandao

last: Li

first: Bo

last: Zhang


title: Cross-lineage Potential of Ascl1 Uncovered by Comparing Diverse Reprogramming Regulatomes [scRNA-seq]

overall_design: Single-cell RNA-seq profiles of A+M infected and MGT infected fibroblast were generated at day 3 post infection by 10x Genomics Chromium System.

last: Wang

first: Benjamin

last: keepers

first: Jiandong

last: Liu


title: In vivo single cell transcriptomics reveals Klebsiella pneumoniae-governed polarization of ontogenetically distinct macrophage lineages by targeting an evolutionary conserved type I IFN-IL10-STAT6 axis to promote infection.

city: Belfast

first: Jose

last: Bengoechea

state: Northern Ireland

address: 97 Lisburn Road

department: WWIEM

institute: Queen's University Belfast

summary: Mice were infected with Klebsiella pneumoniae and interstitial and alveolar macrophages isolated and subjected to single cell RNA sequencing to investigate the transcriptomes of Klebseilla-associated and uninfected bystander cells.

overall_design: C57BL/6 age and sex matched animals  were infected intranasally  with  K. pneumoniae Kp52145 expressing mCherry  After 24 h, lungs were homogenized, pooled and red cells lysed  before pre-sorting using CD11c Microbeads, UltraPure (Miltenyi Biotech) according to manufacturer’s instructions. Cell suspensions were incubated with combinations of the following rat anti-mouse antibodies: against cell surface markers Ly6C APC/Cy7 (clone HK1.4, Ref: 128026), CD11b APC (Ref: 101212), CD11c Pacific Blue (Ref: 117322), SiglecF FITC (Ref: 155504, BioLegend).  Ly6C+CD11b+CD11c+SIGLECF- Interstitial Macrophages (IMs) and Ly6C+CD11b-CD11c+Siglec F+ Alveoar macrophages (AMs) were sorted from PBS control mice. From infected animals, four separate populations were retrieved namely IMs associated with Kp52145 (Ly6C+CD11b+CD11c+SIGLECF-Kp52145+), bystander IMs (Ly6C+CD11b+CD11c+SIGLECF-Kp52145-), Kp52145-associated AMs (Ly6C+CD11b-CD11c+Siglec F+Kp52145+) and bystander AMs (Ly6C+CD11b-CD11c+Siglec F+Kp52145-) populations.

first: Amy

last: Dumigan

first: Oisín

last: Cappa

first: Brenda

last: Morris

first: Joana

last: Sá Pessoa

first: Ricardo

last: Calderon-Gonzalez

first: Grant

last: Mills

first: Rebecca

last: Lancaster

first: David

last: Simpson

first: Adrien

last: Kissenpfennig

middle: A


title: Cross-lineage Potential of Ascl1 Uncovered by Comparing Diverse Reprogramming Regulatomes

first: LI

last: QIAN


title: Cross-lineage Potential of Ascl1 Uncovered by Comparing Diverse Reprogramming Regulatomes [ChIP-seq II]

overall_design: H3K27ac, Ascl1, and Mef2c ChIP-seq libraries of Mef2c infected, Ascl1 infected, A+M infected, and MGT infected fibroblast were generated at day 3 post infection  using published ChIP-seq protocol

first: Haofei

first: Li

last: Qian


title: Cross-lineage Potential of Ascl1 Uncovered by Comparing Diverse Reprogramming Regulatomes [RNA-seq III]

overall_design: RNA-seq libraries of neonatal cardiomyocytes using the Roche KAPA Stranded mRNA-Seq kit


title: Cross-lineage Potential of Ascl1 Uncovered by Comparing Diverse Reprogramming Regulatomes [RNA-seq II]

overall_design: RNA-seq libraries of iN, IHep, and iCM were generated at day 3 post infection  using  the Roche KAPA Stranded mRNA-Seq kit


title: Cross-lineage Potential of Ascl1 Uncovered by Comparing Diverse Reprogramming Regulatomes [scATAC-seq]

overall_design: Single-cellATAC-seq profiles of A+M infected and MGT infected fibroblast were generated at day 3 post infection by 10x Genomics Chromium System.


title: Cross-lineage Potential of Ascl1 Uncovered by Comparing Diverse Reprogramming Regulatomes [RNA-seq I]

overall_design: RNA-seq libraries of Mef2c infected, Ascl1 infected, A+M infected, and MGT infected fibroblast were generated at day 3 post infection using the Roche KAPA Stranded mRNA-Seq kit


title: The hypoxia induced changes in miRNA in RNA-induced silencing complexes and HIFs induced miRNAs in human endothelial cells

city: GDANSK

first: Rafal

last: Bartoszewski

address: Hallera 107

country: Poland

institute: Medical University of Gdansk

type: Non-coding RNA profiling by high throughput sequencing

summary: What governs the transition between the two HIFs (the HIF switch) and the role of miRNAs in this regulation is not completely clear. Using genome-wide expression studies on the miRNA content of RNA-induced silencing complex (RISC) in HUVECs exposed to hypoxia compared to the global miRNA-Seq analysis revealed dramatic differences between the two. In our analyses, compared the miRNA and mRNA levels in RISC at 2 hours (mainly HIF-1 driven), 8 hours (HIF-1 and HIF-2 elevated), and 16 hours (mainly HIF-2 driven) in a gene ontology context. This allowed for determining the direct impact of the miRNAs in modulating the cellular signaling pathways involved in the adaptive response. Furthermore, we demonstrate that the hypoxic levels of the vast majority of HIF-1-dependent miRNAs (including miR-210-3p) are also HIF-2 dependent, and that HIF-2 specifically governs the expression of 11 specific miRNAs

overall_design: Examination of miRNA profiles in HUVECs exposed to hypoxia, hypoxia mimetics, with and without HIF1A and EPAS1 silencing


title: Cross-lineage Potential of Ascl1 Uncovered by Comparing Diverse Reprogramming Regulatomes [ChIP-seq I]

overall_design: H3K27ac ChIP-seq libraries of iN, IHep, and iCM were generated at day 3 post infection  using published ChIP-seq protocol


title: The hypoxia induced changes in mRNA in RNA-induced silencing complexes  in hypoxia exposed human endothelial cells

overall_design: Examination of mRNA profiles in HUVECs exposed to hypoxia, hypoxia mimetics, with and without HIF1A and EPAS1 silencing


title: Treatment of human polymorphonuclear neutrophils with platelet-derived mitochondria or damage-associated molecular patterns

city: Moncton

first: Eric

middle: P

last: Allain

state: New Brunswick

address: 330 University ave

department: Medical Genetics

institute: Vitalité Health Network

summary: Inflammation is an essential process of the host defense against infections, illness, or tissue injuries. However, unregulated inflammation has been associated with chronic inflammatory autoimmune diseases, such as rheumatoid arthritis, multiple sclerosis, and atherosclerosis. Polymorphonuclear neutrophils (PMNL) are amongst the first immune cells involved in the acute inflammatory response used to fight bacterial infections. Once activated, PMNL releases inflammatory mediators, enzymes and large quantities of microparticles in the extracellular milieu to recruit various immune cells required to fight the invading pathogens. Recent evidence also shows that platelets (PLTs), well known for their coagulation proprieties, are also implicated in the body’s inflammatory response. Interestingly, activated PLTs can release fully functional mitochondria in the extracellular milieu. Known as the powerhouse of the cell, the mitochondria share similar characteristics with bacteria. Therefore, we hypothesize that PLTs-derived mitochondria present in the extracellular milieu, acting in a similar way as bacteria, induce a sterile inflammatory response that involves the PMNL. The objective of this study was to investigate the sterile inflammatory response of PMNL caused by the exposure to PLTs-derived extracellular mitochondria. Blood was obtained from healthy consenting donors, then PMNL and PLTs-derived mitochondria were isolated and purified. Following the co-incubation of PMNL with various physiological doses of PLTs-derived mitochondria, a characterization of the interaction between PMNL and PLTs-derived mitochondria and an investigation of the inflammatory proprieties of PMNL were performed using flow cytometry, transmission electron microscopy, and high-resolution respirometry. While the transcriptomic analysis indicated that several mitochondrial genes had increased expression, no mitochondrial-dependent increase in oxygen consumption was observed by high-resolution respirometry experiments. However, our data show that PLTs-derived mitochondria significantly induce, in a dose-dependent manner, the release of PMNL microparticles. This study provides new insight into the role of PLTs-derived mitochondria in the context of sterile inflammation.

overall_design: PMNLs were freshly isolated and treated with either platelet-derived mitochondria or DAMPs. Controls were untreated resting PMNLs. RNA was subsequently extracted and subjected to rRNA-depletion, library preperation and RNA-sequencing.

first: Luc

last: Boudreau

first: Marie-France

middle: N

last: Soucy

first: Jacob

last: Léger

first: Robert

last: Foulem

first: Marc

last: Surette


title: Selective targeting of visceral adiposity by polycation nanomedicine

first: Kam

last: Leong

address: 3600 Broadway, RM450C

department: Biomedical Engineering

institute: Columbia University

summary: Obesity is a pandemic health problem with poor solutions, especially for targeted treatment. Here we develop a polycation-based nanomedicine to selectively target visceral adiposity, the more metabolically detrimental and manipulation-resistant fat. We demonstrated that the polycationic polymer polyamidoamine (PAMAM) generation 3 (P-G3) was specifically enriched in the visceral fat due to its high charge density when delivered intraperitoneally. Moreover, P-G3 treatment of obese mice inhibited visceral adiposity, increased energy expenditure, prevented obesity, and alleviated the associated metabolic dysfunctions. In vitro adipogenesis models and single-cell RNA sequencing (scRNA-seq) revealed that P-G3 paradoxically uncouples the defining function of adipocyte - lipid synthesis and storage - from adipocyte development to create unique “dwarf” adipocytes that possess normal adipocyte functions but are deficient in hypertrophic growth at least through synergistically modulating NAD and mTOR pathways. The visceral fat distribution of P-G3 was further enhanced by modifying P-G3 with cholesterol to form lipophilic nanoparticles, which were also effective in treating obesity. Our study highlights an unexpected strategy to tackle visceral adiposity and champions a new direction of exploring cationic nanomaterials for treating metabolic diseases.

overall_design: 3T3-L1 cells were cultured and differentiated into adipocytes. Cells (treated with or without PAMAM polymers) were collected at differentiation Day 0, 3, and 6 as preadipocytes, early adipogenesis, and mature adipocytes for single cell sequencing.

first: Wan

last: Qianfen

first: Huang

last: Baoding

first: Xiao

last: Yang

first: Qiang

last: Li


title: ERK signalling orchestrates neural differentiation by promoting the polycomb repressive complex [dataset 1]

first: Kate

last: Storey

summary: In this experiment patterns of chromatin accessibility were compared in (H9) human ES cell derived neuromesodermal progenitors (NMP-L)s and derived neural progenitors (NP)s at different days during the neural differentiation procedure (day 5, day 6 and day 8) and also  in NPs at day 5 and 6 exposed to carrier control with DMSO or the MEK inhibitor PD184352.

overall_design: In this experiment we compared chromatin accessibility in NMP-Ls, NPs day 5, day 6 and day 8 as well as in NPs day 5 and 6 with DMSO or MEK inhibtor treatment. Experiments wer done in biological duplicates. With untreated and DMSO treated cells fuctioning as the controls for MEK inhibitor treated cells.

first: Claudia

last: Semprich

first: Vicki

last: Metzis

first: Harshil

last: Patel

first: James

last: Briscoe


title: TCR repertoire sequencing analysis using  RNA on fibrotic livers

city: Zurich

first: Jing

last: Chen

state: Other

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zurich

summary:
Fibrosis is the final path of nearly every form of chronic disease and accounts for up to 45% of all deaths in the developed world. However, antifibrotic therapies that target fibrogenic cells are lacking. We tested whether specific immunization against ADAM12 can elicit an antigen-specific cytotoxic T cell response to ameliorate liver fibrosis. In this study, we performed T cell receptor (TCR) alpha- and beta-chain repertoire sequencing on fibrotic livers to further characterize the T cell response and to detect potential TCR clonotypes.
We observed TCR clonality of liver-infiltrating T cells from v-A12- and control-vaccinated mice with minimal overlap to v-CTRL mice in two α-chain sequences. However, the vast majority of expanded clones from v-A12-vaccinated animals showed a unique sequence pattern. Moreover, there was no overlap in the β-chain sequences between v-A12-vaccinated and control mice, suggesting a vaccination-induced expansion of antigen-specific TCR clonotypes.

overall_design: Livers were collected and used for total RNA extraction. Then total RNA was used for TCR alpha- and beta-chain sequencing. Comparative gene expression analysis of TCR alpha- and beta-chain seq data for livers from these four groups (sham_ v-CTRL, sham_v-A12, CCl4_v-CTRL and CCl4_v-A12) were performed.

first: Christian

last: Stockmann

first: Michal

last: Sobecki

first: Ewelina

last: Krzywinska


title: Differential gene expressionin cMet-enriched T cell populations

city: London

first: Federica

last: Marelli-Berg

address: Charterhouse Square

department: William Harvey Research Institute

institute: Centre for Biochemical Pharmacology  Heart Centre

summary: Control (cMet+ T cells less than 0.5%) and cMet-enriched (7%) T cells were activated with plate-bound anti-CD3/CD28 and gene tracription was measured

overall_design: Federica,Marelli-Berg

first: Eriomina

last: Shahaj

first: Kevin

last: Blighe


title: DNA replication timing directly regulates the frequency of oncogenic chromosomal translocations [RNA-seq]

city: Vienna

first: Tobias

last: Neumann

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

summary: Many cancers originate from misregulation of gene expression caused by chromosomal translocations which result from ligation of DNA double-strand breaks (DSBs). Indeed, translocations may be causal in ~20% of human cancer morbidity 1. Although the sources of DSBs are numerous2-5, we have virtually no knowledge of the steps linking DSB formation to DSB ligation. Here, we show that early replication timing of translocation partner loci, mediated by the activity of replication origins, is a critical regulator of lymphomagenic Myc translocations generated by activation-induced deaminase (AID) during antibody maturation in B-cells. Reduced levels of the replicative helicase, the minichromosome maintenance (MCM) complex6, impairs translocation genesis, decreases firing of replication origins at AID target genes and globally abrogates the replication timing program without altering cell proliferation, gene expression or genome architecture. Strikingly, deleting a single origin of replication at Myc induces a switch from early-to-late replication at Myc with concomitantly impaired translocation frequency. This phenotype is reversed by restoring early replication at Myc thereby demonstrating a direct, causal role of replication origin activity and replication timing in translocation genesis. Finally, this replication timing-mediated step acts downstream of DSBs and is independent of DSB frequency, constituting a novel regulatory step in translocation biogenesis.

overall_design: RNA-Seq LacZ and Mcm infected CH12 cells and C13 and C23 clones

first: Mihaela

last: Peycheva

first: Daniel

last: Malzl

first: Mariia

last: Nazarova

first: Ursula

last: Schoeberl

first: Rushad

last: Pavri


title: DNA replication timing directly regulates the frequency of oncogenic chromosomal translocations [PRO-cap]

overall_design: PRO-cap of WT CH12 cells


title: DNA replication timing directly regulates the frequency of oncogenic chromosomal translocations [Repli-seq]

overall_design: Repli-seq in LacZ and Mcm infected CH12 cells and C13, C2ki and C13ki clones


title: DNA replication timing directly regulates the frequency of oncogenic chromosomal translocations [SNS-seq]

overall_design: SNS-seq inLacZ and Mcm infected CH12 cells


title: BAF complex maintains glioma stem cells in pediatric H3K27M-glioma [ATAC-seq]

first: Joana

last: Marques

overall_design: DNA accessibility assessed by ATACseq of BT869 cells upon SMARCA4 knockout or treatment with BRG1 antagonists.

first: Eshini

last: Panditharatna

first: Li

last: Jiang

first: Caleb

last: Lareau

first: Mariella

last: Filbin


title: In vivo G-CSF Treatment Activates GR-SOCS1 Axis Suppressing IFN-γ Secretion by Natural Killer Cells [CUT&TAG]

status: Public on Sep 14 2022

city: Beijing

first: Ting

last: Peng

address: Beijing haidiang

institute: PKU

summary: Natural killer (NK) cells are lymphocytes of the innate immune system that are involved in controlling tumors or microbial infections through the production of interferon gamma (IFN-γ). Granulocyte-colony stimulating factor (G-CSF) inhibits IFN-γ secretion by NK cells, but the mechanism underlying this effect remains unclear. Here, by comparing the multi-omics profiles of human NK cells before and after in vivo G-CSF treatment, we identified a pathway that was activated in response to G-CSF treatment, which suppressed IFN-γ secretion in NK cells. Specifically, our integrative genomic strategy revealed glucocorticoid receptor (GR) activation in NK cells that mediated the genomic response to G-CSF treatment. Activated GRs can inhibit secretion of IFN-γ by promoting interactions between suppressor of cytokine signaling 1 (SOCS1) promoter and enhancer, as well as increase the expression of SOCS1. Experiments in mice confirmed that G-CSF in vivo treatment significantly down-regulated IFN-γ secretion and up-regulated GR and SOCS1 expression in NK cells. In addition, GR blockade (RU486) significantly reversed the effects of G-CSF, demonstrating that GR up-regulates SOCS1 and inhibits the production of IFN-γ by NK cells.

overall_design: This study was designed to explore the mechanism of the suppression effect  of G-CSF on IFN-γ production. To this end, we generated multi-omics profile of HSC donor derived bone marrow NK cells before and after G-CSF treatment and further validated our findings in mice.


title: DNA replication timing directly regulates the frequency of oncogenic chromosomal translocations

summary: Chromosomal translocations result from the joining of DNA double-strand breaks (DSBs) and frequentlycause cancer. However, the steps linking DSB formation to DSB ligation remain undeciphered. Wereport that DNA replication timing (RT) directly regulates lymphomagenicMyctranslocations duringantibody maturation in B cells downstream of DSBs and independently of DSB frequency. Depletion ofminichromosome maintenance complexes alters replication origin activity, decreases translocations,and deregulates global RT. Ablating a single origin atMyccauses an early-to-late RT switch, loss oftranslocations, and reduced proximity with the immunoglobulin heavy chain (Igh) gene, its majortranslocation partner. These phenotypes were reversed by restoring early RT. Disruption of early RT alsoreduced tumorigenic translocations in human leukemic cells. Thus, RT constitutes a general mechanismin translocation biogenesis linking DSB formation to DSB ligation.

overall_design: LAM-HTGTS  in LacZ and Mcm infected CH12 cells, C13 deltaori and C23 deltaori clones, C13 restored and C2 restored clones using a Myc-bait;  LacZ and Mcm infected CH12 cells, C13 deltaori and C13 restored clones using a Irf2bp2-bait


title: RNAseq in lung cancer pneumospheres treated with PD-L1s

city: Milano

first: Matteo

last: Cereda

address: Via Celoria, 26

department: Biosciences

country: Italy

institute: University of Milan

summary: We evaluated the differential expression of protein coding genes in NSCLC pneumospheres upon treatment  with PD-L1s

overall_design: Pneumospheres were generated seeding NSCLC cells in Ultra-Low Attachment flasks, in serum free DMEM-F12 medium containing fibroblast growth factor, epithelial growth factor and B-27™ Supplement. NSCLC pneumospheres were stimulated by synthetic PD-L1 soluble form (PD-L1s) (25 μg/ml, R&D system) in 0% FBS culture medium for 15 min.

first: Dario

last: Sangiolo

first: Ramona

last: Rotolo

first: Valeria

last: Leuci

first: Chiara

last: Donini

last: Galvagno

first: Serena

last: Peirone


title: In vivo G-CSF Treatment Activates GR-SOCS1 Axis Suppressing IFN-γ Secretion by Natural Killer Cells [RNA-seq]


title: Gene expression data from 1 year old Hdc+/+ and Hdc-/- stomach.

first: Kwang

last: Kim

address: 50 Yonsei-ro

institute: Yonsei University College of Medicine

summary:
Histamine defeciency result to hypertrophic gastropathy in the stomach.  We use  gene array to distover the major cause of stomach lesion in Hdc-/-.
Tesult shows that chronic inflammation and dysregulation of macrophage functions are the major trigger for hypertrophic gastropathy in Hdc--/- stomach.

overall_design: RNA from one year old Hdc+/+ and Hdc-/- FVB mouse stomach tissues were extracted and hybridization on Affymetrix microarrays.

first: Soo

last: Cho


title: DNA replication timing directly regulates the frequency of oncogenic chromosomal translocations [HiC]

first: Tobias

last: Neumann

overall_design: HiC in LacZ and Mcm infected CH12 cells and C13 clone

first: Mihaela

last: Peycheva

first: Daniel

last: Malzl

first: Mariia

last: Nazarova

last: Schoeberl


title: TBX20 Consolidates Cardiac Reprogramming Factors to Enhance Contractility and Energy Metabolism in Human Induced Cardiomyocytes [ATAC-Seq]

city: Birmingham

first: Changde

last: Cheng

state: Alabama

address: 1824 6th Ave S, WTI 510G

department: Department of Medicine - Hematology & Oncology

institute: The University of Alabama at Birmingham

summary: Background: Direct cardiac reprogramming of fibroblasts into cardiomyocytes has emerged as one of the promising strategies to remuscularize the injured myocardium. Yet, it is still insufficient to generate functional induced cardiomyocytes (iCMs) from human fibroblasts using conventional reprogramming cocktails, such as our previously published combination consisting of MEF2C, GATA4, TBX5 and microRNA miR-133 (MGT133).   Results: To discover potential missing factors for human direct reprogramming, we performed transcriptomic comparison between human iCMs and functional cardiomyocytes (CMs). We identified T-box transcription factor TBX20 as the top CM gene that is unable to be activated by MGT133. TBX20 is required for normal heart development and cardiac function in adult CMs but its role on cardiac reprogramming remains undefined. Here, we found that transduction of MGT133+TBX20 in human cardiac fibroblasts resulted in enhanced reprogramming featured with significantly activated contractility gene programs and signatures more similar to ventricular CMs. Human iCMs produced with MGT133+TBX20 more frequently demonstrated beating and calcium oscillation in co-culture with pluripotent stem cell derived CMs. More mitochondria and higher mitochondrial respiration were also detected in iCMs after TBX20 overexpression. Mechanistically, comprehensive transcriptomic, chromatin occupancy and epigenomic integration revealed that TBX20 localized to the cis-regulatory enhancers of under-expressed cardiac genes, such as MYBPC3, MYH7 and MYL4, to activate gene expression via strengthening the occupancy and co-occupancy of transcription factors. Furthermore, we identified TBX20-regulated enhancers and confirmed the synergistic effect of MGT and TBX20 on enhancer activation.   Conclusions: TBX20 promotes cardiac cell fate conversion via direct activating cardiac enhancers. Human iCMs generated with TBX20 showed enhanced cardiac function in terms of contractility and mitochondrial respiration.

overall_design: Examination of genome-wide accessibility of induced cardiomyocytes derived from human fibroblasts.  Biological triplicate were used for statistical analysis.

first: Yawen

last: Tang

first: Sajesan

last: Aryal

first: Rui

last: Lu

first: Yang

last: Zhou


title: In vivo G-CSF Treatment Activates GR-SOCS1 Axis Suppressing IFN-γ Secretion by Natural Killer Cells [Hi-C]

first: Ting

last: Peng


title: TBX20 Consolidates Cardiac Reprogramming Factors to Enhance Contractility and Energy Metabolism in Human Induced Cardiomyocytes [RNA-Seq]

overall_design: Time Course mRNA profiles in human induced cardiomyocytes at reprogramming day 0, 3, 9 and 14. RNA-seq analyses were performed with three biological replicates.


title: TBX20 Consolidates Cardiac Reprogramming Factors to Enhance Contractility and Energy Metabolism in Human Induced Cardiomyocytes [scRNA-Seq]

overall_design: Single cell transcriptomic analysis of human induced cardiomyocytes


title: Effect of inactivation of Mst1 and Mst2 in the mouse adrenal cortex

city: Saint-Hyacinthe

first: Nour

last: Abou Nader

state: Québec

address: 3200 rue sicotte

department: Biomédecine vétérinaire

institute: Université de Montréal

summary:
The Hippo Pathway has been found to play an important role in adrenal gland development and maintenance in mice.
In this study, we further explored the role of the Hippo pathway in the adrenal gland using a transgenic mouse model where we knocked out the upstream kinases of the pathway, Mst1 and Mst2.

overall_design: Nr5a1-Cre and Mst1(flox/flox);Mst2(flox/flox) were selectively bred over generations to obtain Mst1(flox/flox);Mst2(flox/flox);Nr5a1-Cre mutant mice. Controls are considered the Mst1(flox/flox);Mst2(flox/flox) mice. At 2 months of age, mice were dissected and adrenal glands were isolated and conserved at -80°C.

first: Alexandre

last: Boyer


title: Comparative Study of the Expression Profiles of miRNAs of Milk-Derived Exosomes of Yak and Jeryak

status: Public on Sep 13 2022

city: Lanzhou

first: Xingdong

last: Wang

state: 未选择

address: No.335 Jiangouyan, Qilihe District

institute: CAAS: Chinese Academy of Agricultural Sciences

summary: The Jeryak is the hybrid offspring of yaks and Jersey cattle and exhibit improved milk and meat yields. Biomolecules carried within milk exosomes are important for cell growth, development, immune regulation, and various pathophysiological processes. Previous studies showed that miRNAs regulate mammary gland development, lactation, and milk quality. This study explored the relationship between milk exosomes miRNAs and lactation performance. A comparison of the milk content showed that yak milk was of a better quality compared to Jeryak milk (casein, fat, TS, SNF, lactose). Milk collected in December was superior to that collected in June for both yak and Jeryak, except for lactose concentrations. Exosomes were extracted by density gradient centrifugation and miRNA expression profiles in milk exosomes from three yaks and three Jeryaks collected in June and December were detected by small RNA sequencing. In all, 22, 120, 78, and 62 differentially expressed miRNAs (DEMs) were identified in Jun_ JY vs. Jun_ Y (P1: Jeryak in June vs. Yak in June), Jun_ JY vs. Dec_ JY (P2: Jeryak in June vs. Jeryak in December), Dec_ JY vs. Dec_ Y (P3: Jeryak in December vs. Yak in December), and Jun_ Y vs. Dec_ Y (P4: Yak in June vs. Yak in December) groups. These DEMs were enriched in functions and signaling pathways related to lactation performance. In conclusion, these findings are a reference tool to study the molecular basis of lactation performance.

sample_organism:
Bos grunniens
Bos grunniens x Bos taurus

overall_design: miRNA sequencing of milk exosomes of yak and Jeryak in June and December

first: Wenwen

last: Ren

first: Ping

last: Yan

first: Chunnian

last: Liang


title: Development of the chicken lateral plate mesoderm and forelimb mesenchyme

city: Clayton

first: Axel

last: Newton

state: Victoria

address: 19 Innovation Walk

country: Australia

institute: Monash University

summary: The lateral plate mesoderm (LPM) is a transient tissue that produces a diverse range of differentiated structures, including the limbs. However, the molecular mechanisms that drive early LPM specification and development are poorly understood. In this study, we utilize single-cell transcriptomics to define the cell-fate decisions directing LPM specification, subdivision, and early initiation of the forelimb mesenchyme in chicken embryos. We establish a transcriptional atlas and global cell-cell signalling interactions in progenitor, transitional and mature cell types throughout the developing forelimb field.

overall_design: This dataset contains single cells from developing chicken forelimb field tissues covering embryonic days 1.5, 2.5 and 3.5 or stages HH10, HH14 and HH18 respectively. Cells were isolated and barcoded using the 10x Chromium platform

first: Sarah

last: Williams

first: Andrew

middle: T

last: Major

first: Craig

last: Smith


title: Differential DNA Methylation Drives Allelic Architecture for Grb10-Ddc Locus in the Developing Heart

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: While it is understood that the genome is organized into large domains, little is known about cell-type specific interactions at individual loci in mammalian development. Imprinted loci represent a compelling feature of chromatin conformation, illustrating how genes are controlled in local domains to drive parental-specific transcriptional programs important for growth: a clear example being the imprinted Grb10-Ddc locus. Using hybrid mouse crosses and genetic engineering, we uncovered an insulator at Grb10 that is tissue-specific and dynamically controlled by DNA methylation. Insulator CBR2.3 acquires paternal-specific hypomethylation post-implantation, assembling a higher-order structure on the paternal chromosome. Deletion of paternal CBR2.3 converts the chromatin domain to the maternal configuration, redirecting Grb10-Ddc enhancer function, resulting in major cardiac phenotypes. We conclude that CBR2.3 functions as a shared, paternal and tissue-specific insulator for Grb10-Ddc expression in heart, contributing to fundamentally different chromosomal conformations that impact enhancer activity in vivo.

overall_design: Capture-C on F1 hybrid hearts derived from reciprocal crosses between C57BL/6 (B6) mice and animals homozygous for the Japanese Fancy (JF1/Ms) strain.

first: Aimee

last: Juan

first: Yee

middle: H

last: Foong

first: Joanne

last: Thorvaldsen

first: Nicolae

last: Leu

first: Joel

last: Rurik

first: Li

last: Li

first: Casey

last: Rosier

first: Jonathan

last: Epstein

first: Marisa

last: Bartolomei


title: In vivo G-CSF Treatment Activates GR-SOCS1 Axis Suppressing IFN-γ Secretion by Natural Killer Cells [ATAC-seq]

first: Ting

last: Peng


title: IKBKE contributes to neuropsychiatric manifestations in lupus-prone mice

city: Sapporo

first: Kohei

last: Karino

state: Hokkaido

address: Kita 15, Nishi 7, Kita-ku

institute: Hokkaido university

summary:
Objectives. Systemic lupus erythematosus (SLE) is a systemic autoimmune disease characterized by multi-organ dysfunction. Neuropsychiatric SLE (NPSLE) occurs in 30~40% of patients with lupus and is the most severe presentation of SLE, frequently resulting in limitation of daily life. Recent studies have shown that microglia, tissue-resident macrophages in the central nervous system, are involved in the pathogenesis of NPSLE. Herein, we explored new therapeutic targets for NPSLE focusing on microglia.
Methods. RNA sequencing of microglia in MRL/lpr, lupus-prone mice, as well as that of microglia cultured in vitro with cytokines were performed. A candidate gene, which could be a therapeutic target for NPSLE, was identified and its role on microglial activation and phagocytosis was investigated using specific inhibitors and siRNA. The effect of intracerebroventricular administration of the inhibitor on the behavioural abnormalities of MRL/lpr was also evaluated.
Results. Transcriptome analysis revealed the upregulation of Ikbke, which encodes the inhibitor of nuclear factor kappa-B kinase epsilon (IKBKE) in both microglia from MRL/lpr mice and cytokine-stimulated microglia in vitro. Intracerebroventricular administration of an IKBKE inhibitor ameliorated cognitive function and suppressed microglial activation in MRL/lpr mice. Mechanistically, IKBKE inhibition reduced glycolysis, which dampened microglial activation and phagocytosis.
Conclusions. These findings suggest that IKBKE plays a vital role in the pathogenesis of NPSLE via microglial activation, and it could serve as a therapeutic target for NPSLE.

overall_design: Microglial RNA profiles of 16-week old MRL/lpr, 16-week old MRL/MpJ, neonatal MRL/lpr stimulated with  with IFNg, IL-6, IFNa and TNFa alone or in a mixture.  3 samples per group.

first: Michihito

last: Kono

first: Yuki

last: Kudo

first: Masatoshi

last: Kanda

first: Shuhei

last: Takeyama

first: Nobuya

last: Abe

first: Kuniyuki

last: Aso

first: Yuichiro

last: Fujieda

first: Masaru

last: Kato

first: Kenji

last: Oku

first: Olga

last: Amengual

first: Tatsuya

last: Atsumi


title: Generation and comparative analysis of an Itga8-CreERT2 mouse with preferential activity in vascular smooth muscle cells

city: Augusta

first: Ganesh

middle: Daulatrao

last: Warthi

state: Georgia

address: 1460 Laney Walker BLVD

department: Vascular biology Center

institute: Augusta University

summary: All current smooth muscle cell (SMC) restricted Cre mice recombine floxed alleles in vascular and visceral SMCs. We generated a tamoxifen-inducible CreERT2 mouse, Itga8-CreERT2, and compared its activity to the widely used Myh11-CreERT2 mouse. Both CreERT2 mice showed similar activity in vascular SMCs; however, Itga8-CreERT2 displayed low activity in visceral SMC-containing tissues (e.g., intestine). Myh11-CreERT2 (but not Itga8-CreERT2) mice exhibited high levels of CreERT2 protein, tamoxifen-independent activity, and an altered transcriptome. Whereas Myh11-CreERT2-mediated knockout of Srf resulted in a lethal intestinal phenotype, loss of Srf with Itga8-CreERT2 (SrfItga8) revealed viable mice with attenuated vascular SMC contractile gene expression, but no evidence of intestinal pathology. Male and female SrfItga8 mice presented with vascular contractile incompetence; however, only male SrfItga8 mice showed systemic changes in blood pressure. These results establish the Itga8-CreERT2 mouse as an alternative to existing SMC Cre strains where gene loss may result in visceral myopathies that obfuscate accurate phenotyping in vascular SMCs.

first: Joseph

last: Miano

first: Qing

middle: R

last: Lyu


title: Comparative genomics of melanoma subtypes

city: Herston

first: Felicity

last: Newell

address: 300 Herston Rd

institute: QIMR Berghofer Medical Research Institute

type: Methylation profiling by genome tiling array

summary: This study examined whole genome sequencing, RNAseq and methylation data for melanoma subtypes. Illumina MethylationEPIC BeadChip array analysis of 144 melanoma tumors was carried out as part of the study.

overall_design: Illumina Infinium MethylationEPIC BeadChip array analysis of 144 melanoma tumours.

first: Peter

last: Johansson

first: James

last: Wilmott

first: Katia

last: Nones

first: Vanessa

last: Lakis

first: Antonia

last: Pritchard

first: Serigne

last: Lo

first: Robert

middle: V

last: Rawson

first: Stephen

last: Kazakoff

first: Andrew

middle: J

last: Colebatch

first: Lambros

last: Koufariotis

last: Ferguson

first: Scott

last: Wood

first: Conrad

last: Leonard

first: Matthew

last: Law

first: Kelly

last: Brooks

first: Natasa

last: Broit

first: Jane

last: Palmer

first: Kasey

last: Couts

first: Ismael

last: Vergara

first: Georgina

last: Long

last: Barbour

first: Omgo

middle: E

last: Nieweg

first: Brindha

last: Shivalingam

first: William

last: Robinson

first: Jonathan

last: Stretch

last: Spillane

first: Robyn

last: Saw

first: Kerwin

middle: F

last: Shannon

first: John

last: Thompson

first: Graham

last: Mann

last: Pearson

first: Richard

last: Scolyer

first: Nicola

last: Waddell

first: Nicholas


title: An altered basis of tRNA processing is linked to a distinct La protein in T. thermophila

city: Sherbrooke

first: Étienne

last: Fafard-Couture

address: 3201 Jean-Mignault

department: Biochemistry and functional genomics

institute: University of Sherbrooke

summary: La proteins bind the UUU-3’OH sequence found at the 3’-end of nascent RNA polymerase III transcripts, including pre-tRNAs, using a tandem arrangement of a winged-helix fold La motif (LaM) and an adjacent RNA recognition motif (RRM). La binding in diverse species results in protection of the 3’-end from exonucleases, stabilization of the pre-tRNA species and promotion of pre-tRNA folding until the UUU-3’OH containing trailer is endonucleolytically cleaved. Based on sequence conservation in the LaM, the Tetrahymena thermophila protein MLP1 (and related factors in other alveolates) has been hypothesized to function as a genuine La protein, despite the absence of the adjacent RRM found in La proteins of all prior investigated species. We show that MLP1 functions as a genuine La protein in that it binds and affects the processing of pre-tRNAs in T. thermophila and when expressed as a heterologous factor in fission yeast, however, unlike in other examined eukaryotes, depletion of MLP1 results in 3’-trailer stabilization. We also observed that 3’-trailers in T. thermophila are uniquely shortened relative to other examined eukaryotes, and that 5’-leaders in this species have evolved to disfavour pre-tRNA leader/trailer pairing. Our data suggest that the variant MLP1 architecture relative to other genuine La proteins is linked to an altered mechanism of tRNA processing in T. thermophila.

overall_design: Size-selected and fragmented TGIRT-Seq librairies were generated from RNA samples originating from wild type (WT), partial knockout of MLP1 (KO) and MLP1 immunoprecipitation (MLP1_IP) Tetrahymena thermophila samples with three biological replicates each.

first: Kyra

last: Kerkhofs

first: Jyoti

last: Garg

first: Jean-Marc

last: Deragon

first: Sherif

last: Abou-Elela

first: Michelle

middle: S

last: Scott

first: Ron

last: Pearlman

first: Mark

last: Bayfield


title: Multi-omics: In vivo G-CSF Treatment Activates GR-SOCS1 Axis Suppressing IFN-γ Secretion by Natural Killer Cells

first: Ting

last: Peng

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

overall_design: Refer to individual Series


title: BAF complex maintains glioma stem cells in pediatric H3K27M-glioma [scRNA-seq]

city: Boston

first: Joana

last: Marques

address: 360 Longwood Avenue

institute: Dana-Farber Cancer Institute

summary: Diffuse midline gliomas (DMGs) are uniformly fatal pediatric central nervous system cancers, refractory to standard of care therapeutic modalities. The primary genetic drivers are a set of recurrent amino acid substitutions in genes encoding histone H3 (H3.3 and H3.1, K27M), which are currently undruggable. These H3K27M oncohistones perturb normal chromatin architecture, resulting in an aberrant epigenetic landscape, which we interrogated here for epigenetic dependencies using a CRISPR screen in patient-derived H3K27M-glioma neurospheres. We show that H3K27M-glioma cells are dependent on core components of the mammalian SWI/SNF (BAF) chromatin remodeling complex for maintaining glioma stem cells in a cycling, oligodendrocyte precursor cell (OPC)-like state. Genetic perturbation of the BAF catalytic subunit SMARCA4 (BRG1), as well as pharmacological suppression opposes proliferation, promotes differentiation, and improves overall survival of patient-derived xenograft (PDX) models. In summary, we demonstrate that therapeutic inhibition of BAF complex has translational potential for children with H3K27M-gliomas.

overall_design: Gene expression profiling by single cell RNAseq of BT869 cells upon SMARCA4 knockout.

first: Eshini

last: Panditharatna

first: Li

last: Jiang

middle: G

first: Mariella

last: Filbin


title: Effect of divergence in fertility on miRNA profIling in spermatozoa of bulls

city: Co. Meath

first: Kate

last: Keogh

address: Dunsany

department: Animal and Bioscience Department

country: Ireland

institute: Teagasc Grange

summary: The aim of this study was to examine changes in the miRNA transcriptional profile of spermatozoa in Holstein-Friesian bulls. Spermatozoa from bulls divergent for feritlity status were used for this study with 10 High fertility bulls and 10 Low fertility bulls. RNA was extracted and subsequently subjected to miRNAseq analysis. 13 miRNA were identified as differentially expressed in the spermatozoa between bulls of high and low feritlity status.

overall_design: In total 20 spermatozoa RNA samples were analysed. 10 samples were derived from bulls which ranked for high fertility status (High, n=10) and 10 samples were derived from low fertility status bulls (Low, n=10).   Total RNA was extracted from a pool of frozen-thawed semen from three different ejaculates per bull.

first: Eimear

last: Donnellan

first: Jean-Philippe

last: Perrier

first: Miriam

last: Štiavnická

first: Caitríona

last: Collins

first: Elaine

last: Dunleavy

first: Eli

last: Sellem

first: Naomi

middle: C

last: Bernecic

first: Patrick

last: Lonergan

first: David

last: Kenny

first: Sean

last: Fair


title: scRNA-seq of male mouse aorta collected over the light-dark cycle

first: Garret

middle: A.

last: FitzGerald

address: 3400 Civic Center Boulevard

overall_design: Male C57BL6 mice were entrained to a 12:12 light-dark (LD) cycle for 2 weeks. Mice were sacrificed at Zeitgeiber times (ZTs) 0, 6, 12, and 18 (2 mice per time point), and whole aorta was dissected. Single-cell suspensions were collected for each aorta, and cells from the same time points were pooled together prior to single-cell RNA-sequencing.

first: Soon

middle: Y

last: Tang

first: Ronan

last: Lordan

last: Anderson


title: Phenotypic selection during laboratory evolution of yeast populations leads to a genome-wide sustainable chromatin compaction shift

city: Illkirch-Graffenstaden

last: Moreno Fortuno

state: Bas Rhin

address: 1 Rue Laurent Fries

institute: INSTITUT DE GÉNÉTIQUE ET DE BIOLOGIE MOLÉCULAIRE ET CELLULAIRE

summary: Based on inheritance of acquired characteristics, Lamarckian theory of evolution explains the evolution of biological systems through epigenetics. In a previous study, we have shown how microbial evolution has resulted in a persistent reduction in expression after repeatedly selecting for the lowest PGAL1-YFP-expressing cells. Applying the ATAC-seq assay on samples collected from this 28-days evolution experiment, here we show how genome-wide chromatin compaction change during evolution under selection pressure. We found that the chromatin compaction was altered not only on GAL network genes directly impacted by the selection pressure, showing an example of non-genetic memory, but also at the whole genome level. The GAL network genes experienced chromatin compaction accompanying the reduction in PGAL1-YFP reporter expression; strikingly, the fraction of global genes with differentially compacted chromatin states accounted for about a quarter of the total genome.  Moreover, some of the ATAC-seq peaks followed well-defined temporal dynamics. Comparing the peak’s intensity in consecutive days, we found most of the differential compaction to occur between days 0 and 3 when the selection pressure was first applied, and between days 7 and 10 when the pressure was lifted. Among the gene sets enriched for the differential compaction events, some had increased chromatin availability once selection pressure was applied and decreased availability after the pressure was lifted (or vice versa). These results intriguingly show that, despite the lack of targeted selection, transcriptional availability of a large fraction of the genome change in a very diverse manner during evolution and these changes can occur in a relatively short number of generations.

overall_design: Comparative ATAC-seq profiling of the original WP35 yeast strain (Day0) and its evolved derivatives (Day3, Day7, Day10, Day28), with two independent biological replicates per timepoint

last: Moreno

first: Murat

last: Acar


title: Listeria monocytogenes infection alters content and function of extracellular vesicles produced by trophoblast stem cells

status: Public on Sep 12 2022

city: East Lansing

first: Jonathan

last: Hardy

state: Michigan

address: 775 Woodlot Drive

department: Microbiology and Molecular Genetics

institute: Michigan State University

summary: Placental immunity is critical for fetal health during pregnancy, as invading pathogens spread from the parental blood to the fetus through this organ. However, inflammatory responses in the placenta can adversely affect both the fetus and the pregnant person, and the balance between protective placental immune response and detrimental inflammation is poorly understood. Extracellular vesicles (EVs) are membrane-enclosed vesicles that play a critical role in placental immunity. EVs produced by placental trophoblasts mediate immune tolerance to the fetus and to the placenta itself, but these EVs can also activate detrimental inflammatory responses. The regulation of these effects is not well-characterized, and the role of trophoblast EVs (tEVs) in the response to infection has yet to be defined. The Gram-positive pathogen Listera monocytogenes (Lm) infects the placenta, serving as a model to study tEV function in this context. We investigated the effect of Lm infection on the production and function of tEVs, using a trophoblast stem cell (TSC) model. We found that tEVs from infected TSCs can induce the production of the pro-inflammatory cytokine TNF-α in recipient cells. Surprisingly, this tEV treatment could confer increased susceptibility to subsequent Lm infection, which has not previously been reported as an effect of EVs. Proteomic analysis and RNA-sequencing revealed that tEVs from infected TSCs had altered cargo compared to those from uninfected TSCs. However, no Lm proteins were detected in tEVs from infected TSCs. Together, these results suggest an immunomodulatory role for tEVs during prenatal infection.

overall_design: Gene expression analysis of RNA-sequencing for extracellular vesicles from trophoblast stem cells. 3 trophoblast extracellular vesicle from Listeria monocytogenes infected trophoblast stem cells and 3 uninfected controls.

last: Kaletka

first: Kun

last: Lee

first: Josephine

last: Altman

first: Masamitsu

last: Kanada

middle: W


title: Long non-coding RNA LINC01882 ameliorates aGVHD via skewing CD4+ T Cells differentiation towards Treg cells

city: wuhan

first: yao

last: teng

state: hubei

address: tongji medical school

institute: wuhan union hosipital

summary:
To investigate the  function of long non-coding RNA LINC01882 in the regulation of CD4+T cell differentiation, we established LINC01882-overexpressed CD4+T cells by  infecting with lentivirus.
We then performed microRNA gene expression profiling analysis using data obtained from microRNA sequencing.

overall_design: Comparative gene expression profiling analysis of microRNA sequencing  data for LINC01882-overexpressed activited CD4+Tcells and its control.

first: Yao

last: Teng

first: Linghui

last: Xia

first: Qiuling

last: Wu


title: The novel lncRNA ALPHA specifically targets chikungunya virus to control infection

first: Sara

last: Cherry

address: 472A Stemmler Hall

department: Pathology and Laboratory Medicine

summary: We set out to determine whether lncRNAs can contribute to additional antiviral immune strategies independently of canonical innate signaling. High-throughput genetic screening of 2200 human lncRNAs led to the identification of the cytoplasmic antiviral lncRNA Antiviral LncRNA Prohibiting Human Alphaviruses (ALPHA) which is transcriptionally induced by alphaviruses and functions independently of IFN to specifically inhibit the replication of CHIKV and its closest relative, O’nyong’nyong virus (ONNV), but not other viruses. Furthermore, we showed that ALPHA interacts with CHIKV genomic RNA and restrains viral RNA replication. Together, our findings reveal that ALPHA and potentially other lncRNAs can mediate non-canonical antiviral immune responses against specific viral pathogens.

overall_design: RNA sequencing from human brain microvascular endothelial cells (HBMEC) in the presence and absence of chikungunya virus (CHIKV) or the phylogenetically disparate arbovirus, Zika virus (ZIKV)

first: Megha

last: Basavappa

first: Max

middle: B

last: Ferretti

first: Mark

last: Dittmar

first: Julian

last: Stoute

first: Megan

last: Sullivan

first: Kanupriya

last: Whig

first: Hui

last: Shen

first: Kathy

last: Liu

last: Schultz

first: Daniel

last: Beiting

first: Kristen

last: Lynch

first: Jorge

last: Henao-Mejia


title: Global transcriptome analyses and intracellular regulatory mechanisms of glycine betaine and mycosporine-2-glycine expression in the halotolerant cyanobacterium Halothece sp. PCC 7418 exposed to abiotic stresses II

status: Public on Sep 11 2022

city: Nagoya

first: Hakuto

last: Kageyama

state: Aichi

address: 1-501, Shiogamaguchi, Tempaku-ku

institute: Meijo University

summary: Halotolerant species are of interest since they occur naturally in environments with excess toxic ions. The cyanobacterium Halothece sp. PCC 7418 (hereafter referred to as Halothece) exhibits remarkable halotolerance and was used to examine stress-responsive regulatory mechanisms. The effects of sa;t-down shock on Halothece transcriptomes were examined using RNA sequencing.

overall_design: Halothece sp. PCC7418 cells were exposed to various abiotic stress conditions. Then, total RNA was extracted and analyzed by RNA-seq analysis.

first: Rungaroon

last: Waditee-Sirisattha


title: Perturbations in the T cell receptor β repertoire during malaria infection in children: a preliminary study.

city: Kigali

first: Abdoelnaser

middle: Mahmmod

last: Degoot

state: Kigali

address: KN 3Rd

department: Research Department

country: Rwanda

institute: African Institute for Mathematical Sciences

summary: The changes occurring in the T cell repertoire during clinical malaria infection in children remain unknown. In this study, we undertook the first detailed comparative study of the T cell repertoire in African children with and without clinical malaria to test the hypothesis that clonotypic expansions that occur during P. falciparum infection will contribute to the generation of a T cell repertoire that is unique to each disease state. We profiled the complementarity-determining region 3 (CDR3) of the TCRβ chain sequences from children with Plasmodium falciparum infections (asymptomatic, uncomplicated and severe malaria) and compared these with sequences from healthy children. Strikingly, we discovered that children with symptomatic malaria has a lower TCR diversity and frequency of shared (or “public”) TCR sequences compared to asymptomatic children. Also, TCR diversity was inversely associated with parasitemia. Furthermore, by clustering TCR sequences based on their predicted antigen specificities, we identified a specificity cluster, with a 4-mer amino acid motif, that is overrepresented in the asymptomatic group compared to the diseased groups. Further investigations into this finding may help in delineating important antigenic targets for vaccine and therapeutic development. The results show that the T cell repertoire in children is altered during malaria, suggesting that exposure to P. falciparum antigens disrupts the adaptive immune response, which is an underlying feature of the disease.

overall_design: Cross-sectional study to  characterize T cell phenotypic responses in children with P. falciparum infections

first: Augustina

last: Frimpong

first: Michael

last: Ofori

first: Kwadwo

last: Kusi

first: Buri

last: Gershom

first: Jacob

last: Quartey

first: Erick

last: Keyi-Baafour

first: Nhi

last: Nguyen

first: Wilfred

last: Ndifon


title: Global transcriptome analyses and intracellular regulatory mechanisms of glycine betaine and mycosporine-2-glycine expression in the halotolerant cyanobacterium Halothece sp. PCC 7418 exposed to abiotic stresses

summary: Halotolerant species are of interest since they occur naturally in environments with excess toxic ions. The cyanobacterium Halothece sp. PCC 7418 (hereafter referred to as Halothece) exhibits remarkable halotolerance and was used to examine stress-responsive regulatory mechanisms. The effects of five different stimuli on Halothece transcriptomes were examined using RNA sequencing. In response to diverse stresses, there were both common and stress-specific transcriptional responses.


title: Multiomic Analysis of Adult Diapause in Drosophila melanogaster Identifies Hallmarks of Cellular Quiescence [RNA-Seq]

status: Public on Sep 10 2022

city: Providence

first: Corinne

last: Hutfilz

state: Rhode Island

address: 171 Meeting St.

country: USA

institute: Brown University

summary: Diapause and diapause-like states constitute natural, inducible, and evolutionarily conserved examples of lifespan plasticity that are well-suited to represent physiologically accurate models for longevity. We integrated ATAC-seq and RNA-seq technologies to probe the transcriptional regulatory pathways controlling lifespan plasticity in diapause.

overall_design: Comparison of chromatin accessibility profiles from w1118 virgin female adult Drosophila in diapause or in regular conditions, additionally supplemented with either S-methoprene or ethanol (vehicle) for a total of 4 experimental conditions.

first: Hutfilz

last: Corinne


title: A specific Argonaute phosphorylation regulates the binding to microRNAs during C. elegans development.

city: Québec

first: Miguel

last: Quévillon Huberdeau

address: 9 Rue McMahon

department: Département de biologie moléculaire, de biochimie médicale et de pathologie

institute: Université Laval

summary: Argonaute proteins are at the core of the microRNA-mediated gene silencing pathway essential for animals. In C. elegans, the microRNA-specific Argonautes ALG-1 and ALG-2 regulate multiple processes required for proper animal developmental timing and viability. Here, we identified a new phosphorylation site, serine 642, on ALG-1 that modulates microRNA association. Mutating ALG-1 serine 642 into a phospho-mimicking residue impairs microRNA binding and causes embryonic lethality and post-embryonic phenotypes that are common with alteration of microRNA functions. Monitoring microRNA levels in alg-1 phosphorylation mutant animals reveal that miRNA passenger strands strongly increase but are not preferentially loaded into ALG-1, indicating that the miRNA binding defects could also lead to miRNA duplexes accumulation. Our genetic and biochemical experiments support the protein kinase A KIN-1 as the putative kinase that phosphorylates ALG-1 serine 642. Altogether, our data indicate that PKA triggers the ALG-1 phosphorylation to regulate its microRNAs association during C. elegans development.

overall_design: Develop a novel protocol to clone small RNA and mRNA

middle: Q

last: Huberdeau

first: Vivek

middle: N

last: Shah

first: Smita

last: Nahar

first: Astrid

last: Bruckmann

first: Foivos

last: Gypas

first: Kotaro

last: Nakanishi

first: Helge

last: Grosshans

first: Gunter

last: Meister

first: Martin

last: Simard


title: Multiomic Analysis of Adult Diapause in Drosophila melanogaster Identifies Hallmarks of Cellular Quiescence [ATAC-seq]