title: Role of E2F6 in gene expression and DNA methylation during mouse development

city: Illkirch

first: Michael

last: Weber

address: 300 Bd Sebastien Brant

department: UMR7242 Biotechnology and Cell Signalling

institute: CNRS

summary: In the mouse, long-term silencing by CpG island DNA methylation is specifically targeted to germline genes in somatic cells, however the molecular mechanisms of this specificity remain unclear. Here we demonstrate that the transcription factor E2F6, a member of the polycomb repressive complex 1.6 (PRC1.6), is critical to target and initiate epigenetic silencing at germline genes in early embryogenesis. Genome-wide, E2F6 binds preferentially to CpG islands in embryonic cells. E2F6 cooperates with MGA to silence a subgroup of germline genes in mouse embryonic stem cells and in vivo, a function that critically depends on the E2F6 marked box domain. Furthermore, inactivation of E2f6 leads to a failure to deposit CpG island DNA methylation at these genes during implantation. Finally, we show that E2F6 is required to initiate epigenetic silencing in early embryonic cells but becomes dispensable for the maintenance in differentiated cells. Our findings elucidate the mechanisms of epigenetic targeting of germline genes and provide a paradigm for how transient repression signals by DNA-binding factors in early embryonic cells are translated into long term epigenetic silencing during mammalian development.

overall_design:
We mapped E2F6 binding sites in mouse ES cells by ChIP-seq.
We studied the role of E2F6 in gene expression by performing RNA-seq in triplicates in WT and E2f6-/- mouse ES cells and E8.5 embryos.
To study the role of E2F6 in DNA methylation, we performed Whole Genome Bisulfite Sequencing (WGBS) in a WT and E2f6-/- embryo, as well as Reduced Representation Bisulfite Sequencing (RRBS) in WT and E2F6-/- ES cells, E8.5 embryos (two replicates), adult tissues (brain, muscle, kidney, three replicates), primary MEFs (two replicates) and MEF Crispr-Cas9 clones (two replicates).

last: Dahlet

first: Peter

last: Hansen

first: Matthias

last: Truss


title: NSCLP-Twins

status: Public on Apr 24 2021

city: Miami

first: Derek

last: Van Booven

state: FL

address: 1501 NW 10th Ave

country: USA

institute: University of Miami

type: Methylation profiling by high throughput sequencing

summary: this study analyzes the WGBS of twins discordant for non syndromic cleft lip and palate

overall_design: WGBS was performed on twin saliva samples

first: Juan

last: Young

first: Susan

last: Blanton

first: Jacqueline

last: Hecht


title: Single cell immune profiling of human cervix biopsies

city: Seattle

first: Tao

last: Peng

state: WA

address: 1100 Fairview Ave N/FHCRC/E5-110

department: Medicine

institute: University of Washington

type: Expression profiling by high throughput sequencing

summary: We have used 10x singel cell immune profiling methods to analyze gene expression and TCR clonotypes simultaneously of freshly isolated human ectocervix biopsies. Our main goal is to define phenotypes and clonotypes of different subsets of tissue resident CD8 T cells in normal human cervix tissues.

overall_design: We analyzed single cell gene expression and TCR clonotypes of 10 cervix samples from eight subjects.


title: HOXA13 in etiology and oncogenic potential of Barrett’s esophagus [BAR-T]

city: ROTTERDAM

first: Vincent

last: Janmaat

address: Dr. Molewaterplein 40

department: Gastroenterology and Hepatology

country: Netherlands

institute: Erasmus MC

summary: Barrett’s esophagus in gastrointestinal reflux patients constitutes a columnar epithelium with distal characteristics, prone to progress to esophageal adenocarcinoma. HOX genes are known mediators of position-dependent morphology. Here we show HOX collinearity in the adult gut while Barrett’s esophagus shows high HOXA13 expression in stem cells and their progeny. HOXA13 overexpression appears sufficient to explain both the phenotype (through downregulation of the epidermal differentiation complex) and the oncogenic potential of Barrett’s esophagus. Intriguingly, employing a mouse model that contains a reporter coupled to the HOXA13 promotor we identify single HOXA13-positive cells distally from the physiological esophagus, which is mirrored in human physiology, but increased in BE. Additionally, we observe that HOXA13 expression confers a competitive advantage to cells. We thus propose that Barrett’s esophagus and associated esophageal adenocarcinoma is the consequence of expansion of this gastro-esophageal HOXA13-expressing compartment following epithelial injury.

overall_design: mRNA profiles of wild type BAR-T versus HOXA13 knock-out BAR-T monoclonal cell lines.

middle: T

first: Maikel

middle: P

last: Peppelenbosch


title: HOXA13 in etiology and oncogenic potential of Barrett’s esophagus [EPC2]

overall_design: mRNA profiles of wild type EPC2-hTERT versus HOXA13 knock-out EPC2-hTERT monoclonal cell lines.


title: HOXA13 in etiology and oncogenic potential of Barrett’s esophagus [KH2 mESC non diff]

overall_design: mRNA profiles of control KH2 mESC's versus HOXA13 overexpressing KH2 mESC's.


title: Genomic Landscape, Evolution and Chemoresistance of Yolk Sac Tumors

city: Beijing

first: Jiaxin

last: Yang

address: Shuaifuyuan No.1

country: China

institute: PUMCH

summary: Yolk sac tumors (YSTs) are a major histological subtype of malignant ovarian germ cell tumors, and compared to other subtypes, patients with YST have a worse prognosis. The molecular basis of this disease has not been characterized at the genomic level. Here we characterized 41 clinical tumor samples (and related normal samples) from 30 YST patients, with distinct responses to cisplatin_x001f__x001F_-based chemotherapy, through a combination of whole-exome and RNA sequencing. We show that microsatellite instability status and mutational signature are informative of chemoresistance. We identify somatic driver candidates, including significantly mutated genes KRAS and KIT and copy-number alteration drivers, such as deleted ARID1A and PARK2, and amplified ZNF217, CDKN1B, and KRAS. Interestingly, YSTs appear to have very infrequent TP53 mutations, whereas the tumors from patients with abnormal gonadal development are characterized by both KRAS and TP53 mutations as well as abnormal sex-specific genes. The differential expression analysis of primary sensitive tumors versus relapsed tumors and in vitro experiments suggest a role of OVOL2 overexpression in YST resistance to cisplatin. Our study lays a critical foundation for understanding key molecular aberrations and developing novel therapeutic strategies for this disease.

overall_design:
We characterized 41 clinical tumor samples (and related normal samples) from 30 YST patients, with distinct responses to cisplatin-based chemotherapy, through a combination of whole-exome and RNA sequencing.

>>> The raw sequence data reported in this study have been deposited in the Genome Sequence Archive of the BIG Data Center, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, under accession number HRA000131, and are publicly accessible at http://bigd.big.ac.cn/gsa . All relevant data are available from the authors <<<

first: Xuan

last: Zong

first: Ying

last: Zhang

first: Xinxin

first: Dongyan

last: Cao

first: Mei

last: Yu

first: Jinhui

last: Wang

first: Hongyue

last: Li

first: Xuejiao

last: Guo

first: Han

last: Liang


title: HOXA13 in etiology and oncogenic potential of Barrett’s esophagus [KH2 mESC diff]

overall_design: KH2 mESC diff CONTROL and HOXA13


title: Genome wide analysis of gene expression in SK-N-BE(2)-C cells after treatment with vorinostat (SAHA)

status: Public on Apr 23 2021

city: Heidelberg

first: Johannes

last: Ridinger

address: Im Neuenheimer Feld 280

department: CCU Pediatric Oncology

country: Germany

institute: German Cancer Research Center

summary: Analysis of gene expression changes after treatment of neuroblastoma cell line SK-N-BE(2)-C afer 24h and 6d treatment with vorinostat to check for changes in expression of genes regulating autophagy

overall_design: total RNA was isolated from SK-N-BE(2)-C cells treated with DMSO or vorinostat for 24h and 6d respectively.

first: Ina

last: Oehme

first: Olaf

last: Witt

first: Andreas

last: Schober

first: Inga

last: Rettig


title: Construction of a Mammalian Embryo from Embryonic Stem Cells Instructed by Morphogen Gradients

status: Public on Apr 25 2021

city: Charlottesville

first: Bernard

middle: Victor

last: Thisse

state: VA

address: 1340 Jefferson Park ave

department: Cell Biology

institute: University of Virginia

summary: Generating properly organized and differentiated embryonic structures in vitro from aggregates of pluripotent cells remains a major challenge. In a living embryo, the interplay in between signaling molecules known as morphogens and their antagonists lead to gradients of activity that instruct cells about their fate, leading to patterning and morphogenesis. Here we show that experimentally engineering a morphogen signaling center within an aggregate of mouse pluripotent stem cells is sufficient to mimic the function of an embryo organizer and to trigger embryonic development. The resulting embryoids are remarkably well patterned along anterior-posterior and dorsal-ventral axes, generate three germ layers through a process of gastrulation and differentiate germ layer derivatives (including notochord, vasculature, neural tube, neural crest, endoderm) similar to an authentic embryo at E9-E9.5.

overall_design: Trancriptome of pools of 12 Embryoids were compared to the ones of pool of 12 controls (aggregates of embryonic stem cells not instructed by a morphogen signaling center)  7 days (D7) or 8 days (D8)  after aggregation of stem cells (from the E14TG2a line) in hanging drops. Triplicates were analyzed for each experimental condition.

first: Jonathan

last: Fillatre

first: Ricardo

last: Morales-Borges

first: Jinwoo

last: Lee

first: Christine


title: Global Profiling of RNA-Binding Protein Target Sites by LACE-seq

first: Yuanchao

last: Xue

address: Datun Road #15

department: Institute of Biophysics

institute: Chinese Academy of Sciences

summary: RNA-binding proteins (RBPs) have essential functions during germline and early embryo development. However, current methods are unable to identify the in vivo targets of an RBP in those rare cells. Here, by coupling RBP-mediated reverse transcription termination with linear amplification of cDNA ends and sequencing, we present the LACE-seq method for identifying RBP-regulated RNA networks at or near the single-oocyte level. We determined the binding sites and regulatory mechanisms for several RBPs, including Argonaute 2 (Ago2), Mili, Ddx4, and PTBP1, in mature oocytes. Unexpectedly, transcriptomic and proteomic analysis of Ago2-/- oocytes revealed that Ago2 interacted with endogenous small interfering RNAs (endo-siRNAs) to repress mRNA translation globally. Furthermore, the Ago2 and endo-siRNA complexes could fine-tune the transcriptome by slicing long terminal repeat retrotransposon-derived chimeric transcripts. The precise mapping of RBP binding sites in a few cells opens the door for studying the roles of RBPs in embryonic development and reproductive diseases.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
We first developed a linear amplification of cDNA ends and sequencing (LACE-seq) methodology to identify RBP targets at or near the single-cell level. Next, we determined the binding sites for several RBPs, including Argonaute 2 (Ago2), MILI, Ddx4, and PTBP1 (also known as PTB) in single or dozens of fully-grown mouse oocytes. Two biological repeats, labeled as Rep 1 and Rep 2, were generated for each sample. For measuring Ago2 regulated genes in fully-grown oocytes, we also performed single-cell RNA-seq analysis on five control and Ago2-null oocytes. To identify endo-siRNAs loaded into Ago2, we performed single-cell CAS-seq using Ago2 immunoprecipitated small RNAs from MII oocyte and labeled as Ago2_IP_Oocyte. To evaluate the specificity of LACE-seq, we performed Ago2 LACE-seq in oocytes from Ago2 conditional knockout (cKO) mice and PTBP1 LACE-seq in K562 cells treated with PTBP1 shRNA.
RNA-seq analysis of Meiosis II oocytes from Ago2 cKO (Ago2 loxP/loxP,Zp3-cre) and Control(Ago2 loxP/+) female mice.

first: Ruibao

last: Su

first: Lihua

last: Fan

first: Changchang

first: Lei


title: HOXA13 in etiology and oncogenic potential of Barrett’s esophagus

first: Vincent

last: Janmaat

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

overall_design: Refer to individual Series


title: Gene expression profiles in mouse hepatocytes

status: Public on Apr 26 2021

city: Sapporo

first: Norihisa

last: Ichinohe

state: Hokkaido

address: South-1, West-17, Chuo-ku,

department: Department of Tissue Development and Regeneration

country: Japan

institute: Sapporo Medical University School of Medicine

summary: Hepatocytes consist of subpopulations namely mature hepatocytes and small hepatocytes. Alhtough they have differet proliferative capabiliary in vitro, the difference between two populations has not been examined by transcrptome.

overall_design: Idenfitication for heterogenity of adult mouse hepatocytes

first: Naoki

last: Tanimizu

first: Yasushi

last: Sasaki


title: Nitrogen starvation-responsive microRNAs are affected by transgenerational stress in durum wheat seedlings

status: Public on Apr 21 2021

city: Urrbrae

first: Haipei

last: Liu

state: South Australia

address: PMB1 Waite Building, School AFW

country: Australia

institute: The University of Adelaide

type: Non-coding RNA profiling by high throughput sequencing

summary: Stress events have transgenerational effects that influence plant growth in the subsequent generation. In Mediterranean regions, water-deficit and heat (WH) stress is a frequent issue that negatively affects crop yield and quality. Nitrogen (N) is an essential plant macronutrient and often a yield-limiting factor for crops. Here, the response of durum wheat seedlings to N starvation under the transgenerational effects of WH stress were investigated in two genotypes. Both genotypes showed significant reduction in seedling height, leaf number, shoot and root weight (fresh and dry), primary root length and chlorophyll content under N starvation stress. However, in the WH stress-tolerant genotype, the reduction rate of most traits were lower in progeny from the stressed parents than progeny from the control parents. Small RNA sequencing identified 1,534 microRNAs in different treatment groups. Differentially expressed microRNAs (DEMs) were characterized subject to N starvation, parental stress and genotype factors, with their target genes identified in silico. GO and KEGG enrichment analyses revealed the biological functions associated with DEM-target modules in stress adaptation processes, which could contribute to the phenotypic differences observed in two genotypes. The study provides the first evidence of the transgenerational effects of WH stress on N starvation response in durum wheat.

overall_design: Analysis of small RNA transcriptome in eight biological pools (two genotypes by two parental treatment by two progeny treatment)

first: Amanda

middle: J

last: Able

first: Jason

middle: A


title: Transcriptome profiling of miR-541 kd mouse cortical cells

status: Public on Apr 22 2021

city: Pisa

first: Federico

last: Cremisi

address: Piazza dei Cavalieri, 7

department: Science

country: Italy

institute: Scuola Normale

summary: Using an in vitro model of mouse corticogenesis from mouse embryonic stem cells  (ESCs), we investigated the gene expression changes exerted by the inactivation of the Eutherian-specific microRNA miR-541. The microRNA mmu-miR-541-5p was inhibited by the transfection of an antago-miR into  ESC-progenitors at 12 days of in vitro differentiation  (DIV12) and and the cell transcriptome of transfected cells was compared to the transcriptome of control-transfected cells 5 days after transfection (DIV17). The comparison between control and miR-541 kd cells highlighted  classes of differentially expressed genes related to axon elongation and neural development GO terms.

overall_design: Transcriptome datasets of mouse embryonic cortical cells transfected with antago-miR against mmu-miR-541-5p or with control antago-miR

first: Manuella

last: Martins

first: Silvia

last: Galfrè

first: Marco

last: Terrigno

first: Luca

last: Pandolfini

first: Irene

last: Appolloni

first: Keagan

last: Dunville

first: Andrea

last: Marranci

first: Milena

last: Rizzo

first: Alberto

last: Mercatanti

first: Laura

last: Poliseno

first: Francesco

last: Morandin

last: Pietrosanto

first: Manuela

last: Helmer-Citterich

first: Paolo

last: Malatesta

first: Robert

last: Vignali


title: MicroRNA expression in a model of mouse corticogenesis

summary: We established an in vitro model of mouse corticogenesis starting from mouse embryonic stem cells  (ESCs). We analyzed miRNAomes of dividing and post-mitotic ESC-cortical cells and miRNAomes of E12 and P0 mouse cortex.  By comparing  the microRNA expression profiles of  progenitors and precursors at different times of  in vitro differentiation to the microRNA expression profiles of E12 and P0 mouse cortex we validated the model of mouse in vitro corticogenesis and provided  microRNA expression datasets of  early mouse embryonic cerebral cortex. Moreover, by the miR-CATCH method we analyzed the enrichement of microRNAs after the binding to the 3’UTR of Satb2. This allowed  to identify microRNAs that directly inhibit SATB2 expression.

overall_design: miRNAomes of developing mouse cortex, cortical progenitor and precursor cells, and Satb2-interacting miRNAs.


title: Skin and gut imprinted T helper cell subsets exhibit distinct functional phenotypes in central nervous system autoimmunity

city: Munich

first: Thomas

last: Korn

state: Bavaria

address: Ismaninger Str. 22

department: Neurology

institute: Technical University of Munich

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We developed an experimental framework to probe the idea that the site of priming in the systemic immune compartment is a determinant of T helper cell-induced immunopathology in remote organs. By site-specific in vivo labeling of antigen-specific T cells in inguinal (i) or gut draining mesenteric (m) lymph nodes, we show that i-T cells and m-T cells isolated from the inflamed central nervous system in a model for Multiple Sclerosis are distinct.

overall_design: Comparison of DNA accessibility by Omni-ATAC-seq in sorted effector i- and m-T cells (mD2RED CD4+ CD44high) and naive i- and m-T cells (mD2RED CD4+ CD44int) from spleen.

first: Michael

last: Hiltensperger

first: Gildas

last: Lepennentier

first: Helena

middle: D

last: Moreno


title: Single-cell RNA-sequencing of mouse embryoids at Day 8

first: Bernard

last: Thisse

address: 1340 Jefferson Park Avenue

summary: Generating properly organized and differentiated embryonic structures in vitro from aggregates of pluripotent cells remains a major challenge to overcome. In the living embryo, the interplay between morphogens and their antagonists set up gradients of activity that instruct cells about their fate, leading to patterning and morphogenesis. Here we show that experimentally engineering a morphogen signaling center within an aggregate of mouse pluripotent stem cells is sufficient to mimic in vitro the function of an embryo organizer and to trigger embryonic development. The resulting embryoids are extensively patterned along their anterior-posterior and dorsal-ventral axes, with formation of three germ layers through a process of gastrulation and differentiation of germ layer derivatives similar to those of a neurula-stage mouse embryo.

overall_design: Dissociated cells from a pool of 90 embryoids at Day 8 of development fixed in methanol.

first: Peng-fei

last: Xu

first: Ricardo

last: Moraes Borges

first: Jonathan

last: Fillatre

first: Christine


title: Gene expression dynamics underlying cell fate emergence in 2D micropatterned human embryonic stem cell gastruloids

city: St Louis

first: Kyaw Thu

last: Minn

address: 1 Brookings Drive

institute: WUSTL

summary: We applied BMP4 to circular micropattern cultures to differentiate human embryonic stem cells (H1 hESCs) into microcolonies termed ‘gastruloids’, comprising germ layer and extraembryonic cells. Time-course single cell RNA-sequencing was performed at 0h (immediately before BMP4 treatment), 12h, and 24h after BMP4 treatment. Combining these 0h, 12h, and 24h datasets with previously generated 44h datasets, we report transcriptomic dynamics over the course of BMP4-driven differentiation in micropatterned cultures.

overall_design: Single-cell RNA sequencing was performed on gastruloid cells differentiated from H1 hESCs at 0h (immediately before BMP4 treatment), 12h, and 24h of BMP4 treatment.

first: Sabine

last: Dietmann

first: Samantha

last: Morris


title: Gene expression profiling of Smad1/5 cKO and Acvr2a cKO mice

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: We generated mice with single or double conditional inactivation of SMAD1 and SMAD5 using progesterone receptor (PR) cre (Smad1flox/flox;Smad5flox/flox;Pgr-cre+/-, or “Smad1/5 cKO”). Female mice with single SMAD1 or SMAD5 deletion were subfertile, whereas Smad1/5 cKO were infertile and had no visible implantation sites at 4.5 days post-coitum (dpc), indicating functional redundancy of SMAD1 and SMAD5. Histological and molecular analyses of the Smad1/5 cKO uteri during pregnancy determined that the infertility was the result of impaired uterine receptivity. During the window of implantation, uteri of Smad1/5 cKO mice responded abnormally to estradiol (E2) and to progesterone (P4), retained luminal PR expression, and displayed cytoplasmic FOXO1 mis-localization. Furthermore, uteri of Smad1/5 cKO mice did not respond to an artificial decidual stimulus and the stroma failed to differentiate. To determine the cell surface receptor complex that controls BMP signaling during implantation, we generated mice with conditional deletion of Acvr2a and Acvr2b using Pgr-cre+/-. We determined that Acvr2b cKO females were subfertile, while Acvr2a cKOs were infertile and displayed a range of ovarian and uterine abnormalities, including endometrial and implantation defects that phenocopied those of Smad1/5 cKO mice. Transcriptomic profiling of the Smad1/5 cKO and Acvr2a cKO uterus showed that genes involved in epithelial cell remodeling and microvilli/ciliated cell function were overrepresented in both genotypes. These results demonstrate that BMP signals mediated via ACVR2A and SMAD1/5 control endometrial receptivity and embryo implantation by remodeling the apicobasal polarity of the epithelium during the window of implantation.

overall_design: Multiple group comparison

first: Fengju

last: Chen

first: Diana

last: Monsivais

first: Martin

last: Matzuk


title: m6A RNA methylation of major satellite repeat transcripts facilitates chromatin association and RNA:DNA hybrid formation in mouse heterochromatin

city: Freiburg im Breisgau

first: Galina

last: Erikson

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

overall_design:
Analysis of m6A-modified transcripts in mouse embryonic stem cells (mutants for Mettl3, Mettl14 and corresponding wild types)

Analysis of gene expression in mouse embryonic stem cells (mutants for Mettl3, Mettl14 and corresponding wild types)

first: Katarzyna

last: Duda

last: Jenuwein


title: Conservation and divergence of vulnerability and responses to stressors between human and mouse astrocytes

city: Los Angeles

first: Jiwen

last: Li

address: 635 Charles E. Young Dr. S.

institute: UCLA

summary: Astrocytes were purified from mouse cortices and human cortex tissue by immunopanning with HepaCAM. All treatments were proceeded on 3DIV in serum-free medium. Astrocytes were treated by TNFα for 48hr, by Poly I:C for 72hr, or by hypoxia for 72hr. Acutely purified atrocytes RNA was harvest immediately after HepaCAM immunopanning. Serum selected astrocytes RNA was collected after 4-6 days culturing in serum medium. Serum-free cultured astrocytes RNA was collected on 5-6 DIV. Serum-selection purified human astrocytes were transplanted into P2-11 Rag2 immunodeficient mouse brains, and after about 8 months, transplanted human and host mouse astocytes RNA was collected acutely on HepaCAM immunopanning dish.

overall_design: For each kind of treatments and relative controls, there are four patient samples. Six TNFα treated mouse samples and six relative control samples. Four Poly I:C treated mouse samples and four relative control samples. Four hypoxia treated mouse samples and four relative control samples. There are four acutely purified human samples from four patients, three serum selected human astrocyte samples from three patients, and five serum-free cultured samples from five patients.. Three transplanted human samples from three patients and three mouse host samples.

first: J

first: Y

last: Zhang


title: GATA3 Cut and Run in naïve human T cells

status: Public on Apr 20 2021

city: London

first: Paul

last: Lavender

address: 5th Floor, Tower Wing, Great Maze Pond

department: School of Immunology and Microbial Sciences

country: United Kingdom

institute: King's College London

overall_design: Naïve human T cells

first: Audrey

last: Kelly


title: Blood RNA signature RISK4LEP predicts leprosy years before clinical onset

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

institute: Leiden University Medical Center

summary: Exploratory RNA expression analysis during development of leprosy allows identification of RISK4LEP, a 4-gene blood RNA signature predicting leprosy years before clinical onset.

overall_design: Comparison of blood transcriptomics in leprosy progressors before symptoms (First), at diagnosis (Second) and household contact controls (HHC)

first: Maria

last: Tió-Coma

first: Szymon

middle: M

last: Kiełbasa

first: Annemieke

last: Geluk


title: Effect of N1-acetylspermidine treatment on the translatome of hair follicle stem cell organoid cultures

city: Cologne

first: Franziska

last: Metge

address: Joseph-Stelzmann-Str 9b

department: Bioinformatics Corefacility

institute: Max Planck Institute for Biology of Ageing

summary: Stem cell differentiation has been shown to involve an increase in mRNA translation. Amongst others, the rate of translation is influenced by availability of the natural polyamines putrescine, spermidine, and spermine that are essential for cell growth and modulate stem cell maintenance. However, the link between polyamines and translation in cell fate decisions remains obscure. Here, we used hair follicle stem cell (HFSC) organoids to study the role of polyamines as key regulators of mRNA translation in stem cell fate decisions. HFSCs showed lower translation and reduced polyamine levels than progenitor cells. Surprisingly, we found that reduced translation achieved by changed polyamine availability and stemness do not correlate in the organoids. We identified N1-acetylspermidine as regulator of cell fate decisions. To investigate the effect on translation upon N1-AcSpd supplementation, we performed ribosome foot pronting. We confirmed the increase in proliferation identified by 3'RNA-sequencing on the translatome level. N1-AcSpd treatment partially aligns the translatome of progenitor cells to that of HFSCs. Overall, this study delineates the diverse routes of polyamine metabolism-mediated regulation of stem cell fate decisions.

overall_design: RNA-Seq / Ribo-Seq of sorted HFSC organoids (alpha6+CD34- and alpha6+CD34+ cells), 8 samples, 2 biological replicates, untreated and treated with N1-acetylspermidine for 72h, samples for Ribo-Seq and RNA-Seq were obtained from the same lysis

first: Kira

last: Allmeroth

first: Maxime

last: Derisbourg

last: Denzel


title: Global analysis of RNA-dependent RNA Polymerase-dependent small RNAs reveals new substrates and functions for these proteins and SGS3 in Arabidopsis

city: Philadelphia

first: Xia

last: Hua

state: PA

address: 433 S University Ave

institute: University of Pennsylvania

summary: In plants, smRNAs are often derived from long double-stranded RNA (dsRNA) molecules synthesized by one of the six genomically-encoded RNA-dependent RNA Polymerase (RDR) proteins. However, the full complement of the RDR-dependent smRNAs and functions that these proteins and their RNA-binding co-factors play in plant RNA silencing has not been fully uncovered. To address this gap, we performed a global genomic analysis of all six RDRs and two of their co-factors to find new substrates for RDRs and targets of the resulting RDR-derived siRNAs to uncover new functions for these proteins in plants. Based on these analyses, we identified substrates for the three RDR clade proteins (RDR3 - 5), which had not been well-characterized previously. We also identified new substrates for the other three RDRs (RDR1, 2, and 6) as well as the RDR2 co-factor RNA-DIRECTED DNA METHYLATION 12 (RDM12) and the RDR6 co-factor SUPRESSOR OF GENE SILENCING 3 (SGS3). These findings revealed that the target substrates of SGS3 are not limited to those solely utilized by RDR6, but that this protein seems to be a more general co-factor for the RDR family proteins. Additionally, we found that RDR6 and SGS3 are involved in the production of smRNAs that target transcripts related to abiotic stresses including water deprivation, salt stress, and ABA response, and as expected the levels of these mRNAs are increased in rdr6 and sgs3 mutant plants. Correspondingly, plants that lack these proteins (rdr6 and sgs3 mutants) are hypersensitive to ABA treatment, tolerant to high levels of PEG8000, and have higher survival rate under salt treatment in comparison to wild-type (Col-0). In total, our analyses have provided an extremely data-rich resource for uncovering new functions of RDR-dependent RNA silencing in plants, while also revealing a previously unexplored link between the RDR6/SGS3-dependent pathway and plant abiotic stress responses.

overall_design: Small RNA sequencing (15 bp-50 bp) and toal RNA sequencing in T-DNA knockout mutants of six RDRs, SGS3, and RDM12 in Arabidopsis thanliana 30 days unopened flower buds

first: Nathan

last: Berkowitz

first: Matthew

middle: R

last: Willmann

first: Xiang

last: Yu

first: Eric

last: Lyons

first: Brian

last: Gregory


title: Validation of protein arginine methyltransferase 5 (PRMT5) as a candidate therapeutic target in the spontaneous canine model of non-Hodgkin lymphoma [ATAC-seq]

city: Columbus

first: Ayse

middle: Selen

last: Yilmaz

state: OH

address: 1800 Cannon Drive

department: Biomedical Informatics

institute: OSU

summary: Targeting PRMT5 in canine lymphoma: we characterized expression patterns of PRMT5 in canine lymphomas and correlated these with histological subtypes using tissue microarrays. We characterized expression of PRMT5 in three canine lymphoma-derived cell lines and primary lymph node biopsies. We have demonstrated that inhibition of PRMT5 leads to growth suppression and induction of apoptosis in canine lymphoma cell lines and primary canine lymphoma cells in a time and dose-dependent manner, while selectively decreasing global marks of symmetric dimethylarginine (SDMA) and histone H4 arginine 3 symmetric di-methylation. We performed ATAC-sequencing with pathway enrichment analysis to characterize genome-wide changes in chromatin accessibility after PRMT5 inhibition. We performed gene expression microarrays with pathway analysis to characterize whole transcriptome changes in canine lymphoma cell lines treated with PRMT5 inhibitors. This work validates PRMT5 as a promising therapeutic target for canine lymphoma and supports the continued used of the spontaneously occurring canine lymphoma model for the preclinical development of PRMT5 inhibitors for the treatment of human NHL.

overall_design: ATAC-sequencing was performed on the canine B-cell lymphoma cell lines CLBL-1 and 17-71 after treated with 100 nM of PR220, a selective protein arginine methyltransferase (PRMT5) inhibitor.

first: Shelby

middle: L

last: Sloan

middle: S

first: Hatice

middle: G

last: Ozer

first: William

middle: C

last: Kisseberth

first: Robert

last: Baiocchi


title: Gray but not white matter astroglia-specific connexin 43 ablation ameliorates neuroinflammation

city: Fukuoka

first: Ryo

last: Yamasaki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-Ku

institute: Kyushu University


title: Effect of flg22 peptide over transcriptome and nucleosome landscape of Arabidopsis on Col-0 and chromatin remodelling ATPase EDA16 mutants

city: Paris

first: Lorenzo

last: Concia

email: colore@gmail.com, concia@bio.ens.psl.eu

address: 46 Rue d'Ulm

department: Institut de Biologie

country: France

institute: École Normale Supérieure

summary: Activation of plant immunity by bacterial MAMPs such as flg22 affects nucleosome positioning over thousands of loci and is correlated with the transcription of immune-related genes. Data for chromatin remodelling ATPase EDA16 truncated and over-expressor mutants as well as Col-0 (control) are provided.

overall_design: 2-week-old seedlings were treated with 100 nM flg22 or mock-treated for 2 hours. Material was frozen and ground in liquid nitrogen splitting sample into 2 batches; one for RNA-seq and one for MNase-seq. Col-0, eda16-OE (SAIL_40_F09) and eda16-∆Hc (SAIL_735_G06) seedlings were used. This experiment was carried out in duplicate with 24 samples in total (12 samples for RNA-seq and 12 samples MNase-seq). Samples single-end sequenced with NextSeq 500 Illumina sequencer

first: Alonso

last: Pardal

first: Sophie

last: Piquerez

first: Moussa

last: Benhamed

first: Vardis

last: Ntoukakis


title: Gray but not white matter astroglia-specific connexin 43 ablation ameliorates neuroinflammation [Affymetrix]

summary: Objective: We previously reported that white matter connexin43 (Cx43) may related to the severity of the multiple sclerosis (MS), whereas the role of gray matter Cx43 in demyelinating disease is unknown. It was considered MS lesions were only exist in white matter, but recent studies revealed that demyelinating lesions are also exist in the cerebral cortex. This fact suggest the possibility that gray matter is somewhat related to the pathophysiology of MS. In this study, we aimed to clarify the role of gray matter Cx43 in a mouse model of MS (experimental autoimmune encephalomyelitis [EAE]).  Methods: We developed Cx43F/F;Glutamate aspartate transporter (GLAST)-CreER(T2)KI/+ mice as gray matter specific Cx43 conditional knock-out (Cx43cKO) mice. We induced MOG-EAE 10 days after tamoxifen injection, and analyze its clinical course and pathology. We used Cx43F/F mice as controls.  Results: EAE was significantly milder in gray matter astrocyte-specific Cx43cKO mice from acute phase to chronic phase, as compared with control mice. Pathology demonstrated less demyelinating lesions and infiltrating cells. Infiltrating immune cells did not express Cx43 in the active demyelinating lesions of the lumbar cord in both groups. The expression level of Cx43 was similar between these two groups in the spleen and the inguinal lymph nodes.  Interpretation: Acute KO of gray matter specific Cx43 before induction of EAE reduce its aggressiveness. This finding may suggest the possibility that gray matter Cx43 modify the MS pathophysiology.

overall_design: We used connexin 43 inducible conditional knockout-mice to see the difference in disease severity of EAE with or without the white matter connexin 43. MG_Cx43_f_f_pre_signal means isolated-microglial samples from control mice without immunization. MG_Cx43_icKO_pre_signal means isolated-microglial samples from Cx43 icKO mice without immunization. MG_Cx43_f_f_acute_signal means isolated-microglial samples from control mice in the acute phase of the disease. MG_Cx43_icKO_acute_signal means isolated-microglial samples from Cx43 icKO mice in the acute phase of the disease.

first: Hayato

last: Une


title: Validation of protein arginine methyltransferase 5 (PRMT5) as a candidate therapeutic target in the spontaneous canine model of non-Hodgkin lymphoma [array]

overall_design: RNA was isolated from the canine B-cell lymphoma cell lines CLBL-1 and 17-71 after treated with 100 nM of PR220, a selective protein arginine methyltransferase (PRMT5) inhibitor. Whole transcriptome profiling was preformed using Affymetrix microarrays to evaluate changes in gene expression after PRMT5 inhibition.


title: The combined action of CTCF and its testis-specific paralog BORIS is essential for spermatogenesis

city: Washington

first: Samuel

last: Rivero-Hinojosa

state: District of Columbia

address: 111 Michigan Ave NW

department: Children’s Research Institute, Center for Cancer and Immunology Research

institute: Children’s National Health System

summary: CTCF is a key organizer of the 3D genome. Its specialized paralog, BORIS, heterodimerizes with CTCF but is expressed only in male germ cells and in cancer states. Unexpectedly, BORIS-null mice have only minimal germ cell defects. To understand the CTCF-BORIS relationship, mouse models with varied CTCF and BORIS levels were generated. Whereas Ctcf+/+Boris+/+, Ctcf+/-Boris+/+, and Ctcf+/+Boris-/- males are fertile, Ctcf+/-Boris-/- (Compound Mutant; CM) males are sterile. Testes with combined depletion of both CTCF and BORIS show reduced size, defective meiotic recombination, increased apoptosis, and malformed spermatozoa. Although CM germ cells exhibit only 25% of CTCF WT expression, chromatin binding of CTCF is preferentially lost from CTCF-BORIS heterodimeric sites. Furthermore, CM testes lose the expression of a large number of spermatogenesis genes and gain the expression of developmentally inappropriate genes that are “toxic” to fertility. Thus, a combined action of  CTCF and BORIS is required to both repress pre-meiotic genes and activate post-meiotic genes for a complete spermatogenesis program.

overall_design: Genome-wide mapping of CTCF and BORIS sites and mRNA expression profiles in Ctcf (+/+)Boris(+/+),  Ctcf (+/-)Boris(+/+),  Ctcf +/+Boris(-/-), and Ctcf (+/-)Boris(-/-) [also called 'DKO' or 'CM'] mouse whole testes, round spermatids , and spermatocytes

first: Elena

last: Pugacheva

first: Victor

last: Lobanenkov


title: Gray but not white matter astroglia-specific connexin 43 ablation ameliorates neuroinflammation [Agilent]

summary:
Objective: We previously reported that white matter connexin43 (Cx43) may related to the severity of the multiple sclerosis (MS), whereas the role of gray matter Cx43 in demyelinating disease is unknown. It was considered MS lesions were only exist in white matter, but recent studies revealed that demyelinating lesions are also exist in the cerebral cortex. This fact suggest the possibility that gray matter is somewhat related to the pathophysiology of MS. In this study, we aimed to clarify the role of gray matter Cx43 in a mouse model of MS (experimental autoimmune encephalomyelitis [EAE]).
Methods: We developed Cx43F/F;Glutamate aspartate transporter (GLAST)-CreER(T2)KI/+ mice as gray matter specific Cx43 conditional knock-out (Cx43cKO) mice. We induced MOG-EAE 10 days after tamoxifen injection, and analyze its clinical course and pathology. We used Cx43F/F mice as controls.
Results: EAE was significantly milder in gray matter astrocyte-specific Cx43cKO mice from acute phase to chronic phase, as compared with control mice. Pathology demonstrated less demyelinating lesions and infiltrating cells. Infiltrating immune cells did not express Cx43 in the active demyelinating lesions of the lumbar cord in both groups. The expression level of Cx43 was similar between these two groups in the spleen and the inguinal lymph nodes.
Interpretation: Acute KO of gray matter specific Cx43 before induction of EAE reduce its aggressiveness. This finding may suggest the possibility that gray matter Cx43 modify the MS pathophysiology.

overall_design: We used connexin 43 inducible conditional knockout-mice to see the difference in disease severity of EAE with or without the white matter connexin 43. Cx43F_F means control mice brain sample without deletion of Cx43 expression. Cx43cKO means Cx43 depleted mice. 1 means pre-immunized, 2 means the onset phase of the disease, and 3 means the peak stage of the disease.


title: Profiling the inflammatory signatures of bulk MC38, Pan02 and KPC tumors from wild-type mice and Sirpα-KO mice before and after radiation therapy

status: Public on Apr 19 2021

city: Atlanta

first: zhen

last: bian

state: Georgia

address: Department of Biology, 161 Jesse Hill Jr. Dr

institute: Georgia State University

summary: The inflammatory gene expression profile in MC38, Pan02 and KPC tumors from wild-type mice and Sirpα-KO mice before and after radiation was analyzed by nCounter Analysis System using nCounter Mouse Immunology kit including 561 immunology-related mouse genes .

overall_design: MC38, Pan02 or KPC tumors (sizes 250-300mm3) in wild-type mice and Sirpα-KO mice were treated with a fraction of 8Gy X-ray radiation. Tumors were resected 12h  and 18h post irradiation (n=2 mice per time point), followed by isolation of total RNA. RNA samples of the two time points were pooled and analyzed with Nanostring nCounter assays. Therefore, each set of Nanostring data represents transcription profile of four RNA samples (four mice).

first: Zhen

last: Bian

first: Yuan

last: Liu


title: CD27hiCD38hi plasmablasts are activated B cells of mixed origin with distinct function [Smart-seq]

status: Public on Apr 16 2021

city: Singapore

first: Jinmiao

last: Chen

address: 8a Biomedical Grove

department: SigN

country: Singapore

institute: A*STAR

summary: Using Smart-seq2 single cell sequencing we reported that plasmablasts from dengue-infected individuals separate into 4 distinct clusters with distinct function.

overall_design:
DEG analysis from single-cell sorted Plasmablasts (CD19+IgD-CD27hiCD38hi) from 7 patients with primary or secondary dengue infection.

**Submitter declares that the raw data were deposited in the European Genome-phenome Archive (EGA ID EGAS00001005258) due to patient privacy concerns.**

first: Angeline

last: Rouers

first: Katja

last: Fink

first: Raman

last: Sethi


title: CD27hiCD38hi plasmablasts are activated B cells of mixed origin with distinct function [10X Genomics]

summary: Using 10X Genomics we identified B cells with a plasmablasts signature (based on CD38, CD27 and PRDM1 expression) and extract these cells to assign them to our Smart-seq analysis run in parallel.

overall_design:
Gene expression in plasmablasts from 2 dengue-infected patients (1 primary and 1 secondary).

**Submitter declares that the raw data are being deposited in the European Genome-phenome Archive (EGA ID EGAS00001005258) due to patient privacy concerns.**


title: CD27hiCD38hi plasmablasts are activated B cells of mixed origin with distinct function

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

overall_design: Refer to individual Series


title: Tracing the origin of hair follicle stem cells

city: Chuo-ku, Kobe

first: Hironobu

last: Fujiwara

address: 2-2-3 Minatojima-minamimachi

department: Center for Biosystems Dynamics Research

institute: RIKEN

summary: The scRNA-seq data are an integral part of the manuscript with the above title. Using a photo-labelling technique and RamDA-seq as described in the overall design, we obtained accurate scRNA-seq data from developing hair follicles (HFs), reflecting the spatiotemporal dynamics of cellular state transition during HF morphogenesis. Single cell transcriptome analysis identified cell types, which cannot be distinguished by known makers, their signature markers, and transcriptional state changes in developing HFs. By integration of the data from single cell live imaging, our findings revealed the origin and developmental trajectories of tissue stem cells (SCs), leading to a new model of HF development and SC induction with unprecedented resolution.

overall_design:
Embryonic skin tissues contain a mix of different HF types at different developmental stages, rendering separation and transcriptional profiling of HFs at specific developmental stages difficult. We thus developed a transgenic mouse line expressing a photo-convertible fluorescent protein, nuclear Kikume Green-Red, which enables identification and photo-labelling of target HFs under a confocal microscope. Entire single whisker HFs at E12.0, E13.0, E13.5, E14.0, E15.0, and E17.0 were photo-converted. Basal epidermal cells of each photo-labelled HF (E12.0–E17.0, ITGA6+/CD31-/kikGR-red+ cells; E11.5, ITGA6+/CD31- cells) were isolated as single cells by FACS. All scRNA-seq libraries were constructed for RamDA-seq, a novel sensitive and accurate total scRNA-seq method. We obtained single cell full-length total RNA sequencing of developing whisker HFs as follows: E11.5, 94 cells; E12.0, 280 cells; E13.0, 276 cells; E13.5, 189 cells; E14.0, 183 cells; E15.0, 362 cells; E17.0, 282 cells (total: 1,666 single cells).

Please note that total 1,666 samples were included in the data analysis, however, the processed data file contains only 1614 data columns due to low-quality samples (indicated as the sample 'characteristics: data quality = low').

first: Ritsuko

last: Morita

first: Tetsutaro

last: Hayashi

first: Mana

last: Umeda

first: Mika

last: Yoshimura

first: Itoshi

last: Nikaido


title: Genome-wide analysis of gene expression profiles were conducted under different salt and drought stresses of Chlorella sp. TLD6B

city: Shihezi

first: Hong

last: Li

state: Xinjiang

address: Beisi road

department: School of Pharmacy

institute: Shihezi University

summary: By applying Illumina Novaseq 6000, Chlorella sp. TLD6B cells of the control group on day zero and 18, as well as under low salt stress (NaCl1) and under high salt stress (NaCl2) on day 18 were selected for transcriptome sequencing analysis. Meanwhile, 0.05 g/mL ( PEG1) and 0.1 g/mL PEG-6000 (medium for drought stress, PEG2 ) were used to prepare the drought-stressed Chlorella sp. TLD6B cells. Each treatment had two replicates. Clean data were filtered after the removal of adapters, poly-N strands, and low-quality reads. There were no reference genomes for Chlorella sp. TLD6B, and de novo assembly for clean reads was performed by using Trinity. The sequences were compared with databases such as NR, NT, Swiss-Pro, GO, KEGG, PFAM, and KOG using Blast X (e-value ≤ 10-5). The GO annotation of unigenes was obtained using BLAST2GO. FPKM method was used for the analysis of gene expression levels (Trapnell et al., 2010). Out of six samples, a total of 963,078,184 raw reads were generated. A total of 947,225,244 clean reads were obtained based on the base quality score and read length. Meanwhile, the GC percentage in clean reads reached nearly 66.0%, with Q20 being above 96%. A total of 219,577 transcripts with an average length of 1,394 bp were obtained. In total, 155,503 non-redundant unigenes were assembled for the following analyses. The length of the unigenes ranged from 200 bp to 23,825 bp, with an average length of 1,842 bp. Under different salt stress, verification had been conducted with qRT-PCR on nine unigenes of different pathways, which were related to lipid metabolism. The detection results by qRT-PCR were highly correlated with RNA-Seq results (r = 0.890, r2 = 0.791), which indicated that the RNA-Seq data of Chlorella sp. TLD6B under salt stress were accurate and reliable. Our study represents the first detailed analysis of Chlorella sp. TLD6B under salt stress transcriptomes. Hierarchical clustering of differentially expressed genes uncovered several currently uncharacterized genes that may contribute to the function about lipid accumulation of Chlorella sp. TLD6B under salt stress.

overall_design: Detection of Chlorella sp. TLD6B under salt stress and drought stress.

first: Jun

last: Tan

first: Jianfeng

last: Gao


title: Downregulation of lncRNA XR_429159.1 could promote brain metastasis in patients with limited-stage small-cell lung cancer

city: Jinan

first: Yaru

last: Tian

address: Jiyan Road

institute: Shandong Cancer Hospital

summary:
Purpose: To identify the aberrant long non-coding RNA (lncRNA) and explore the predictive value of lncRNA on the risk of brain metastases (BMs) for patients with limited-stage small cell lung cancer (SCLC).
Patients and Methods: We executed an array of lncRNA and mRNA chip assays on peripheral blood mononuclear cells of SCLC patients with BM comparing to others without BMs to identify the lncRNAs relating to BMs. Then validation was conducted in clinical data to confirm the relationship of lncRNAs and BMs furtherly. We estimated the cumulative incidence of BMs using the Kaplan-Meier method and differences between the groups were analyzed using the log-rank test.
Results: The expression of 67 lncRNAs (27 up, 40 down) and 47 mRNAs (20 up, 27 down) were different significantly in BM groups comparing to the group without BMs (fold change ≥ 2.0, p value ≤0.05) which were found by lncRNA and mRNA chip assays initially. Four lncRNAs were verified by qRT-PCR to confirm the accuracy of the microarray data and then the results of 11 pairs of patients (11 patients with BMs, while 11 patients without BMs) showed that low expression of LncRNA XR_429159.1 was the high-risk factor of BM. Further clinical data showed that the BM incidence of 25 patients with low level LncRNA XR_429159.1 was 31% at 1-year, and that was 14.3% in the 18 patients with high level LncRNA XR_429159.1, p = 0.035.
Conclusion: Our present study identified that low expression of lncRNA XR_429159.1 was the high-risk factor of BM in patients with limited-stage SCLC.

overall_design: Six SCLC patients with BMs and 6 SCLC patients without BMs

first: Ji

first: Wang

last: Jing

first: Wenxiao

last: Jia

first: Xiaoyang

last: Zhai

first: Hui

last: Zhu

first: Jinming

last: Yu


title: Myeloid Arginase 1 Insufficiency Exacerbates Amyloid-β Associated Neurodegenerative Pathways and Glial Signatures in a Mouse Model of Alzheimer's Disease: A Targeted Transcriptome Analysis

status: Public on Apr 15 2021

city: Lexington

first: Chao

last: Ma

state: KY

address: Sanders-Brown Bldg. R430, 800 S. Limestone St.

department: Department of Neuroscience

institute: University of Kentucky

summary: Brain myeloid cells, include infiltrating macrophages and resident microglia, play an essential role in responding to and inducing neurodegenerative diseases, such as Alzheimer’s disease (AD). Genome-wide association studies (GWAS) implicate many AD casual and risk genes enriched in brain myeloid cells. Coordinated arginine metabolism through arginase 1 (Arg1) is critical for brain myeloid cells to perform biological functions, whereas dysregulated arginine metabolism disrupts them. Altered arginine metabolism is proposed as a new biomarker pathway for AD. We previously reported Arg1 deficiency in myeloid biased cells using lysozyme M (LysM) promoter-driven deletion worsened amyloidosis-related neuropathology and behavioral impairment. However, it remains unclear how Arg1 deficiency in these cells impacts the whole brain to promote amyloidosis. Herein, we aim to determine how Arg1 deficiency driven by LysM restriction during amyloidosis affects fundamental neurodegenerative pathways at the transcriptome level. By applying several bioinformatic tools and analyses, we found that amyloid-β (Aβ) stimulated transcriptomic signatures in autophagy-related pathways and myeloid cells' inflammatory response. At the same time, myeloid Arg1 deficiency during amyloidosis promoted gene signatures of lipid metabolism, myelination, and migration of myeloid cells. Focusing on Aβ associated glial transcriptomic signatures, we found myeloid Arg1 deficiency up-regulated glial gene transcripts that positively correlated with Aβ plaque burden. We also observed that Aβ preferentially activated disease-associated microglial signatures to increase phagocytic response, whereas myeloid Arg1 deficiency selectively promoted homeostatic microglial signature that is non-phagocytic. These transcriptomic findings suggest a critical role for proper Arg1 function during normal and pathological challenges associated with amyloidosis. Furthermore, understanding pathways that govern Arg1 metabolism may provide new therapeutic opportunities to rebalance immune function and improve microglia/macrophage fitness.

overall_design: A total of 12 samples were analyzed from four groups of mice (nTg/Arg1+/+/LysMcreTg/+, nTg/Arg1fl/+/LysMcreTg/+, APP+/-/Arg1+/+/LysMcreTg/+, APP+/-/Arg1fl/+/LysMcreTg/+). Each group contained three biological samples representing six mice, since an equal mass of RNA from two mice were pooled and matched for genotype, gender, and age. So one pooled RNA sample represents two mice. The control samples were selected based on the required multiple comparison analysis.

first: Daniel

last: Lee


title: Validation of protein arginine methyltransferase 5 (PRMT5) as a candidate therapeutic target in the spontaneous canine model of non-Hodgkin lymphoma

first: Ayse

last: Yilmaz


title: CSF CD4+ T cells in MS

status: Public on Apr 14 2021

city: Planegg-Martinsried

first: Eduardo

last: Beltrán

state: Bayern

address: Großhaderner Str. 9

department: Institute of Clinical Neuroimmunology

institute: University Hospital, LMU Munich

summary: Single-cell transcriptome profiling of disease-related lymphocytes in patients with multiple sclerosis

first: Beltrán

last: Eduardo


title: Development of a transcriptomic biomarker to detect histone deacetylase inhibitors (HDACi) in TK6 cells

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

summary: Transcriptomic signatures, or biomarkers, of toxicity can facilitate rapid mechanistic analysis of chemicals using high-content transcriptomic data and identification of potential hazards to human health. We developed an 81-gene transcriptomic biomarker, named TGx-HDACi, to detect histone deacetylase inhibitors (HDACi) in TK6 human lymphoblastoid cells after 4 hours of chemical exposure. This work leveraged an established transcriptomic biomarker of DNA damage, TGx-DDI, which was developed by Heng Hong Li et al. (2015); TGx-DDI contains 63 genes and can distinguish between DNA damage-inducing (DDI) and non-DDI agents after 4 hours of exposure in TK6 cells. TGx-HDACi was derived from Templated Oligo-Sequencing (TempO-Seq) whole transcriptome gene expression profiles of 20 reference compounds, consisting of 10 HDACi and 10 non-HDACi compounds. Fourteen of the TGx-HDACi reference compounds are also part of the 28-compound reference set for TGx-DDI. The nearest shrunken centroid (NSC) method was applied to the gene expression profiles and 81 genes were identified that accurately identified HDACi compounds in the NSC probability analysis. The classification performance of TGx-HDACi was validated using an additional set of 11 test compounds (4 HDACi and 7 non-HDACi). Thus far, TGx-HDACi has demonstrated 100% accuracy. The availability of TGx-HDACi increases the diversity of tools that can facilitate mode of action analysis of toxicants using gene expression profiling.

sample_organism:
Homo sapiens
blank sample

platform_organism:
Homo sapiens
blank sample

overall_design: TK6 human lymphoblastoid cells were exposed to the 20 TGx-HDACi reference compounds (10 HDACi and 10 non-HDACi) and 11 validation compounds (4 HDACi and 7 non-HDACi) for 4h and whole transcriptomes were profiled using a TempO-Seq whole transcriptome kit (BioSpyder, Carlsbad, CA).  Prior to whole transcriptome profiling, range finding experiments were performed to select one concentration for each compound. TK6 cells were exposed to increasing concentrations of each chemical for 4h. Cell viability was measured at 24h (4h exposure followed by 20h recovery in media) by MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay and gene expression of three indicator genes was measured at 4h by TaqMan qPCR assays. For HDACi compounds, RGL1, NEU1, and GRP183 were used as indicators of transcriptional response to HDACi exposure at 4h. The three genes were selected based on DNA microarray profiles of TK6 cells exposed to four HDACi compounds (trichostatin A, oxamflatin, apicidin, and HC toxin) for 4h, generated in a previous study [Li et al. 2015]; the three genes had the largest fold change in expression in the four microarray profiles and were not altered by non-HDACi exposures in the study. For non-HDACi compounds, cellular stress response genes ATF3, CDKN1A, and GADD45A were used as indicators genes [Li et al. 2015]. The selected concentrations for TempO-Seq analysis induced the highest fold changes in the three indicator genes after 4h exposure, without overt cytotoxicity in the MTT assay after a 20h-recovery (less than 50% reduction in viability at 24 h).  Cells were exposed to the selected concentration of each compound on three separate occasions to generate three replicate RNA samples for each treatment.

first: Eunnara

last: Cho

first: Andrea

last: Rowan-Carroll

first: Andrew

last: Williams

first: J

last: Corton

first: Heng

middle: H

first: Albert

last: Fornace Jr.

first: Cheryl

last: Hobbs

first: Carole

last: Yauk


title: Transcriptome analysis of maize Gibberella stalk rot

status: Public on Apr 13 2021

city: Nanjing

first: wang

last: yinying

state: Jiangsu

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

department: College of Agriculture

institute: Nanjing Agricultural University

summary: Gibberella stalk rot (GSR) caused by Fusarium graminearum is one of the most devastating diseases causing significant yield loss of maize, and GSR resistance is a quantitative trait controlled by multiple genes. Although a few QTLs/resistance genes have been identified, the molecular mechanisms underlying GSR resistance remain largely unexplored. To identify potential resistance genes and to better understand the molecular mechanism of GSR resistance, a transcriptomic was conducted using two inbred lines with contrast GSR resistance, K09 (resistant) and A08 (susceptible) upon infection with F. graminearum. While substantial number of differentially expressed genes (DEGs) associated with various defense-related signaling pathways were identified between two lines, multiple hub genes likely associated with GSR resistance were pinpointed using Weighted Gene Correlation Network Analysis (WGCNA). ZmHIR3 showed strong correlation with multiple key genes.

overall_design: The RNA-seq analysis using A08 and K09 at different time points (6h,12h,24h,48h and 72h) after infection with F. graminearum.

first: Yali

last: sun

first: Xinsen

last: Ruan

first: Qing

last: Wang

first: Xiquan

last: Gao


title: Activation-induced deaminase is critical for the establishment of DNA methylation patterns prior to the germinal center reaction

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

summary: Activation-induced deaminase (AID) initiates antibody diversification in germinal center B cells by deaminating cytosines, leading to somatic hypermutation and class-switch recombination. Loss-of-function mutations in AID lead to hyper-IgM syndrome type 2 (HIGM2), a rare human primary antibody deficiency. AID-mediated deamination has been proposed as leading to active demethylation of 5-methycytosines in the DNA, although evidence both supports and casts doubt on such a role. In this study, using whole-genome bisulfite sequencing of HIGM2 B cells, we investigated direct AID involvement in active DNA demethylation. HIGM2 naïve and memory B cells both display widespread DNA methylation alterations, of which approximately 25% are attributable to active DNA demethylation. For genes that undergo active demethylation that is impaired in HIGM2 individuals, our analysis discards AID involvement. We demonstrate that the widespread alterations in the DNA methylation and expression  profiles of HIGM2 naïve B cells result from premature overstimulation of the B-cell receptor prior to the germinal center reaction. Our data support a role for AID in B cell central tolerance in preventing the expansion of autoreactive cell clones, affecting the correct establishment of DNA methylation patterns.

overall_design: RNA-Seq of Control and HIGM2 naïve and memory B cells.


title: Human Induced Pluripotent Stem Cell-derived Hepatocyte-like Cells Provide Insights on Parenteral Nutrition Associated Cholestasis in the Immature Liver

city: Milwaukee

first: Sridhar

last: Rao

state: WI

address: 8727 Watertown Plank Road

department: Blood Research Institute

institute: BloodCenter of Wisconsin

summary: Our findings provide insights into altered bile acid and lipid metabolizing processes in the immature human liver and support the use of iHLC as a relevant in vitro system for modeling the developing liver to study lipid metabolism and PNAC.

overall_design:
RNA-seq on iPSC-derived hepatocyte-like cells and fetal liver.

The adult sample is reanalysis of GSM1067795.

first: Kirthi

last: Pulakanti


title: Transcriptomic profile in the fetal cerebral cortex after maternal sevoflurane

city: Shanghai

first: Ming

last: Jiang

address: Dong'an Road 130

institute: Fudan University

summary: It has been reported that 0.75-2% of pregnant women undergo non-obstetric surgeries in the first two trimester which is the period for neurogenesis. Radial glial progenitors (RGPs) give rise to most if not all pyramidal neurons in embryonic brains. Here, we evaluated the acute alterations in RGPs after maternal sevoflurane exposure by analyzing transcriptomic profile.

overall_design: Pregant mice in sevoflurane group were exposed to 2.5% sevoflurane for six-hour while control group in 100% Oxygen on gestational day 14.5. At the end of the exposure, the fetal cerebral cortex of two groups were isolated and analyzed for RNA sequencing.

first: Tianxiang

last: Tang

first: Fang

last: Fang

first: Jing

last: Cang


title: Identification of a T-bet hi Quiescent Exhausted CD8 T Cell Subpopulation That Can Differentiate into TIM3 + CX3CR1 + Effectors and Memory-like Cells

city: Saint Louis

first: Takeshi

last: Egawa

state: MO

address: 660 South Euclid

department: Pathology and Immunology

institute: Washington University School of Medicine

summary: Persistent Ag induces a dysfunctional CD8 T cell state known as "exhaustion" characterized by PD-1 expression. Nevertheless, exhausted CD8 T cells retain functionality through continued differentiation of progenitor into effector cells. However, it remains ill-defined how CD8 T cell effector responses are sustained in situ. In this study, we show using the mouse chronic lymphocytic choriomeningitis virus infection model that CX3CR1+ CD8 T cells contain a T-bet-dependent TIM3-PD-1lo subpopulation that is distinct from the TIM3+CX3CR1+PD-1+ proliferative effector subset. The TIM3-CX3CR1+ cells are quiescent and express a low but significant level of the transcription factor TCF-1, demonstrating similarity to TCF-1hi progenitor CD8 T cells. Furthermore, following the resolution of lymphocytic choriomeningitis virus viremia, a substantial proportion of TCF-1+ memory-like CD8 T cells show evidence of CX3CR1 expression during the chronic phase of the infection. Our results suggest a subset of the CX3CR1+ exhausted population demonstrates progenitor-like features that support the generation of the CX3CR1+ effector pool from the TCF-1hi progenitors and contribute to the memory-like pool following the resolution of viremia.

overall_design: Spenocytes from 21 dpi with LCMV-c13 were sorted to obtain gp-33 specific CD8 T cells. Sorted cells were subjected to single cell RNA sequencing on the droplet based 10X Genomics platform.

first: Saravanan

last: Raju

first: Yu

last: Xia

first: Bence

last: Daniel

first: Kathryn

middle: E

last: Yost

first: Elliot

last: Bradshaw

first: Elena

last: Tonc

first: Daniel

last: Verbaro

first: Kohei

last: Kometani

first: Wayne

last: Yokoyama

first: Tomohiro

last: Kurosaki

first: Ansuman

last: Satpathy


title: Gastruloids generated without exogenous Wnt activation develop anterior neural tissues [EmbryoidsTruseq2]

status: Public on Apr 12 2021

city: Lausanne

first: Nicolas

last: Broguiere

address: AI 1208 Station 15

department: Sciences de la vie

country: Switzerland

institute: EPFL

summary: Here we describe an approach to generate gastruloids that have a more complete antero-posterior development. We used bioengineered hydrogel microwell arrays to promote the robust derivation of mouse ESCs into post-implantation epiblast-like (EPI) aggregates in a reproducible and scalable manner. These EPI aggregates break symmetry and axially elongate without external chemical stimulation. Inhibition of WNT signaling in early stages of development leads to the formation of gastruloids with anterior neural tissues.

overall_design: Testing the effect of XAV939 on the development of mouse epiblast-like aggregates.

first: Mehmet

middle: U

last: Girgin

first: Lorenzo

last: Mattolini

first: Matthias

last: Lutolf


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

city: Zurich

first: Tanja

last: Rothgangl

address: Winterthurerstrasse, 190

department: Pharmacology and Toxicology

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:
Macaca fascicularis
Homo sapiens
Mus musculus

overall_design: NGS data from >= 3 biological replicates

first: Gerald

last: Schwank


title: The SAGA complex regulates early steps in transcription via its deubiquitylase module subunit USP22

city: Philadelphia

first: Priyankara

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: SAGA is a modular cofactor complex that is essential for eukaryotic transcription. SAGA’s complement of ~20 proteins exist within four structurally and functionally distinct modules, two of which are catalytic. Within the KAT module, GCN5 acetylates histone tails, leading to increased chromatin accessibility and bromodomain protein recruitment. The DUB module contains the ubiquitin hydrolase USP22. In yeast, the USP22 ortholog deubiquitylates H2B, resulting in Pol II S2 phosphorylation and subsequent transcriptional elongation. We report here that metazoan SAGA, and USP22 specifically, are required at a more proximal stage in activator-driven transcription, i.e. pre-initiation complex (PIC) assembly. A combination of genome-wide and proteomic analyses revealed that H2B deubiquitylation is not linked to USP22-dependent transcription. Instead, USP22 controls Mediator tail subunit ubiquitylation. Mechanistically, USP22 controls loading of Mediator tail and GTFs onto promoters, with Mediator core recruitment being USP22-independent. These findings place human SAGA function at the earliest steps in activator-driven transcription.

overall_design: Hi-CHIP for H3K4me3 in USP22 wild type and knockdown conditions before and after ER stress response

first: Steven

middle: B

last: McMahon

first: Timothy

last: Stanek


title: Spatio-temporal landscape of mouse epididymal cells and specific mitochondria-rich segments defined by large-scale single-cell RNA-seq

city: Nantong

first: Hao

last: Chen

state: Jiangsu Province

address: NO.16, Wenfeng xi Road

department: Medical school

institute: Nantong University

summary: In total, 40,623 cells were detected and further clustered into 8 identified cell populations. Focused analyses revealed the subpopulations of principal cells, basal cells, clear/narrow cells, and halo/T cells. Notably, two subtypes of principal cells, the Prc7 and Prc8 subpopulations were enriched as stereocilia-like cells according to GO analysis. Further analysis demonstrated the spatially specific pattern of the DEGs in each cell cluster. Unexpectedly, the abundance of mitochondria and mitochondrial transcription (MT) was found to be higher in the corpus and cauda epididymis than in the caput epididymis by scRNA-seq, immunostaining, and qPCR validation. In addition, the spatio-temporal profile of the DEGs from the P42 and P56 epididymis, including transiting spermatozoa, was depicted.

overall_design: Five 42 days (P42) and ten 56 days (P56) old of wild-type C57Bl/6J mice were sacrified, then the epididymis were dissected and divided into three segments (caput, corpus, and cauda). Ten epididymis from five mice were cut into the different segment and immediately transferred into the GEXSCOPETM Tissue Preservation Solution (Singleron Biotechnologies) in an Eppendorf tube labeled as EP (caput), EO (corpus) and ED (cauda) on ice. For P56 epididymis, samples were two replicates. The procedure was repeated in a mice until all segments were collected in each tube. The pooled segments were further to the procedure of tissue dissociation and single cell preparation.

first: Gangcai

last: Xie


title: RNA Atlas of Bacterial Human Pathogens Uncovers Stress Dynamics Linked to Bacterial Infections

city: Umea

first: Kemal

last: Avican

address: Building 6L

department: Department of Molecular Biology

country: Sweden

institute: Umea University

summary: Pathogenic bacteria encounter a variety of stressful host environments during infection. Their responses to meet these challenges protect them from deadly damages and aid in adaption to harmful environments. Bacterial products critical for this protection are therefore interesting as suitable targets for new antimicrobials. To shed light on the complex array of molecular pathways involved in bacterial stress responses we challenged 32 diverse human pathogenic bacteria to 11 infection related stress conditions and catalogued their transcriptomes. Initial analyses of the comprehensive data set showed that beside coding RNAs, known and yet unknown putative novel ncRNAs comprise a significant part of the responses. We also computed a scores for all genes to be used for predictions for their probability to be regulated at certain stresses. The core scores enabled identification of universal stress responders representing conserved gene products involved in basic mechanisms important for responses to multiple stresses. Further, the environmental specific core scores made it possible to predict functions of yet non-characterized and also hypothetical gene products. All data are collected in the PATHOGENEX interactive RNA atlas, which is made available to the research community providing ample opportunities for discovering new aspects of regulatory networks in pathogenic bacteria as well as identification of novel players critical for bacterial infectivity and maintenance of infections.

sample_organism: Staphylococcus aureus subsp. aureus MRSA252

sample_organism: Staphylococcus aureus subsp. aureus MSSA476

overall_design: Stress response of 32 human bacterial pathogens to 11 infection relevant stress conditions.

first: Maria

last: Fällman


title: The DNA methylome and transcriptome of hyper-IgM syndrome type 2 B cells

first: Esteban

last: Ballestar

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


title: miRNA expression analysis of HeLa cells treated with secretome of Salmonella infected cells

city: Chennai

first: Areejit

last: Samal

state: Tamil Nadu

address: 4th Cross Road

department: Computational Biology

country: India

institute: The Institute of Mathematical Sciences (IMSc)

summary: To have a global picture of the miRNAs regulated upon treatement with secretome of Salmonella infected cells, we assessed small RNA changes, by RNA-sequencing, of HeLa cells treated with sectretome of Salmonella infected cells or mock-treated cells

overall_design: miRNome profile of cells treated with secretome of Salmonella infected or mock-treated cells were generated by RNA-sequencing

first: Ana

last: Eulalio

first: Miguel

last: Mano


title: Overexpression of human BAG3P209L in mice causes restrictive cardiomyopathy due to sarcomere disruption and protein aggregate formation

city: Pittsburgh

first: guang

last: li

address: 530 45th St. 8116 Rangos Research Center

institute: university of pittsburgh

summary: An amino acid exchange (P209L) in the HSPB8 binding site of the human cochaperone Bcl2-associated athanogene 3 (BAG3) gives rise to severe dominant childhood cardiomyopathy. To phenocopy the human disease in mouse and gain insight into its mechanisms, we have generated humanized transgenic mouse models. Expression of human BAG3P209L-eGFP in mice caused Z-disc disintegration and formation of protein aggregates. This was accompanied by massive fibrosis resulting in a severe, early-onset restrictive cardiomyopathy with increased mortality, as observed in patients. RNA-Seq and proteomic analysis revealed changes in the protein quality control system and increased autophagy in hearts from hBAG3P209L-eGFP overexpressing mice. Also, the mutation renders hBAG3P209L less soluble in vivo and induces protein aggregation, but does not abrogate hBAG3 binding properties. Thus, we have established a mouse model recapitulating mimicing the human disease and found that the disease mechanism is due to accumulation of hBAG3P209L and mouse BAG3, causing sequestering of components of the protein quality control system and the autophagy machinery leading to the reduction of the stability and functional organization of sarcomeres. We have also tested a gene therapy approach utilizing expression of shRNA against hBAG3 in cardiac muscle via AAV and demonstrate that this halted and even partially reversed major phenotypic features of the disease.

overall_design: Comparative analysis of the single cell mRNA-sequencing profile of transgenic CMs (PGKcre:BAG3P209L_homo_GFP_bright, PGKcre:BAG3P209L_homo_GFP_dim, PGKcre:BAG3P209L_het_GFP_bright, PGKcre:BAG3P209L_het_GFP_dim) and control CMs.

first: Michael

last: Hesse

first: Bernd

middle: K

last: Fleischmann

first: Guang

last: Li

first: Sean

last: Wu


title: miRNA expression analysis of Salmonella Typhimurium infected cells

summary: To have a global picture of the miRNAs regulated upon Salmonella infection, we assessed small RNA changes, by RNA-sequencing, of HeLa cells infected with Salmonella Typhimurium compared with mock-treated cells . In addtion to the total population, we evaluated miRNA expression in the fraction of HeLa cells with internalized bacteria (Salmonella-positive), as well as in bystander cells, separated by fluorescence activated cell sorting (FACS)

overall_design: miRNome profile of Salmonella infected cells (total), mock-treated cells (mock), sorted cells with internalized bacteria (Salmonella positive) and sorted cells without internalized bacteria (bystander) cells were generated by RNA-sequencing


title: miRNA expression analysis of E2F1 knockdown cells compared to control siRNA treated cells

summary: To have a global picture of the miRNAs dependent on the transcription factor E2F1, we assessed small RNA changes, by RNA-sequencing, of HeLa cells transfected with an siRNA targeting E2F1 or a control siRNA.

overall_design: miRNome profile of E2F1 knockdown HeLa cells and HeLa cells transfected with control siRNA were generated by RNA sequencing


title: PGE2 supplementation of oocyte culture media improves the developmental and cryotolerance performance of bovine blastocysts derived from a serum-free in vitro production system, mirroring the inner cell mass transcriptome

status: Public on Apr 10 2021

city: JOUY-en-JOSAS

first: gilles

last: charpigny

state: ILe de France

address: domaine de Vilvert

department: Physiologie Animale Systeme Elevage

institute: INRAE

summary: We focused our investigation of an embryo's response to different in vitro environments on changes to the transcriptomic profile of the inner cell mass (ICM), i.e. that part of the blastocyst giving rise to the epiblast and then to all future intraembryonic tissues. We used RNA-sequencing analysis to examine the gene expression of ICM derived under the different IVP conditions. The study evaluated the effects of a serum-free (SF) IVP system including defined oocyte culture media supplemented or not with PGE2, on gene expression of the ICM when compared with standard serum-containing (SC) IVP.

overall_design: Cumulus-oocyte-complexes (COC) were randomly assigned to three in-vitro-produced (IVP) treatment groups : standard serum-containing conditions including the serum supplementation (“SC”), experimental serum-free IVP conditions (“SF”), and experimental serum-free IVP conditions associated with PGE2 supplementation (“SF + PGE2”). After a 22h maturation period, COC were transfered to embryo culture medium and incubated for 7 days to reach blastocyst stage. Four independent sessions of in vitro embryo production, each including the three IVP conditions were performed in order to produce pools (3, 4 and 4 for the “SC”, “SF” and “SF + PGE2” treatment groups, respectively) of 8 to 11 fresh dissected ICM. Their transcriptomic profiles were established by RNA sequencing.

first: Gilles

last: Charpigny

first: Brigitte

last: Marquant-Le-Guienne

first: Christophe

last: Richard

first: Pierre

last: Adenot

first: Olivier

last: Dubois

first: Valérie

last: Gélin

first: Nathalie

last: Peynot

last: Daniel

first: Vincent

last: Brochard

first: Fabienne

last: Nuttinck


title: A gene set signature for the risk of progression in IgM MGUS to Waldenström Macroglobulinemia by microarray of B cells and plasma cells

status: Public on Apr 09 2021

city: Milano

first: Alessansdra

last: Trojani

address: Piazza dell'Ospedale Maggiore, 3

institute: Department of Hematology, ASST Grande Ospedale Metropolitano Niguarda

summary:
IgM monoclonal gammopathy of undetermined significance (IgM MGUS) is an early precursor stage of the rare lymphoma Waldenström Macroglobulinemia (WM). Although comparative gene expression studies on WM, IgM MGUS, and normal B cells identified several genes differently expressed, reliable predictors of progression from IgM MGUS to WM have not yet been identified. We performed a microarray study on CD19+ and CD138+ cells of WM vs. IgM MGUS vs. CTRLs to determine gene signatures for both cell populations.
We demonstrated that hematopoietic antigens, cell-adhesion molecules, Wnt signaling, BCR signaling, calcium signaling, coagulation cascade, and pathways responsible for cell cycle and proliferation were significantly enriched for genes expressed in B cells of WM vs. IgM MGUS vs. CTRLs. Notably, we showed nine genes which displayed the same expression levels in both WM and IgM MGUS compared to CTRLs, suggesting their possible role in the risk of transformation in IgM MGUS to WM.

overall_design: We performed GEP of 36 patients with WM, 13 patients with IgM MGUS, and 7 healthy subjects (CTRLs) using Affymetrix Human Genome U133 plus 2.0 array with the Gene Chip platform. Our aims were to identify gene expression signatures which characterize the 3 groups, and to determine possible genes involved in the risk of progression of IgM MGUS to WM.

first: Alessandra

first: Barbara

last: Di Camillo

first: Luca

last: Bossi

first: Livia

last: Leuzzi

last: Tedeschi

first: Antonino

last: Greco

first: Anna

last: Frustaci

first: Marina

last: Deodato

first: Alessandro

last: Beghini

first: Roberto

last: Cairoli


title: The effect of DMD on THP1 macrophages in response to IMQ.

city: Taoyuan City

first: Shih-Yi

last: Chuang

address: No.259, Wenhua 1st Rd., Guishan Dist.

country: Taiwan

institute: Chang Gung University

summary: To clarify the role of DMD in macrophages in response to IMQ, we performed transcriptomic analysis by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) from IMQ-induced THP1 macrophages with or without DMD treatment in vitro.

overall_design: THP-1 was differentiated into macrophages by treating cells with 100 ng/ml of PMA for 24-36 h, followed by overnight incubation in fresh medium. THP1 cells were pretreated with DMD following in the presence of IMQ.  0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA)  Raw signal data was normalized by quantile normalization for differential expressed genes discovering.For functional assay, we provied enrichment test for differential expressed genes (For most model organisms). Welgen Biotech used clusterProfiler for enrichment test for gene ontology (GO) and pathway (KEGG).


title: Transcriptome-wide RNA structure probing reveals the structural basis of Dicer binding and cleavage

city: Stanford

first: Mark

last: Kay

state: CA

address: 269 Campus Drive

institute: Stanford University

summary: RNA structure is vital for its function. Current transcriptome-wide RNA structure probing methods only capture partial structure information. Measuring RNA structure in full length is critical to the function and regulation study of small RNAs and short fragments of functional sites. Here, we present icSHAPE-MaP, an approach combining in vivo click selective 2′-hydroxyl acylation and mutational profiling to probe intact RNA structures. We further showcase the RNA structural landscape of substrates bound by human Dicer, by combining RNA immunoprecipitation pull-down and small RNA structure profiling through icSHAPE-MaP. Structural categories of Dicer substrates were unveiled with distinct patterns in correlation to their binding affinity and cleavage efficiency. And by tertiary structural modeling for pre-miRNAs, one of the major binding and cleavage substrates for Dicer, we find the spatial distance measuring as an important parameter for Dicer cleavage-site selection.

overall_design: icSHAPE-MaP of six samples for small RNAs (sRNAs, <200 nt) from HEK293T cells, including two treated with DMSO as control, two treated with NAI-N3 in the culture medium, and two treated with NAI-N3 after RNA extraction and refolding in vitro; Dicer-RIP-icSHAPE-MaP of eight samples from Dicer deficient 293T cells, including two RIP samples treated with DMSO as control, three RIP samples treated with NAI-N3, and three input samples as the control for RIP; sRNA-seq of eight samples (40-200 nt in size) from Dicer deficient 293T cells, including four with Dicer wildtype (WT) reconstitution and four with catalytic-dead Dicer reconstitution; miRNA-seq (~20 nt in size ) of 12 samples from HEK293T cells, including two replicates for the overexpression of each miR-217 variant (total five variants plus WT).

first: Qing-Jun

last: Luo

first: Jinsong

last: Zhang

first: Pan

last: Li

first: Qiangfeng


title: PD-L1 alteration in lung cancer affects tumorigenicity lung tumors

status: Public on Apr 08 2021

city: Rehovot

first: Yosef

last: Yarden

address: Herzl St 234

department: Biological Regulation

country: Israel

institute: Weizmann Institute of Science

summary: Cancer immunotherapy has focused on inhibitors of checkpoint proteins, such as Programmed Death Ligand 1 (PD-L1). Unlike RAS-mutated lung cancers, EGFR mutant tumors have generally low response to immunotherapy. Because treatment outcomes vary by EGFR allele, we assumed that intrinsic and microenvironmental factors are involved. Among all non-immunological signaling pathways we surveyed in patients’ datasets, EGFR signaling best associated with high PD-L1. Correspondingly, active EGFRs stabilized PD-L1’s transcripts and depleting PD-L1 severely inhibited EGFR-driven tumorigenicity and metastasis in mice. The underlying mechanisms involve recruitment of phospholipase C-g1 (PLC-g1) to a cytoplasmic motif of PD-L1, which enhances PLC-g1 activation by EGFR. Once stimulated, PLC-g1 activates calcium flux, RHO GTPases and protein kinase C, which promotes an aggressive phenotype. Furthermore, anti-PD-L1 antibodies can inhibit these intrinsic functions of PD-L1. Our results portray PD-L1 as a molecular amplifier of EGFR signaling and lay the foundation for understanding resistance of EGFR+ tumors to immunotherapy.

overall_design: PC9ER cells either overexpressing PDL1 or inhibition of si-PDL1 total RNA seq profiles.

first: Soma

last: Gosh

first: Diana

last: Drago


title: Independent component analysis of E. coli’s transcriptome reveals the cellular processes which respond to heterologous gene expression

city: La Jolla

first: Wun Kiat Justin

last: Tan

state: California

address: 9500 Gilman Drive #0412, PFBH 414

country: USA

institute: UCSD

summary: Heterologous gene expression to expand the native genetic capability of E. coli is the backbone of protein expression and metabolic engineering. The goal of this study was to determine how the identity of the heterologous gene expressed affected the host cell transcriptome. We generated a library of E. coli expressing 46 heterologous genes through an identical rhamnose inducible expression system and perform high throughput RNAseq as well as independent component analysis to elucidate the major variances in the transcriptome. We find that the major variations during heterologous gene expression can be divided into 5 main cellular responses: Fear vs greed, metal homeostasis, respiration, protein folding and amino acid and nucleotide metabolism.

overall_design: RNAseq of 46 lines of heterologous gene expressing lines of E. coli using the same expression system

first: Justin

first: Bernhard

middle: O

last: Palsson


title: Tracking of CD4+ T cells during CNS autoimmunity

city: Planegg-Martinsried

first: Eduardo

last: Beltrán

address: Großhaderner Str. 9

institute: University Hospital, LMU Munich

summary: Here, we use in vivo labeling at defined anatomical sites for "provance" tracking of immune cells across compartmental borders in the context of experimental autoimmune encephalomyelitis (EAE). Specifically, we labeled T cells in mesenteric or inguinal lymph nodes (LNs) of T cell conditional mitoDendra2 reporter mice via photoconversion at disease onset and re-isolated photoconverted T cells form the LNs, spleen and CNS two days later and we performed scRNA-seq on them. Our experimental system will help to better understand the phenotype and function of T cells migration into the CNS as a consequence of priming in a distinct peripheral immune compartment.

overall_design: Two single-cell RNA experiments were performed. In the first, scRNA-seq and Cell Hashing libraries were prepared using the 10x Chromium Single Cell 3' Solution (Chromium Single Cell 3' v3 combined with Cell Hashing as per established protocols (doi: 10.1186/s13059-018-1603-1). In the second, scRNA-seq, scTCR-seq and Cell Hashing libraries were prepared using the 10x Chromium Single Cell 5' Solution (Chromium Next GEM Single Cell VDJ v1.1 with Feature Barcoding technology for Cell Surface Protein)

first: Michael

last: Hiltensperger

first: Thomas

last: Korn


title: Contextual cues from cancer cells govern CAF heterogeneity

city: Houston

first: Chenghang

last: Zong

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

overall_design: Refer to individual Series


title: Salmonella FinO ProQ IP

city: Würzburg

first: Jörg

last: Vogel

address: Josef-Schneider-Straße 2

department: Institute for Molecular Infection Biology

institute: Würzburg University

summary: IP (as previously described Chao et al., 2012; Smirnov et al., 2016) of ProQ-3xFLAG and FinO-3xFLAG in Salmonella SL1344 at different growth conditions.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: growth, IP, seq

first: Youssef

last: El Mouali

first: Milan

last: Gerovac


title: IL-26 mediates epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI) resistance through endoplasmic reticulum stress signaling pathway in triple negative breast cancer cells

status: Public on Apr 07 2021

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary: We investigated how gefitinib-treatment and/or IL-26 stimulation affected gene expression in HCC70 cells by DNA microarray analysis.

overall_design: Human breast carcinoma cell lines HCC70 were treated with media as a gefitinib or IL-26 for 3 hr, and total RNA was isolated for a total of 4 samples.

first: T

last: Itoh

first: C

last: Morimoto

first: K

last: Ohnuma


title: Capturing human trophoblast development with naive pluripotent stem cells in vitro

city: Kyoto

first: Yasuhiro

last: Takashima

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

institute: Kyoto University


title: Capturing human trophoblast development with naive pluripotent stem cells in vitro [scRNA-Seq]

summary: We report global transcriptional alteration and transcriptional trajectories from naive human pluripotent stem cells-derived trphectoderm to cytotrophoblast. By graph-based cell identities of total samples on the Seurat platform, we identified 9 main clusters, and further revealed the pseudotime differentiation during trophectoderm-cytotrophoblast transition.

overall_design: Analyzing transcriptional profiles during naive human pluripotent stem cells-derived trophectoderm-cytotrophoblast transition using scRNA-seq. We generated chromium single cell 3' v3.1 libraries from randomly captured trophoblast-like cells and sequenced them using Illumina HiSeq 4000.  Finally, we profiled 14,164 cells (nTE_D2: 2,378 cells; nTE_D3: 5,148 cells; nCT_D5:3,529 cells; nCT_D10: 3,109 cells) with a range of 56,312 – 130,971 mean reads per cell for each sample, whereby approximately 5,500–8,000 median genes per cell for each sample were detected.

first: Shingo

last: Io

first: Mio

last: Kabata

first: Takuya

last: Yamamoto


title: Inhibition of TGF-β/Smad3 signaling disrupts cardiomyocyte cell cycle progression and EMT-like migration during ventricle regeneration

city: Wuhan

first: Ruilin

last: Zhang

address: 185 Donghu Road

institute: Wuhan University

summary: Transcriptome sequencing of SIS3-treated uninjured (5dpf) and injured (2dpt) zebrafish hearts.

overall_design: Gene expression profiles of DMSO- or SIS3-treated uninjured and injured hearts were generated by deep sequencing, using Illumina HiSeq X Ten.

first: Yuanyuan

last: Peng

first: Wenyuan

last: Wang


title: Temporal evolution of cellular heterogeneity during the progression to advanced, AR-negative prostate cancer [scRNA-seq]

city: New York

first: Nicholas

last: Brady

state: NY

address: 1188 York Ave

department: Pathology and Laboratory Medicine

institute: Weill Cornell Medicine

summary: Despite advances in the development of highly effective androgen receptor (AR)-directed therapies for the treatment of men with advanced prostate cancer, acquired resistance ultimately ensues. A significant subset of patients with resistant disease develop AR-null, androgen-indifferent tumors that lose their luminal identify and display neuroendocrine features (neuroendocrine prostate cancer (NEPC)). Utilizing a genetically engineered mouse model, we have characterized the synergy between N-Myc overexpression and RB1 loss-of-function which results in the formation of AR-negative, poorly differentiated tumors with high metastatic potential. Single-cell-based approaches revealed striking changes to the transcriptome and chromatin accessibility during the transition to NEPC. Global DNA methylation and the N-Myc cistrome are redirected following RB1 loss. Altogether, our data provide new insight into the progression to NEPC.

overall_design: scRNA-seq in mouse prostate tumors

first: Alyssa

last: Bagadion

first: Richa

last: Singh

first: David

last: Rickman


title: Temporal evolution of cellular heterogeneity during the progression to advanced, AR-negative prostate cancer [RNA-seq]

overall_design: RNA-seq in mouse prostate tumors


title: Small molecule Y-320 stimulates ribosome biogenesis, protein synthesis and aminoglycoside-induced premature termination codon readthrough

city: Vancouver

first: Stephane

last: Flibotte

state: BC

address: 2370-6270 University Blvd.

department: Faculty of Science

institute: University of British Columbia

summary: Premature termination codons (PTC) cause over 10% of genetic disease cases. Some aminoglycosides that bind to the ribosome decoding centre can induce PTC readthrough and restore low levels of full-length functional proteins. However, concomitant inhibition of protein synthesis limits the extent of PTC readthrough that can be achieved by aminoglycosides like G418. Using a cell-based screen, we identified a small molecule, the phenylpyrazoleanilide Y-320, that potently enhances TP53, DMD and COL17A1 PTC readthrough by G418. Unexpectedly, Y-320 increased cellular protein levels and protein synthesis, measured by SYPRO Ruby protein staining and puromycin labelling, as well as ribosome biogenesis measured using antibodies to rRNA and ribosomal protein S6. Y-320 did not increase the rate of translation elongation and it exerted its effects independently of mTOR signaling. At the single cell level, exposure to Y-320 and G418 increased ribosome content and protein synthesis which correlated strongly with PTC readthrough. As a single agent, Y-320 did not affect translation fidelity measured using a luciferase reporter gene but it enhanced misincorporation by G418. RNA-seq data showed that Y-320 upregulated the expression of CXC chemokines CXCL10, CXCL8, CXCL2, CXCL11, CXCL3, CXCL1 and CXCL16. Several of these chemokines exert their cellular effects through the receptor CXCR2 and the CXCR2 antagonist SB225002 reduced cellular protein levels and PTC readthrough in cells exposed to Y-320 and G418. These data show that the self-limiting nature of PTC readthrough by G418 can be compensated by Y-320, a potent enhancer of PTC readthrough that increases ribosome biogenesis and protein synthesis. They also support a model whereby increased PTC readthrough is enabled by increased protein synthesis mediated by an autocrine chemokine signaling pathway. The findings also raise the possibility that inflammatory processes affect cellular propensity to readthrough agents and that immunomodulatory drugs like Y-320 might find application in PTC readthrough therapy.

overall_design: RNA-Seq analysis compared HDQ-P1 cells treated with 1 µM Y-320 for 48 h to untreated cells, each condition was repeated in triplicates.

first: Sara

last: Hosseini-Farahabadi

first: Alireza

last: Baradaran-Heravi

first: Kunho

last: Choi

first: Michel

last: Roberge

first: Carla

last: Zimmerman


title: Temporal evolution of cellular heterogeneity during the progression to advanced, AR-negative prostate cancer [RRBS]

overall_design: RRBS in LNCaP human prostate cancer cells and mouse prostate tumors


title: Clump sequencing exposes the spatial expression programs of intestinal secretory cells

first: Keren

last: Bahar-Halpern

institute: Weizmann Institute

summary: We molecularly characterized Clumps and single cells from Jejunum. This enable us to uncover the zonation of rare secretory cells on crypt to villus axis.

overall_design: mRNA profiles from clumps and single cells, EDTA isolated jejunum epithelial clumps and single cells were sequenced in several batches in an Illumina NextSeq.

first: Rita

last: Manco

first: Inna

last: Averbukh

last: Halpern

first: Porat

last: Ziv

first: Ido

last: Amit

first: Shalev

last: Itzkovitz


title: Temporal evolution of cellular heterogeneity during the progression to advanced, AR-negative prostate cancer [scATAC-seq]

last: Brady

overall_design: scATAC-seq in mouse prostate tumors


title: Temporal evolution of cellular heterogeneity during the progression to advanced, AR-negative prostate cancer [ChIP-seq]

overall_design:
N-Myc ChIP-seq in mouse prostate tumors
Please note that each processed data was generated from both input and IP samples, and is linked to the corresponding IP sample records.

last: Bagadion


title: Capturing human trophoblast development with naive pluripotent stem cells in vitro [RNA-Seq]

first: Yasuhiro

last: Takashima

summary: Recent reports suggested human embryonic development is not always consistent with mouse. However, experimental approach to in vivo human embryos is extremely limited. Therefore, it is important to develop an appropriate in vitro cell culture system to analyse human pre-implantation development. In this report, we use human naive pluripotent stem cells (PSCs), which share features with pre-implantation epiblasts and show in vitro lineage specification of human trophoblast lineages. We successfully differentiated naive PSCs into trophectoderm, cytotrophoblast, syncytiotrophoblast, and extravillous trophoblast. Cytotrophoblasts could be cultured for long term as stem cells.

overall_design: Analyzing transcriptional profiles in naive PSCs, primed PSCs, naive PSCs-derived TE (nTE), nTE-derived CT (nCT), nTE-derived ST (nST), nTE-derived EVT (nEVT), primed PSCs-derived cells (pBAP), placenta-derived CT (CT30), and in vivo CT.

first: Shingo

last: Io

first: Takuya

last: Yamamoto