title: Loss of Tmem106b leads to cerebellum Purkinje cell death and motor deficits

city: Jacksonville

first: Yingxue

last: Ren

state: FL

address: 4500 San Pablo Rd S

institute: Mayo Clinic

summary: The loss of Tmem106b results in an age-dependent loss of cerebellar Purkinje cells accompanied with motor function deficits. Tmem106b deficiency also results in lysosomal enlargement in both Purkinje cells and microglia, and increased neuroinflammation including complement system activation. These data suggest that, in addition to myelination, Tmem106b also plays important role in maintaining the health and survival of cerebellar Purkinje cells during aging.

overall_design: we performed transcriptomic analyses of RNA from cerebellar tissues harvested from 15-month-old Tmem106b mice [3 Tmem106b+/+ (WT), and 3 Tmem106b-/- (KO), 2 males and 1 females per genotype].

first: Rosa

last: Rademakers

first: Alexandra

last: Nicholson

first: Hung

last: Phuoc

first: Mieu

last: Brooks

first: Wenhui

last: Qiao

first: Zachary

middle: S

last: Quicksall

first: Billie

last: Matchett

first: Ralph

last: Perkerson

first: Aishe

last: Kurti

first: Shunsuke

last: Koga

first: Monica

last: Castanedes-Casey

first: Virginia

last: Phillips

first: Ariston

middle: L

last: Librero

first: Cristhoper

last: Fernandez De Castro

first: Matthew

last: Baker

first: Shanu

last: Roemer

first: Melissa

last: Murray

first: Yan

middle: W

last: Asmann

last: Fryer

first: Guojun

last: Bu

first: Dennis

last: Dickson

first: Xiaolai

last: Zhou


title: EML4-ALK induces cellular senescence in mortal normal human cells and promotes anchorage-independent growth in hTERT-transduced normal human cells

status: Public on Jan 20 2021

city: Bethesda

first: Josh

last: Stone

state: MD

address: 9000 Rockville Pike

department: CCR

country: USA

institute: National Cancer Institue

type: Expression profiling by high throughput sequencing

summary: Background: Chromosomal inversions involving anaplastic lymphoma kinase (ALK) and echinoderm microtubule associated protein like 4 (EML4) generate a fusion protein EML4-ALK in non-small cell lung cancer (NSCLC). The understanding of EML4-ALK function can be improved by a functional study using normal human cells.  Methods: Here we for the first time conduct such study to examine the effects of EML4-ALK on cell proliferation, cellular senescence, DNA damage, gene expression profiles and transformed phenotypes.  Results: The lentiviral expression of EML4-ALK in mortal, normal human fibroblasts caused, through its constitutive ALK kinase activity, an early induction of cellular senescence with accumulated DNA damage, upregulation of p16INK4A and p21WAF1, and senescence-associated -galactosidase (SA-β-gal) activity. In contrast, when EML4-ALK was expressed in normal human fibroblasts transduced with telomerase reverse transcriptase (hTERT), which is activated in the vast majority of NSCLC, the cells showed accelerated proliferation and acquired anchorage-independent growth ability in soft-agar medium, without accumulated DNA damage, chromosome aberration, nor p53 mutation. EML4-ALK induced the phosphorylation of STAT3 in both mortal and hTERT-transduced cells, but RNA sequencing analysis suggested that the different signaling pathways contributed to the different phenotypic outcomes in these cells. While EML4-ALK also induced anchorage-independent growth in hTERT-immortalized human bronchial epithelial cells in vitro, the expression of EML4-ALK alone did not cause detectable in vivo tumorigenicity in immunodeficient mice.  Conclusions: Our data indicate that the expression of hTERT is critical for EML4-ALK to manifest its in vitro transforming activity in human cells. This study provides the isogenic pairs of human cells with and without EML4-ALK expression.

overall_design: We performed the RNA sequencing of primary tumors from 8 cells.

first: Akihiko

last: Miyanaga

first: Masaru

last: Matsumoto

first: Jessica

last: A. Beck

first: Izumi

last: Horikawa

first: Mohammed

last: Khan

first: Curtis

last: C. Harris


title: Synchrony and asynchrony between an epigenetic clock and developmental timing [RNA-Seq]

status: Public on Jan 21 2021

city: Happy Valley

first: Alex

middle: Daniel

last: Chitsazan

state: OR

address: 2720 S Moody Ave

institute: Oregon Health and Science University

summary: Epigenetic changes have been used to estimate chronological age across the lifespan, and some studies suggest that epigenetic "aging" clocks may already operate in developing tissue. To better understand the relationship between developmental stage and epigenetic age, we utilized the highly regular sequence of development found in the mammalian neural retina and a well-established epigenetic aging clock based on DNA methylation. Our results demonstrate that the epigenetic age of fetal retina is highly correlated with chronological age. We further establish that epigenetic aging progresses normally in vitro, suggesting that epigenetic aging is a property of individual tissues. This correlation is also retained in stem cell-derived retinal organoids, but is accelerated in individuals with Down's syndrome, a progeroid-like condition. Overall, our results suggest that epigenetic aging begins as early as a few weeks post-conception, in fetal tissues, and the mechanisms underlying the phenomenon of epigenetic aging might be studied in developing organs.

overall_design: We analysed RNA-seq data of  fetal retinas (n=6) trisomy 21 retinas (n=4), and stem cell-derived retinal organoids (n=5, cell lines: H9).

first: Akina

last: Hoshino

first: Steve

last: Horvath

first: Akshayalakshmi

last: Sridhar

first: Thomas

last: Reh


title: Genome-wide formation of G-quadruplex DNA structures originating from Long Interspersed Elements in Alzheimer’s disease neurons

city: Montreal

first: Gilbert

last: Bernier

state: Quebec

address: 5690 rosemont boulevard

country: Canada

institute: HMR

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report the formation of G4 structures in mature neurons derived from AD iPSc cells

overall_design: examination of G4 structures using 1H6 antibody using mature neurons derived from normal or AD iPSCs

first: Roy

last: Hanna

first: Anthony

last: Flamier

first: Andrea

last: Barabino


title: Different resource allocation in a Bacillus subtilis population displaying bimodal motility

city: Amsterdam

first: Biwen

last: Wang

address: Work, Science Park 904,1098 XH,Amsterdam,The Netherlands

department: Swammerdam Institute for Life Science

country: Netherlands

institute: University of Amsterdam

summary: To cope with sudden changes in their environment, bacteria can use a bet-hedging strategy by dividing the population into cells with different properties. This so called bimodal or bistable cellular differentiation is generally controlled by positive feedback regulation of transcriptional activators. Due to continued turnover of the cytoplasmic content, it is difficult for these activators to reach an activation threshold concentration when cells are growing exponentially. This is one reason why bimodal differentiation is primarily observed from the onset of the stationary phase when exponential growth ceases. An exception is the bimodal induction of motility in Bacillus subtilis, which occurs early during exponential growth. Several mechanisms have been put forward to explain this, including double negative-feedback regulation and the stability of the mRNA molecules involved. In this study, we used fluorescence-assisted cell sorting to compare the transcriptome of motile and non-motile cells and noted that expression of ribosomal genes is lower in motile cells. This was confirmed using an unstable GFP reporter fused to the strong ribosomal rpsD promoter. We propose that the reduction in ribosomal gene expression in motile cells is the result of a diversion of cellular resources to the synthesis of the chemotaxis and motility systems. In agreement, single-cell microscopic analysis indicates that motile cells are slightly shorter than non-motile cells, an indication of slower growth. We speculate that this growth rate reduction can contribute to the bimodal induction of motility during exponential growth.

overall_design: We used reporter strain bSS339, containing the gfp gene under control of the strong SigD-activated flagellin promoter Phag. Cells were grown until an OD of ~0.5 after which the culture was subjected to fluorescence-assisted cell sorting (FACS) and separation into GFP-on (motile) and GFP-off (non-motile) cells. RNA-seq was applied to GFP-on and GFP-off subpopulations respectively with ERCC spike-in RNAs as internal controls and transcriptomes between motile and non-motile was compared. Two independent biological replicates were performed.

first: Simon

last: Syvertsson

first: Jojet

last: Staal

first: Yongqiang

last: Gao

first: Remco

last: Kort

first: Leendert

last: Hamoen


title: Combination therapies induce cancer cell death through the integrated stress response and disturbed pyrimidine metabolism

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

summary: By accentuating drug efficacy and impeding resistance mechanisms, combinatorial, multi-agent therapies have emerged as key approaches in the treatment of complex diseases, most notably cancer. Using high-throughput drug screens, we uncovered distinct metabolic vulnerabilities and thereby identified drug combinations synergistically causing a starvation-like lethal catabolic response in tumor cells from different cancer entities. Domperidone, a dopamine receptor antagonist, as well as several tricyclic antidepressants (TCAs), including Imipramine, induced cancer cell death in combination with the mitochondrial uncoupler Niclosamide ethanolamine (NEN) through activation of the integrated stress response pathway and the catabolic CLEAR network. Using transcriptome and metabolome analyses, we characterized a combinatorial response, mainly driven by the transcription factors Chop and TFE3, which resulted in cell death damage through enhanced pyrimidine catabolism as well as reduced pyrimidine synthesis. Remarkably, the drug combinations sensitized human organoid cultures to the standard-of-care chemotherapy Paclitaxel. Thus, our combinatorial approach could be clinically implemented into established treatment regimen, which would be further facilitated by the advantages of drug repurposing.

overall_design: We performed gene expression microarray analysis in HCT116 cells treated with NEN, Domperidone or with a combination of both.

first: Goetz

last: Hartleben

first: Kenji

last: Schorpp

first: Barbara

last: Betz

first: Zahra

last: Dantes

first: Ina

last: Rothenaigner

first: José

middle: M

last: Monroy Kuhn

first: Sean

last: Lin

first: Susanne

last: Seitz

first: Janina

last: Tokarz

first: Anna

last: Artati

first: Jerzy

last: Adamsky

first: Anja

last: Zeigerer

first: Dominik

last: Lutter

first: Martin

last: Irmler

first: Kamyar

last: Hadian

first: Max

last: Reichert

first: Stephan

last: Herzig

first: Mauricio

last: Berriel Diaz


title: Single-cell RNA-sequencing of iBlastoids generated by reprogramming

status: Public on Jan 19 2021

city: Clayton

first: Jan

last: Schroeder

state: VIC

address: Building 75 Innovation Walk

department: Anatomy & Developmental Biology

country: Australia

institute: Monash University

summary: Here, we report an in vitro model of the human blastocyst by reprogramming fibroblasts, termed iBlastoids. Comprehensive characterization of these iBlastoids demonstrated that they can accurately represent the overall architecture of human blastocysts including an inner cell mass-like structure, marked by classic EPI-associated genes surrounded by an outer layer of cells with key molecular characteristics of the TE and a cavity resembling the blastocoel. Single-cell transcriptomics confirmed the presence of EPI, PE and TE-like cells and unveiled a high correlation between blastocysts and iBlastoids. Finally, iBlastoids are capable of modeling in vitro, several molecular and morphological aspects of blastocyst implantation. In summary, we have developed a scalable and tractable model to study  the human blastocyst, and we envision that iBlastoids will facilitate further studies of the molecular and functional processes during early human development.

overall_design: Examination of the single-cell transcriptome of iBlastoids generated from two individuals (32F and 38F)

first: Xiaodong

last: Liu

first: Jia

middle: P

last: Tan

last: Schröder

first: John

middle: F

last: Ouyang

first: Owen

middle: J

last: Rackham

first: Jose

last: Polo


title: Gene expression profile of brain and hippocampus of B-cell sufficient and B-cell deficient 3xTgAD mice

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Brain and hippocampus gene expression was quantified in female and male 3xTgAD mice with and without B-cell deficiency as compared with sex- and age-matched B-cell sufficient (WT) and B-cell deficient (JHT) mice. (JHT)

overall_design: Hippocampus (HIPP) and brain (BRAIN) tissue from male (N=6) and female (N=9) mice from four genotypes - wildtype mice (WT, C57BL/6j), triple-transgenic Alzheimer's Disease mouse model (3xTgAD), or a B cell knock-out genotype (JHT), and a JHT x 3xTgAD cross (JHT_3xTgAD)

first: Ki

last: Kim

first: Emeline

last: Ragonnaud

first: Monica

last: Bodogai

first: Elin

last: Lehrmann

first: Arya

last: Biragyn


title: Mapping the origin and fate of myeloid cells in distinct compartments of the eye by single-cell profiling

city: Freiburg

first: Roman

last: Sankowski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University of Freiburg Medical Center

summary: Similar to the brain, the eye is considered an immune-privileged organ where tissue-resident macrophages provide the major immune cell constituents. However, little is known about spatially restricted macrophage subsets within different eye compartments with regard to their origin, function and fate during health and disease. Here, we combined single-cell analysis, fate mapping, parabiosis and computational modelling to comprehensively examine myeloid subsets in distinct parts of the eye during homeostasis. This approach allowed us to identify myeloid subsets displaying diverse transcriptional states. During choroidal neovascularization, a typical hallmark of neovascular age-related macular degeneration (AMD), we recognized disease-specific macrophage subpopulations with distinct molecular signatures. Our results highlight the heterogeneity of myeloid subsets and their dynamics in the eye. This provides new insights into the innate immune system in this organ and may offer new therapeutic targets for ophthalmological diseases.

overall_design: CD45+ cells isolated from different eye compartments (including retina, cornea and ciliary body) at baseline or at 2 timepoints after laser lesioning of the retina. Data are representative of ca.6 mice from three independent experiments. CEL-Seq2 protocol was used for single cell sequencing (Hashimshony et al. 2016).

first: Peter

last: Wieghofer

first: Marco

last: Prinz


title: Investigation of the transcriptional effect of artificial activation of Czf1 in Candida albicans

city: Würzburg

first: Joachim

last: Morschhäuser

address: Josef-Schneider-Str 2, Bau D15

department: Institute for Molecular Infection Biology

institute: University of Würzburg

summary: Goal: Phenotypic evidence suggested that the transcription factor Czf1 influences the integrity of the cell wall. RNA-seq was performed to identify cell-wall related genes whose expression changes when Czf1 is artificially activated.  Result: The set of genes whose expression is increased at least 4-fold is significantly enriched for genes whose GO (gene ontology) terms are "cell surface" and "cell wall", as well as several known and putative mannosyltransferases.

overall_design: The SC5314 wild type was compared two two independently constructed strains which express an artificially activated Czf1 (containing a C-terminal fusion of the Saccharomyces cerevisiae Gal4 Activation Domain) under the control of the constitutive ADH1 promoter. All three strains (WT, CZF1GAD1A and B) were sequenced in triplicate from RNA isolated from cultures originating from  a single colony.

first: Austin

last: Mottola


title: Retinitis pigmentosa (RP) mouse cone transcriptom change with Txnip treatment

city: Boston

first: Yunlu

last: Xue

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard University

summary:
Purpose: To identifiy mRNA changes in retinitis pigmentosa (RP) cone photoreceptors with Txnip overexpression treatment, which improved RP cone survival and visual acuity.
Methods: two RP mouse strains, rd1 and Rho-/-, were injected with AAV-Txnip or AAV-H2BGFP control subretinally at P0. Retinas were dissected out at P21 for rd1 and P90 for Rho-/-. 1,000 H2BGFP labeled cones per retina sample were FACS sorted out, and subject for RNA-sequencing.
Results: >1,400 genes in P21 rd1 and >700 genes in Rho-/-  were found differentially expressed with Txnip treatment.
Conclusions: 25 genes are in common between P21 rd1 and P90 Rho-/- with Txnip treatment. On this list, notably, three mitochondrial Electron Transport Chain (ETC) genes were up-regulated.

overall_design: Cone photoreceptor mRNA profiles of 21-day old rd1 and 90-day old Rho-/- mice  with or without AAV-Txnip treatment.

first: Constance

last: Cepko


title: Alzheimer's disease

first: Gilbert

last: Bernier

summary: ES-derived neural cells

overall_design: Alzheimer's disease vs. healthy controls


title: Type I IFNs facilitate innate immune control of opportunistic bacteria in the macrophage cytosol

first: Iain

last: Fraser

address: 9000 Rockville Pike, Bldg. 4, Rm. 109A, MSC-0421

department: NIAID

institute: NIH

summary: The mammalian immune system is constantly challenged by signals from both pathogenic and non-pathogenic microbes. Many of these non-pathogenic microbes have pathogenic potential if the immune system is compromised. The importance of type I interferons (IFNs) in orchestrating innate immune responses to pathogenic microbes has become clear in recent years. However, the control of opportunistic pathogens – and especially intracellular bacteria – by type I IFNs remains less appreciated. In this study, we use the opportunistic, Gram-negative bacterial pathogen Burkholderia cenocepacia (Bc) to show that type I IFNs are capable of limiting bacterial replication in macrophages, preventing illness in immunocompetent mice. Sustained type I IFN signaling through cytosolic receptors allows for increased expression of autophagy and linear ubiquitination mediators, which slows bacterial replication. Transcriptomic analyses and in vivo studies also show that LPS stimulation does not replicate the conditions of intracellular Gram-negative bacterial infection as it pertains to type I IFN stimulation or signaling. This study highlights the importance of type I IFNs in protection against opportunistic pathogens through innate immunity, without the need for damaging inflammatory responses.

overall_design: Timecourse RNAseq analysis of WT and Ifnar1-/- mouse macrophages exposed to Salmonella enterica subsp. enterica serovar Typhimurium (STm), Burkholderia thailandensis (Bt), and lipopolysaccharide (LPS)

first: Michael

middle: G

last: Dorrington

first: Justin

middle: B

last: Lack

first: Bin

last: Lin

first: Jonathan

last: Liang

first: Tregei

last: Starr

first: Orna

last: Ernst

first: Alexandra

middle: H

last: Miller

first: Olivia

last: Steele-Mortimer

middle: D


title: Gene expression profiling of alveolar macrophages from normal lung and metastasis-associated macrophages

city: New Haven

first: Dejian

last: Zhao

state: CT

address: 333 Cedar St

institute: Yale School of Medicine

summary: To profile the gene expression of macrophages associated with lung metastases and identify mechanisms by which macrophages regulate metasetatic growth

overall_design: Lung metastases were induced by tail vein injection of syngenic mouse mammary tumor cells, dissected and processed in parallel with normal lungs for FACS sorting for the CD11B+ and CD11C+ subsets of CD45+;F4/80+;LY6C-;MRC1+;FSC hi cells. RNA from these cells was analyzed by RNA-seq.

first: Wei

last: Zheng

first: Hui

last: Zhang

first: Prameladevi

last: Chinnasamy

first: Nicholas

last: Sibinga

first: Jeffrey

last: Pollard


title: RNA-seq data from mouse newborn rib chondrocytes

city: Suita

first: Kenji

last: Hata

state: Osaka

address: 1-8 Yamadaoka

department: Biochemistry

country: Japan

institute: Osaka University graduate school of dentistry

summary: To understand the targets of Sox5, Sox6 and Sox9, we overexpressed Sox5/6/9 in mouse newborn rib chondrocytes and expression analysis by RNA-seq.

overall_design: mRNA profiles of primary chondrocytes infected with mock and Sox5/6/9 adenoviruses


title: Expression analysis of genes related to cold tolerance in Dendroctonus valens

city: Beijing

first: dongfang

last: zhao

address: No.35 Tsinghua East Road. Haidian Distric

country: China

institute: Beijing Forestry University

summary: To identify genes relevant to cold tolerance and the process of overwintering, we sequenced the transcriptomes of wintering and non-wintering adult and larval D. valens using the Illumina HiSeq platform. Differential expression analysis methods for other non-model organisms were used to compare transcript abundances in adults and larvae at two time periods, followed by the identification of functions and metabolic pathways related to genes associated with cold tolerance. We detected 4387 and 6091 differentially expressed genes (DEGs) between sampling dates in larvae and adults, respectively, and 1140 common DEGs, including genes encoding protein phosphatase, very long-chain fatty acids protein, cytochrome P450, and putative leucine-rich repeat-containing proteins. In a GO enrichment analysis, 1,140 genes were assigned to 44 terms, with significant enrichment for cellulase activity, hydrolase activity, and carbohydrate metabolism. KEGG classification and enrichment analyses showed that the lysosomal and purine metabolism pathways involved the most DEGs, the highly enriched terms included autophagy - animal, pentose and glucuronate interconversions and lysosomal processes. We identified 138 candidate genes associated with cold tolerance, including genes with established roles in this trait (e.g., genes encoding trehalose transporter, fructose-1,6-bisphosphatase, and trehalase). Our comparative transcriptome analysis of adult and larval D. valens in different conditions provides basic data for the discovery of key genes and molecular mechanisms underlying cold tolerance.

overall_design: Transcriptome differences between adult and larval of D.valens two time periods.

first: Dongfang


title: A synthetic mechanogenetic gene circuit for autonomous drug delivery in engineered tissues

city: Saint Louis

first: Bo

state: MO

address: 660 S. Euclid Avenue

department: Developmental Biology

institute: Washington University School of Medicine

summary:
Mechanobiologic signals play critical roles in regulating cellular responses under both physiologic and pathologic conditions.  Using a combination of synthetic biology and tissue engineering, we developed a mechanically-responsive bioartificial tissue that responds to mechanical loading to produce a pre-programmed therapeutic biologic drug. By deconstructing the signaling networks induced by activation the mechanically-sensitive ion channel transient receptor potential vanilloid 4 (TRPV4), we synthesized synthetic TRPV4-responsive genetic circuits in chondrocytes.  These cells were then engineered into living tissues that respond to mechanical compression to drive the production of the anti-inflammatory drug interleukin-1 receptor antagonist.
Mechanical loading of these tissues in the presence of the cytokine interleukin-1 protected constructs from inflammatory degradation. This “mechanogenetic” approach enables long-term autonomous delivery of therapeutic compounds that is driven by physiologically-relevant mechanical loading with cell-scale mechanical force resolution. The development of synthetic mechanogenetic gene circuits provides a novel approach for the autonomous regulation of cell-based drug delivery systems.

overall_design: A custom mechanical compression device was used for sinusoidal compression of 24-individual tissue constructs simultaneously [1] using a closed loop displacement-feedback system.

first: Robert

last: Nims

first: Lara

last: Pferdehirt

first: Amy

last: McNulty

first: Farshid

last: Guilak


title: Control of a programmed cell death pathway in Pseudomonas aeruginosa by a ppGpp-responsive antiterminator [RNA-Seq]

first: Simon

last: Dove

address: 300 Longwood Ave

department: Division of Infectious Diseases

institute: Boston Children's Hospital and Harvard Medical School

summary: In the opportunistic pathogen Pseudomonas aeruginosa the alp system encodes a programmed cell death (PCD) pathway that is switched on in a subset of cells in response to DNA damage. Here we show that the central regulator of this pathway, AlpA, exerts its effects by acting as an antiterminator rather than a transcription activator. In particular, we present evidence that AlpA positively regulates the alpBCDE cell lysis genes, as well as genes in a second newly identified operon, by recognizing specific DNA sites within the promoter, then binding RNA polymerase directly and allowing it to bypass intrinsic terminators positioned downstream. We further show that the activity of AlpA is potentiated by the alarmone ppGpp, which is produced by the cell in response to stress. Through its responsiveness to ppGpp, AlpA can integrate environmental cues into the decision to execute a PCD pathway that is linked to the virulence of the organism.

overall_design: Comparison of transcripts between wild-type Pseudomonas aeruginosa PAO1 ectopically expressing AlpA compared to empty vector control and the same comparison in cells lacking relA

first: Jennifer

last: Pena

first: Kirsty

middle: A

last: McFarland

first: Tracy

middle: K

last: Kambara

first: Kathryn

last: Ramsey

first: Padraig

last: Deighan


title: PlexinA4-Semaphorin3A mediated crosstalk between main cortical interneuron classes is required for superficial interneurons lamination

city: Geneva 4

first: Alexandre

last: Dayer

state: GE

address: Rue Michel-Servet 1

department: Basic Neuroscience

country: Switzerland

institute: University of Geneva

summary: In the mammalian cerebral cortex, the developmental events governing the allocation of different classes of inhibitory neurons into distinct cortical layers are poorly understood. Here we report that the guidance receptor PlexinA4 is upregulated in serotonin receptor 3a-expressing (HTR3A) cortical interneurons (hINs) as they invade the cortical plate and that it regulates their laminar allocation to superficial cortical layers. We find that the PlexinA4 ligand Semaphorin3A acts as a chemorepulsive factor on hINs migrating into the nascent cortex and demonstrate that Semaphorin3A specifically controls their laminar positioning through PlexinA4. We identify that deep layer interneurons constitute a major source of Semaphorin3A in the developing cortex and demonstrate that cell-type specific genetic deletion of Semaphorin3A in these interneurons specifically affects the laminar allocation of hINs. These data demonstrate that in the neocortex, deep layer interneurons control the laminar allocation of hINs into superficial layers.

overall_design: hINs from E14.5, E18.5 and P2 (from controls and Htr3a-KO brains) have been dissociated and FACS-sorted to isolate cells migrating tangentially, invading the cortical plate and settling into the cortex, respectively. Triplicates from 3 different litters were obtained by pooling at least 4 brains. RNA was extracted with Quiagen Rneasy mini kit and quality assessed with Agilent 2100 Bioanalyser. Total RNA was amplified and labeled with Affymetrix small-scale protocol. Biotynilated cDNA was fragmented and hybridized to Mouse Genome 430 2.0 Array (Affymetrix) according to manufacturer's protocol. GeneChips were incubated with biotin-labeled cRNAs probes and stained with streptavidin-phycoerythrin conjugated with antibody amplification using Affymetrix GeneChip Fluidis Station 450. GeneChips were scanned on GC3000 scanner, signal intensities analyzed with Partek Genomic Suite v. 6.6 beta and data normalized using robust multi-array average (RMA).

first: Greta

last: Limoni

first: Sahana

last: Murthy

first: Denis

last: Jabaudon

first: Mathieu

last: Niquille


title: Control of a programmed cell death pathway in Pseudomonas aeruginosa by a ppGpp-responsive antiterminator

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

overall_design: Refer to individual Series


title: RNA m6A methylation orchestrates cancer growth and metastasis via macrophage reprogramming

city: Xi’an

first: Huilong

last: Yin

state: Shaanxi

address: No.169, Changle West Road

institute: Fourth Military Medical University

summary: The CD45+ immune-infiltrated cells in B16 tumors from WT or KO mice were enriched. Then, pooled samples of mice per group were analyzed by single cell RNA sequencing （scRNA-seq）

overall_design: scRNA-seq analysis of tumor immune microenvironment in METTL3 deficient mice

first: Rui

last: Zhang

first: Angang

last: Yang


title: Integrative pan cancer analysis reveals epigenomic variation in cancer type and cell specific chromatin domains

city: Detroit

first: Benjamin

last: Kidder

state: MI

address: 4100 John R St

department: Oncology

institute: Wayne State University

summary: Epigenetic mechanisms contribute to the initiation and development of cancer, and epigenetic variation promotes dynamic gene expression patterns that facilitate tumor evolution and adaptation. While the NCI-60 panel represents a diverse set of human cancer cell lines that has been used to screen chemical compounds, a comprehensive epigenomic atlas of these cells has been lacking. Here, we report an integrative analysis of 60 human cancer epigenomes, representing a catalog of activating and repressive histone modifications. We identify genome-wide maps of canonical sharp and broad H3K4me3 domains at promoter regions of tumor suppressors, H3K27ac-marked conventional enhancers and super enhancers, and widespread inter-cancer and intra-cancer specific variability in H3K9me3 and H4K20me3-marked heterochromatin domains. Furthermore, we identify features of chromatin states, including chromatin state switching along chromosomes, correlation of histone modification density with genetic mutations, DNA methylation, enrichment of DNA binding motifs in regulatory regions, and gene activity and inactivity. These findings underscore the importance of integrating epigenomic maps with gene expression and genetic variation data to understand the molecular basis of human cancer. Our findings provide a resource for mining epigenomic maps of human cancer cells and for identifying epigenetic therapeutic targets.

overall_design: ChIP-Seq of NCI-60 cancer cells


title: Control of a programmed cell death pathway in Pseudomonas aeruginosa by a ppGpp-responsive antiterminator [RNAtag-seq]

overall_design: Comparison of transcripts between wild-type PAO1 and PAO1 lacking alpA in the presence of ciprofloxacin


title: PD-1-targeted immunotherapy in NASH-triggered liver cancer induces pro-tumorigenic environment through CD8+PD-1+ T-cells

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Whereas some cancer types (e.g. melanoma) can be efficiently treated with immunotherapy, others lack measurable positive effects (e.g. PDAC ). Moreover, stratification of responders/non-responders is only possible in some cancer types (e.g. melanoma).  Hepatocellular carcinoma (HCC) has a dismal prognosis, limited treatment options and survival benefit, and represents a potential cancer entity for successful immunotherapy. Here, we investigated NASH -triggered HCC in the context PD-1-targeted immunotherapy. Using flow cytometry, single cell RNA sequencing, immunohistochemistry and mass spectrometric analyses, we found a progressive increase of CD8+PD-1+ effector T-cells with a unique profile of exhaustion and activation markers rising with murine and human NASH severity. Notably, late-stage HCC treatment with PD-1-targeted immunotherapy enhanced hepatic carcinogenesis in mice. To dissect potential mechanisms of action during tumor-initiation and -progression we analyzed the effects of PD-1-targeted immunotherapy at HCC initiation. Anti-PD-1 treatment induced a pro-tumorigenic environment, enhanced necro-inflammation and increased NAFLD -activation score (NAS), leading to increased liver cancer incidence, tumor number and nodule size. In contrast, anti-CD8  treatment reduced NAS and abrogated the development of liver cancer, thus identifying CD8+PD-1+ T-cells as drivers of liver cancer in NASH-triggered HCC. Increased apoptotic signaling, STAT3 phosphorylation and hepatic proliferation were detected in intra-tumoral liver tissue upon PD-1-targeted immunotherapy. In line, PD-1-/- mice challenged with a NASH diet displayed early onset of hepatocarcinogenesis, corroborating the pro-tumorigenic role of absent or reduced PD-1. Mechanistically PD-1-targeted immunotherapy increased hepatic abundance of CD8+PD-1+Tox+CXCR6+CD8+PD-1+TNF+CD39+Gzmb+  T cells found in NASH livers, creating a pro-tumorigenic liver environment .

overall_design: Hepatic CD4+ or CD8+ T-cells of 12 months NASH-diet + 8 weeks treatment (IgG, α-PD-1 or α-CD8)  mice were isolated by liver perfusion, mechanical + enzymatic digestion and percoll gradient enrichment and subsequently single-cell sorted (sorted gate: L/D-,CD11b-,CD11c-,CD19-,CD45+,CD4+ or CD8+ cells) and frozen on dry-ice .

first: Dominik

last: Pfister

first: Nicolas

last: Nunez

first: Olivier

last: Govaere

first: Ankit

last: Sinha

first: Matthias

last: Pinter

first: Marta

last: Szydlowska

first: Ekaterina

last: Friebel

first: Aleksandra

last: Deczkowska

first: Assaf

last: Weiner

first: Mathias

last: Heikenwalder


title: BAF subunit switching regulates chromatin accessibility to control cell cycle exit in the developing mammalian cortex [RNA-seq]

status: Public on Jan 18 2021

city: Geneva

first: Simon

last: Braun

address: rue Michel Servet 1

summary: mSWI/SNF or BAF chromatin regulatory complexes are dosage-sensitive regulators of human neural development frequently mutated in autism and intellectual disability. Cell cycle exit and differentiation of neural stem/progenitor cells is accompanied by BAF subunit switching to generate neuron-specific nBAF complexes. We manipulated the timing of BAF subunit exchange in vivo and found that early loss of the npBAF subunit BAF53a stalls cell cycle exit to disrupt neurogenesis. Loss of BAF53a results in decreased chromatin accessibility at specific neural transcription factor binding sites, including the pioneer factors Sox2 and Ascl1, due to Polycomb accumulation. This results in repression of cell cycle genes, thereby blocking cell cycle progression and differentiation. Cell cycle block upon Baf53a deletion could be rescued by premature expression of the nBAF subunit BAF53b but not by other major drivers of proliferation or differentiation. Wnt, EGF, FGF, Sox2, myc or Pax6 all fail to maintain proliferation in the absence of BAF53a, highlighting a novel mechanism underlying neural progenitor cell cycle exit in the continued presence of extrinsic proliferative cues.

overall_design: We conducted RNAseq on Baf53aHet and Baf53aKO mouse forebrains from embryonic day E15.5


title: m6A-seq analysis of Wild Type and Mettl3-/- BMDMs (bone-marrow-derived macrophages) Transcriptomes

type: Methylation profiling by high throughput sequencing

summary: To investigate the role of METTL3-mediated m6A modification in macrophage, we performed m6A-sequencing to map the m6A modification in bone-marrow-derived macrophages (BMDMs) in wild type (WT) and Mettl3-/- mice.

overall_design: m6A-seq profiles of BMDMs in 8 weeks wild type (WT) and Mettl3-/- (KO) mice were generated by deep sequencing, with biologic replicates.


title: BAF subunit switching regulates chromatin accessibility to control cell cycle exit in the developing mammalian cortex [ATAC-seq]

overall_design: We conducted ATACseq on Baf53aHet and Baf53aKO mouse forebrains from embryonic day E15.5


title: Genome-wide Binding Potential and Regulatory Activity of the Glucocorticoid Receptor’s Monomeric and Dimeric Forms

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

summary: A widely regarded model for glucocorticoid receptor (GR) action postulates that dimeric binding to DNA regulates unfavorable metabolic pathways while monomeric receptor binding promotes repressive gene responses related to its anti-inflammatory effects. This model has been built upon the characterization of the GRdim mutant, reported to be incapable of DNA binding and dimerization. Although quantitative live-cell imaging data shows GRdim as mostly dimeric, genomic studies, on the basis of recovery of enriched half-site response elements, suggest monomeric engagement on DNA. Here, we performed genome-wide studies on GRdim and a constitutively monomeric mutant. Our results show that impairing dimerization affects binding to even open chromatin. Also, GRdim does not exclusively bind half-response elements. Our results do not support a physiological role for monomeric GR and are consistent with a common mode of receptor binding via higher order structures that drives both the activating and repressive actions of glucocorticoids.

overall_design: Genome-wide occupancy profiling of GR and active histone marks by ChIP-seq from mouse mammary adenocarcinoma cell lines (3617) knock-out of endogenous GR (3617-KOGR) and stably integrated with GFP-tagged GR mutants, in biological duplicates, using Illumina NextSeq. GR binding data from the 3617-KOGR cells was used as control for GR (GSE108634; GSM2907216-GSM2907223) and input sample from 3617-KOGR cells were used as controls for the rest (GSE108634; GSM2907274). Chromatin accessibility examined by ATAC-seq from GRdim cell line, in biological duplicates, using Illumina HiSeq4000. Gene expression profiling from GR mutant cell lines by RNA-seq, in biological triplicates, using Illumina HiSeq2500.


title: RNA sequencing of ADIPOR2 knockout HEK293 cells undergone various treatments with palmitic acid

city: Gothenburg

first: Marc

last: Pilon

address: Medicinaregetan 9 (BOX462)

department: Chemistry and Molecular Biology

country: Sweden

institute: University of Gothenburg

summary: How cells maintain vital membrane lipid homeostasis while obtaining most of their constituent fatty acids from a varied diet remains largely unknown. Here, we used transcriptomics, lipidomics, growth and respiration assays and membrane property analyses in human HEK293 cells or human umbilical vein endothelial cells (HUVEC) to show that the function of AdipoR2 is to respond to membrane rigidification by regulating many lipid metabolism genes. We also show that AdipoR2-dependent membrane homeostasis is critical for growth and respiration in cells challenged with saturated fatty acids. Additionally, we found that AdipoR2 deficiency causes transcriptome and cell physiological defects similar to those observed in SREBP-deficient cells upon SFA challenge. Finally, we compared several genes considered important for lipid homeostasis, namely AdipoR2, SCD, FADS2, PEMT and ACSL4, and found that AdipoR2 and SCD are the most important among these to prevent membrane rigidification and excess saturation when human cells are challenged with exogenous SFAs. We conclude that AdipoR2-dependent membrane homeostasis is especially important for the non-toxic uptake of SFAs.

overall_design: Triplicate samples of knockout (KO) and wildtype (WT) cells treated with BSA (control) or Palmitic acid (PA) for 0, 3, 9 and 24h

first: Henrik

last: Palmgren

first: Mario

last: Ruiz


title: Control of a programmed cell death pathway in Pseudomonas aeruginosa by a ppGpp-responsive antiterminator [ChIP-Seq]

last: Dove

overall_design: Identification of DNA associated with the Pseudomonas aeruginosa protein AlpA

first: Jennifer

last: Pena

first: Kirsty

last: McFarland

first: Tracy

last: Kambara

first: Kathryn

last: Ramsey

first: Padraig

last: Deighan


title: BAF subunit switching regulates chromatin accessibility to control cell cycle exit in the developing mammalian cortex


title: Activation of the antiviral factor RNase L triggers translation of non-coding mRNA sequences

city: Bethesda

first: Nicholas

middle: R

last: Guydosh

address: 8 Center Dr, Bldg 8, 220

department: NIDDK

institute: National Institutes of Health

summary: Ribonuclease L (RNase L) is activated as part of the innate immune response and plays an important role in the clearance of viral infections. When activated, it endonucleolytically cleaves both viral and host RNAs, leading to a global reduction in protein synthesis. However, it remains unknown how widespread RNA decay, and consequent changes in the translatome, promote the elimination of viruses. To study how this altered transcriptome is translated, we assayed the global distribution of ribosomes in RNase L activated human cells with ribosome profiling. We found that RNase L activation leads to a substantial increase in the fraction of translating ribosomes in ORFs internal to coding sequences (iORFs) and ORFs within 5’ and 3’ UTRs (uORFs and dORFs). Translation of these alternative ORFs was dependent on RNase L’s cleavage activity, suggesting that mRNA decay fragments are translated to produce short peptides that may be important for antiviral activity.

overall_design: 30 Ribsome profiling datasets on 2-5A or poly I:C treated or untreated A549 lung carcinoma cells.

first: Agnes

last: Karasik

first: Grant

last: Jones

first: Andrew

middle: V

last: DePass


title: Genome wide expression change by ZNF213  knockdown in MCF-7 cells

city: Shenzhen

first: Juntao

last: Xu

state: Guangdong

address: Yuehai Subdistrict, Nanshan District

institute: Philrivers

summary: We aim to the investigate the role of ZNF213 in breast cancer progression. MCF-7 cells were used as the model , ZNF213 was silenced by siRNA.

overall_design: The MCF-7 cells were treated with 50nM stramble siRNA and siZNF213. After 48 hours, cells were harvested and the total RNA was extacted by Qiagen kit. The RNA sample was sent to BGI for RNA expression anaylsis.

first: Jian

last: Zhu

first: Hui

last: Wang


title: Expression data from human venous and arterial endothelial cells

city: Atlanta

first: Michael

last: Koval

state: GA

address: 205 Whitehead Bldg, 615 Michael St

department: Pulmonary Medicine

institute: Emory University School of Medicine

summary:
The vascular tree has considerable diversity, with discrete regions having different physiologic characteristics and permeability. Of note are venules that are significantly more sensitive to pro-inflammatory cytokines than arterioles.
We used microarrays to identify molecular signatures that distinguish primary human venous endothelial cells from arterial endothelial cells. We used microarrays to identify genes differentially expressed by venous vs arterial human endothelial cells.

overall_design: Human umbilical vein endothelial cells (HUVEC; Cell Applications 200K-05), human saphenous vein endothelial cells (HSaVEC; PromoCell C-12231), human aortic endothelial cells (HAoEC; PromoCell C-12271) and human coronary arterial endothelial cells (HCoEC; Lonza CC-2585) were cultured in Microvascular Endothelial Cell Growth Medium-2 (complete medium, EGM-2MV, Lonza) and then used for RNA extraction and hybridization on Affymetrix microarrays.

first: Brant

middle: E

last: Isakson

first: Alexander

last: Lohman


title: Vascular smooth muscle-derived TRPV1-expressing progenitors are a new source of cold induced thermogenic adipocytes

first: Yu-Hua

last: Tseng

address: 1 Joslin Place

institute: Joslin Diabetes Center Harvard Medical School

summary: Brown adipose tissue (BAT) functions in energy expenditure in part due its role in thermoregulation. The prominent capacity of BAT to enhance fuel utilization and energy expenditure makes it an attractive target for treating obesity and metabolic disorders. Prolonged cold exposure induces de novo recruitment of brown adipocytes and activates their thermogenic activity. However, the exact source of cold-induced brown adipocytes is not completely understood. In this study, we sought to investigate the cellular origin of cold-induced brown adipocytes using single-cell RNA sequencing. We identified two distinct types of adipocyte progenitors that contribute to de novo recruitment of brown adipocytes in response to cold challenge. One is the previously known Pdgfra-expressing mesenchymal progenitors and the other is a vascular smooth muscle-derived adipocyte progenitor (VSM-APC) population, which expresses the temperature-sensitive ion channel transient receptor potential cation channel subfamily V member 1 (Trpv1). Using flow cytometry and lineage tracing, we demonstrated that the Trpv1pos VSM-APCs were indeed distinct from the Pdgfrapos progenitors and could contribute to brown adipocytes with greater thermogenic potential. Together, these findings illustrate a landscape of thermogenic adipose niche at the single cell resolution and identify a new cellular origin for the development of brown adipocytes.

overall_design: To characterize the cellular composition of the BAT niche during cold-induced remodeling, we applied scRNA-seq to cells isolated from the stromal vascular fraction of BAT (BAT-SVF) from mice housed at either thermoneutral (TN: 30 °C for 1 week), room temperature (RT: 22 °C) or cold (5 °C for 2 days or 7 days).

first: Farnaz

last: Shamsi

first: Mary

last: Piper


title: Transcriptional profiling of astrocyte subtypes in naive mice and during experimental autoimmune encephalomyelitis

city: Groningen

first: Bart

last: Eggen

state: Groningen

address: Antonius Deusinglaan 1

department: Department of Biomedical Sciences

institute: UMCG Groningen

summary:
We isolated and gene expression profiled distinct astrocyte subtypes from three central nervous system regions: forebrain, hindbrain, and spinal cord, using a FACS-based protocol. Cell surface expression of Glast/Slc1a3 (G) and Acsa-2/Atp1b2 (A) was used to distinguish subpopulations of astrocytes. Furthermore, we assessed the transcriptome of cultured primary neonatal astrocytes.
The local brain environment proved key in establishing different transcriptional programs in astrocyte subtypes. Functional differences between subtypes were also apparent in experimental autoimmune encephalomyelitics (EAE) mice, where these astrocyte subtypes showed distinct responses.
While gene expression signatures associated with blood-brain-barrier maintenance were lost during EAE, signatures contributing to neuroinflammation were increased specifically in astrocytes in the spinal cord.

overall_design: Two main experiments: 1) Transcriptional profiles of astrocyte subpopulations (ACSA+Glast- and ACSA+Glast+) isolated from FVB/N mice from forebrain, hindbrain, and spinal cord, and primary neonatal astrocytes. 2) Transcriptional profiles of astrocyte subpopulations (ACSA+Glast- and ACSA+Glast+) from hindbrain and spinal cord from C57BL/6J mice during four stages of EAE (unimmunized control, stage 1, stage 4, chronic stage).

first: Erik

last: Boddeke

first: Susanne

last: Kooistra


title: Time series genome-wide transcriptome analysis of mouse eyes kept under different seasonal conditions

city: Nagoya

first: Kousuke

last: Okimura

address: Furocho

institute: Nagoya University

summary: We measured time series transcriptome level in mouse eyes kept under short day and cool (SC), winter-like conditions, and long day and warm (LW), summer-like conditions.

overall_design: Comparison of gene expression of  mouse eyes kept under winter-like conditions and summer-like conditions with time series.

first: Takashi

last: Yoshimura


title: SLPI is a novel bone-coupling factor that controls parathyroid hormone-induced bone formation

status: Public on Jan 17 2021

first: Daisuke

last: Okuzaki

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Osteoclastic bone resorption and osteoblastic bone formation/replenishment are closely coupled in bone metabolism. Anabolic parathyroid hormone (PTH), which is commonly used for treating osteoporosis, shifts the balance from osteoclastic to osteoblastic, although the mechanisms underlying this phenomenon are unclear. Here we identified a serine protease inhibitor, secretory leukocyte protease inhibitor (SLPI), as a novel coupling factor that is involved in the PTH-mediated shift to the osteoblastic phase. SLPI was highly upregulated in osteoblasts by PTH, and genetic ablation of SLPI severely impaired PTH-induced bone formation. SLPI induction in osteoblasts enhanced osteoblast differentiation intracellularly and was also secreted extracellularly, attracting neighboring osteoclasts to suppress osteoclastic function. Intravital bone imaging revealed that the PTH-mediated association between osteoblasts and osteoclasts was disrupted in the absence of SLPI. Collectively, these results demonstrate that SLPI, a previously unrecognized bone-coupling factor, mediates the communication of osteoblasts with osteoclasts to promote PTH-induced bone formation.

overall_design: We evaluated transcripts in osteoblasts by RNA-seq, using an iPTH mouse model (Iida-Klein et al. 2002) treated with iPTH or vehicle for 3 weeks.

first: Akito

last: Morimoto

first: Junichi

last: Kikuta


title: Transient “rest” induces functional reinvigoration and epigenetic remodeling in exhausted CAR-T cells Mediate Enhanced Antitumor Activity [ATAC-seq, ChIP-seq]

status: Public on Jan 16 2021

city: Stanford

first: Evan

last: Weber

state: California

address: 265 Campus Drive, SIM1, Room G2105

department: Stanford Cancer Institute

institute: Stanford University

summary: T cell exhaustion limits immune responses against cancer and is a major cause of resistance to CAR-T cell therapeutics. Using a model wherein tonic CAR signaling induces hallmark features of exhaustion, we employed a drug-regulatable CAR to test the impact of transient cessation of receptor signaling (i.e. “rest”) on the development and maintenance of exhaustion. Induction of rest in exhausting or already-exhausted CAR-T cells resulted in acquisition of a memory-like phenotype, improved anti-tumor functionality, and wholescale transcriptional and epigenetic reprogramming. Similar results were achieved with the Src kinase inhibitor dasatinib, which reversibly suppresses CAR signaling. The degree of functional reinvigoration was proportional to the duration of rest and was associated with expression of transcription factors TCF1 and LEF1. This work demonstrates that transient cessation of CAR-T cell signaling can enhance anti-tumor potency by preventing or reversing exhaustion and challenges the paradigm that exhaustion is an epigenetically fixed state.

overall_design: ATAC-seq profiling and ChIP-seq profiling of CAR-T cells cultured under different conditions

first: Kevin

last: Parker

first: Elena

last: Sotillo

first: Julia

last: Belk

first: Bence

last: Daniel

first: Hima

last: Anbunathan

first: Howard

middle: Y

last: Chang

first: Ansuman

middle: T

last: Satpathy

first: Crystal

last: Mackall


title: Transient “rest” induces functional reinvigoration and epigenetic remodeling in exhausted CAR-T cells Mediate Enhanced Antitumor Activity [RNA-seq]

middle: W

overall_design: RNAseq profiling of HA CAR T cells at days 7, 11, and 15 in culture with transient rest and/or treated with Nivolumab

middle: L


title: Transient “rest” induces functional reinvigoration and epigenetic remodeling in exhausted CAR-T cells Mediate Enhanced Antitumor Activity

overall_design: Refer to individual Series


title: Transient “rest” induces functional reinvigoration and epigenetic remodeling in exhausted CAR-T cells Mediate Enhanced Antitumor Activity [ATAC-seq]

overall_design: ATAC-seq profiling of CAR-T cells cultured under different conditions


title: T cell self-reactivity during thymic development dictates the timing of positive selection

city: Berkeley

first: Zoë

last: Steier

state: CA

address: 378 Stanley Hall

institute: UC Berkeley

summary: Functional tuning of mature T cells based on their degree of self-reactivity is established during positive selection in the thymus, although how positive selection differs for thymocytes with relatively low versus high self-reactivity is unclear. In addition, preselection thymocytes are highly sensitive to low-affinity ligands, but the mechanism underlying their enhanced TCR sensitivity is not fully understood. Here we show that thymocytes with low self-reactivity experience briefer TCR signals and complete positive selection more slowly than those with high self-reactivity. Additionally, we provide evidence that cells with low self-reactivity retain a preselection gene expression signature as they mature, including genes previously implicated in modulating TCR sensitivity and a novel group of ion channel genes. Our results imply that thymocytes with low self-reactivity down-regulate TCR sensitivity more slowly during positive selection, and suggest that modulation of membrane ion channel function may play a role in regulating TCR tuning throughout development.

overall_design: RNA-seq was performed on FACS sorted thymocytes from three OT-1 Rag2KO, three F5 Rag1KO, and three TG6 H2b/d mice (biological replicates). Thymocytes were sorted into 3 populations representing 3 distinct stages of CD8 T cell positive selection prior to sequencing: CD4+CD8+CXCR4+CCR7- (C, early positive selection), CD4+CD8+CXCR4-CCR7+ (B, late positive selection) [TG6 only has two biological replicates for this population], and CD4-CD8+CXCR4-CCR7+ (A, Mature CD8SP). This resulted in 26 samples in total.

first: Lydia

last: Lutes

first: Laura

last: McIntyre

first: Shraddha

last: Pandey

first: James

last: Kaminski

first: Ashley

last: Hoover

first: Silvia

last: Ariotti

first: Aaron

last: Streets

first: Nir

last: Yosef

first: Ellen

last: Robey


title: Single cell analysis of juvenile Nkx3.2 mutant zebrafish craniofacial skeleton

city: New York

first: Joanna

last: Smeeton

state: NY

address: 650 W 168TH ST, ROOM 1103A, William Black Building

department: Rehabilitation and Regenerative Medicine

institute: Columbia University Irving Medical Center

summary: The specification and maintenance of distinct zones of chondrocytes within growth plates and joints ensures proper skeletal development through adulthood. Rare mutations in the transcription factor NKX3.2 underlie Spondylo-megaepiphyseal-metaphyseal dysplasia (SMMD), which is characterized by skeletal defects including scoliosis, large epiphyses, wide growth plates, and supernumerary joints in the distal limbs. Embryonic knockdown of nkx3.2 function in zebrafish had revealed a requirement in jaw joint specification, yet embryonic lethality of nkx3.2 knockdown zebrafish and mouse Nkx3.2 mutants had precluded an analysis of post-embryonic functions. Here we report adult viable nkx3.2 zebrafish mutants that display ectopic cartilage overgrowth in place of a missing jaw joint, as well as severe dysmorphologies of the facial skeleton, skullcap, and spine. We also isolate rare viable nkx3.2 knockdown animals that lack the jaw joint but fail to display ectopic cartilage growth and scoliosis, indicating post-embryonic roles for Nkx3.2 beyond jaw joint specification. Consistently, we observe nkx3.2 expression in the subarticular zone of the adult jaw joint and in pre-hypertrophic growth plate chondrocytes. Single-cell RNA sequencing reveals an upregulation of stress-induced pathways in mutants, including the prostaglandin D2 synthase ptgdsb.1 and the mTOR regulator sestrin1, which we confirm by in situ RNA analysis of the defective jaw joint region. Our data reveal a zebrafish model for the joint and spine defects of SMMD and point to post-embryonic roles for Nkx3.2 in buffering the stress response and dampening proliferation in joint-adjacent chondrocytes.

overall_design: Single cell RNA sequencing of FACS isolated cartilages (fli:GFP/sox10:DsRed+) from wildtype and nkx3.2 mutants

first: Gage

last: Crump


title: Biological constraints on GWAS SNPs at suggestive significance thresholds reveal true BMI loci [hMSC_adipocytes_atacseq]

city: Philadelphia

first: Matthew

middle: C

last: Pahl

state: PA

address: 3615 Civic Center Blvd

department: Center for Spatial and Functional Genomics

institute: Children's Hospital of Philadelphia

summary: We investigated whether intersecting functional genomic data (ATAC-seq + promoter focused Capture C) with increasingly powered publically available GWAS for Body Mass Index and Waist to Hip Ratio could identify additional true postiive subsignficant signals (5x10-8< P value < 5x10-4) without increasing the GWAS sample size

overall_design: We performed ATAC-seq  and Promoter Focused Capture C on MSC dervived adipocytes from healthy donors

first: Reza

last: Hammond

first: Chun

last: Su

last: Pippin

first: Yadav

last: Wagley

first: Alessandra

last: Chesi

first: Kurt

last: Hankenson

first: Struan

last: Grant


title: Ayurvedic herbal preparation supplementation does not improve metabolic health in impaired glucose tolerance subjects; observations from a randomised placebo controlled trial

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: The increased usage of alternative Ayurvedic treatments as potential health-beneficial therapies emphasizes the importance of studying its efficacy in sound placebo-controlled intervention trials. An example of such a traditional Ayurvedic herbal preparation is Mohana Choorna, a mixture composed of 20 different herbs and used to prevent and treat type 2-diabetes (T2D). We studied the efficacy of “Mohana Choorna” on T2D-related parameters in subjects with impaired glucose tol-erance. In a double blind, placebo-controlled cross-over trial, 19 overweight (BMI > 27 kg/m2) subjects aged 50–70 years with an impaired glucose tolerance received two four-week interven-tions, i.e., herbal or placebo with a four-week wash-out between interventions. HbA1c, glucose, insulin, triglycerides, cholesterol, blood pressure and augmentation index were measured before and after both interventions at fasting and during a glucose tolerance test. After both interventions, urine was collected to measure treatment exposure using LCMS-based metabolomics and whole genome gene-expression in adipose tissue of 13 subjects. The herbal intervention did not affect plasma glucose triglycerides, cholesterol, blood pressure or the augmentation index but showed a trend towards an increased insulin, HOMA-IR and postprandial insulin levels (p = 0.054, p = 0.056 and p = 0.095 respectively). An increase in expression of inflammation-related gene sets in adipose tissue was observed after the herbal intervention compared to placebo. Urine metabolomic analysis did not reveal a correlation of the presence of specific plant metabolites with “health markers”. Our findings suggest that there is no substantiating evidence to claim that four weeks’ use of the Ayurvedic herbal supplement Mohana Choorna beneficially affects glucose homeo-stasis.

overall_design: Microarray analysis was performed on subcuteaneous adipose tissue from overweight middle age subjects with an impaired glucose tolerance  in cross-over trial with a herbal supplement.

first: Diederik

last: Esser

first: Juri

last: Matualatupau

first: Ric

last: de Vos

first: Ron

last: Wehren

first: Jos

last: van der Stappe

first: Ingrid

last: van der Meer

first: Lydia

last: Afman


title: A Multi-Omics Approach to Epstein-Barr Virus (EBV) Immortalization of B-Cells Reveals Viral-Induced Changes in Chromatin Accessibility and Nucleotide Metabolism

status: Public on Jan 15 2021

first: Priyankara

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Epstein-Barr Virus (EBV) immortalizes resting B-lymphocytes through a highly orchestrated process involving extensive reprogramming of host transcription and metabolism. Here, we use multiple omics-based approaches concurrently across the time course of B-cell infection to investigate the underlying mechanisms that control EBV-induced B-cell immortalization. ATAC-seq revealed that over a third of accessible chromatin is altered with the most perturbed sites overlapping Ets-family, including PU.1 and RUNX1 transcription factors.  EBV nuclear antigens (EBNAs) clustered with different gene categories and RNA-seq identified the transcriptional response of these gene.  Focusing on EBNA1 revealed a selection of gene targets involved in nucleotide metabolism.  Metabolomics indicated that adenosine and purine metabolism are significantly altered by EBV immortalization, and we validated that adenosine deaminase (ADA) is a direct and critical target of EBNA1 and the EBV-directed immortalization process. These findings reveal that purine metabolism and ADA inhibitors may be a useful therapeutic for EBV-driven lymphoid cancers

overall_design: ATAC-seq and RNA-seq of B cells during 0, 2, 7 and 21 days of EBV infection

first: Paul

last: Lieberman

first: Jason

last: Lamontagne


title: Biological constraints on GWAS SNPs at suggestive significance thresholds reveal true BMI loci [hMSC_adipocytes_captureC]

first: Matthew

last: Pahl

first: Reza

last: Hammond

last: Su

first: James


title: Atrial and ventricular transcriptomic alterations in a cardiac mouse model of myotonic dystrophy expressing 960 CUG repeats

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 3181 SW Sam Jackson Park Rd

department: Department of Biomedical Engineering

institute: Oregon Health & Science University

summary:
Purpose: The goal of this study was to characterize the atrial and ventricular transcriptomic changes in a cardiac mouse model of myotonic dystrophy. The mouse model utilizes a bitransgenic system for doxycycline (dox) inducible and cardiomyocyte specific expression of pathogenic RNA containing 960 CUG repeats. Bitransgenic animals (called CUG960 mice) homozygous for the TREDT960I transgene (containing 960 interrupted CTG repeats) and hemizygous for reverse transactivator (rtTA) transgene containing a cardiomyocyte-specific alpha myosin heavy chain promoter are given dox food for expression of CUG repeat RNA. Mice hemizygous for rtTA transgene (MHCrtTA) given dox food were used as controls.
Methods:We performed RNA-seq for high-resolution analysis of transcriptomic alterations in atria and ventricles of CUG960 experimental and MHCrtTA control mice given dox chow since postnatal day 1 (PN1) for a period of 10 weeks.
Results: We identified pathogenic CUG repeat RNA induced gene expression and alternative splicing changes in ion transport genes that are associated with inherited cardiac conduction diseases, including a subset of genes involved in calcium handling.
Conclusions: We identified potential tissue-specific mechanisms contributing to the cardiac disease relevant phenotypes in an animal model of DM1.

overall_design: Mouse atrial and ventricular cardiac muscle mRNA profiles of  CUG960 experimental and MHCrtTA control mice were generated by deep sequencing using Illumina Novaseq 6000.

first: Ashish

middle: N

last: Rao

first: Xiangnan

last: Guan

first: Thomas

last: Cooper


title: Loss of a-actinin-3 during human evolution provides superior cold resilience and muscle heat generation

city: Parkville

first: Peter

middle: John

last: Houweling

state: Does Not Apply

address: Flemington Road

department: Cell Biology

institute: Murdoch Childrens Research Institute

summary:
To examine if the loss of alpha-actinin-3, a fast skeletal muscle protein, modifies core body temperture following acute cold exposure in humans and a mice
Using an Actn3 KO mice model we explore the effects of cold exposure on brown adipose tissue function following exposure to cold (4oC) for 5 hours, compared to control mice housed at either thermoneutrality (30oC) or standard room temperature (22oC)

overall_design: WT and Actn3 KO mice were exposed to altered environmental temperatures and core body tempertaure was recovredd over a 5 hour peroid. Following euthenasia, brown adipose tissue was collected and frozen in liquid nitrogen prior to RNA being extracted.

first: Harrison

last: Wood

first: Chrystal

last: Tiong

first: Kathryn

last: North


title: PiggyBac (PB) genetic screening allows identification of putative metastatic genes

city: Basel

first: Mohamed

last: Bentires-Alj

address: Hebelstrasse 20

department: DBM

institute: University Hospital Basel

summary: Next-Generation Sequencing was applied to investigate candidate breast cancer metastatic genes. PB targeted sequencing of primary tumours and metastases (3 lung metastases, 6 lung macro-metastases and 9 LM cell lines) allowed to identify Nfib as a candidate metastasis inducer.

overall_design: PB-Seq in 16 different primary tumours, 3 lung metastases, 6 lung macro-metastases and 9 LM cell lines to candidate genes enriched at metastatic sites compared to tumours.

first: Michael

last: Stadler

first: Atul

last: Sethi


title: RNA-Seq of 2 lung metastatic breast cancer cell lines and their Nfib Kos.

summary: Next Generation Sequencing was applied to investigate molecular mechanisms underlying the increased metastatic colonization driven by Nfib. Global transcriptional profiling of the lung metastatic cell lines and respective KOs allowed to identify Ero1l as a mediator of metastasis upon Nfib upregulation.

overall_design: RNA-Seq in 2 different lung metastatic breast cancer cell lines and respective KOs to investigate NFIB signalling role in metastasic colonitazion.


title: RNA-Seq of 3 breast cancer models to investigate NFIB signalling role in metastatic colonization.

summary: Next Generation Sequencing was applied to investigate molecular mechanisms underlying the increased metastatic colonization driven by Nfib. Global transcriptional profiling of primary tumours derived from Nfib high-expression models (LM1 and LM9) and Nfib low-expression models (HR1) allowed to identify Ero1l as a mediator of metastasis upon Nfib upregulation.

overall_design: RNA-Seq in 3 different breast cancer models to investigate NFIB signalling role in metastasic colonitazion.


title: Voluntary wheel running did not alter gene expression in 5xFAD mice, but in wild-type animals exclusively after one-day exercise bout

status: Public on Jan 14 2021

city: Mainz

first: Anna

last: Wierczeiko

address: Hanns-Dieter-Hüsch-Weg 15

department: Institute for Human Genetics

institute: University Medical Center, Johannes Gutenberg University Mainz

summary:
Physical activity is considered a promising preventive intervention to reduce the risk of developing Alzheimer’s disease (AD). However, the positive effect of exercise therapy has not been proven conclusively yet, likely due to confounding factors such as varying activity regimens and life or disease stages.
To examine the impact of different exercise regimens in the early disease stages, we subjected young 5xFAD and wild-type mice to 1-day (acute, 3-month-old) and 30-day (chronic, 2-month-old) voluntary wheel running and compared them with age-matched sedentary controls.
We observed a significant increase in brain lactate levels in acutely trained 5xFAD mice relative to all other experimental groups. Subsequent RNA-seq analysis from brain did not reveal major differences in transcriptomic regulation between training durations in 5xFAD mice. In contrast, acute training yielded large gene expression differences in wild-type animals relative to their chronically trained and sedentary counterparts. The comparison of 5xFAD and wild-type mice showed the highest transcriptional differences in the chronic and sedentary groups, whereas acute training was associated with much fewer DEGs.
In conclusion, our results suggest that different training durations did not affect the global transcriptome of 3-month-old 5xFAD mice, whereas acute running seemed to induce a similar transcriptional stress state in wild-type animals as already known for 5xFAD mice.

overall_design: Brain mRNA profiles of 3-month-old wild type (WT) and 5xFAD male mice after three different training levels

first: Lena

last: Gammel

first: Konstantin

last: Radyushkin

first: Vu

last: Nguyen

first: Hristo

last: Todorov

first: Susanne

last: Gerber

first: Kristina

last: Endres


title: MDMX acts as a pervasive preleukemic-to-acute myeloid leukemia transition mechanism

city: Bronx

first: Ulrich

last: Steidl

address: 1300 Morris Park Ave.

institute: Albert Einstein College of Medicine

summary: The p53 inhibitor MDMX is overexpressed in the vast majority of patients with acute myeloid leukemia (AML). Utilizing hematopoietic stem cells from four non-leukemic/pre-leukemic murine models, we performed bulk transcriptomic analysis to evaluate the impact of Mdmx overexpression.

overall_design: Flk2- Lin-Sca-1+Kit+ (LSK) cells were sorted from the bone marrow of wild-type, Mdmx-Tg, Pu.1-URE-/-, Mdmx-Tg/Pu.1-URE-/- murine models. Three replicates were sequenced for each cohort.

first: Koki

last: Ueda

first: Rajni

last: Kumari

first: Emily

last: Schwenger

first: Justin

last: Wheat

first: Oliver

last: Bohorquez

first: Swathi

last: Rao Narayanagari

first: Samuel

middle: J

last: Taylor

first: Luis

last: Carvajal

first: Kith

last: Pradhan

first: Boris

last: Bartholdy

first: Tihomira

middle: I

last: Todorova

first: Hiroki

last: Goto

first: Daqian

last: Sun

first: Jiahao

last: Chen

first: Jidong

last: Shan

first: Yinghui

last: Song

first: Cristina

last: Montagna

first: Shunbin

last: Xiong

first: Guillermina

last: Lozano

first: Andrea

last: Pellagatti

first: Jacqueline

last: Boultwood

first: Amit

last: Verma


title: A CSB-PAF1C axis restores processive transcription elongation after DNA damage repair

city: Leiden

first: Martijn

middle: S.

last: Luijsterburg

state: zuid-holland

address: Einthovenweg 20

department: Human Genetics

institute: LUMC

summary: The coordinated transcription of genes involves the regulated release of RNA polymerase II (RNAPII) from promoter-proximal sites into active elongation. DNA lesions in transcribed strands block elongation and induce a strong transcriptional arrest. The transcription-coupled repair (TCR) pathway efficiently removes transcription-blocking DNA lesions, but this is not sufficient to resume transcription. Through proteomics screens, we find that the TCR-specific CSB protein loads the evolutionary conserved PAF1 complex (PAF1C) onto RNAPII in promoter-proximal regions in response to DNA damage. PAF1C is dispensable for TCR-mediated repair, but is essential for recovery of RNA synthesis after UV irradiation, suggesting an uncoupling between DNA repair and transcription recovery. Moreover, we find that PAF1C promotes RNAPII pause release in promoter-proximal regions and subsequently acts as a processivity factor that stimulates transcription elongation throughout genes. Our findings expose the molecular basis for a non-canonical PAF1C-dependent pathway that restores transcription throughout the human genome after genotoxic stress.

overall_design: BrU-seq and ChIP-seq in human cell lines either untreated (mock) or 3h, 8h or 26h after UV-C treatment with varying dose (as indicated per sample). ChIP-seq was performed targeting RPB1 or PAF1 in either WT or CSB knockout U2OS cells or in U2OS cells in which PAF1 was depleted using the auxin-inducible degron system. BrU-seq was also performed on U2OS cells with and without auxin-induced depletion of PAF1.

first: Diana

last: van den Heuvel

middle: S


title: Mucosal-Associated Invariant T Cell Effector Function Is an Intrinsic Cell Property That Can Be Augmented by the Metabolic Cofactor α-Ketoglutarate

city: Clayton

first: Monash

middle: Bioinformatics

last: Platform

state: VIC

address: Wellington Road

institute: Monash Bioinformatics Platform

summary: Mucosal-associated invariant T (MAIT) cells are an innate-like population of unconventional T cells that respond rapidly to vitamin B metabolite antigens or cytokine stimulation. Due to this reactivity and surface expression of CD45RO+, CD45RA−, CD127+, they are described as effector memory cells. Yet, there is a lack of uniformity in the MAIT cell effector response. it is unclear what factors contribute to setting MAIT cells effector capacity and whether it is fixed or can be modified. To address this, we have taken a systematic approach to examine MAIT cells effector capacity across healthy individuals in response to ligand and cytokine stimulation. We demonstrate the heterogenous nature of MAIT cells effector capacity, and that the ability to produce an effector response was not directly attributable to TCR clonotype or coreceptor expression. Global gene transcription analysis revealed that the MAIT cells effector capacity produced in response to TCR stimulation was associated with the expression of the epigenetic regulator lysine demethylase 6B (KDM6B). Addition of a KDM6B inhibitor does not alter MAIT cell effector function. However, addition of the KDM6B cofactor α-ketoglutarate greatly enhanced MAIT cells effector capacity in a KDM6B-dependent manner. These results demonstrate that the MAIT cells effector response is epigenetically regulated and can be targeted for enhancement.

overall_design: PBMC stimulated and MAIT cells sorted based on cytokine production.

first: Lauren

last: Howson

first: Jasmine

last: Li

first: Anouk

last: von Borstel

first: Adele

last: Barugahare

first: Jeffrey

last: Mak

first: David

middle: P

last: Fairlie

first: James

last: McCluskey

first: Stephen

last: Turner

first: Martin

last: Davey

first: Jamie

last: Rossjohn


title: Machine Learning Identifies Candidates for Drug Repurposing in Alzheimer's Disease

city: Boston

first: Clemens

last: Hug

state: MA

address: 200 Longwood Avenue

department: Harvard Program in Therapeutic Science

institute: Harvard Medical School

summary: Clinical trials of novel therapeutics for Alzheimer's Disease (AD) have consumed a large amount of time and resources with largely negative results. Repurposing drugs already approved by the Food and Drug Administration (FDA) for another indication is a more rapid and less expensive option. In this study, we profile 80 FDA-approved and clinically tested drugs in neural cell cultures, with the goal of producing a ranked list of possible repurposing candidates.

overall_design: An in-vitro differentiated mixture of neuron and glial cells derived from the ReNcell VM neural progenitor cell line was treated with 80 different compounds and mRNA levels measured using RNA-seq.

first: Steve

last: Rodriguez

middle: B

first: Sarah

middle: A

last: Boswell

first: Kyle

last: Evans

first: Peter

middle: K

last: Sorger

first: Mark

last: Albers

first: Artem

last: Sokolov


title: Unique features of co-existence of classical neutrophils and polymorphonuclear myeloid-derived suppressor cells in cancer

first: Priyankara

last: Wickramasinghe

summary: In this study, using single cell RNAseq, cell mass-spectrometry, flow cytometry, and functional analysis, we characterized the heterogeneity of polymorphonuclear neutrophils (PMN) in cancer. We described three populations of PMN in tumor-bearing mice: classical PMN, polymorphonuclear myeloid derived suppressor cells (PMN-MDSC), and activated PMN-MDSC with potent immune suppressive activity. In spleens of mice, PMN-MDSC gradually replaced PMN during tumor progression. Activated PMN-MDSC were found only in tumors where they were present at the very early stages of the disease. These populations of PMN in mice could be separated based on the expression of CD14. In peripheral blood of cancer patients, we identified two distinct populations of PMN with characteristics of classical PMN and PMN-MDSC. Gene signature of tumor PMN-MDSC was similar to that in mouse activated PMN-MDSC and was closely associated with negative clinical outcome in cancer patients.  Thus, we provided evidence that PMN-MDSC is a distinct population of PMN with unique features and potential for selective targeting opportunities

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Single cell RNA-seq of polymorphonuclear neutrophils (PMN) from naïve and tumor burden (TB) mice
Single cell RNA-seq of polymorphonuclear neutrophils (PMN) blood of healthy and tumor burden patients

first: Dmitry

last: Gabrilovich

first: Filippo

last: Veglia


title: RNAseq of wild type (WT) and Dll4+/- mouse lung

city: Kansas City

first: Venkatesh

last: Sampath

address: 2401 Gillham Road

department: Neonatology

institute: Children's Mercy Hospital

summary: We report the application of RNA sequencing for high-throughput profiling of gene epxression in WT and Dll4 +/- lung

overall_design: mRNA profiles of 6-day old WT and Dll4+/- mice

first: Sheng

last: Xia

first: Heather

last: Menden

first: Daniel

last: Heruth


title: Single cell chromatin accessibility identifies pancreatic islet cell type- and state-specific regulatory programs of diabetes risk [Hi-C]

city: La Jolla

last: Gaulton

address: 9500 Gilman Drive

department: Pediatrics

institute: University of California, San Diego

summary: Single-nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq) creates new opportunities to dissect cell type-specific mechanisms of complex diseases. Since pancreatic islets are central to type 2 diabetes (T2D), we profiled 15,298 islet cells by using combinatorial barcoding snATAC-seq and identified 12 clusters, including multiple alpha, beta and delta cell states. We cataloged 228,873 accessible chromatin sites and identified transcription factors underlying lineage- and state-specific regulation. We observed state-specific enrichment of fasting glucose and T2D genome-wide association studies for beta cells and enrichment for other endocrine cell types. At T2D signals localized to islet-accessible chromatin, we prioritized variants with predicted regulatory function and co-accessibility with target genes. A causal T2D variant rs231361 at the KCNQ1 locus had predicted effects on a beta cell enhancer co-accessible with INS and genome editing in embryonic stem cell-derived beta cells affected INS levels. Together our findings demonstrate the power of single-cell epigenomics for interpreting complex disease genetics.

overall_design: Hi-C of ES-derived beta cells

first: Joshua

last: Chiou


title: Satellite cell expansion is mediated by P-eIF2α-dependent Tacc3 translation

city: Montréal

first: Claudia

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

institute: Lady Davis Institute for Medical Research

summary: Translational control of gene expression is an important regulator of adult stem cell quiescence, activation and self-renewal. In skeletal muscle, quiescent satellite cells maintain low levels of protein synthesis, mediated in part through the phosphorylation of eIF2α (P-eIF2α). Pharmacological inhibition of the eIF2α phosphatase with the small molecule sal003 maintains P-eIF2α and permits the expansion of satellite cells ex vivo. Paradoxically, P-eIF2α also increases the translation of specific mRNAs, which is mediated by P-eIF2α-dependent read-through of inhibitory upstream open reading frames (uORFs). Here, we ask whether P-eIF2α-dependent mRNA translation enables expansion of satellite cells. Using transcriptomic and proteomic analyses, we show a number of genes associated with the assembly of the spindle pole to be upregulated at the level of protein, without corresponding change in mRNA levels, in satellite cells expanded in the presence of sal003. We show that uORFs in the 5′ UTR of mRNA for the mitotic spindle stability gene Tacc3 direct P-eIF2α-dependent translation. Satellite cells deficient for TACC3 exhibit defects in expansion, self-renewal and regeneration of skeletal muscle.

overall_design: Satellite cells of adult Pax3GFP/+ mice after 4-day culture in presence of 10 μM sal003 (4 replicates) or under normal conditions (DMSO, 4 replicates) for a total of 8 samples.

first: Ryo

last: Fujita

first: Solène

last: Jamet

first: Graham

last: Lean

first: Harry

middle: M

last: Cheng

first: Steven

last: Hébert

first: Colin

last: Crist


title: Single cell RNA-seq data on human innate lymphoid cells II.

city: London

first: Janice

last: Layhadi

address: South Kensington Campus

department: National Heart and Lung Institute

country: United Kingdom

institute: Imperial College London

summary: Allergic rhinitis is a prevalent condition affecting up to 25% of the global population. The role of innate lymphoid cells in the pathogenesis of allergic diseases have been previously described, however, a single cell transcriptomic analysis to investigate differences between allergic and non-atopic healthy individuals have yet to be fully investigated. Using a combination of single cell RNA/protein and FACS validation, we provide evidence that there is a predominance and dysregulation of a type 2 response in the ILCs of allergic patients.

overall_design: Single cell RNA sequencing was performed by isolating human innate lymphoid cells (ILCs) by FACS sorting from peripheral blood mononuclear cells. Libraries (3' GEX and protein libraries) were prepared using Chromium single cell 3' Reagent Kits according to manufacturer's protocol (10x Genomics). The generated scRNAseq libraries were sequenced using HiSeq 4000 sequencers.   Human samples were processed and sequenced for allergic group (n=2) and non-allergic healthy control (n=1).

first: Mohamed

middle: H

last: Shamji


title: Single cell RNA-seq data on human innate lymphoid cells.

summary: Allergic rhinitis is a prevalent condition affecting up to 25% of the global population. Whilst common pharmacotherapies such as anti-histamines and corticosteroids can act as temporary symptom reliever, it does not work in 20% of patients. In these patients, allergen immunotherapy is recommended. The role of innate lymphoid cells in allergen specific immunotherapy which can result in the induction of tolerance towards the sensitizing allergen remains unclear. Using a combination of single cell RNA/protein and FACS validation, we provide evidence that the competence of ILC2 to produce IL-10 is dysregulated in allergic individuals and can be restored in patients who receive grass pollen immunotherapy. We also identified that this mechanism is associated with modification in retinol metabolic pathway, cytokine-cytokine receptor interaction and JAK-STAT signalling pathways in the ILCs.

overall_design: Single cell RNA sequencing was performed by isolating human innate lymphoid cells (ILCs) by FACS sorting from peripheral blood mononuclear cells. ILCs were cultured in vitro with IL-2/IL-7/IL-33/RA for 7 days and libraries (3' GEX and protein libraries) were prepared using Chromium single cell 3' Reagent Kits according to manufacturer's protocol (10x Genomics). The generated scRNAseq libraries were sequenced using HiSeq 4000 sequencers.   2 biologically independent human samples were processed and sequenced for each treatment groups (placebo-treated at 12m, active-treated at 12m and active-treated at 24m).


title: Gene transcription in wild-type (WT) and c-abl/arg knockout MEFs

city: Beijing

first: Hainan

last: Liu

address: Taiping Road, Haidian District

institute: Beijing Institute of Biotechnology

summary:
Abl kinases, which are required for multiple cellular processes, including proliferation, apoptosis, adhesion, cell migration, and stress responses,  widely participate in the regulation of gene transcription.
To illustrate the role of Abl kinase in gene expression, the transcription of approximately 22,000 genes in wild-type (WT) and c-abl/arg knockout MEFs was detected using Affymetrix GeneChips (Mouse Genome 430 2.0).

overall_design: Wild-type and c-abl/arg knockout MEFs (Mouse Embryonic Fibroblasts) were extracted RNA and hybridizated on Affymetrix microarrays. We sought to illustrate the role of Abl kinases in gene expression. To that end, we respectively extract the RNA of wild-type MEFs (MEF-WT) and c-abl/arg knockout MEFs (DKO) with three repeats, named with MEF-WT-1, MEF-WT-2, MEF-WT-3, DKO-1, DKO-2 and DKO-3.


title: Complexity and tumor potential of human embryonic sympatho-adrenal area including neural crest and mesodermal derivatives

city: Vienna

first: Artem

middle: V

last: Artemov

address: Spitalgasse 4

department: Center for Brain Research

country: Austria

institute: Medical University of Vienna

summary: We addressed heterogeneity of neural crest- and mesoderm-derived lineages developing into adrenal glands, kidneys, endothelium and hematopoietic tissue for understanding transitions, integration and tumor-initiating states between week 6 and 14 of human development. We identified new transitions connecting intermediate mesoderm and progenitors of organ primordia, hematopoietic system and endothelial subtypes. Unexpectedly, we revealed that in humans, contrary to mice, nerve-associated Schwann cell precursors give rise to highly-proliferative sympathoblasts within adrenal gland, which in turn could transit into neuroendocrine chromaffin cells. The analysis of cell state signatures in relation to survival curves of patients suggested Schwann cell precursor-derived sympathoadrenal subtypes as origin for different neuroblastoma tumors.

overall_design: We isolated individual cells from dissected intact adrenal glands with surrounding tissue from human embryos at post-conception weeks 6, 8, 9, 11, 12, 14 and subjected them to single cell transcriptomics sequencing using 10x Chromium approach.

first: Polina

last: Kameneva

first: Erik

last: Sundstrom

first: Igor

last: Adameyko


title: Single-cell chromatin accessibility identifies pancreatic islet cell type- and state-specific regulatory programs of diabetes risk [RNA-seq]

first: Kyle

overall_design: RNA-seq of ES-derived beta cells with KCNQ1enh deletion (n=6; 3 clones each differentiated two times) and scrambled control (n=2; 1 clone differentiated two times).


title: Sugarcane drought experiment under field conditions

city: Sao Paulo

first: Augusto

middle: Lima

last: Diniz

state: SP

address: Av Lineu Prestes

department: Biochemistry

country: Brazil

institute: University of Sao Paulo

summary: A field experiment was conducted at the Federal University of Alagoas in Maceio, Brazil. varieties RB86-7515, RB85-5536 and RB92-579 were distributed in a randomized block design with four replicates in two conditions: irrigated (control) and non-irrigated (treatment).

overall_design: This experiment included the expression analysis of leaves and internode I from 6-month-old plants. Total RNA was extracted using the TriZol method, treated with DNase I and purified. Hybridization experiments were conducted on a customized 4x44K oligoarray (Agilent Technologies) for sugarcane (CaneRegNet). The oligoarrays were read using the GenePix 4000B scanner device (Molecular Devices) and the fluorescence data was processed by Feature Extraction software 9.5.3 (Agilent Technologies).

first: Maximiller

last: Dal-Bianco


title: GPER1 inhibits placental type I IFN responses to preserve fetal health during maternal infection

city: Durham

first: Nicholas

last: Heaton

state: NC

address: 213 Research Drive, 426 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

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

overall_design: Refer to individual Series


title: GPER1 inhibits placental type I IFN responses to preserve fetal health during maternal infection [RNAseq]

summary: Inhibition of GPER1 in pregnant mice significantly alters inflammation and angiogenesis in the placenta, but does not significantly impact the lung

overall_design: Pregnant mice were treated with either a GPER1 antagonist (G15) or vehicle control and then infected with IAV before collection of lungs and placental tissues for transcriptional profiling

first: Alfred

middle: T

last: Harding


title: Innate immune responses by bronchial epithelial cells exposed to the bacterial component flagellin

status: Public on Jan 13 2021

city: Amsterdam

first: Joe

last: Butler

address: Meibergdreef 9

department: Infectious diseases

institute: Amsterdam UMC

summary: RNAseq was used to measure the transciptional respose of human bronchial epithelium (HBE) to the bacterial component flagellin with particular emphasis on innate immunity and metabolism.

overall_design: Human bronchial epithelium (HBE) were isolated from 3 volunteers. Each donor's HBE were exposed to flagellin or PBS vehicle. In addition we investigated the effect of rapamycin (mTOR inhibitor) and IOX2 (a selective inhibitor of the HIF-1α prolyl hydroxylase-2).


title: GPER1 inhibits placental type I IFN responses to preserve fetal health during maternal infection [GECKOscreen]

summary: Identification of factors that control ifn responses during pregnancy

overall_design: A549 cells containing an interferon responsive reporter and CRISPR Cas9 technology were transduced with the complete sgRNA library and then treated with interferon alpha. Next, cells that were not responsive to interferon were collected and the sgRNAs enriched in these populations was sequenced.


title: Genome-wide analysis of mRNA expression profile in MDA-MB-231 cells treated with or without 3.75 μM DCC-2036 for 48 hours.

city: Hengyang

first: Yingying

last: Shen

address: 69 Chuanshan Road

department: Institute of Clinical Medicine

institute: The First Affiliated Hospital of University of South China

summary: Our study found that DCC-2036, the novel tyrosine kinase inhibitor, has potent activity against triple negative breast cancer (TNBC). To better understand the molecular mechanisms involving in the effect of DCC-2036 on TNBC cells, the whole genome-wide transcriptome profile of MDA-MB-231 cells (a representative TNBC cell line) cultured with or without DCC-2036 was analyzed by cDNA microarray.

overall_design: Microarray expression profiling of mRNAs were conducted using RNA extracted from MDA-MB-231 cells treated with or without 3.75 μM DCC-2036 for 48 hours for three independent experiments. The sample 2, 4, 6 are drug treatment group (MDA-MB-231 cells exposed to 3.75 μM DCC-2036 for 48 h), and the sample 1, 3, 5 are control group (MDA-MB-231 cells exposed to 0 μM DCC-2036 for 48 h).

first: Wei

last: Zhang

first: Jianghua

first: Yuyang

last: Jiang

first: Xuyu

last: Zu


title: Serine biosynthesis is a metabolic vulnerability in FLT3-ITD-driven acute myeloid leukaemia [MV411_OCI-AML3_DMSO_AC220_24hr]

first: Stefan

last: Bjelosevic

address: 450 Brookline Ave

department: Department of Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary: We performed 3'-RNA-Sequencing on RNA isolated from human MV4-11 and OCI-AML3 cells which had been treated with DMSO or the FLT3 inhibitor Quizartinib (AC220) to perform differential gene expression analysis.

overall_design: Cells were treated with 5 nM Quizartinib (AC220) for 24 hours in vitro. Total RNA was isolated from cells and 3'-RNA libraries were prepared for next-generation sequencing.

first: Emily

last: Gruber

first: Stephin

last: Vervoort

first: Kristin

last: Brown

first: Ricky

middle: W

last: Johnstone


title: Serine biosynthesis is a metabolic vulnerability in FLT3-ITD-driven acute myeloid leukaemia [iFLT3-ITD-Depletion_In VITRO]

summary: We performed 3'-RNA-Sequencing on RNA isolated from murine MLL-AF9/iFLT3-ITD cells where the inducible iFLT3-ITD transgene had been depleted for 24 or 48 hours compared to non-depleted conditions in vitro to perform differential gene expression analysis.

overall_design: Cells were cultured in the presence of 1 µg/mL doxycycline to maintain iFLT3-ITD transgene expression in vitro. Cells were then washed twice with PBS and cultured in the absence of doxycycline to deplete iFLT3-ITD transgene expression for 24 or 48 hours (or maintained in 1 µg/mL doxycycline as a control). Total RNA was isolated from cells and 3'-RNA libraries were prepared for next-generation sequencing.


title: The role of CD74 in Hematopoietic Stem Cells

city: Rehovot

first: Idit

last: Shachar

address: 234 Herzl Street

institute: Weizmann Institute

summary: Hematopoietic stem and progenitors cells (HSPCs) are a small population of undifferentiated cells that have the capacity for self-renewal, and differentiate into all blood cell lineages. These cells are the most useful cells for clinical transplantations and for regenerative medicine. So far, it has not been possible to expand adult hematopoietic stem cells (HSCs) without losing their self-renewal properties. CD74 is a cell surface receptor for the cytokine macrophage migration inhibitory factor (MIF), and its mRNA is known to be expressed in HSCs. Here, we demonstrate that mice lacking CD74 exhibit an accumulation of hematopoietic stem cells in the BM due to their increased potential to repopulate and compete for BM niches. Our results suggest that CD74 regulates the maintenance of the HSCs and CD18 expression. Its absence leads to induced survival of these cells, and accumulation of quiescent and proliferating cells. Furthermore, in in-vitro experiments, blocking of CD74 elevated the numbers of HSPCs. Thus, we suggest that blocking CD74 could lead to improved clinical insight into bone marrow transplant protocols, enabling improved engraftment.

overall_design: Hematopoietic stem cells (CD34-/LSK cells) were isolated from bone marrow of 3 WT mice and 3 CD74-/- mice (by sorting using FACS Aria in 70 micron nozzle).

first: Shirly

last: Becker-Herman


title: Serine biosynthesis is a metabolic vulnerability in FLT3-ITD-driven acute myeloid leukaemia [MV411_OCI-AML3_ATF4_RNAP2_CHIP]

summary: We performed ChIP-seq on MV4-11 or OCI-AML3 cells which had been treated with DMSO or 5 nM of the FLT3 inhibitor Quizartinib (AC220) to determine the location of ATF4 or RNAPII across the genome.

overall_design: Cells were treated with the FLT3 inhibitor Quizartinib (AC220, 5 nM, for 24 hours) prior to cross-linking, isolation and sonication of nuclei and immunoprecipitation of chromatin using antibodies against ATF4 or RNAPII.


title: Transcriptome analysis reveals photoperiod-associated genes expressed in rice anthers

city: shanghai

first: shiyu

last: sun

address: No.800 dong chuan road

institute: Shnaghai jiao tong university

summary: Environmental conditions, such as photoperiod and temperature, can affect male fertility in plants. While this feature is heavily  exploited in rice to generate male-sterile lines for hybrid breeding, the underlying molecular mechanisms remain largely  unknown. In this study, we use a transcriptomics approach to identify key genes and regulatory networks affecting pollen  maturation in rice anthers in response to different day lengths.This work provides a new understanding on photoperiodsensitive pollen development in rice, and our gene expression database will provide a new, comprehensive resource to identify  new environmentally sensitive genes regulating male fertility for use in crop improvement.

overall_design: the mitosis stages I anther were collected at 08:00,12:00,16:00,20:00,00:00, 04:00 in sort-day(12 hours light) and long-day(14 hours dark) condition., each sample have two biological replicates.

first: Shiyu

last: Sun

first: Wang

last: Duoxiang

first: Jingbin

last: Li

first: Yaqi

last: Lei

first: Gang

first: Wengou

last: Cai

first: Xiangxiang

last: Zhao

first: Wanqi

last: Liang

first: Dabing