title: Obesity accelerates hair thinning by stem cell-centric converging mechanism [RNA-seq]

status: Public on Apr 14 2021

city: Bunkyo-ku

first: Hironobu

last: Morinaga

state: Tokyo

address: 1-5-45 Yushima

department: Stem Cell Biology

institute: Tokyo Medical and Dental University

summary: Obesity, a worldwide epidemic, predisposes to many ageing-associated diseases, yet its exact impact on organ dysfunction is largely unknown. Hair follicles, mini-epithelial organs that grow hair, miniaturize by ageing to cause hair loss through the depletion of hair follicle stem cells (HFSCs). Here, we report that obesity-induced stress such as by high-fat diet (HFD) feeding primarily targets HFSCs to accelerate hair thinning. Chronological gene expression analysis revealed that HFD feeding for four consecutive days directs activated HFSCs toward epidermal keratinization by generating excessive reactive oxygen species yet retains HFSC pools in young mice. Integrative analysis with stem cell fate tracing, epigenetic analysis and reverse genetics revealed that further feeding of HFD subsequently induces lipid droplets and NF-B activation within HFSCs via autocrine/paracrine IL1R signaling. Those integrated factors converge on the profound inhibition of Sonic hedgehog (Shh) signal transduction in HFSCs, thereby further depleting lipid-laden HFSCs through their aberrant differentiation and inducing hair follicle miniaturization and eventual hair loss. Conversely, Shh activation by transgenes or compounds rescues HFD-induced hair loss. These data collectively demonstrate that stem cell inflammageing induced by obesity robustly represses organ regeneration signals to accelerate the mini-organ miniaturization, and suggests the importance of daily prevention of organ dysfunction.

overall_design: Gene expression in anagen hair follicle stem cells of the mice fed with normal diet or high fat diet.

first: Emi

last: Nishimura


title: Genomic landscapes of VEGF family members in endothelial cells

status: Public on Apr 15 2021

city: Kuopio

first: Minna

last: Kaikkonen-Määttä

country: Finland

institute: A. I. Virtanen Institute

type: Expression profiling by high throughput sequencing

summary: Role of novel long intergenic (lincRNA) and enhancer RNAs (eRNAs) in the regulation of vascular endothelial growth factors (VEGFs), in endothelial cells.

overall_design: Integration of different sequencing techniques (GRO-Seq, Hi-C and Chip-Seq) in primary endothelial cells (HUVEC), to identify lincRNA and eRNA. Knock out validation studies with CRISPR/Cas9, followed by RNA-Seq in EA.hy926

first: M

first: I

last: Mushimiyimana

first: V

last: Tomas Bosch

first: H

last: Niskanen

first: N

last: Downes

first: P

last: Moreau

last: Laram-Karam

first: S

last: Ylä-Herttuala


title: M1BP cooperates with CP190 to activate transcription at TAD borders and promote chromatin insulator activity (ATAC-seq)

city: bethesda

first: Elissa

last: Lei

state: MD

address: 50 south drive, blg50

department: NIDDK

country: USA

institute: NIH

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Genome organization is driven by forces affecting transcriptional state, but the relationship between transcription and genome architecture remains unclear. Here, we identified the Drosophila transcription factor Motif 1 Binding Protein (M1BP) in physical association with the gypsy chromatin insulator core complex, including the universal insulator protein CP190. M1BP is required for enhancer-blocking and barrier activities of the gypsy insulator as well as its proper nuclear localization. Genome-wide, M1BP specifically colocalizes with CP190 at Motif 1-containing promoters, which are enriched at topologically associating domain (TAD) borders. M1BP is required for CP190 chromatin binding at many shared sites, and CP190 also affects M1BP chromatin association. Both factors are required for Motif 1-dependent gene expression and transcription near TAD borders genome-wide. Finally, loss of M1BP alters local genome compaction. Our results reveal physical and functional interaction between CP190 and M1BP to activate transcription at TAD borders and mediate chromatin insulator-dependent genome organization.

overall_design: Examination of overlapping of M1BP with insulator protein CP190 genome wide in Kc167 embryonic cell lines and also to investigate whether association of these insulator factors are dependent on M1BP or binding of M1BP dependent on CP190. Overall, both M1BP and CP190 regulate together active transcription at TAD borders.

first: Indira

last: Bag

first: Shue

last: Chen

first: Leah

middle: F

last: Rosin

first: Yang

first: Chen-Yu

last: Liu

first: Guo-Yun

last: Yu

middle: P


title: A fusion protein complex that combines IL12, IL15, and IL18 signaling to induce memory-like NK cells for cancer immunotherapy

city: St. Louis

first: Todd

last: Fehniger

state: Missouri

address: 660 South Euclid Avenue

institute: Washington University School of Medicine

summary: NK cells are a promising cellular therapy for cancer, with challenges in the field including persistence, functional activity, and tumor recognition. Briefly priming blood NK cells with rhIL-12, rhIL-15, and rhIL-18 (12/15/18) results in memory-like NK cell differentiation  and enhanced responses against cancer. We developed a novel platform centered upon an inert tissue factor scaffold for production of heteromeric fusion protein complexes (HFPC). The first use of this platform combined IL-12, IL-15 and IL-18 receptor engagement (HCW9201) and the second adds CD16 engagement (HCW9207). HCW9201 and HCW9207 stimulated activation and proliferation signals in NK cells, but HCW9207 had decreased IL-18 receptor signaling. RNAseq and multidimensional mass cytometry revealed strong parallels between HCW9201 and 12/15/18. Moreover, HCW9201 stimulation improved NK cell metabolic fitness, and resulted in the DNA methylation remodeling characteristic of memory-like differentiation. HCW9201- and 12/15/18-primed similar increases in short-term and memory-like NK cell cytotoxicity and IFN-g production against leukemia targets, as well as equivalent control of leukemia in NSG mice. Thus, HFPCs represent a protein engineering approach that solves many problems associated with multi-signal receptor engagement on immune cells, and HCW9201-primed NK cells will be advanced as an ideal approach for clinical GMP-grade memory-like NK cell production for cancer therapy.erm and memory-like NK cell cytotoxicity and IFN-g production against leukemia targets, as well as equivalent control of leukemia in NSG mice. Thus, HFPCs represent a protein engineering approach that solves many problems associated with multi-signal receptor engagement on immune cells, and HCW9201-primed NK cells will be advanced as an ideal approach for clinical GMP-grade memory-like NK cell production for cancer therapy.

overall_design: NK cells (> 95% CD56+CD3-) were isolated from healthy donor PBMCs using RosetteSep (STEMCELL Technologies). ML and control NK were generated essentially as described previously with NK media (Miltenyi) with 5% (v/v) heat-inactivated human AB pooled sera (Millipore Sigma) (CNKM) or RPMI-1640, supplemented with 2 mM L-glutamine, antibiotics (penicillin, 100 U/mL; streptomycin, 100 µg/mL) (ThermoFisher), and 10% (v/v) fetal bovine serum (Cytiva). NK cells were incubated with individual cytokines; IL-12p70 (10 µg/mL), IL-15 (50 µg/mL), and IL-18 (50 µg/mL) (12/15/18) (7); or HFPCs at 50 to 100 nM. After 12-16 hours of activation, NK cells were washed three times and plated in 1 ng/mL rhIL-15 with every other day media exchanges. RNA was isolated for RNA sequencing as described elsewhere.

first: David

last: Russler-Germain

first: Michelle

last: Becker-Hapak


title: Platelets orchestrate the resolution of pulmonary inflammation in mice through Treg repositioning and macrophage education

city: Münster

first: Jan

last: Rossaint

address: Albert-Schweitzer-Campus 1, Bldg. A1

department: Dpt. of Anesthesiology

country: Germany

institute: University of Münster

summary: Our study investigates how interactions of platelets with regulatory T cells (Tregs) modulates the transcriptomic profile of Tregs and pro- and anti-inflammatory macrophages in the lung during resolution of pulmonary inflammation.

overall_design: Pulmonary inflammation was induced by bacterial pneumonia (K. pneumonia) in mice. Single Tregs and Treg-PLT aggregates were isolated from the brochoalveolar lavage (BAL) on day 5 after induction of pneumonia. Pro- and antiinflammatory macrophages were isolated from the BAL on day 5 after induction of bacterial pneumonia from control and platelet-depleted mice.

first: Tobias

last: Tekath


title: Improved transformation efficiency of group A Streptococcus by inactivation of a type I restriction modification system

city: Boston

first: Michael

last: Wessels

state: MA

address: 330 Longwood Ave

department: Medicine

institute: Boston Children's Hospital

summary: Streptococcus pyogenes or group A Streptococcus (GAS) is a leading cause of bacterial pharyngitis, skin and soft tissue infections, life-threatening invasive infections, and the post-infectious autoimmune syndromes of acute rheumatic fever and post-streptococcal glomerulonephritis.  Genetic manipulation of this important pathogen is complicated by resistance of the organism to genetic transformation.  Very low transformation efficiency is attributed to recognition and degradation of introduced foreign DNA by a type I restriction-modification system encoded by the hsdRSM locus.  DNA sequence analysis of this locus in ten GAS strains that had been previously transformed with an unrelated plasmid revealed that six of the ten harbored a spontaneous mutation in hsdR, S, or M.  The mutations were all different, and at least five of the six were predicted to result in loss of function of the respective hsd gene product.  The unexpected occurrence of such mutations in previously transformed isolates suggested that the process of transformation selects for spontaneous inactivating mutations in the Hsd system.  We investigated the possibility of exploiting the increased transformability of hsd mutants by constructing a deletion mutation in hsdM in GAS strain 854, a clinical isolate representative of the globally dominant M1T1 clonal group.  Mutant strain 854hsdM exhibited a 5-fold increase in transformation efficiency compared to the wild type parent strain and no obvious change in growth or off-target gene expression.  We conclude that genetic transformation of GAS selects for spontaneous mutants in the hsdRSM restriction modification system.  We propose that use of a defined hsdM mutant as a parent strain for genetic manipulation of GAS will enhance transformation efficiency and reduce the likelihood of selecting spontaneous hsd mutants with uncharacterized genotypes.

overall_design: Comparison of transcripts between wild-type GAS strain 854 and strain 854 with a defined deletion of hsdM

first: Meredith

middle: B

last: Finn

first: Kathryn

middle: M

last: Ramsey

first: Simon

middle: L

last: Dove

middle: R


title: CD32+CD4+ T cells sharing B cell properties increase in lymphoid tissues during simian immunodeficiency virus infection

status: Public on Apr 16 2021

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

summary: HIV reservoirs in tissues form the major hurdle to an HIV cure. Despite major progress made on the understanding of the establishment and persistence of viral reservoirs, the characterization of composition and dynamics of the viral reservoir is still uncomplete. In addition, most studies in HIV infection are limited to blood. Here we take advantage of non-human primate models to provide a longitudinal analysis on potential viral target cells in distinct body compartments : blood, lymph nodes (LN), spleen ileum, jejunum and liver. We observed an increase in CD32+CD4+ T cells in secondary lymphoid tissues and intestine during primary and chronic pathogenic SIVmac infection. In the natural host (African green monkey, AGM), increase of the CD4+CD32+T cell levels was observed in tissues with higher replication and immune activation. CD32+CD4+ T cells expressed more often markers associated with HIV infected and/or reservoir cells (PD-1, CXCR5 for TFH cells in SLT, and CXCR3 for Th1 cells) than CD32- cells. The tissue CD32+CD4+T cells displayed higher levels of actively transcribed SIV RNA than CD32-CD4+T cells. The genome-wide transcriptome of CD32+CD4+ T cells in spleen from SIV-infected animals indicated that the CD32+CD4+ T cells shared B cell markers. The CD20+ expressing CD32+CD4+ T cells were increased in the tissues but not in the blood during SIV infection. Altogether, the study showed that SIV infection increases the frequencies of CD32+CD4+ T cells in tissues more than in blood. These cells might represent a not well-described subpopulation of activated CD4+ T cells.

sample_organism:
Macaca fascicularis
Chlorocebus sabaeus

platform_organism:
Macaca fascicularis
Chlorocebus sabaeus

overall_design: Transcriptome profiling of different T4 lymphocyte subsets according to CD32 expression in the spleen of pathogenic and nonpathogenic simian models of SIV infection

first: Nicolas

last: Huot

first: Etienne

last: Kornobis

first: Hugo

last: Varet

first: Beatrice

last: Jacquelin

first: Michaela

last: Müller-Trutwin


title: Senescence‐associated β‐galactosidase reveals the abundance of senescent CD8+ T cells in aging humans

city: Piscataway

first: Ricardo

middle: Iván

last: Martínez Zamudio

state: New Jersey

address: 675 Hoes Lane West

department: Pharmacology

institute: Rutgers Biomedical and Health Sciences | Rutgers-Robert Wood Johnson Medical School

summary: Aging leads to a progressive functional decline of the immune system, rendering the elderly increasingly susceptible to disease and infection. The degree to which immune cell senescence contributes to this decline remains unclear, however, since markers that label immune cells with classical features of cellular senescence accurately and comprehensively have not been identified. Using a second‐generation fluorogenic substrate for β‐galactosidase and multi‐parameter flow cytometry, we demonstrate here that peripheral blood mononuclear cells (PBMCs) isolated from healthy humans increasingly display cells with high senescence‐associated β‐galactosidase (SA‐βGal) activity with advancing donor age. The greatest age‐associated increases were observed in CD8+ T‐cell populations, in which the fraction of cells with high SA‐βGal activity reached average levels of 64% in donors in their 60 s. CD8+ T cells with high SA‐βGal activity, but not those with low SA‐βGal activity, were found to exhibit features of telomere dysfunction‐induced senescence and p16‐mediated senescence, were impaired in their ability to proliferate, developed in various T‐cell differentiation states, and had a gene expression signature consistent with the senescence state previously observed in human fibroblasts. Based on these results, we propose that senescent CD8+ T cells with classical features of cellular senescence accumulate to levels that are significantly higher than previously reported and additionally provide a simple yet robust method for the isolation and characterization of senescent CD8+ T cells with predictive potential for biological age.

overall_design: We performed bulk RNA-seq of FACS-isolated CD8+T cells exhibiting low and high senescence associated ß-galactosidase activity.

middle: I

last: Martínez-Zamudio

first: Hannah

middle: K

last: Dewald

first: Themistoklis

last: Vasilopoulos

first: Lisa

last: Gittens-Williams

first: Patricia

last: Fitzgerald-Bocarsly

first: Utz

last: Herbig


title: Analyses of H2A and H2A.Z incorporations into chromatin of permeabilized cells

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

summary: Histone proteins, including their variants, play indispensable roles in chromatin structure and function. The specific histone incorporation is the key to epigenetic features and contributes to cell differentiation and development. To understand how each histone is targeted to and incorporated into the specific chromatin region, we used a new method, in which we introduced epitope-tagged histone complexes in permeabilized cells and let them incorporated into the chromatin. The newly incorporated histone complex is easily distinguished from the parental histones by the epitope-tag. We name this as RhIP (Reconstituted histone complex Incorporation into chromatin of Permeabilized cell) assay. We analyzed the correlation between the histone incorporation and the chromatin structure, using the H2A-H2B and H2A.Z-H2B complexes. The histone incorporation mainly occurred at less condensed chromatin (open), suggesting that the condensed chromatin (closed) is a barrier for histone incorporation. To overcome this barrier, H2A, but not H2A.Z, uses a replication-coupled deposition mechanism. This led to the genome-wide distribution of H2A and the exclusion of H2A.Z from the closed chromatin.

overall_design: RhIP-ChIP-seq of H2A and H2A.Z using asynchronous, early S and late S phase cells.

first: Hiroaki

last: Tachiwana

first: Kazumitsu

last: Maehara

first: Akihito

last: Harada


title: Genome-wide RNA-sequencing differences in nucleus accumbens of smokers vs. nonsmokers

city: Research Triangle Park

first: Dana

last: Hancock

state: NC

address: 3040 E Cornwallis Rd

institute: RTI  International

summary: Cigarette smoking remains the leading cause of preventable death worldwide. Cigarette smoking behaviors (e.g., initiation, nicotine dependence, cessation) are heritable, and many genetic risk loci have been identified. However, the neurobiological mechanisms underlying the genetic risk loci along the trajectory of smoking are largely unknown. RNA-sequencing (RNA-seq) differences between smokers and nonsmokers can provide insight into mechanisms that predispose to smoking behaviors and consequences of the smoking exposure itself. Here, we provide RNA-seq data generated in nucleus accumbens, an addiction-relevant brain tissue, from 223 deceased individuals: 50 current cigarette smokers, 171 nonsmokers, and 2 individuals with undetermined smoking status. DNA methylation data on the Illumina HumanMethylationEPIC array are also available on most of these individuals and made available (GEO accession number GSE147040).

overall_design: RNA-seq data were measured in postmortem nucleus accumbens bulk tissue. The dataset includes 223 deceased individuals, including 50 current cigarette smokers, 171 nonsmokers, and 2 individuals with undetermined smoking status.


title: Selective Activation of CNS and Reference PPARGC1A Promoters Is Associated with Distinct Gene Programs Relevant for Neurodegenerative Diseases

city: Salzburg

first: Selma

last: Soyal

address: Strubergasse 18

department: Institute of Pharmacology and Toxicology

country: Austria

institute: Paracelsus Private Medical University

summary: The transcriptional regulator peroxisome proliferator activated receptor gamma coactivator 1A (PGC-1α), encoded by PPARGC1A, has been linked to neurodegenerative diseases. Recently discovered CNS-specific PPARGC1A transcripts are initiated far upstream of the reference promoter, spliced to exon 2 of the reference gene, and are more abundant than reference gene transcripts in post-mortem human brain samples. The proteins translated from the CNS and reference transcripts differ only at their N-terminal regions. To dissect functional differences between CNS-specific isoforms and reference proteins, we used clustered regularly interspaced short palindromic repeats transcriptional activation (CRISPRa) for selective endogenous activation of the CNS or the reference promoters in SH-SY5Y cells. Expression and/or exon usage of the targets was ascertained by RNA sequencing. Compared to controls, more differentially expressed genes were observed after activation of the CNS than the reference gene promoter, while the magnitude of alternative exon usage was comparable between activation of the two promoters. Promoter- selective associations were observed with canonical signaling pathways, mitochondrial and nervous system functions and neurological diseases. The distinct N-terminal as well as the shared downstream regions of PGC-1α isoforms affect the exon usage of numerous genes. Furthermore, associations of risk genes of amyotrophic lateral sclerosis and Parkinson’s disease were noted with differentially expressed genes resulting from the activation of the CNS and reference gene promoter, respectively. Thus, CNS-specific isoforms markedly amplify the biological functions of PPARGC1A and CNS-specific isoforms and reference proteins have common, complementary and selective functions relevant for neurodegenerative diseases.

overall_design: Selective endogenous activation of the CNS or Reference PPARGC1A promoters in SH-SY5Y cells using CRISPRa.

first: Markus

last: Kwik

first: Stefan

last: Hainzl

first: Jan

last: Oppelt

first: Boris

last: Tichy

first: Ulrich

last: Koller

first: Emanuele

last: Bernardinelli

last: Steiner

first: Greta

last: Zara

first: Charity

last: Nofziger

first: Serge

last: Weis

last: Paulmichl

first: Silvia

last: Dossena

first: Wolfgang

last: Patsch


title: PLZF acetylation levels regulate NKT cell differentiation

status: Public on Apr 21 2021

first: Marc

last: Delord

address: Hopital Saint-Louis, 1 avenue Claude Vellefaux

department: Recherche clinique

institute: Centre hospitalier de Versailles

type: Methylation profiling by high throughput sequencing

summary: The transcription factor PLZF (promyelocytic leukemia zinc finger) is encoded by the BTB 42 domain-containing 16 (Zbtb16) gene. Its repressor function regulates specific transcriptional 43 programs. During the development of invariant natural killer T (NKT) cells, PLZF is 44 expressed and directs their effector program but the detailed mechanisms underlying PLZF 45 regulation of multi-stage NKT cell developmental program are not well understood. This 46 study investigated the role of acetylation-induced PLZF activation on NKT cell development 47 by analyzing mice expressing a mutant form of PLZF mimicking constitutive acetylation (PLZFON mice). NKT populations in PLZFON 48 mice were reduced in proportion and numbers 49 of cells, and the cells present were blocked at the transition from developmental stage 1 to stage 2. NKT cell subset differentiation was also altered, with T-bet+ NKT1 and RORJt + 50 NKT17 subsets dramatically reduced, and the emergence of a T-bet - RORJt - 51 NKT cell subset 52 with features of cells in early developmental stages rather than mature NKT2 cells. Analysis 53 of DNA methylation patterns indicated that activated PLZF establishes a unique DNA 54 methylation signature to regulate NKT cells’ entry into the early stages of development, while 55 repressing maturation. In wild-type NKT cells, deacetylation of PLZF alleviates this 56 repression and allows subsequent NKT cell differentiation. Interestingly, development of 57 other innate lymphoid and myeloid cells, that are dependent on PLZF for their generation, is not altered in PLZFON 58 mice highlighting lineage specific regulation. Overall, we propose that 59 specific epigenetic control of PLZF through acetylation levels is required to regulate normal 60 NKT cell differentiation.

overall_design: MeDIP-Seq analysis of WT vs PLZTon NKT cells

first: Jihene

last: Klibi

first: Claudine

last: Joseph

first: Aurelie

last: Teissandier

first: Bruno

last: Lucas

first: Christine

last: Chomienne

first: Antoine

last: Toubert

first: Deborah

last: Bourc'his

first: Fabien

last: Guidez

first: Kamel

last: Benlagha


title: single-cell RNA-seq data of human B cells in rejecting renal allograft and tonsil biopsies.

city: Chicago

first: Yuta

last: Asano

state: IL

address: 924 E 57th Street

institute: The University of Chicago

summary: Characterization of gene expression signature of intrarenal B cells in comparison with tonsil GC B cells.

overall_design: Eight renal and seven tonsil samples collected in two cohorts. Samples of each cohort were sequenced in four or one separate runs respectively.

first: Joe

last: Daccache

first: Dharmendra

last: Jain

first: Kichul

last: Ko

first: Andrew

last: Kinloch

first: Margaret

last: Veselits

first: Donald

last: Wolfgeher

first: Anthony

last: Chang

first: Michelle

last: Josephson

first: Patrick

last: Cunningham

first: Anat

last: Tambur

first: Aly

middle: A

last: Khan

first: Shiv

last: Pillai

first: Anita

middle: S

last: Chong

first: Marcus

last: Clark


title: Transcriptomic Analysis of pnp-1 mutants in C. elegans

city: San Diego

first: Emily

last: Troemel

state: CA

address: 4202 Bonner Hall, 9500 Gilman #0349

department: Cell and Developmental Biology

institute: University of California, San Diego

summary: We used RNA-seq to identify gene expression changes in C. elegans pnp-1 mutants

overall_design: Total RNA was extracted from synchronized whole C. elegans grown 56 hours post L1 at 20°C. synchronized L1 worms were prepared by bleaching gravid adults to isolate embryos that hatched in M9 buffer into starved, synchronized L1 worms. N2, pnp-1(jy90) and pnp-1(jy121) animals were used. Five biological replicates were used

first: Eillen

last: Tecle

first: Crystal

last: Chhan

first: Latisha

last: Franklin

first: Ryan

last: Underwood

first: Wendy

last: Hanna-Rose


title: High resolution single cell transcriptomics reveals heterogeneity of self-renewing hair follicle stem cells

city: Ithaca

first: Tudorita

last: Tumbar

state: NY

address: 526 Campus Rd

department: Molecular biology and genetics

institute: Cornell University

summary:
Purpose: To dissect the transcriptomic profiles and unravel population-specific transcriptional heterogeneity of self renewing hair follicle stem cells in vivo
Methods: We performed 10x genomics single-cell RNA sequencing (scRNA-seq) of FACS sorted CD34+/K14-H2BGFP+ hair follicle stem cells from mouse skin at mid-anagen. FACS purified CD34+/K14-H2BGFP+ single-cell suspension was processed for the barcoded single-cell 3′ cDNA libraries generation using Chromium Single Cell 3′ gel bead and library Kit v3. The final libraries were quantified using Agilent Bioanalyzer high sensitivity DNA chip and sequenced using an Illumina NextSeq-500. The raw data files were demultiplexed to generate the sample-specific FASTQ files, which were aligned to the mouse reference genome (mm10-3.0.0) using the 10x Genomics Cell Ranger pipeline (v3.1.0).  The raw scRNA-seq data was processed using Cell Ranger from the 10x platform to generate an expression matrix that was further analyzed in R using the Seurat package version 3.1. Only high-quality cells that had between 200 and 5000 genes expressed and had under 10% of the UMIs mapped to mitochondrial genes were retained.
Results: We obtained a total of 6736 high quality cells from two datasets for further analysis by Seurat workflow
Conclusions: Obtained high quality single cell transcriptomic data to dissect molecular heterogeneity of hair follicle stem cells

overall_design: Single cell RNA-seq profiles of sorted hair follicle stem cells at mid anagen stage from wild type (WT) mice

first: Gopal

last: Chovatiya


title: Smart-RRBS for single cell methylome and transcriptome analysis

city: Cambridge

first: Ayush

middle: T

last: Raman

address: 75 Ames St

department: Epigenomics Program

institute: Broad Institute of MIT and Harvard

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

overall_design: Refer to individual Series


title: 3’ RNA-seq of five brain structures after repeated exposure to cocaine

city: Jerusalem

first: Ami

last: Citri

address: Givat Ram

country: Israel

institute: The Hebrew University of Jerusalem

summary:
At the core of addiction, drug experiences induce circuit-specific transcriptional adaptations to hijack the native mechanisms of neuroplasticity and promote maladaptive behaviors.
In the present study, we utilized 3’-RNA-sequencing to define the transcriptional landscapes of five brain nuclei within the reward circuit following distinct cocaine experiences. We exposed mice to cocaine (20 mg/kg, IP), acutely (single exposure), repeatedly (5 daily exposures) as well as to a challenge cocaine (acute exposure after 21 days of abstinence following repeated cocaine).
We then profiled transcription (applying 3’-RNAseq) within key brain structures of the reward circuitry: limbic cortex- medial prefrontal and cingulate together (LCtx), nucleus accumbens (NAc), dorsal striatum (DS), amygdala (Amy), and lateral hypothalamus (LH) at 0, 1, 2, 4 hrs following cocaine exposure.

overall_design: 3’ RNA-seq of transcriptional dynamics across five brain structures following acute, repeated and challenge exposure to cocaine.


title: Temporarily epigenetic repression in Bergmann glia regulates the migration of Granule cells (RNA-seq)

city: Xiamen

first: shaoxuan

last: chen

state: Fujian Province

address: School of Life Sciences, Xiang'an Campus, Xiamen University, Xiang'an District

country: China

institute: xiamen university

summary: Forming tight interaction with both Purkinje and granule cells (GCs), Bergmann glia (BG) are essential for cerebellar morphogenesis and neuronal homeostasis. However, how BG act in this process is unclear without comprehensively transcriptomic landscape of BG. Here, high temporal-resolution investigation of transcriptomes with FACS-sorted BG revealed the dynamic of genes within given functions and pathways enabled BG to assist neural migration and construct neuron-glia network. We found the peak time of GCs migration (P7-10) was strikingly coincided with the downregulation of extracellular matrix (ECM) related genes by prevailing transcriptional repression, and the disrupting of which by Setdb1 ablation at P7-10 in BG led to the significant migration defect of GCs by abnormal ECM expression emphasizing the criticality of Nfix-Setdb1 mediated H3K9me3 repressive complex for the precise regulation of GCs migration in vivo. Thus, BG’s transcriptomic landscapes offer an insight into the mechanism by which BG are in-depth integrated in cerebellar neural network.

overall_design: BGs mRNA profiles of Nestin-∆TK-IRES-GFP or Mash1 cre-ERT2, R26-LSL-tdTomato mice were generated by deep sequencing using BGI-500

first: Boxin

last: Zhang


title: Temporarily epigenetic repression in Bergmann glia regulates the migration of Granule cells (ChIP-seq)

overall_design: Examination of H3K9me3 in Bergmann glial cells


title: Global transcriptome of bone marrow niche cells in homoestatis and human xenografts

city: London

first: Dominique

last: Bonnet

state: London

address: 1 Midland Rd

country: United Kingdom

institute: Francis Crick Institute


title: Global transcriptome of bone marrow Nestin+ mesenchymal stromal cells in homoestatis and human xenografts at early and late time points

summary: We analysed the transcriptional signature of bone marrow Nestin+ mesenchymal stromal cells extracted from the bone marrow of mice engrafted with human AML cell lines and compared it to the one of untransplanted mice

overall_design:
Immunodeficient mice were transplanted with human AML cell lines, human AML cells derived from patients (blood or bone marrow), or with normal human hematopoietic cells (cd34+) derived from cord blood. Mice were sacrificed once assessed the bone marrow engraftment, and the bones were processed to isolate niche cells using the depicted marker. RNA was extracted, sequencing libraries were prepared and sequenced.
"early" stands for isolated at early time points of the leukemic progression
"late" stands for isolated at late time points of the leukemic progression
"ut" stands for untreated
"ch" stands for cherry, the marker we used to isolate the leukemia proximal niche.

first: Diana

last: Passaro

first: Probir

last: Chakravatry

first: Manuel

last: Garcia-Albornoz


title: Comparison of gene expression in symbiotic and non-symbiotic cells of Exaiptasia pallida

city: Heidelberg

first: Annika

last: Guse

address: Im Neuenheimer Feld 230

department: Centre for Organismal Studies

institute: Heidelberg University

summary: Emergence of the symbiotic lifestyle fostered the immense diversity of all ecosystems on Earth, but symbiosis plays a particularly remarkable role in marine ecosystems. Photosynthetic dinoflagellate endosymbionts power reef ecosystems by transferring vital nutrients to their coral hosts. The mechanisms driving this symbiosis, specifically those which allow hosts to discriminate between beneficial symbionts and pathogens, are not well understood. Here, we uncover that host immune suppression is key for dinoflagellate endosymbionts to avoid elimination by the host using a comparative, model systems approach. Unexpectedly, we find that the clearance of non-symbiotic microalgae occurs by non-lytic expulsion (vomocytosis) and not intracellular digestion, the canonical mechanism used by professional immune cells to destroy foreign invaders. We provide evidence that suppression of TLR signalling by targeting the conserved MyD88 adapter protein has been co-opted for this endosymbiotic lifestyle, suggesting that this is an evolutionarily ancient mechanism exploited to facilitate symbiotic associations ranging from coral endosymbiosis to the microbiome of vertebrate guts.

overall_design: The gene expression profiles of symbiotic and aposymbiotic endodermal cells obtained 24 - 48 hours after symbiosis establishment in Aiptaisia larvae were compared. In addition to GEO accession: GSE141133

first: Philipp

last: Voss

first: Sebastian

middle: G

last: Gornik

first: Marie

last: Jacobovitz

last: Rupp

first: Ira

last: Maegele


title: Network-based assessment of HDAC6 activity is highly predictive of pre-clinical and clinical responses to the HDAC6 inhibitor ricolinostat [high throughput sequencing]

city: Memphis

first: Qingfei

last: Pan

state: TN

address: 262 Danny Thomas Place

department: Department of Computational Biology

institute: St. Jude Children's Research Hospital

summary: Despite the anticancer activity of pan-histone deacetylase (HDAC) inhibitors, their clinical use has been limited due to toxicity. However, the development of more specific inhibitors that selectively inhibit individual HDACs is emerging as a novel and well-tolerated alternative. Here, we present the results of the first clinical trial evaluating the activity of ricolinostat (the leading HDAC6 inhibitor) in breast cancer (BC) patients. We have developed a computational network-based algorithm to evaluate the activity of the HDAC6 protein, based on the enrichment of its transcriptional targets in differentially expressed genes (HDAC6 score). Through preclinical in vitro and in vivo studies, we confirmed that the HDAC6 score can stratify the sensitivity of BC cells to ricolinostat treatment and may thus have value as a predictive biomarker. Moreover, analysis of ~3,000 primary human breast cancers showed that ~30% of them present high HDAC6 scores. Based on these results, we designed a phase Ib clinical trial to evaluate the activity of ricolinostat plus nab-paclitaxel in metastatic BC patients. Study results showed that the two agents can be safely combined, that clinical activity is identified specifically in patients with HR+/HER2- disease, and that the HDAC6 score was predictive of response. Expansion of our analysis to other tumor types identified multiple cohorts enriched in high HDAC6 score samples. These results suggest that the HDAC6 score may provide an effective predictive biomarker of ricolinostat sensitivity in multiple human cancers.

overall_design: Gene expression profiles of 1) 10 formalin fixed parafilm embedded biopsy samples from 10 patients of ductal breast cancer who were treated with HDAC6 inhibitor ricolinostat; and 2) 4 breast cancer cell lines treated by ricolinostat for 6 hours and 24 hours and by tunicamycin for 18 hours.

first: Tizita

middle: Z

last: Zeleke

first: Kevin

last: Kalinsky

first: Jose

last: Silva

first: Jiyang

last: Yu


title: Global transcriptome of bone marrow niche cells in homoestatis and human xenografts at late time points

summary: We analysed the transcriptional signature in different niche cells extracted from the bone marrow of mice engrafted with human AML patient-derived samples or AML cell lines and compared it to the one of mice engrafted with human normal hematopoietic cells derived from cord blood or untransplanted mice

overall_design: Immunodeficient mice were transplanted with human AML cell lines, human AML cells derived from patients (blood or bone marrow), or with normal human hematopoietic cells (cd34+) derived from cord blood. Mice were sacrificed once assessed the bone marrow engraftment, and the bones were processed to isolate niche cells using the depicted marker. RNA was extracted, sequencing libraries were prepared and sequenced.


title: Obesity accelerates hair thinning in stem cell-centric converging mechanism

city: Bunkyo-ku

first: Hironobu

last: Morinaga

address: 1-5-45 Yushima

institute: Tokyo Medical and Dental University

summary: Obesity, a worldwide epidemic, predisposes to many ageing-associated diseases, yet its exact impact on organ dysfunction is largely unknown. Hair follicles, mini-epithelial organs that grow hair, miniaturize by ageing to cause hair loss through the depletion of hair follicle stem cells (HFSCs). Here, we report that obesity-induced stress such as by high-fat diet (HFD) feeding primarily targets HFSCs to accelerate hair thinning. Chronological gene expression analysis revealed that HFD feeding for four consecutive days directs activated HFSCs toward epidermal keratinization by generating excessive reactive oxygen species yet retains HFSC pools in young mice. Integrative analysis with stem cell fate tracing, epigenetic analysis and reverse genetics revealed that further feeding of HFD subsequently induces lipid droplets and NF-κB activation within HFSCs via autocrine/paracrine IL1R signaling. Those integrated factors converge on the profound inhibition of Sonic hedgehog (Shh) signal transduction in HFSCs, thereby further depleting lipid-laden HFSCs from the skin surface and inducing hair follicle miniaturization and eventual hair loss. Conversely, Shh activation by transgenes or compounds rescues HFD-induced hair loss. These data collectively demonstrate that stem cell inflammageing induced by obesity robustly represses organ regeneration signals to accelerate the mini-organ miniaturization, and indicates suggests the importance of daily prevention of organ dysfunction.

overall_design: Gene expression in hair follicle stem cells of young mice, aged mice and the mice fed with normal diet or high fat diet were measured.

first: Emi

last: Nishimura


title: Bulk RNA sequencing of subcutaneous, abdominal and perivascular adipose derived stem cells

status: Public on Apr 13 2021

city: Hangzhou

first: Yongli

last: Ji

state: Zhejiang

address: Jiefang Road 88

institute: Zhejiang University

summary: Previous publications demonstrated that there were anatomical, physiological, cellular, clinical and prognostic differences among adipose tissue present in subcutaneous areas, abdominal cavity and outside adventitial layer of artery. Thus, we wondered whether ASCs from subcutaneous adipose tissue, abdominal adipose tissue and perivascular adipose tissue were also different in gene expression. Here we performed bulk RNA-Seq assay for subcutaneous, abdominal and perivascular adipose derived stem cells.

first: Yao

last: Xie

first: Yuankun

last: Ma

first: Jian

last: Shen


title: Comparison of gene expression in Exaiptasia pallida aposymbiotic cells and cells containing Microchloropsis gaditana

last: Guse

overall_design: The gene expression profiles of aposymbiotic endodermal cells and cells containing M. gaditana obtained 24 - 48 hours after uptake in Aiptaisia larvae were compared. In addition to GEO accession: GSE140173


title: Bortezomib induces methylation changes in neuroblastoma cells that appear to play a significant role in resistance development to this compound

city: Szczecin

first: Tomasz

last: Wojdacz

state: Zachodniopomorskie

address: Unii Lubelskiej 1

department: Independent Clinical Epigenetics Laboratory

country: Poland

institute: Pomeranian Medical University

type: Methylation profiling by genome tiling array

summary: Genome-wide patterns of DNA methylation were quantified using the Illumina Infinium HumanMethylationEPIC BeadChip in DNA samples isolated from neuroblastoma cell line SH-SY5Y repeatedly treated with bortezomib (BTZ), lenalidomide and control samples.

overall_design: This data set includes 6 DNA samples isolated from cell line SH-SY5Y treated with BTZ, 6 DNA samples isolated from cell line SH-SY5Y treated with lenalidomide and 6 DNA samples isolated from non-treated cell line SH-SY5Y (control).

first: Karolina

last: Łuczkowska

first: Katarzyna

middle: E

last: Sokolowska

first: Olga

last: Taryma-Lesniak

first: Krzysztof

last: Pastuszak

first: Anna

last: Supernat

first: Jonas

last: Bybjerg-Grauholm

first: Lise

last: Hansen

first: Edyta

last: Paczkowska

first: Bogusław

last: Machaliński


title: Human neurovascular unit chip with a functional blood-brain barrier models brain-infection mechanism of a fungal meningitis pathogen

city: Seoul

first: Kyung-Tae

last: Lee

address: Yonsei-ro 50

department: Biotechnology

country: South Korea

institute: Yonsei University

summary: Reconstitution of a neurovascular unit model with blood-brain barrier (BBB) function is of great importance for drug development targeting cerebral diseases and study of brain disease mechanisms. In this study, we describe a human neurovascular unit chip designed by reconstituting necessary cellular and extracellular components in microfluidic devices. Dynamic three-dimensional co-culture of human cells (neural stem cells, brain microvascular endothelial cells, and brain vascular pericytes) in microfluidics with a stepwise unidirectional flow successfully established the chip with BBB-mimetic structural and functional features to be an effective barrier for drugs and cytokines. Furthermore, we showed the utility of the chip by modeling the neurotropic behaviors and BBB penetration process of a global fungal meningitis pathogen, Cryptococcus neoformans. This chip is the first in vitro experimental model for monitoring neurotropism of C. neoformans and would contribute to the investigation of various cerebral disorders, including microbial infectious diseases and their corresponding drug development.

overall_design: The NSCs in BHEM hydrogel on top of Transwell insert were co-cultured with ECs on the bottom of the Transwell.

first: Jin

last: Kim

first: Yong-Sun

last: Bahn

first: Seung-Woo

last: Cho


title: SDHB gene promoter MethylTarget sequencing of normal pregnancy and recurrent spontaneous abortion patients

city: Shanghai

first: Sha

last: Xu

address: Songhu Road 2005

institute: Fudan University

summary: Our study found that low SDHB expression and high succinate levels are important for maintaining embryo implantation in the first trimester; therefore, high SDHB expression and low succinate levels during early pregnancy may increase the risk of RSA. To investigate why villous SDHB expression increases pathologically in RSA but exhibits dynamically low levels during the first trimester followed by high levels under physiological conditions, we detected CpG site methylation levels in the SDHB promoter region of villi from both individuals with RSA and controls.

overall_design: DNA methylation at specific CpG sites was determined by MethylTarget sequencing (Genesky Biotechnologies Inc., Shanghai, China), using next-generation sequencing-based multiple targeted CpG methylation analysis.

first: Xu

last: Sha

first: Zhao

last: Jianyuan


title: Disruption of YY1-EZH2 Interaction using Synthetic Peptides Inhibits Breast Cancer Development

city: Harbin

first: Guangyue

last: Li

state: heilongjang

address: No.26 Hexing Road Xiangfang District

department: College of Life Science

institute: Northeast Forestry University

summary: Enhancer of zeste homolog 2 (EZH2) is a methyltransferase to mediate lysine 27 trimethylation in histone H3 (i.e., H3K27me3) and repress gene expression. In solid tumors, EZH2 promotes oncogenesis, and is considered a therapeutic target. As a transcription factor, Yin Yang 1 (YY1) recruits EZH2 through its oncoprotein binding (OPB) domain to establish gene repression. In this study, we mapped the YY1 protein binding (YPB) domain on EZH2 to a region of 27 amino acids. Both YPB and OPB domain synthetic peptides could disrupt YY1-EZH2 interaction, markedly reduce breast cancer cell viability, and efficiently inhibit tumor growth in a xenograft mouse model. We analyzed MDA-MB-231 cells treated with YPB, OPB and control peptides by chromatin immunoprecipitation DNA sequencing (ChIP-seq) using an antibody against H3K27me3. YPB and OPB treatments altered H3K27me3 on 465 and 1,137 genes, respectively, compared to the control. Of these genes, 145 overlapped between the two peptides. Among them, PTENP1, the PTEN pseudogene, showed reduced H3K27me3 signal when treated by either YPB or OPB peptide. Consistently, the two peptides enhanced both PTENP1 and PTEN expression with concomitantly reduced AKT activation. Further studies validated PTENP1’s contribution to the anticancer activity of YPB and OPB peptides.

overall_design: ChIP-seq for H3k27me3 in MDA-MB-231 cells treated with YPB, OPB and control peptides

first: Cheng

last: Yi

first: Wenmeng

last: Wang

first: Guangchao

last: Sui


title: Phenotypic manifestation of alpha-synuclein strains derived from Parkinson’s disease and multiple system atrophy in human dopaminergic neurons

city: Oxford

first: Devika

last: Agarwal

address: JR hospital, Headley way

department: The MRC Weatherall Institute of molecular medicine

institute: University of Oxford

summary: Althougha-synuclein is implicated in the pathogenesis of Parkinson’s disease and related disorders, it remains unclear whether specific conformations or levels ofa-synuclein assemblies are toxic and how they cause progressive loss of human dopaminergic neurons. To address this issue, we used iPSC-derived dopaminergic neurons with a-synuclein triplication or controls where endogenous a-synuclein was imprinted into synthetic or disease-relevant conformations. We used a-synuclein fibrils generated de novo or amplified from homogenates of brains affected with Parkinson’s disease (n=3) or multiple system atrophy (n=5). We found that a 2.5-fold increase in a-synuclein levels in a-synuclein gene triplication neurons promoted seeded aggregation in a dose and time-dependent fashion, which was associated with a further increase in a-synuclein gene expression. Progressive neuronal loss was observed only in a-synuclein triplication neurons seeded with brain-amplified fibrils. Transcriptomic analysis and isogenic correction of a-synuclein triplication revealed that intraneuronalalpha-synuclein levels solely and sufficiently explained vulnerability to neuronal death

overall_design: RNASeq experiment to compare the SNCA triplication iPSC line (n=3 biological replicates per condition) at baseline and after induction of alpha-synuclein aggregation for 1 and 2 weeks. This was done to investigate whether there are transcriptomic changes upon alpha-synuclein aggregation within neurons using SNCA Triplication line (SFC831-03-03) when compared to their corresponding baseline Non-seeded controls (NSC) using three different types of fibrils: de novo generated fibrils (FIB), MSA amplified Fibrils (MSA) or PD amlpified Fibrils (PD) at 1 microM. A total of 24 different human iPSC samples were sequenced on the Novaseq 6000 platform.

first: Benedict

last: Tanudjojo

first: Samiha

last: Shaikh

first: Alexis

last: Fenyi

first: Luc

last: Bousset

first: Jade

last: Marsh

first: Christos

last: Zois

first: Sabrina

last: Herman-Ackah

first: Roman

last: Fischer

first: David

last: Sims

first: Ronald

last: Melki

first: George

last: Tofaris


title: Transneuronal Dpr12/DIP-δ interactions facilitate compartmentalized dopaminergic innervation of Drosophila mushroom body axons

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

institute: Weizmann Institute of Science

summary: The mechanisms controlling wiring of neuronal networks are not completely understood. The stereotypic architecture of the Drosophila mushroom-body (MB) offers a unique system to study circuit assembly. The adult medial MB γ-lobe is comprised of a long bundle of axons that wires with specific modulatory and output neurons in a tiled manner defining five distinct zones. We found that the immunoglobulin superfamily protein Dpr12 is cell-autonomously required in γ-neurons for their developmental regrowth into the distal γ4/5 zones, where both Dpr12 and its interacting protein, DIP-δ, are enriched. DIP-δ functions in a subset of dopaminergic neurons that wire with γ-neurons within the γ4/5 zone. During metamorphosis, these dopaminergic projections arrive to the γ4/5 zone prior to γ-axons, suggesting that γ-axons extend through a prepatterned region. Thus, Dpr12/DIP-δ transneuronal interaction is required for γ4/5 zone formation. Our study sheds light onto molecular and cellular mechanisms underlying circuit formation within subcellular resolution.

overall_design: Transcriptional profiling of drosophila γ neurons perturbed by Hr51 RNAi

first: Bavat

last: Bornstein

first: Hagar

last: Meltzer

first: Ruth

last: Adler

first: Idan

last: Alyagor

first: Victoria

last: Berkun

first: Gideon

last: Cummings

first: Fabienne

last: Reh

first: Hadas

last: Keren-Shaul

first: Eyal

last: David

first: Thomas

last: Riemensperger

first: Oren

last: Schuldiner


title: RNA-seq data from submiligram porcine myocardial tissue before and after myocardial infarction

city: Solna

first: Staffan

last: Holmin

state: Non US/Canada

address: Visionsgatan 4, J5:20

country: Sweden

institute: Karolinska Institutet

summary: We have developed an endovascular micro-endomyocardial biopsy device (Micro-EMB) with an outer diameter of 0.4 mm in order to minimize procedural risk, sampling trauma, and increase sampling specificity compared to conventional EMB. Here, we have taken micro-EMB samples from swine myocardium before, during and after myocardial infarction to detect potential gene expression responses.

overall_design: Twentythree blood samples and 62 micro-biopsy samples from the left ventricular myocardial wall were taken from three individual swine. Of the micro-biopsy samples, 6 were taken at baseline, 9 during the one hour occlusion (0 -1 h), 22 at 1 - 3 hours, 21 after two days and 21 after 14 days.    The biopsies were either aimed at the apical region of the heart, which was considered affected by the infarction, or lateral regions of the heart which were considered non-affected by the infarction.

first: Arvin

last: Chireh

first: Rikard

last: Grankvist


title: In vivo adenine base editing of PCSK9 in mice and macaques reduces LDL-cholesterol levels [RNA-seq]

city: Zurich

first: Tanja

last: Rothgangl

address: Winterthurerstrasse, 190

department: Pharmacology and Toxicology

country: Switzerland

institute: UZH Zurich

summary: The majority of known pathogenic point mutations in the human genome are C•G to T•A substitutions. Adenine base editors (ABEs), comprised of nuclease-impaired Cas9 fused to adenine deaminases, enable direct repair of these mutations, making them promising tools for precision in vivo genome editing therapies. However, prior to application in patients, thorough safety and efficacy studies in relevant model organisms are needed. Here, we apply adenine base editing in vivo in the liver of mice and cynomolgus macaques to install a splice site mutation in PCSK9 and reduce blood low-density lipoprotein (LDL) levels, a well-known risk factor for cardiovascular disease. Intravenous delivery of ABE-encoding mRNA and a locus-specific single guide (sg)RNA utilizing lipid nanoparticle (LNP) technology induce up to 67% editing in the liver of mice and up to 34% editing in the liver of macaques, leading to a reduction of plasma PCSK9 and LDL levels. We observed rapid clearance of ABE mRNA after LNP-mediated delivery, and neither sgRNA-dependent nor sgRNA-independent off-target mutations are detected in genomic DNA. Together, our findings support safety and feasibility of adenine base editing to treat patients with monogenetic liver diseases.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: total RNA-seq data from >=3 replicates each

first: Gerald

last: Schwank


title: Canine

city: Bethesda

first: Alexander

middle: Christian

last: Harris

state: Maryland

address: 50 South Drive

department: National Human Genome Research Institute

institute: National Institutes of Health

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

overall_design: Refer to individual Series


title: Regulatory variants associated with canine hematopoietic cancers

summary: Multi-omics approach identifies germline regulatory variants associated with hematopoietic malignancies in dogs

overall_design: 311 Flatcoated Retrievers

first: Jacquelyn

last: Evans

first: Heidi

last: Parker

first: Gerard

last: Rutteman

first: Jocelyn

last: Plassais

middle: C

first: David

last: Sargan

first: Rodney

last: Page

first: Elaine

last: Ostrander


title: Gene expression data from Tyr::CreErT2::BrafV600E Pten F/+ mouse tumors according to defloxing status of Brn2

city: Orsay

first: Lionel

last: Larue

address: Bat 110, Centre universitaire

department: UMR3347 CNRS - U1021 INSERM, Institut Curie

institute: Institut Curie


title: SnRNA-seq analysis of hippocampus in TAFE3 and TAFE4 mice

city: St. Louis

first: Jason

last: Ulrich

address: 425 S. Euclid

institute: Washington University

summary: The apolipoprotein E (APOE) gene is the strongest genetic risk factor for Alzheimer disease (AD). In addition to effects of apoE on amyloid-β, results have shown that apoE markedly influences pathological forms of tau and tau-mediated neurodegeneration with apoE4 having a strong deleterious effect on both parameters. In the brain, apoE is produced and secreted primarily from astrocytes and also by activated microglia though the cell-specific role of each form of apoE in the setting of neurodegeneration has not been determined. We utilized a well- characterized mouse model of tauopathy, P301S Tau transgenic mice expressing floxed APOE-e4 or APOE-e3 alleles. We crossed these mice with Aldh1l1-CreERT2 mice and at 5.5 months of age, after the onset of tau pathology, administered tamoxifen or vehicle. We then compared mice with or without inducible knockout of astrocyte APOE at 9.5 months of age. Single nucleus RNA sequencing analysis revealed striking gene expression changes in all cell types in P301S mice with astrocytic APOE4 playing a role in modulating neuron, astrocyte, and microglial gene expression to a more homeostatic state.

overall_design: Droplet-based 3′ end massively parallel single-cell RNA sequencing was performed by isolating single nuclei from flash-frozen mouse brains through sucrose gradient and libraries were prepared using Chromium Single Cell 5′ Reagent Kits according to manufacturer’s protocol (10x Genomics). The generated scRNAseq libraries were sequenced using Illumina sequencers.

last: Holtzman

middle: D

first: Chao

last: Wang

first: Monica

last: Xiong

first: Maud

last: Gratuze

first: Xin

last: Bao

first: Prabhakar

last: Andhey

first: Melissa

last: Manis

first: Caitlin

last: Schroeder

first: Zhuoran

last: Yin

first: Charlotte

last: Madore

first: Oleg

last: Butovsky

first: Maxim

last: Artyomov


title: Gene expression data from Tyr::CreErT2::BrafV600E Pten F/+ mouse tumors according to defloxing status of Brn2 [cell lines]

summary: To investigate the mechanism underlying the effect of Brn2-loss we extracted mRNA from Braf-Pten-Brn2-wt, Braf-Pten-Brn2-het, and Braf-Pten-Brn2-hom mouse melanomas and performed microarray-based transcriptome analysis.

overall_design: We studied the effect of Brn2 loss on in vivo melanomagenesis by generating the mouse cell lines (Tyr::CreERt2/°; BrafV600E/+; PtenF/+; Brn2+/+) = (Braf-Pten-Brn2-wt), (Tyr::CreERt2/°; BrafV600E/+; PtenF/+; Brn2F/+) =  (Braf-Pten-Brn2-het) and (Tyr::CreERt2/°; BrafV600E/+; PtenF/+; Brn2F/F) = (Braf-Pten-Brn2-hom) by introducing the floxed Brn2 locus into the genome by appropriate crossings (Figure 2 S2A) {Jaegle, 2003 #1672}. Cre-mediated defloxing of Braf, Pten, and Brn2 loci was induced by topical application of tamoxifen during the first three days after birth (Figure 2 S2B). All mice were monitored for the number of tumors/mice, and the growth rate of the first tumor. Cell lines were established from these tumors

first: Michael

last: Hamm

first: Pierre

last: Sohier

first: Jeremy

middle: H

last: Raymond


title: Loss of LUC7L2 and U1 snRNP subunits shifts energy metabolism from glycolysis to OXPHOS

city: Cambridge

first: Alexis

last: Jourdain

address: 415 Main Street

institute: Broad Institute of MIT & Harvard

summary:
Oxidative phosphorylation (OXPHOS) and glycolysis are the two major pathways for ATP production. The reliance
on each varies across tissues and cell states, and can influence susceptibility to disease. At present, the
full set ofmolecular mechanisms governing the relative expression and balance of these two pathways is unknown.
Here, we focus on genes whose loss leads to an increase in OXPHOS activity. Unexpectedly, this
class of genes is enriched for components of the pre-mRNA splicing machinery, in particular for subunits
of the U1 snRNP. Among them, we show that LUC7L2 represses OXPHOS and promotes glycolysis by multiple
mechanisms, including (1) splicing of the glycolytic enzyme PFKM to suppress glycogen synthesis, (2)
splicing of the cystine/glutamate antiporter SLC7A11 (xCT) to suppress glutamate oxidation, and (3) secondary
repression of mitochondrial respiratory supercomplex formation. Our results connect LUC7L2 expression
and, more generally, the U1 snRNP to cellular energy metabolism.

overall_design:
RNA-Seq analysis of LUC7L2 WT HeLa and K562 grown in glucose or galactose, or LUC7L2 KO HeLa and K562 cells grown in glucose.

eCLIP analysis of LUC7L2-interacting RNA in HeLa and K562 cells. Input and eCLIP are provided for each cell type in duplicate (total = 8 samples).

first: Vamsi

last: Mootha


title: In vivo adenine base editing of PCSK9 in mice and macaques reduces LDL-cholesterol levels

first: Tanja

last: Rothgangl

sample_organism:
Macaca fascicularis
Homo sapiens
Mus musculus


title: The Dystonia Gene THAP1 Controls DNA Double Strand Break Repair Choice

first: Wei

last: Wu

state: Shanghai

address: 320 yueyang road

department: Center for Excellence in Molecular Cell Science


title: Bulk RNAseq of AnnexinV+ and AnnexinV- cells from the Mertk-KO corpus callosum at the 4 week cuprizone timepoint

city: South San Francisco

first: Kimberle

last: Shen

address: 1 Dna way

institute: Genentech

summary:
Purpose:  Following 4 weeks of 0.2% cuprizone treatment, Mertk-KO mice accumulate dying cells in the corpus callosum (based on cleaved-cas3 staining). These cells are not seen in Mertk-WT animals at the same cuprizone timepoint. The goal of this study is to identify these dying cells in the Mertk-KO corpus callosum

Methods:  2 biological replicates (mice) were used. Corpus callosa were dissected from Mertk-KO mice after 4 weeks of 0.2% cuprizone treatment. Tissues were dissected into single cells using Miltenyi Neural Tissue Dissociation Kit (P) and stained with Annexin V. The stained cell suspensions were then FAC sorted into Annexin V+ and Annexin V- populations. RNA from these cells were extracted using QIAGEN RNeasy kit.

Results: Bulk RNA-Seq data were analyzed using an in-house pipeline consisting of GSNAP HTSeqGenie. Reads aligning uniquely to exons were counted to each gene, and size-factor normalization was used to calculating nRPKM statistic.

Conclusions: Based on the differences of transcriptomic profiles of AnnexinV+ and AnnexinV- cells, we conclude that the dying AnnexinV+ cells are microglia.

overall_design: Comparison of dying (AnnexinV+) and living (AnnexinV-) cells in the Mertk-KO corpus callosum after 4 weeks of 0.2% cuprizone treatment.

first: Brad

last: Friedman


title: scRNAseq of Mertk-WT and Mertk-KO corpus callosum

summary:
Purpose:  The goal of this study is to characterize the the different CNS cell types in the mouse corpus callosum over three different cuprizone treatment timepoints - (Baseline, 4 weeks, 4 weeks + 3 weeks of recovery) and compare the Mertk-WT vs Mertk-KO response to demyelination.

Methods:  3-4 biological replicates (mice) were used for each timepoint/genotype. Tissues were dissociated into single cells for preparation of 10X libraries and sequenced with HiSeq 2500 (Illumina).

Results: scRNA-Seq data were analyzed with an in-house analysis pipeline. Briefly, reads were demultiplexed based on perfect matches to expected cell barcodes. Transcript reads were aligned to the mouse reference genome (GRCm38) using GSNAP (Wu and Nacu, 2010). Only uniquely mapping reads were considered for downstream analysis. Transcript counts for a given gene were based on the number of unique molecular identifiers (UMIs) for reads overlapping exons in sense orientation. To account for sequencing or PCR errors, one mismatch was allowed when collapsing UMI sequences. Cell barcodes from empty droplets were filtered by requiring a minimum number of detected transcripts. Cells with less than 1000 total UMIs were discarded.

Conclusions: We show differences between Mertk-WT and Mertk-KO cellular profiles, particularly at the 4 week Cuprizone timepoint. In addition, our data show a distinct, yet heterogenous, population of oligodendrocytes that arise in the cuprizone model where remyelination is spontaneous and robust. Our results provide new insights into the cellular response to demyelination, that includes a resource for comparing and interpreting neurodegenerative disease models.

overall_design: 10X Single-cell profiling of Mertk-WT and Mertk-KO corpus callosum tissue at three different timepoints (baseline, 4 weeks, 4 weeks + 3 weeks of recovery)


title: Gene expression data from Tyr::CreErT2::BrafV600E Pten F/+ mouse tumors according to defloxing status of Brn2 [tumors]

first: Lionel

last: Larue

overall_design: We studied the effect of Brn2 loss on in vivo melanomagenesis by generating the mouse lines Tyr::CreERt2/°; BrafV600E/+; Brn2F/+ (Braf-Brn2-het), Tyr::CreERt2/°; BrafV600E/+; Brn2F/F (Braf-Brn2-hom), Tyr::CreERt2/°; BrafV600E/+; PtenF/+; Brn2F/+ (Braf-Pten-Brn2-het) and Tyr::CreERt2/°; BrafV600E/+; PtenF/+; Brn2F/F (Braf-Pten-Brn2-hom) by introducing the floxed Brn2 locus into the genome by appropriate crossings. Cre-mediated defloxing of Braf, Pten, and Brn2 loci was induced by topical application of tamoxifen during the first three days after birth. All mice were monitored for the number of tumors/mice, and the growth rate of the first tumor.


title: Recognition of inherently unstable H2A-nucleosome by Swc2 is a major determinant for unidirectional H2A.Z exchange

status: Public on Apr 12 2021

city: Beijing

first: Zhuqiang

last: Zhang

address: 15 Datun Road, Chaoyang District.

institute: Institute of Biophysics, CAS

summary: The site-specific chromatin incorporation of eukaryotic histone variant H2A.Z is driven by the multi-component chromatin remodeling complex SWR1/SRCAP/ p400. The budding yeast SWR1 complex replaces the H2A-H2B dimer in the canonical nucleosome with the H2A.Z-H2B dimer, but the mechanism governing the directionality of H2A-to-H2A.Z exchange remains elusive. Here, we use single-molecule force spectroscopy to dissect the disassembly/ reassembly of H2A-nucleosome and H2A.Z-nucleosome. We find that the N-terminal 1-135 residues of yeast SWR1-complex-protein-2 (previously termed Swc2-Z) facilitate the disassembly of nucleosomes containing H2A but not H2A.Z. The Swc2-mediated nucleosome disassembly/reassembly requires the inherently unstable H2A-nucleosome, whose instability is conferred by three H2A α2-helix residues Gly47, Pro49 and Ile63 as they selectively weaken the structural rigidity of H2A-H2B dimer. It also requires Swc2-ZN (residues 1-37) that directly anchors to H2A-nucleosome and functions in the SWR1-catalyzed H2A.Z replacement in vitro and yeast H2A.Z deposition in vivo. Our findings providecrucial insights into how SWR1 complex discriminates between the H2A-nucleosome and H2A.Z-nucleosome, establishing a simple paradigm for the governace of unidirectional H2A.Z exchange.

overall_design: H2A.Z ChIP-seq experiments were performed in Saccharomyces cerevisiae with 3 genotypes: WT, Swc2-ΔZ and Swc2-ΔZN. All samples are sequenced with the corresponding input sample. No replicates.

first: Linchang

last: Dai

first: Xue

last: Xiao

first: Lu

last: Pan

first: Liuxin

last: Shi

first: Ning

last: Xu

first: Xiaoli

last: Feng

last: Ma

first: Shuoxing

last: Dou

first: Pengye

last: Wang

first: Bing

last: Zhu

last: Li

first: Zheng

last: Zhou


title: Unique molecular signatures typify skin inflammation induced by chemical allergens and irritants

city: Lyon

first: Simon

last: de Bernard

address: 30 rue Pré Gaudry

institute: AltraBio

summary: A transcriptomic comparative analysis was performed to explore and characterize the molecular signatures of chemical-induced skin inflammation, in order to identify biomarkers that could discriminate allergic from irritant contact dermatitis.

overall_design: Skin biopsy samples from 47 patients with positive patch tests to reference allergens (nickel, n=10; MI, n=6; linalool hydroperoxide, n=10, amoxicillin, n=6; acetazolamide, n=1; piperacillin/tazobactam, n=1; Methylisothiazolinone n=6) or irritants (SLS, n=11; nonanoic acid, n=4; cantharidin, n=7) were collected. Control areas including non-lesional skin or vehicle (petrolatum or isopropanol) patch-tested skin were also collected from the same patients. All these samples were analysed by gene microarray.

first: Marc

last: Vocanson

first: Marine-Alexia

last: Lefevre


title: DNMT3A haploinsufficiency causes dichotomous DNA methylation defects at enhancers in mature human immune cells [RNA-seq]

city: Irvine

first: Minji

last: Byun

state: California

address: 829 Health Science Rd, 311

department: Microbiology and Molecular Genetics

institute: University of California Irvine

summary: DNMT3A encodes an enzyme that carries out de novo DNA methylation, which is essential for the acquisition of cellular identity and specialized functions during cellular differentiation. It is the most common driver gene of age-related clonal hematopoiesis. As such, mature immune cells harboring DNMT3A mutations can be readily detected in elderly individuals. Most acquired DNMT3A mutations are heterozygous and predicted to cause loss-of-function, indicating that haploinsufficiency is the predominant pathogenic mechanism. Yet, whether and how DNMT3A haploinsufficiency affects the function of mature immune cells is poorly understood. Here, we demonstrate that DNMT3A haploinsufficiency impairs the gain of DNA methylation at decommissioned enhancers, while simultaneously and unexpectedly impairs DNA demethylation at thousands of newly activated enhancers in mature human myeloid cells. The DNA methylation defects alter the activity of affected enhancers, leading to abnormal gene expression and impaired immune response. These findings provide insights into the mechanism of immune dysfunction associated with acquired DNMT3A mutations and clonal hematopoiesis.

overall_design: Steady state transcriptome and LPS response of macrophages differentiated from wild-type (DNMT3A+/+), DNMT3A-haploinsufficient (DNMT3A+/-), or DNMT3A-null (DNMT3A-/-) human embryonic stem cells were examined by RNAseq.

first: Jung-Yeon

last: Lim


title: Canine Blood ChIP-seq

first: Alexander

last: Harris

summary: Identification of canine regulatory regions in peripheral blood mononuclear cells from purebred dogs.

overall_design: Examination of 2 histone marks in 8 canine peripheral blood mononuclear cell samples

first: Jacquelyn

last: Evans

first: Jocelyn

last: Plassais

first: Elaine

last: Ostrander


title: DNMT3A haploinsufficiency causes dichotomous DNA methylation defects at enhancers in mature human immune cells [csRNA-seq]

overall_design: Capped small RNA-seq (csRNA-seq) can map and quantify all transcription start sites (TSSs), including those from enhancer RNA and other rapidly processed or degraded transcripts. csRNA-seq was applied to macrophages differentiated from wild-type (DNMT3A+/+), DNMT3A-haploinsufficient (DNMT3A+/-), or DNMT3A-null (DNMT3A-/-) human embryonic stem cells to quantaify enhancer RNA and assess enhancer activity.

first: Sascha

last: Duttke

first: Christopher

last: Benner


title: DNMT3A haploinsufficiency causes dichotomous DNA methylation defects at enhancers in mature human immune cells [BiSulfite-seq]

overall_design: Whole-genome bisulfite sequencing (WGBS) was performed for macrophages differentiated from wild-type (WT), DNMT3A-haploinsufficient (HET), or DNMT3A-null (KO) H1-hESCs (three independent clones per group).


title: Gene expression profiles of normal and activity-silenced mitral cells at P3 and P6

city: Fukuoka

first: Takeshi

last: Imai

address: Maidashi3-1-1, Higashi-ku

department: Graduate School of Medical Sciences

institute: Kyushu University

summary: Mitral cells in the mouse olfactory bulb are known to remodel their primary dendrites and form lateral dendrites during postnatal development. These processes are suppressed when neuronal activity is silenced by overexpression of Kir2.1 in mitral cells, indicating that neuronal activity in mitral cells is required. However, it is unclear what changes in gene expression lead to the remodeling of mitral cell dendrites in an activity-dependent manner. To address this, we performed a microarray-based analysis of gene expression in mitral cells during normal development and under the activity-silenced condition.

overall_design: We analyzed four groups: EYFP+ mitral cells at P3, EYFP+ mitral cells at P6, Kir2.1-expressing EYFP+ mitral cells at P3, and Kir2.1-expressing EYFP+ mitral cells at P6. We used 40 mitral cells for each group. After cDNA synthesis from single cells, the 40 cDNA samples were divided into 4 biological replicates, each of which contains cDNA from 10 mitral cells.

first: Satoshi

last: Fujimoto


title: MAP3K7 loss drives enhanced androgen signaling and independently confers risk of recurrence in prostate cancer with joint loss of CHD1

city: Aurora

first: Lauren

last: Jillson

state: Colorado

address: 12801 E 17th Avenue, Room L18-6213, Mail stop 8303

department: Pharmacology

institute: University of Colorado Anschutz Medical Campus


title: RNA-Seq of LNCaP human prostate cancer cells with knockdown of MAP3K7 and/or CHD1

summary:
Purpose: The goal of this study is to identify transcriptome-wide changes that occur in a human prostate cell line with knockdown of MAP3K7(TAK1) and CHD1, in the presence and absence of androgens. We utilize this cell line as a model of an aggressive prostate cancer subtype consisting of deletions of both MAP3K7 and CHD1 in human patients. RNAseq comparing shControl, shMAP3K7(TAK1), shCHD1, and both (shMAP3K7/shCHD1) was used to identify transcriptome changes resulting from loss of each of these genes, as well as their effects on androgen signaling.
Abstract of associated study: Prostate cancer (PCa) genomic subtypes that stratify aggressive disease and inform treatment decisions at the primary stage are currently limited. Previously, we functionally validated an aggressive subtype present in 15% of PCa characterized by dual deletion of MAP3K7 and CHD1.  Recent studies in the field have focused on deletion of CHD1 and its role in androgen receptor (AR) chromatin distribution and resistance to AR-targeted therapy, however, CHD1 is rarely lost without co-deletion of MAP3K7. Here we show that in the clinically relevant context of co-loss of MAP3K7 and CHD1 there are significant, collective changes to aspects of AR signaling. While CHD1 loss mainly impacts the expansion of the AR cistrome, loss of MAP3K7 drives increased AR target gene expression. PCa cell line models engineered to co-suppress MAP3K7 and CHD1 also demonstrated increased AR-v7 expression and resistance to the AR-targeting drug enzalutamide. Furthermore, we determined that low protein expression of both genes is significantly associated with biochemical recurrence (BCR) in a clinical cohort of radical prostatectomy specimens. Low MAP3K7 expression, however, was the strongest independent predictor for risk of BCR over all other tested clinicopathologic factors including CHD1 expression. Collectively, these findings illustrate the importance of MAP3K7 loss in a molecular subtype of PCa that poses challenges to conventional therapeutic approaches.

overall_design: mRNA profiles of LNCaP human prostate cancer cells engineered with shControl, shMAP3K7, shCHD1, and both (shMAP3K7 and shCHD1), with and without 1nM R1881 were generated by RNAsequencing and compared to identify differentially expressed genes between the groups.

first: James

last: Costello

first: Scott

last: Cramer


title: ChIP-seq of the androgen receptor (AR) in LNCaP human prostate cancer cells with knockdown of MAP3K7 and/or CHD1

summary:
Purpose: The goal of this study is to identify genome-wide changes in AR chromatin binding that occur in a human prostate cell line with knockdown of MAP3K7(TAK1) and CHD1, in the presence and absence of androgens. We utilize this cell line as a model of an aggressive prostate cancer subtype consisting of deletions of both MAP3K7 and CHD1 in human patients. ChIP-seq comparing AR chromatin binding in shControl, shMAP3K7(TAK1), shCHD1, and both (shMAP3K7/shCHD1) was used to identify AR cistrome changes resulting from loss of each of these genes.
Abstract of associated study: Prostate cancer (PCa) genomic subtypes that stratify aggressive disease and inform treatment decisions at the primary stage are currently limited. Previously, we functionally validated an aggressive subtype present in 15% of PCa characterized by dual deletion of MAP3K7 and CHD1.  Recent studies in the field have focused on deletion of CHD1 and its role in androgen receptor (AR) chromatin distribution and resistance to AR-targeted therapy, however, CHD1 is rarely lost without co-deletion of MAP3K7. Here we show that in the clinically relevant context of co-loss of MAP3K7 and CHD1 there are significant, collective changes to aspects of AR signaling. While CHD1 loss mainly impacts the expansion of the AR cistrome, loss of MAP3K7 drives increased AR target gene expression. PCa cell line models engineered to co-suppress MAP3K7 and CHD1 also demonstrated increased AR-v7 expression and resistance to the AR-targeting drug enzalutamide. Furthermore, we determined that low protein expression of both genes is significantly associated with biochemical recurrence (BCR) in a clinical cohort of radical prostatectomy specimens. Low MAP3K7 expression, however, was the strongest independent predictor for risk of BCR over all other tested clinicopathologic factors including CHD1 expression. Collectively, these findings illustrate the importance of MAP3K7 loss in a molecular subtype of PCa that poses challenges to conventional therapeutic approaches.

overall_design: ChIP-seq of the androgen receptor (AR) in LNCaP human prostate cancer cells engineered with shControl, shMAP3K7, shCHD1, and both (shMAP3K7 and shCHD1), with and without 1nM of the synthetic androgen R1881. The roles of MAP3K7 and/or CHD1 in altering the AR cistrome were assessed.

first: Etienne

last: Danis


title: RNA-Seq of LAPC4 human prostate cancer cells with knockdown of MAP3K7 and CHD1

summary:
Purpose: The goal of this study is to identify transcriptome-wide changes that occur in a human prostate cell line with knockdown of MAP3K7(TAK1) and CHD1, in the presence and absence of androgens. We utilize this cell line as a model of an aggressive prostate cancer subtype consisting of deletions of both MAP3K7 and CHD1 in human patients. RNAseq comparing shControl and shMAP3K7/shCHD1 was used to identify transcriptome changes resulting from loss of these genes, as well as their effects on androgen signaling.
Abstract of associated study: Prostate cancer (PCa) genomic subtypes that stratify aggressive disease and inform treatment decisions at the primary stage are currently limited. Previously, we functionally validated an aggressive subtype present in 15% of PCa characterized by dual deletion of MAP3K7 and CHD1.  Recent studies in the field have focused on deletion of CHD1 and its role in androgen receptor (AR) chromatin distribution and resistance to AR-targeted therapy, however, CHD1 is rarely lost without co-deletion of MAP3K7. Here we show that in the clinically relevant context of co-loss of MAP3K7 and CHD1 there are significant, collective changes to aspects of AR signaling. While CHD1 loss mainly impacts the expansion of the AR cistrome, loss of MAP3K7 drives increased AR target gene expression. PCa cell line models engineered to co-suppress MAP3K7 and CHD1 also demonstrated increased AR-v7 expression and resistance to the AR-targeting drug enzalutamide. Furthermore, we determined that low protein expression of both genes is significantly associated with biochemical recurrence (BCR) in a clinical cohort of radical prostatectomy specimens. Low MAP3K7 expression, however, was the strongest independent predictor for risk of BCR over all other tested clinicopathologic factors including CHD1 expression. Collectively, these findings illustrate the importance of MAP3K7 loss in a molecular subtype of PCa that poses challenges to conventional therapeutic approaches.

overall_design: mRNA profiles of LAPC4 human prostate cancer cells engineered with shControl or shMAP3K7 and shCHD1, with and without 1nM R1881 were generated by RNAsequencing and compared to identify differentially expressed genes between the groups.


title: RNA-Seq of 22RV1 human prostate cancer cells with knockdown of MAP3K7 and CHD1

overall_design: mRNA profiles of 22RV1 human prostate cancer cells engineered with shControl or shMAP3K7 and shCHD1, with and without 1nM R1881 were generated by RNAsequencing and compared to identify differentially expressed genes between the groups.


title: Lineage tracing reveals the pro-tumorigenic niche role of tissue resident macrophages in early lung cancer lesions [scRNA-seq]

city: New York

first: Maria

last: Casanova Acebes

state: New York

address: 1470 Madison Ave

department: Oncological Sciences

institute: Mount Sinai School of Medicine

summary: To explore the diversity of the MF compartment in human non-small cell lung carcinoma lesions (NSCLC), we first performed an unbiased single cell RNA-sequencing (scRNAseq) analysis of CD45+ tumor-associated leukocytes. We identified distinct MF populations enriched in human tumors and found related MF phenotypes in mouse lung tumors. Using lineage-tracing, we discovered these discrete MF populations differ in origin and have a distinct temporal and spatial distribution in the TME. Longitudinal tumor imaging revealed that upon tumor cell seeding, TRMF accumulate in proximity to tumor cells to promote tumor cell epithelial mesenchymal transition and invasiveness, while also inducing a potent T regulatory (Treg) response that protects tumor cells from adaptive immunity. TRMF depletion prior to tumor implantation, while sparing Mo-MF, did not affect tumor cell seeding but significantly reduced Treg numbers, dampened the Treg regulatory program, promoted the accumulation of CD8+ T cells in tumor lesions, and reduced tumor invasiveness and growth. During tumor growth, TRMF redistributed at the periphery of the TME, which becomes dominated by Mo-MF both in mouse and human NSCLC lesions, and TRMF depletion in later stage tumors, had little effect on tumor growth. This study identifies the distinct contribution of the TRMF lineage to early lung cancer invasiveness and establish TRMF as a potential novel target to treat early lung cancer lesions.

overall_design: Sorted enriched macrophages and monocytes in the lung (LinNEG, CD11b+CD11c+) from naïve C57BL/6 naïve and tumor bearing mice (KP tumors d30) were generated by deep sequencing using Illumina Nextseq 500.

first: María

last: Casanova-Acebes

first: Andrew

last: Leader


title: Lineage tracing reveals the pro-tumorigenic niche role of tissue resident macrophages in early lung cancer lesions [MC68]

overall_design: Sorted enriched macrophages and monocytes in the lung (LinNEG, CD11b+CD11c+) from naïve Cx3CR1CreER-LSL-R26-YFP and tumor bearing mice (KP tumors d30) were generated by deep sequencing using Illumina Nextseq 500.


title: Lineage tracing reveals the pro-tumorigenic niche role of tissue resident macrophages in early lung cancer lesions [MC29]

overall_design: Sorted enriched macrophages and monocytes in the lung (LinNEG, CD11b+CD11c+) from naïve Map17CreER-LSL-R26-tdTom and tumor bearing mice (KP tumors d30) were generated by deep sequencing using Illumina Nextseq 500.


title: Lineage tracing reveals the pro-tumorigenic niche role of tissue resident macrophages in early lung cancer lesions II

overall_design: Sorted lung TRMs from naïve wild type (WT) and tumor bearing mice (KP-TRMs : KP tumors  harvested at d15 and at d35) were generated by deep sequencing using Illumina Nextseq 500.


title: Lineage tracing reveals the pro-tumorigenic niche role of tissue resident macrophages in early lung cancer lesions III

overall_design: The chromatin accessibility profiles of sorted lung TRMs from naïve wild type (WT) and KP-TRMs  (KP tumors D15 and KP tumors D30), were generated by deep sequencing in triplicates using Illumina Nextseq 500 and with an average of 10 million paired-end reads per sample.


title: Transcriptome and translatome profiling of Mtb-infected human DC identifies GSK-3beta as a molecular switch of rapamycin-driven immune stimulation

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

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

country: Italy

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

summary:
In human primary dendritic cells (DC) rapamycin - an autophagy inducer and protein synthesis inhibitor - overcomes the autophagy block induced by Mycobacterium tuberculosis (Mtb) and promotes Th1 response via IL-12 secretion. Here, the immunostimulatory activity of rapamycin in Mtb-infected DC was investigated by analyzing the transcriptome and the translatome profiles.
Several differentially expressed genes (DEGs) were found in transcriptome and translatome of Mtb-infected DC, showing an additional increase in presence of rapamycin, which was instead ineffective in uninfected cells. The majority of DEGs identified in the translatome resulted also present in the transcriptome-modulated genes, suggesting that both RNAs are actively translated mRNAs. The DEG in silico analysis showed significant changes in intracellular cascades related to cytokine production, cytokine-induced signaling and immune response to pathogens. In particular, rapamycin treatment of Mtb-infected DC caused a significant enrichment of IFN-beta, IFN-lambda and IFN-stimulated genes in the polysome-associated RNA fraction. In addition, IL-12, IL-23, IL-1B, IL-6, and TNF-A were induced at RNA and protein level by rapamycin in Mtb-infected DC, while IL-10 was reduced. Interestingly, upon siRNA or pharmacologically GSK-3beta inhibition, rapamycin-driven modulation of the pro- and anti-inflammatory cytokine balance was lost, thus indicating that in Mtb-infected DC GSK-3beta functions as molecular switch for the regulation of cytokine milieu.
In conclusion, our study sheds light on the molecular mechanism by which autophagy contributes to DC activation during Mtb infection and highlights that rapamycin and its analogs as well as GSK-3beta modulators are promising compounds for host-directed therapy in the control of Mtb infection.

overall_design: Matched transcriptome and translatome profiles of human primary Dendrtitic cells infected with Mtb and treated with rapamycin, four biological replicates for each condition.

first: Marilena

middle: P

last: Etna

first: Orazio

last: Palumbo

first: Raffaella

last: Stallone

first: Massimo

last: Carella

first: Rodolfo

last: Negri

first: Eliana

last: Coccia


title: Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes

city: Seattle

first: Robert

last: Waterston

state: WA

address: Foege Building S-350D, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

summary: Recently developed single cell technologies allow researchers to characterize cell states at ever greater resolution and scale. C. elegans is a particularly tractable system for studying development, and recent single cell RNA-seq studies characterized the gene expression patterns for nearly every cell type in the embryo and at the second larval stage (L2). Gene expression patterns are useful for learning about gene function and give insight into the biochemical state of different cell types; however, in order to understand these cell types, we must also determine how these gene expression levels are regulated. We present the first single cell ATAC-seq study in C. elegans. We collected data in L2 larvae to match the available single cell RNA-seq data set, and identify tissue-specific chromatin accessibility patterns that align well with existing data, including the L2 single cell RNA-seq results. Using a novel implementation of the Latent Dirichlet Allocation algorithm, our chromatin accessibility data provide new insights into which genomic loci may be participating in cell type-specific gene regulation, with promise for better understanding of cellular differentiation and gene regulation in the worm.

overall_design: Survey of chromatin accessibility for all tissues in C. elegans nematodes at the second larval stage (L2) by sciATAC-seq of 30,930 cells.

first: Timothy

middle: J

last: Durham

first: Riza

middle: M

last: Daza

first: Lou

last: Gevirtzman

first: Darren

last: Cusanovich

first: William

last: Stafford Noble

first: Jay

last: Shendure


title: Lineage tracing reveals the pro-tumorigenic niche role of tissue resident macrophages in early lung cancer lesions VI

first: Maria

last: Casanova Acebes


title: RORa regulates developmental and angiotensin II-induced cardiac hypertrophy

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: RORasg/sg mice have small cardiomyocytes and hypocontractile hearts with increased fibrosis. Microarrays revealed broad deficits of sarcomeric RNAs and key myogenic transcription factors, suggesting that the loss of RORa leads to impaired developmental hypertrophy through transcriptional regulation. RORasg/sg mice developed exaggerated ventricular remodeling in response to Agn II infusion. We identify novel cardioprotective roles for RORa in promoting developmental and preventing pathological cardiac hypertrophy, mediated in part through regulation of the IL-6-STAT3 pathway in cardiomyocytes and cardiac fibrosis

overall_design: Heart total RNAs were purified from 5 WT and 4 RORasg/sg mice. Then the samples were applied to Agilent mouse genome chip.

first: Ju-Youn

last: Beak

first: Hong-Soon

last: Kang

first: Anton

last: Jetten


title: DNMT3A haploinsufficiency causes dichotomous DNA methylation defects at enhancers in mature human immune cells [tiling array]

first: Minji

last: Byun

overall_design: Bisulphite converted DNA from 40 samples were hybridised to the Illumina Infinium MethylationEPIC Beadchip.

first: Jung-Yeon

last: Lim


title: A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2 [gene expression levels]

status: Public on Apr 11 2021

city: Boston

first: Yered

middle: Hammurabi

last: Pita-Juarez

state: MA

address: 330 Brookline Ave

department: Pathology

institute: Beth Israel Deaconess Medical Center

summary: The SARS-CoV-2 pandemic has caused over 1 million deaths globally, mostly due to acute lung injury and acute respiratory distress syndrome, or direct complications resulting in multiple-organ failures. Little is known about the host tissue immune and cellular responses associated with COVID-19 infection, symptoms, and lethality. To address this, we collected tissues from 11 organs during the clinical autopsy of 17 individuals who succumbed to COVID-19, resulting in a tissue bank of approximately 420 specimens. We generated comprehensive cellular maps capturing COVID-19 biology related to patients’ demise through single-cell and single-nucleus RNA-Seq of lung, kidney, liver and heart tissues, and further contextualized our findings through spatial RNA profiling of distinct lung regions. We developed a computational framework that incorporates removal of ambient RNA and automated cell type annotation to facilitate comparison with other healthy and diseased tissue atlases. In the lung, we uncovered significantly altered transcriptional programs within the epithelial, immune and stromal compartments and cell intrinsic changes in multiple cell types relative to lung tissue from healthy controls. We observed evidence of alveolar type 2 (AT2) differentiation replacing depleted alveolar type 1 (AT1) lung epithelial cells, as previously seen in fibrosis, and a concomitant increase in myofibroblasts reflective of defective tissue repair. Viral reads were enriched in lung mononuclear phagocytic cells and endothelial cells, and these cells expressed distinct viral RNA host response transcriptional programs. We corroborated the compositional and transcriptional changes in lung tissue through spatial analysis of RNA profiles in situ and distinguished unique tissue host responses between regions with and without viral RNA, and in COVID-19 donor tissues relative to healthy lung. Finally, we analyzed genetic regions implicated in COVID-19 GWAS with transcriptomic data to implicate specific cell types and genes associated with disease severity. Overall, our COVID-19 cell atlas is a foundational dataset to better understand the biological impact of SARS-CoV-2 infection across the human body and empowers the identification of new therapeutic interventions and prevention strategies.

overall_design:
This dataset contains gene expression levels from ROIs from autopsy FFPE lung tissues from a cohort of 5 patients with positive SARS-CoV-2 nasopharyngeal swab on admission. A total of 80 ROIs were collected and segmented to 80 AOIs.

WTA = Nanostring GeoMx Digital Spatial Profiling (DSP) Whole Transcriptome Atlas  (WTA) Panel

first: Ioannis

last: Vlachos


title: Lineage tracing reveals the pro-tumorigenic niche role of tissue resident macrophages in early lung cancer lesions

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

overall_design: Refer to individual Series


title: A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2 [protein levels]

first: Samouil

last: Farhi

state: Massachusetts

address: 415 Main St.

institute: Broad Institute of MIT and Harvard

overall_design: This dataset contains protein levels from ROIs from 9 SARS-CoV-2 infected patient LUL FFPE samples collected during rapid autopsy, and 3 non-infected control parenchyma samples. Up to 26 ROIs were collected within each patient sample, segmented to PanCK+ and PanCK- AOIs, for n = 330 AOIs total. RNA Scope on serial sections was used to guide ROI selection. Coordinates reported are stage coordinates of collection, invert for approximate imaged location. Matched regions were acquired with mRNA profiling by NanoString CTA and WTA assays, reported in GSE162911. Mapping between datasets is in supplementary file ROI matching to RNA data.xlsx.

first: Toni

last: Delorey

first: Carly

last: Ziegler

first: Graham

last: Heimberg

first: Rachelly

last: Normand

first: Yiming

last: Yang

first: Asa

last: Segerstolpe

first: Domenic

last: Abbondanza

first: Stephen

last: Fleming

first: Ayshwarya

last: Subramanian

first: Karthik

last: Jagadeesh

first: Kushal

last: Dey

first: Michal

last: Slyper

first: Daniel

last: Montoro

last: Pira-Juarez

first: Devan

last: Phillips

first: Pritha

last: Sen

first: Zohar

last: Bloom-Ackerman

first: Andrea

last: Ganna

first: James

last: Gomez

first: Erica

last: Normandin

first: Pourya

last: Naderi

first: Yury

last: Popov

first: Sebastian

last: Niezen

first: Linus

last: Tsai

first: Katherine

last: Siddle

first: Malika

last: Sud

first: Victoria

last: Tran

first: Shamsudheen

last: Vellarikkal

first: Liat

last: Amir-Zilbertstein

first: Deepak

last: Atri

first: Nick

last: Barkas

first: Olga

middle: R

last: Brook

first: Jonathan

last: Chen

first: Prajan

last: Divakar

first: Phylicia

last: Dorceus

first: Jesse

last: MEngreitz

first: Donna

last: Fitzgerald

first: Robin

last: Fropf

first: Steven

last: Gazal

first: Joshua

last: Gould

first: John


title: Lineage tracing reveals the pro-tumorigenic niche role of tissue resident macrophages in early lung cancer lesions I

first: Maria

last: Casanova Acebes

overall_design: We analized in vitro 3D-matrigel co-cultures of KP-GFP tumoral cells (spheroids) alone or co-cultured with lung TRMs (alveolar macrophages) or bone-marrow monocytes to evaluate the direct effect of different populations of macrophages on cancer cells.

first: María

last: Casanova-Acebes


first: Samouil

last: Farhi

sample_organism:
Homo sapiens
blank sample

platform_organism:
Homo sapiens
blank sample

overall_design: This dataset contains gene expression levels from ROIs from 9 SARS-CoV-2 infected patient LUL FFPE samples collected during rapid autopsy, and 3 non-infected control parenchyma samples. In addition to this core sample set we report one trachea CTA slide, one heart left ventricle WTA slide, one LUL CTA repeat with different segmentation, one LLL slide and one RUL slide. Up to 26 ROIs were collected within each patient sample, segmented to AOIs according to the descriptions below. In total we report n = 375 AOIs for CTA and n = 409 AOIs for WTA. RNA Scope on serial sections was used to guide ROI selection. Additional sample properties, and mapping to protein data in this super series is reported in sheets of Nanostring_Count_Matrices.xlsx.

first: Toni

last: Delorey

first: Carly

last: Ziegler

first: Graham

last: Heimberg

first: Rachelly

last: Normand

first: Yiming

last: Yang

first: Asa

last: Segerstolpe

first: Domenic

last: Abbondanza

first: Stephen

last: Fleming

first: Ayshwarya

last: Subramanian

first: Karthik

last: Jagadeesh

first: Kushal

last: Dey

first: Michal

last: Slyper

first: Daniel

last: Montoro

first: Yered

last: Pira-Juarez

first: Devan

last: Phillips

first: Pritha

last: Sen

first: Zohar

last: Bloom-Ackerman

first: Andrea

last: Ganna

first: James

last: Gomez

first: Erica

last: Normandin

first: Pourya

last: Naderi

first: Yury

last: Popov

first: Sebastian

last: Niezen

first: Linus

last: Tsai

first: Katherine

last: Siddle

first: Malika

last: Sud

first: Victoria

last: Engreitz


title: Expression data from WT and BFAR-deficient naïve CD4+ T cells stimulated in Th9 differentiation condition for 3 days

city: Shanghai

first: Siyu

last: Pei

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

summary: We conducted gene expression profile analysis by using WT and BFAR-deficient naive CD4+ T cells.Gene ontology (GO) analysis revealed the most prominent biological processes altered in naive CD4+ T cells cultured in Th9 condition were associated with immune system process.

overall_design: Genome-wide expression profiling of WT and BFAR-deficient naïve CD4+ T cells stimulated in Th9 differentiation condition for 3 days were generated by RNA-sequencing analysis

first: Yichuan

last: Xiao


title: A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2

first: Samouil

last: Farhi


title: Next Generation Sequencing Facilitates Quantitative Analysis of the implication of LAIR-1 in sorted mouse pulmonary ILC2 Transcriptomes

status: Public on Apr 10 2021

city: Los Angeles

first: Georges Doumet

last: HELOU

address: 1450 Biggy St, NRT5505, Keck School of Medicine

department: Molecular Microbiology and Immunology

institute: University of Southern California

summary: Type-2 innate lymphoid cells (ILC2s) are central players in type-2 asthma. They initiate eosinophil infiltration and airway hyperreactivity (AHR) through cytokine secretion. Leukocyte-associated immunoglobulin-like receptor 1 (LAIR-1) is an inhibitory receptor considered as immune checkpoint in different inflammatory diseases. Here we assessed the role of LAIR-1 in murine ILC2s. WT and LAIR-1 KO mice were intranasally challenged with IL-33 and pulmonary ILC2s were sorted to perform  RNA sequencing. Our results unravel a novel regulatory axis in ILC2s with the capacity to reduce their activation.

overall_design: mRNA profiles of sorted mouse pulmonary ILC2s from WT and LAIR-1 KO mice were generated by deep sequencing, in triplicate, using a NextSeq 500 (Illumina) system.

first: D

last: Helou

first: O

last: Akbari