title: Clonal expansion and activation of tissue-resident memory-like Th17 cells expressing GM-CSF in the lung of severe COVID-19 patients

city: Hamburg

first: Yu

last: Zhao

address: Falkenried 94

department: Institute of Medical Systems Biology

institute: University Medical Center Hamburg-Eppendorf

summary: Hyperinflammation contributes to lung injury and subsequent acute respiratory distress syndrome (ARDS) with high mortality in severe COVID-19. To understand the underlying mechanisms, we investigated the role of the lung-specific immune response. Here we profiled lymphocytes and myeloid cells in the bronchoalveolar lavage (BAL) fluid and blood of COVID-19 patients. By tracking T cell clones across tissues, we identified clonally expanded tissue-resident memory-like Th17 cells (Trm17 cells) in the lung even after viral clearance. These Trm17 cells are characterized by a potentially pathogenic cytokine profile with expression of IL17A and CSF2 (GM-CSF). Interactome analysis revealed that Trm17 cells interact with macrophages and cytotoxic CD8+ T cells, which have been associated with disease severity and lung damage. High IL-17A and GM-CSF protein levels in the serum of COVID-19 patients correlated with severe clinical course. This study suggests pulmonary Trm17 cells as one of the orchestrators of the hyperinflammation in severe COVID-19 and that these cells and their cytokines, such as GM-CSF, are promising biomarkers and potential targets for a COVID-19 therapy.

overall_design: SRA accession: SRP306287; BioProject accession: PRJNA701725; Sort CD45 positive cells the bronchoalveolar lavage fluid and blood of COVID-19 patients and bacteria pnemonia patients, then perform 5'-RNA single cell transcriptome, CITE-seq and TCR sequening (10x genomics).

first: Fabian

last: Hausmann

first: Nicola

last: Gagliani

first: Christian

last: Krebs


title: GATA transcription factors, SOX17 and TFAP2C, drive the human germ-cell specification program

status: Public on Feb 15 2021

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

type: Expression profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

summary: The in vitro reconstitution of human germ-cell development provides a robust framework for clarifying key underlying mechanisms. Here, we explored transcription factors (TFs) that engender the germ-cell fate in their pluripotent precursors. Unexpectedly, SOX17, TFAP2C, and BLIMP1, which act under the BMP signaling and are indispensable for human primordial germ-cell-like cell (hPGCLC) specification, failed to induce hPGCLCs. In contrast, GATA3 or GATA2, immediate BMP effectors, combined with SOX17 and TFAP2C, generated hPGCLCs. GATA3/GATA2 knockouts dose-dependently impaired BMP-induced hPGCLC specification, whereas GATA3/GATA2 expression remained unaffected in SOX17, TFAP2C, or BLIMP1 knockouts. In cynomolgus monkeys, a key model for human development, GATA3, SOX17, and TFAP2C were co-expressed exclusively in early PGCs. Crucially, the TF-induced hPGCLCs acquired a hallmark of bona fide hPGCs to undergo epigenetic reprogramming and mature into oogonia/gonocytes in xenogeneic reconstituted ovaries. By uncovering a TF circuitry driving the germ line program, our study provides a paradigm for TF-based human gametogenesis.

overall_design: Refer to individual Series


title: Pluripotent stem cell derived models of neurological diseases reveal early transcriptional heterogeneity

status: Public on Feb 14 2021

city: Jerusalem

first: Matan

last: Sorek

address: Edmond J. Safra Campus

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

summary: Identification of transcriptional heterogeneity changes in Huntington's disease (HD) and Autism Spectrum Disorder (ASD) human embryonic stem cells(hESC)- and induced pluripotent stem cells(iPSC)-derived neural progenitor cells

overall_design: RNA seq libraries from 426 single cells and population controls with Smart-Seq2

first: Walaa

last: Oweis

first: Shahar

last: Simon

first: Malka

last: Nissim-Rafinia

first: Cynthia

middle: C

last: Hession

first: Xian

last: Adiconis

first: Sean

middle: K

last: Simmons

first: Xi

last: Shi

first: Congyi

last: Lu

first: Neville

middle: E

last: Sanjana

first: Jen

middle: Q

last: Pan

first: Feng

last: Zhang

first: Joshua

middle: Z

last: Levin

first: Eran

last: Meshorer


title: Targeting cholesterol metabolism as efficient antiviral strategy against the Hepatitis E virus

status: Public on Feb 12 2021

city: Bonn

first: Denna

last: Tabari

address: Kurt-Georg-Kiesinger Allee 3

country: Germany

institute: Federal Institute for Drugs and Medical Devices

summary: We used whole genome expression profiling to analyze the effects of Hepatitis E Virus (HEV) on the mRNA transcriptome of A549/D3 cells - particularly to identify differentially expressed genes which are associated with cholesterol metabolism.

overall_design: Gene expression profiles of persistently HEV-infected A549 cells (Johne R, Reetz J, Ulrich RG, Machnowska P, Sachsenröder J, Nickel P et al. An ORF1-rearranged hepatitis E virus derived from a chronically infected patient efficiently replicates in cell culture. Journal of viral hepatitis 2014;21(6):447–56.) were analyzed after 4 and 12 days of culturing. At the same timepoints gene expression profiles of uninfected A549/D3 (Schemmerer M, Apelt S, Trojnar E, Ulrich RG, Wenzel JJ, Johne R. Enhanced Replication of Hepatitis E Virus Strain 47832c in an A549-Derived Subclonal Cell Line. Viruses 2016;8(10).) cells were analyzed. 3 biological replicates were used.

first: Mirco

last: Glitscher

first: David

last: Heiler Martin

first: Kathrin

last: Woytinek

first: Benjamin

last: Schmidt

first: Catharina

last: Scholl

first: Julia

last: Stingl

first: Evelyn

last: Seelow

first: Mira

last: Choi

first: Eberhard

last: Hildt


title: Analysis of senescence transcriptome upon knockdown of XPO7 [RNA-seq]

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

summary: We depleted XPO7 by shRNA in IMR90 ER:RAS cells. 5 days after RAS induction by treatment with 4OHT we collected RNA. XPO7 depletion alleviates senescence induction.

overall_design: 4 conditions in triplicate. IMR90 ER:RAS cells, either: non-induced control cells (non-senescent), 4OHT induced cells (Senescent, induced), IMR90 ER:RAS cells,  4OHT-induced  and  with XPO7 depletion (by expressing shXPO7_3), IMR90 ER:RAS cells,  4OHT-induced  and  with XPO7 depletion (by expressing shXPO7_5)

first: Andrew

last: Innes

first: Jesus

last: Gil

first: Gopuraja

last: Dharmalingam

first: Husayn

middle: A

last: Pallikonda


title: Next-Generation Sequencing Facilitates Quantitative Analysis of Rbbp4F/F (Control) and Rbbp4-/- Embryonic Stem Cells Transcriptomes

status: Public on Feb 19 2021

city: Nanjing

first: Su

last: Ting

address: No. 12, Xuefu Road, Pukou District

department: Model Animal Research Center

country: China

institute: Nanjing University

summary: Purpose: The goals of this study are to compare Rbbp4-/- with Rbbp4F/F embryonic stem cells transcriptome profiling (RNA-seq) to evaluate the target genes regulated by Rbbp4.

overall_design: mRNA profiles of Rbbp4F/F and Rbbp4-/- embryonic stem cells were generated by deep sequencing, in triplicate, using Illumina Novaseq6000.

first: Yikai

last: Huang

first: JinZhong

last: Qin


title: Virus infection of the CNS disrupts the immune-neural-synaptic axis via induction of pleiotropic gene regulation of host responses

status: Public on Feb 18 2021

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

country: USA

institute: NIH

summary: Treatment for many viral infections of the central nervous system (CNS) remains only supportive. Here we address a remaining gap in our knowledge regarding how the CNS and immune systems interact during viral infection. By examining the regulation of the immune and nervous system processes in a nonhuman primate model of West Nile virus neurological disease, we show that virus infection disrupts the homeostasis of the immune-neural-synaptic axis via induction of pleiotropic genes with distinct functions in each component of the axis. This pleiotropic gene regulation suggests an unintended off-target negative impact of virus-induced host immune responses on the neurotransmission, which may be a common feature of various viral infections of the CNS.

overall_design: time course with WNV infection and mock treated

first: Olga

last: Maximova

first: Daniel

first: John

last: Kash

first: Kishore

last: Kanakabandi

first: Yongli

last: Xiao

first: Mahnaz

last: Minai

first: Ian

middle: N

last: Moore

first: Jeff

last: Taubenberger

first: Craig

last: Martens

first: Jeffrey

middle: I

last: Cohen

first: Alexander

middle: G

last: Pletnev


title: The role of mammalian DNA methyltransferases in the regulation of temporal order of DNA replication [microarray]

city: Tsu

first: Shin-ichiro

last: Takebayashi

state: Mie

address: 2-174, Edobashi

department: Graduate School of Medicine

institute: Mie University

summary:
Multiple epigenetic pathways underlie the temporal order of DNA replication (replication timing) in the context of development and disease. DNA methylation by DNA methyltransferases (DNMTs) and downstream chromatin reorganization and transcriptional changes are thought to impact DNA replication, yet this remains to be comprehensively tested. Using cell biological and genome-wide approaches to measure replication timing, we identified a number of genomic regions undergoing subtle but reproducible replication timing changes in various DNMT-mutant mouse ES cell lines that include a line with a drug-inducible DNMT3a2 expression system. Replication timing within pericentromeric heterochromatin (PH) correlates with redistribution of H3K27me3 induced upon DNA hypomethylation: later replicating PH coincides with H3K27me3 enriched regions. In contrast, this relationship with H3K27me3 was not evident at chromosomal arm regions that undergo either early-to-late (EtoL) or late-to-early (LtoE) replication timing switching upon loss of DNMTs. Interestingly, transcriptional up- and down-regulation frequently coincide with earlier and later shifts in replication timing of chromosomal arm regions, respectively. Our study revealed previously unrecognized complex and diverse roles of DNMTs in shaping the mammalian DNA replication landscape.
We investigated the effect of Dnmt3a2 expression in the transcription profile of Dnmt3a and 3b double knockout (DKO) ES cells.

overall_design: Dnmt3a−/−Dnmt3b−/− DKO ES cell clones stably expressing RU486 (mifepristone, a progesterone receptor antagonist)-inducible DNMT3a2 were generated by electroporation-mediated introduction of an expression plasmid for DNMT3a2 fused with the ligand-binding domain of the human progesterone receptor driven by the CAG promoter, followed by selection with blasticidin. To induce DNMT3a2 protein, obtained ES cells (clone 1723) were cultured in ES medium containing 1 µM RU486 for 14 days on feeder MEFs. As a control, cells were treated with ethanol. RNA was isolated from these cells and hybridized to Affymetrix microarrays


title: The role of mammalian DNA methyltransferases in the regulation of temporal order of DNA replication [BrdU-IP]

summary: Multiple epigenetic pathways underlie the temporal order of DNA replication (replication timing) in the context of development and disease. DNA methylation by DNA methyltransferases (DNMTs) and downstream chromatin reorganization and transcriptional changes are thought to impact DNA replication, yet this remains to be comprehensively tested. Using cell biological and genome-wide approaches to measure replication timing, we identified a number of genomic regions undergoing subtle but reproducible replication timing changes in various DNMT-mutant mouse ES cell lines that include a line with a drug-inducible DNMT3a2 expression system. Replication timing within pericentromeric heterochromatin (PH) correlates with redistribution of H3K27me3 induced upon DNA hypomethylation: later replicating PH coincides with H3K27me3 enriched regions. In contrast, this relationship with H3K27me3 was not evident at chromosomal arm regions that undergo either early-to-late (EtoL) or late-to-early (LtoE) replication timing switching upon loss of DNMTs. Interestingly, transcriptional up- and down-regulation frequently coincide with earlier and later shifts in replication timing of chromosomal arm regions, respectively. Our study revealed previously unrecognized complex and diverse roles of DNMTs in shaping the mammalian DNA replication landscape.

overall_design: Analysis of early and late replicating chromosomal regions in mouse embryonic stem cells


title: Comparison of wild type “empty” and Furin super-enhancer deleted SE EL-4 cell lines

city: Tampere

first: Ilkka

last: Junttila

state: Tampere

address: Arvo Ylpön katu 34

department: Institute of Medical and Life Science

country: Finland

institute: University of Tampere

type: Non-coding RNA profiling by high throughput sequencing

summary: Exceedingly abundant p300 histone acetylase binding was reported upstream Furin in mouse Th1 cells. We aimed to investigate the role of this genomic area in RNA expression by deleting it from EL-4 mouse thymoma cells and comparing the RNA expression profiles in steady-state and after PMA/ionomycin stimulation.

overall_design: Three independent wild type “empty” and Furin super-enhancer deleted SE EL-4 cell clones were left unstimulated or stimulated with PMA/ionomycin for 6 hours. Total RNA was isolated and sent to NovoGene for RNA sequencing using the Illuminia PE150 platform.

first: Zsuzsanna

last: Ortutay

first: Marko

last: Pesu


title: Azathioprine Blocks the Aberrantly Elevated Lipid Metabolism and Induces Apoptosis in Glioblastoma [RNA-Seq]

status: Public on Feb 16 2021

city: Daejeon

first: Hye Jin

last: Nam

email: nhj0120@gmail.com, hjnam@krict.re.kr

state: Not US or Canada

address: 141 Gajeongro, Yuseong

country: South Korea

institute: Korea Research Institute of Chemical Technology

summary: Glioblastoma multiforme (GBM) is the most aggressive type of brain tumor with poor survival rate and temozolomide (TMZ) has been used as the standard chemotherapy for GBM treatment. However, a large number of patients either respond poorly to TMZ and/or develop resistance after long-term use, urging the need for the development of potent drugs with novel mechanisms of action. Here, using high-throughput compound screening (HTS), we found azathioprine, an immunosuppressive medication, to be a promising therapeutic agent for TMZ-resistant GBM treatment. Through integrative genome-wide analysis and global proteomic analysis, we identified the elevated lipid metabolism due to hyperactive EGFR/AKT/SREBP-1 signaling pathway being inhibited by azathioprine. In addition, azathioprine causes ER stress-induced apoptosis. Orthotopic xenograft models injected with patient-derived GBM cells exhibits reduced tumor volumes and increased apoptosis by azathioprine. These overall data indicate that azathioprine could be a powerful therapeutic option for TMZ-resistant GBM patients.

overall_design: Gene expression profiling of 559T and 592T cells untreated or treated with azathioprine for 48 hours.

first: Hye

middle: J

first: Heeyeong

last: Cho


title: Radiation-induced differentiation of normal  human skin fibroblasts.

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary:
(1) Gene expression profiles during radiation-induced premature, terminal differentiation of exponentially growing progenitor fibroblasts to postmitotic functional cells after single dose (4 Gy) or two fractions (2×4 Gy).
(2) Comparison with gene expression profile of confluent cells after fractionated irradiation with 3×4 Gy

overall_design: Two independent repeat experiments (#1 and #2)  for (1) and (2) were performed with GS4 fibroblasts. Further three independent repeats (#3, #4, #5) of (1) for day 3, only, were performed with GS3, GS4, and GS5, fibroblasts

last: Herskind


title: Spontaneously resolved atopic dermatitis shows melanocyte and immune cell activation distinct from healthy control skin

city: Vienna

first: Katharina

last: Rindler

address: Waehringer Guertel 18-20

department: Dermatology

country: Austria

institute: Medical University of Vienna

summary: Atopic dermatitis (AD) typically starts in infancy or early childhood, showing spontaneous remission in a subset of patients, while others develop lifelong disease. Despite an increased understanding of AD, factors guiding its natural course are only insufficiently elucidated. We thus performed suction blistering in skin of adult patients with stable, spontaneous remission from previous moderate-to-severe AD during childhood. Samples were compared to healthy controls without personal or familial history of atopy, and to chronic, active AD lesions. Skin cells and tissue fluid obtained were used for single-cell RNA sequencing and proteomic multiplex assays, respectively. We found overall cell composition and proteomic profiles of spontaneously healed AD to be comparable to healthy control skin, without upregulation of typical AD activity markers (e.g., IL13, S100As, and KRT16). Among all cell types in spontaneously healed AD, melanocytes harbored the largest numbers of differentially expressed genes in comparison to healthy controls, with upregulation of potentially anti-inflammatory markers such as PLA2G7. Conventional T-cells also showed increases in regulatory markers, and a general skewing toward a more Th1-like phenotype. By contrast, gene expression of regulatory T-cells and keratinocytes was essentially indistinguishable from healthy skin. Melanocytes and conventional T-cells might thus contribute a specific regulatory milieu in spontaneously healed AD skin.

overall_design:
Skin cells from patients with spontaneously resolved atopic dermatitis were compared to healthy controls without personal or familial history of atopy, and to chronic, active AD lesions.

>>>Raw data are unavailable due to patient privacy concerns<<<

first: Thomas

last: Krausgruber

first: Felix

middle: M

last: Thaler

first: Natalia

last: Alkon

first: Christine

last: Bangert

first: Harald

last: Kurz

first: Nikolaus

last: Fortelny

middle: B

last: Rojahn

first: Constanze

last: Jonak

first: Johannes

last: Griss

first: Christoph

last: Bock

first: Patrick

last: Brunner


title: Bromodomain proteins regulate human cytomegalovirus latency and reactivation allowing epigenetic therapeutic intervention.

status: Public on Feb 11 2021

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

institute: Weizmann Institute

summary: We report the application of RNA sequencing technology for high-throughput profiling of both host and human cytomegalovirus (HCMV) transcript levels in latenly infected CD14+ monocytes after treatment with histone deacetylase inhibitors (CHR-4487) and BET-bromodomain inhibitors (GSK726).

overall_design: Examination of changes to the HCMV latent transcriptome with epigenetic inhibitor treatment.

first: Ian

last: Groves

first: Aharon

last: Nachshon

first: Batsheva

last: Rozman

first: Michal

last: Schwartz

first: Sarah

last: Jackson

first: Emma

middle: L

last: Poole


title: Comparison of extracellular vesicle miRNA cargo of Adult and Fetal MSCs

status: Public on Feb 10 2021

city: Rotterdam

first: Jeroen

last: van de Peppel

address: 's Gravendijkwal 230

country: Netherlands

institute: ErasmusMC

summary:
Recently, we and others have illustrated that extracellular vesicles (EVs) have the potential to support hematopoietic stem and progenitor cell (HSPC) expansion; however, the mechanism and processes responsible for the intercellular communication by EVs are still unknown. In the current study, we investigate whether primary human bone marrow derived mesenchymal stromal cells (BMSC) EVs isolated from two different origins, fetal (fEV) and adult (aEV) tissue, can increase the relative low number of HSPCs found in umbilical cord blood (UCB) and which EV-derived components are responsible for ex vivo HSPC expansion. Interestingly, aEVs but and to a lesser extent fEVs, showed supportive ex vivo expansion capacity of UCB-HSPCs. Taking advantage of the two BMSC sources with different supportive effects, we analyzed the EV cargo and investigated how gene expression is modulated in HSPCs after incubation with aEVs and fEVs.
Proteomics analyses of the protein cargo composition of the supportive aEV versus the less-supportive fEV identified 90% of the Top100 exosome proteins present in the ExoCarta database. Gene Ontology (GO) analyses illustrated that the proteins overrepresented in aEVs were annotated to oxidation-reduction process, mitochondrial ATP synthesis coupled proton transport, or protein folding. In contrast, the proteins overrepresented in fEVs were annotated to extracellular matrix organization positive regulation of cell migration or transforming growth factor beta receptor (TGFBR) signaling pathway.
Small RNA sequencing identified different molecular signatures between aEVs and fEVs. Interestingly, the microRNA cluster miR-99b/let-7e/miR-125a, previously identified to increase the number of HSPCs by targeting multiple pro-apoptotic genes, was highly and significantly enriched in aEVs.
Although we identified significant differences in the supportive effects of aEVs and fEVs, RNAseq analyses of the 24hrs treated HSPCs indicated that a limited set of genes was differentially regulated when compared to cells that were treated with cytokines only. Together, our study provides novel insights into the complex biological role of EVs and illustrates that aEVs and fEVs differentially support ex vivo expansion capacity of UCB-HSPCs. Together opening new means for the application of EVs in the discovery of therapeutics for more efficient ex vivo HSPC expansion.

overall_design: Examination of the miRNA content of extracellular vesicles isolated from Adult and Fetal MSC and the cellular content, respectively.

first: Corina

last: Ghebes

first: Carlijn

last: Voermans


title: Gene expression profiling in human induced pluripotent stem cell-derived cardiomyocytes(hiPS-CMs) after different topographic substrates stimulation

city: Suita

first: Jong-Kook

last: LEE

address: 2-2 Yamada-oka

department: Cardiovascular Regenerative Medicine

institute: Osaka University Graduate School of Medicine

summary:
Purpose: To induce hiPS-CMs maturation by using engineering technics, including culturing on the anisotropic pattern, has been widely explored. However, the underlying mechanisms of the benefits driven by the aligned topographic stimuli are still pending. To obtain insights into the underlying molecular pathways/signaling involved in the facilitation of hiPS-CMs maturation driven by specific topographic stimuli, we performed RNA-seq for the hiPS-CMs samples after culturing on the different patterns
Methods: hiPS-CMs cultured on the flat bottom 24-well plate (MS-80240; Sumilon)/random nanofiber substrate (NanoECM, 2401; Funakoshi)/aligned nanofiber substrate (NanoAligned, 2402; Funakoshi) for one week. Then the cells were harvested as Flat, Random, Align group samples. Total RNA was extracted using the RNeasy Plus mini kit (740990.250; Takara), the concentration of RNA was measured by using NanoDrop (2000/2000c Spectrophotometers, Thermo Fisher). The Illumina package bcl2fastq software was used for base-calling. The raw reads were mapped to the human reference genome sequences (GRCh38) using TopHat ver. 2.1.1 in combination with Bowtie2 ver. 2.3.4.1
Results: The principal component analysis(PCA) analysis revealed that the hiPS-CMs from flat and random patterns showed the most variance. And the differentially expressed genes (DEGs) were detected with theDESeq2 package, showed that the flat group samples occupied most of the enrichment gene expression. The enriched DEGs termed by Gene Ontology(GO) Biological Process revealed that the upregulated genes in flat group are mainly related to the regulation of cell movement, including extracellular matrix organization, cell adhesion, and cell migration. The well-known cardiac maturation markers such as MYH7 and TNNI3 showed significantly upregulated in align group, as well as cardiac structural(MLC2, TNNT2, GJA1), and calcium handling relevant genes( CASQ2, CAMK2B, CAV3) also showed a higher expression than that of in flat group. The most up-regulated gene sets related pathways in align group include cardiac development and heart morphogenesis, negative regulation of binding, and microtubule-based process. In contrast, the relative down-regulated gene enriched pathways in align group are mostly involved in KRT gene family, which also plays a role in cell movement
Conclusions: hiPS-CMs by culturing on the aligned pattern for a short-term have facilitated maturation of hiPS-CMs. The up-regulated gene sets in align group related to regulating cell cycle pathways. The genome-wide expression analysis provided insights into the underlying molecular pathways/signaling involved in the specific topographic stimuli induced maturation of hiPS-CMs

overall_design: mRNA profiles of hiPS-CMs in flat, random, and align patterns

first: Jun

last: Li

last: Lee


title: Analysis of the senescence transcriptome in TRF2dBdM-induced senescence and replicative senescence [microarray]

first: LMS

last: Bioinformatics Core

summary: We stably infected IMR90 fibroblasts with lentiviral vectors expressing doxycycline-inducible TRF2dBdM or vector control. Cells were treated with 1mg/ml of doxycycline for 7 days to induce senescence in the cells expressing TRF2dBdM before collecting RNA. IMR90 cells, either young (passage 10, population doubling ~20) or old  (passage 24, population doubling ~40-48) were also used as a model of replicative senescence. The transcriptomes were analyzed using RNA microarrays.

overall_design: 12 samples examined: 3 Empty vector (control), 3 TRF2dBdM (senescent), 3 young, 3 old.

first: Andrew

last: Innes

first: Jesus

last: Gil

first: Gopuraja

last: Dharmalingam

first: Husayn

last: Pallikonda


title: Gene expression analyses of hematopoietic stem and progenitor cells treated with extracellular vesicles isolated from adult and fetal MSCs

summary: Recently, we and others have illustrated that extracellular vesicles (EVs) have the potential to support hematopoietic stem and progenitor cell (HSPC) expansion; however, the mechanism and processes responsible for the intercellular communication by EVs are still unknown. In the current study, we investigate whether primary human bone marrow derived mesenchymal stromal cells (BMSC) EVs isolated from two different origins, fetal (fEV) and adult (aEV) tissue, can increase the relative low number of HSPCs found in umbilical cord blood (UCB) and which EV-derived components are responsible for ex vivo HSPC expansion. Interestingly, aEVs and to a lesser extent fEVs, showed supportive ex vivo expansion capacity of UCB-HSPCs. Taking advantage of the two BMSC sources with different supportive effects, we analyzed the EV cargo and investigated how gene expression is modulated in HSPCs after incubation with aEVs and fEVs.   Proteomics analyses of the protein cargo composition of the supportive aEV versus the less-supportive fEV identified 90% of the Top100 exosome proteins present in the ExoCarta database. Gene Ontology (GO) analyses illustrated that the proteins overrepresented in aEVs were annotated to oxidation-reduction process, mitochondrial ATP synthesis coupled proton transport, or protein folding. In contrast, the proteins overrepresented in fEVs were annotated to extracellular matrix organization positive regulation of cell migration or transforming growth factor beta receptor (TGFBR) signaling pathway.   Small RNA sequencing identified different molecular signatures between aEVs and fEVs. Interestingly, the microRNA cluster miR-99b/let-7e/miR-125a, previously identified to increase the number of HSPCs by targeting multiple pro-apoptotic genes, was highly and significantly enriched in aEVs.  Although we identified significant differences in the supportive effects of aEVs and fEVs, RNAseq analyses of the 24hrs treated HSPCs indicated that a limited set of genes was differentially regulated when compared to cells that were treated with cytokines only. Together, our study provides novel insights into the complex biological role of EVs and illustrates that aEVs and  fEVs differentially support ex vivo expansion capacity of UCB-HSPCs. Together opening new means for the application of EVs in the discovery of therapeutics for more efficient ex vivo HSPC expansion.

overall_design: HSPCs from 3 different donors were incubated with cytokines only, aEVs and fEVs for 24 hours and gene expression profiles were generated.


title: TET2 is a component of the ER complex and controls 5mC to 5hmC conversion at ER cis-regulatory regions [MMS/RRHP]

city: Cambridge

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

institute: Cancer Research UK, Cambridge Institute

summary: Estrogen receptor-a (ER) drives tumour development and metastasis in ER positive (ER+) breast cancer. GATA3 is a transcription factor that has been closely linked to ER function, but the role of GATA3 in ER transcriptional activity is not clear. We sought to identify the contribution of GATA3 to the ER complex by conducting quantitative multiplexed rapid immunoprecipitation mass spectrometry of endogenous proteins (qPLEX-RIME) to assess changes to the ER complex in response to GATA3 depletion. Unexpectedly, very few proteins were dissociated from the ER complex in the absence of GATA3, with the only major change being depletion of TET2 from the ER complex. In breast cancer cells and Patient-Derived Xenograft (PDX) tissue, TET2 binding events were shown to constitute a near-total subset of ER binding events, and loss of TET2 was functionally associated with reduced activation of proliferative pathways. To investigate the TET2-ER relationship, the role of TET2 in regulating DNA modifications in ER+ breast cancer cells was examined. TET2 knockdown did not appear to result in changes to global DNA methylation, however, oxidation of methylated DNA to 5-hydroxymethylcytosine (5hmC) was significantly reduced after TET2 depletion and these events occurred at ER enhancers. These findings implicate TET2 in the production and maintenance of 5hmC at ER sites, providing a potential mechanism for TET2-mediated regulation of ER target genes.

overall_design: Methyl-Midi SeqTM (MMS) or Reduced Representation Hydroxymethylation Profiling (RRHP) in MCF7 cells in response to treatment with either a non-targeting siRNA control, or siRNA against TET2.

first: Rebecca

last: Broome

first: Igor

last: Chernukin

middle: S


title: BRG1 knockdown inhibits proliferation through multiple cellular pathways in prostate cancer

city: Adelaide

first: Joanna

last: Achinger-Kawecka

state: SA

address: AHMS Building, North Terrace

country: Australia

institute: South Australian Immunogenomics Cancer Institute

summary: Deregulation of the chromatin remodeller BRG1 contributes to a wide range of malignancies. In prostate cancer BRG1 is over expressed, however, the underlying function and cellular consequences of this are still being uncovered. Here, we have investigated the role of BRG1 in transcription regulation in prostate cancer. We found that BRG1 is over expressed in both the TCGA prostate cancer cohort as well as a panel of prostate cancer and transformed prostate cell lines. We then utilised a temporal model of BRG1 depletion followed by mRNA-seq to examine changes in gene expression. Surprisingly, we detected a modest overall effect, however, a number of genes associated with proliferation and cell cycle progression were down regulated. We find these genes were in part, co-regulated by AR and FOXA1. Corresponding cell cycle analysis conferred G1 arrest, and altered nuclei morphology with depletion of BRG1. This data provides mechanistic insight into the function of BRG1 in prostate cancer.

overall_design: RNA-seq was conducted in LNCaP cells following SMARCA4/BRG1 knock-down.

first: Katherine

last: Giles


title: TET2 is a component of the ER complex and controls 5mC to 5hmC conversion at ER cis-regulatory regions

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Epigenetic silencing of miR-144/451a cluster contributes to HCC progression via paracrine HGF/MIF-mediated macrophage remodeling [miRNA-seq]

status: Public on Feb 09 2021

city: Xi'an

first: Li

middle: hui

last: chen

address: No.169 Changlexi Road

department: Biochemistry and Molecular Biology

institute: Fourth Military Medical University

summary: The HCC and adjacent NH tissues were isolated from 9 HCC patients and RNA was extracted from the paired samples.

first: Huichen

first: Lei

last: Liu


title: Development of Double-positive Thymocytes at Single-cell Resolution

status: Public on Feb 13 2021

city: Hefei

first: Kun

last: Qu

address: University of Science and Technology of China, No.96, JinZhai Road Baohe District

summary: We applied single-cell sequencing to mouse thymocytes and analyzed the transcriptome data using Seurat. By applying unsupervised clustering, we defined thymocyte subtypes and validated DP cell subtypes by flow cytometry. We classified the cell cycle phases of each cell according to expression of cell cycle phase-specific genes. For immune synapse detection, we used immunofluorescent staining and ImageStream-based flow cytometry. We studied and integrated human thymocyte data to verify the conservation of our findings and also performed cross-species comparisons to examine species-specific gene regulation. We classified blast, rearrangement and selection subtypes of DP thymocytes and used the surface markers CD2 and Ly6d to identify these subtypes by flow cytometry. Based on this new classification, we found that the proliferation of blast DP cells is quite different from that of double-positive cells and other cell types, which tend to exit the cell cycle after a single round. At the DP cell selection stage, we observed that CD8-associated immune synapses formed between thymocytes, indicating that CD8sp selection occurred among thymocytes themselves. Moreover, cross-species comparison revealed species-specific transcription factors (TFs) that contribute to the transcriptional differences of thymocytes from humans and mice. Our study classified DP thymocyte subtypes of different developmental stages and provided new insight into the development of DP thymocytes at single-cell resolution, furthering our knowledge of the fundamental immunological process of thymopoiesis.

overall_design: single-cell RNA and ATAC sequencing of mouse thymocytes

first: Y

first: K

first: L

last: Zhu

first: B

first: D

last: Zong

first: P

last: Cai

first: C

last: Jiang

last: Du

first: J

last: Lin


title: Modeling expression ranks for noise-tolerant differential expression analysis of scRNA-Seq data

city: Delhi

first: Debarka

last: Sengupta

state: Delhi

address: IIIT Delhi, Okhla Phase 3

department: Computational Biology and Computer Science

country: India

institute: Indraprastha Institute of Information Technology

summary: Systematic delineation of complex biological systems is an ever-challenging and resource-intensive process. Single-cell transcriptomics allows us to study cell-to-cell variability in complex tissues at an unprecedented resolution. Accurate modeling of gene expression plays a critical role in the statistical determination of tissue-specific gene expression patterns. In the past few years, considerable efforts have been made to identify appropriate parametric models for single cell expression data. The zero-inflated version of Poisson/Negative Binomial and Log-Normal distributions have emerged as the most popular alternatives due to their ability to accommodate high dropout rates, as commonly observed in single cell data. While the majority of the parametric approaches directly model expression estimates, we explore the potential of modeling expression-ranks, as robust surrogates for transcript abundance. Here we examined the performance of the Discrete Generalized Beta Distribution (DGBD) on real data and devised a Wald-type test for comparing gene expression across two phenotypically divergent groups of single cells. We performed a comprehensive assessment of the proposed method, to understand its advantages as compared to some of the existing best practice approaches. Besides striking a reasonable balance between Type 1 and Type 2 errors, we concluded that ROSeq, the proposed differential expression test is exceptionally robust to expression noise and scales rapidly with increasing sample size. For wider dissemination and adoption of the method, we created an R package called ROSeq, and made it available on the Bioconductor platform.

overall_design: Two single cell dataset are included: (1) 150 single human foreskin BJ fibroblast cells (2) 352 single K562 cells were profiled using Fluidigm based single cell RNA-seq protocol to characterized cellular heterogeneity of two phenotypically divergent cells. In addition, RNA expression profiling of bulk cells (3 replicates for BJ and 4 replicates for K562) were performed in tubes. Polaris™ integrated fluidic circuit (IFC) was used to sequester up to 48 single cells per cell type per one IFC run using Polaris system. The captured single cells were processed for cell lysis, reverse transcription (RT), and full-length transcriptome amplification using template-switching chemistry. Following harvest from the IFC, sequencing libraries are generated using a modified Nextera® protocol and sequenced on Illumina® NextSeq 500 platform.

first: Krishan

last: Gupta

first: Naveen

last: Ramalingam


title: TET2 is a component of the ER complex and controls 5mC to 5hmC conversion at ER cis-regulatory regions [ChIP-Seq]

first: Jason

last: Carroll

overall_design: ChIP-seq in breast cancer cell lines, either untreated, or in response to TET2 knockdown or fulvestrant treatment. Additionally, ChIP-seq in untreated PDX samples.

first: Rebecca

first: Igor

last: Chernukhin


title: CDK9 inhibitor induces the apoptosis of acute lymphocytic leukemia by inhibiting c-Myc-mediated glycolytic metabolism

city: Shanghai

first: xia

last: jing

address: 1678 Dongfang Road

institute: Shanghai Children’s Medical Center

summary:
Purpose:the inhibitory effect of CDK9i on the energy metabolism of B-ALL cells remains unclear. To address this question, we collected SNS-032- and DMSO-treated cells for RNA sequencing
Methods:REH cells were seeded at a density of 1× 106 cells/ml and treated with 200nm SNS_032 or DMSO for 24h.
Results:CDK9i perturbs the glycolytic metabolism of B-ALL cells in vitro.

overall_design: REH total mRNA profiles treated with 200nm SNS_032 or DMSO for 24h.

first: Wen-Li

last: Huang

first: Tuersunayi

last: Abudureheman

first: Sa

last: Guo

first: Gang

last: Yin

first: Cai-Wen

last: Duan


title: Dynamic Epigenetic Changes during a Relapse and Recovery Cycle in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome

city: Dunedin

first: Amber

last: Helliwell

address: 710 Cumberland Road

department: Biochemistry Department

country: New Zealand

institute: University of Otago

summary:
Purpose: ME/CFS is a debilitating and complex disease. The majority of patients exist in a chronic state of health where they are affected by relapse events. Precision medicine following patients can capture changes in the DNA methylation indicative of biological dysfunction
Methods: DNA was extracted from the PBMCs of 2 ME/CFS patients and a age/gender matched control at five different time points. After performing RRBS the sequence was aligned to hg19 genome using Bismark. The data was analyzed using a Chi squared test through DMAP in order to determine variation between the patient and control groups across 40-220bp fragments of the genome.
Results: A total of 17 and 14 statistically significant variably methylated fragements were indentified in each patient that strongly associated with a relapse event. These fragements were found on regions of regulatory importance of the genome that associated with immune (primarily inflammatory) and metabolic function.
Conclusions:  Our study represents the first investigation of ME/CFS patients using reduced representation bisulfite sequencing along a longitudinal timeframe. We captured a number of major variably methylated fragments in each patient that associated with their relapse events. Our results identified a number of differentially methylated regulatory elements and gene bodies that highlight the disturbed pathophysiology in ME/CFS. DNA methylation that differentiates disease variability in ongoing ME/CFS may have practical applications for strategies to deacrease the frequency and severity of relapse events.

overall_design: RRBS Analysis of 2 ME/CFS patients and matched control over eleven months

first: Warren

last: Tate

first: Aniruddha

last: Chatterjee

first: Peter

last: Stockwell

first: Tina

last: Edgar


title: Transcriptomic analysis of primary Müller glial cells (pMGCs) and human induced pluripotent stem cell-derived Muller glial cells (hiMGCs)

city: Paris

first: Xavier

last: Guillonneau

address: 17 rue Moreau

department: Institut de la vision

country: France

institute: INSERM

summary: Muller glial cells (MGCs) are responsible for the homeostatic and metabolic support of the retina. Despite the importance of MGCs in retinal disorders, reliable and accessible human cell sources to be used to model MGC-associated diseases are lacking. Although primary human MGCs (pMGCs) can be purified from post-mortem retinal tissues, the donor scarcity limits their use. To overcome this problem, we developed a protocol to generate and bank human induced pluripotent stem cell-derived MGCs (hiMGCs). Using a transcriptome analysis, we showed that the 3 genetically independent hiMGCs generated were homogeneous and showed phenotypic characteristics and transcriptomic profile of pMGCs. These cells expressed key MGC markers, including Vimentin, CLU, DKK3, SOX9, SOX2, S100A16, ITGB1 and CD44 and could be cultured up to passage 8. Under our culture conditions, hiMGCs and pMGCs expressed low transcript levels of RLPB1, AQP4, KCNJ1, KCJN10 and SLC1A3. Thus, hiMGCs could be an alternative to pMGCs and an extremely valuable tool to help to understand and model glial cell involvement in retinal disorders, including DR.

overall_design: Examination of Müller glial cell transcriptome by RNAseq analysis

first: G

last: Blot

first: J

last: Roger

first: S

last: Reichman

first: X


title: RNAseq analysis of blood from HIV-infected-only and HIV-flu-coinfected patients and healthy controls

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

department: Virology

institute: University Münster

summary:
Gene expression changes in the blood was studied by RNAseq
Results: Highly damped host immune response in HIV patients after influenza infection

overall_design: Peripheral blood was collected from patients, RNA was isolated and sequenced.


title: Gene expression profiling of shRNA transduced rat hippocampal neurons

city: Kodaira

first: Hitomi

last: Matsuno

state: Tokyo

address: 4-1-1 Ogawa-Higashi

department: Department of Mental Disorder Research

institute: NCNP National Institute of Neuroscience

summary: Sirtuin 6 (SIRT6), a member of the sirtuin family, acts as nicotinamide adenine dinucleotide-dependent protein deacetylase, mono-adenosine diphosphate-ribosyltransferase, and fatty acid deacylase and plays critical roles in inflammation, aging, glycolysis, and DNA repair. Accumulating evidence has suggested that SIRT6 is involved in brain functions such as neuronal differentiation, neurogenesis, and learning and memory. However, the precise molecular roles of SIRT6 during neuronal circuit formation are not well understood. In this study, we attemped to elucidate the molecular roles of SIRT6 on neurite development using a primary culture of hippocampal neurons. We observed that SIRT6 was abundantly localized in the nucleus, and its expression was markedly increased during neurite outgrowth and synaptogenesis. Using shRNA-mediated SIRT6 knockdown, we showed that the dendritic length and number of dendrite branches were significantly reduced in SIRT6 knockdown neurons. Microarray and subsequent gene ontology analysis revealed that reducing SIRT6 caused the downregulation of immediate early genes (IEGs) and alteration of several biological processes including MAPK (ERK1/2) signaling. We found that nuclear accumulation of phosphorylated ERK1/2 was significantly reduced in SIRT6 knockdown neurons. Overexpression of SIRT6 promoted dendritic length and branching, but the mutants lacking deacetylase activity had no significant effect on the dendritic morphology. Collectively, the presented findings reveal a role of SIRT6 in dendrite morphogenesis and suggest that SIRT6 may act as an important regulator of the ERK1/2 signaling pathway that mediates IEG expression, which leads to dendritic development.

overall_design: To understand the molecular function of SIRT6 in neuronal morphogenesis, we performed microarray analysis using total RNA isolated from shRNA transduced rat hippocampal neurons.


title: Ribonuclease J modulates cell shape, exotoxin production, and virulence in Corynebacterium diphtheriae

status: Public on Feb 08 2021

city: Bielefeld

first: Manuel

last: Wittchen

address: Universitaetsstr. 27

department: Center for Biotechnology

institute: Bielefeld University

summary: RNA degradation is a crucial process in bacterial cells for maintaining proper transcriptome homeostasis and coping with changing environments. A specialized ribonuclease known as RNase J (RnJ) participates in mRNA turnover in many Gram-positive bacteria; however, nothing is known about this process in Corynebacterium diphtheriae, nor is the identity of this RNase. We report here that C. diphtheriae DIP1463 encodes a predicted RnJ homolog, comprised of an N-terminal beta-lactamase domain, followed by beta-CASP and C-terminal domains. We show that a recombinant protein encompassing the beta-lactamase domain possessed 5’-exoribonuclease activity, which was abolished by alanine-substitution of conserved catalytic residues His186 and His188. Intriguingly, deletion of DIP1463/rnj in C. diphtheriae caused slow growth and augmented cell width. Comparative RNA-seq analysis revealed that RnJ controls a large regulon encoding many factors predicted to be involved in biosynthesis, regulation, transport, and iron acquisition. One up-regulated gene in ∆rnj mutant is ftsH, coding for the cell division protein FtsH, an inner membrane protease. Interestingly, overexpression of FtsH in the wild-type strain also caused cell-width augmentation. However, unlike the rnj mutant, which was attenuated in a Caenorhabditis elegans model of infection, the FtsH-overexpressing strain exhibited the same virulence phenotype as the wild-type strain. Remarkably, under iron-depleted conditions, production of the exotoxin diphtheria toxin was significantly reduced in the rnj mutant compared to the wild-type strain, likely due to dysregulated secretion of the toxin. Evidently, RNase J is a key ribonuclease that post-transcriptionally influences the expression of factors vital to C. diphtheriae physiology and virulence.

overall_design: Examination of RNase J deficient mutant compared to wildtype in biological triplicates

first: Truc

middle: T

last: Luong

first: Minh

last: Nguyen

first: Yi-Wei

last: Chen

first: Chungyu

last: Chang

first: Ju

middle: H

last: Lee

first: HyLam

last: Ton-That

first: Melissa

last: Cruz

first: Danielle

last: Garsin

first: Asis

last: Das

first: Andreas

last: Tauch

first: Hung


title: small non-coding RNA expression profile in F1 progeny from irradiated adults zebrafish

city: Oslo

first: Leonardo

middle: Martin

last: Martin

address: Ullevålsveien 72

department: Basic Sicences and Aquatic medicine

country: Norway

institute: Norwegian University of Life Sciences

summary: In order to investigate transcriptomic mechanisms underlying radiation exposure, we exposed zebrafish (~6 month old) to 8.7 mGy/h of g-radiation (5.2 Gy total dose) during gametogenesis for 27 days. F1 offspring from exposed parents were sampled at 5.5 hpf (late blastula/early gastrula) one year after parental exposure, for small RNA sequence analysis to determine changes in the sncRNA expression profile. Pairwise comparison between F1 generation from exposed (F1-γ), and control (F1-C) parents, revealed several classes of sncRNAs and one class of lncRNA differentially expressed. Overall, 22 miRNAs, 11 piRNA clusters, 19 snRNAs, and 21 lincRNA were found differentially expressed. When linking the DEmiRs to our previously published mRNA data, a total of 672 differentially expressed mRNAs could be linked to the DEmiRs, of which 380 followed the canonical inverse relation in miRNA-mRNA interaction. Pathway analysis revealed these 380 mRNAs involved in insulin receptor, NFkB and PTEN signaling, linking to apoptosis and cancers. The 84.2% of differentially expressed snRNAs were down-regulated in the F1-γ group, 68.8% of which were U1 and U2 snRNAs. In addition, 45% of differentially expressed DEpiRNA clusters were found associated to 9 TEs (LTR, LINE, and TIR) (p=0.0024). DEpiRNA clusters were expressed from the opposite strand of the associated TEs, indicating expression of DEpiRNAs in response to activation of TEs. Finally, 66.7% and 33.3% of lincRNAs in F1-γ were down- and up-regulated respectively. The cancer and development related lincRNAs malat-1 was found among the most down-regulated genes, denoting a link between lincRNAs expression and altered phenotypes reported previously in our parallel studies.

overall_design: One year after parental exposure during gametogenesis to 60Co source at 8.7 mGy/h (5.2 Gy total dose), three biological replicates of F1 embryos were collected in pools of 100 individuals from both exposed and control groups. Total RNA corresponding to sampled embryos in each experimental group was extracted and sent for small RNA sequencing under platform Illumina 4000. The 6 small RNA libraries obtained from 3 biological replicates in each experimental group were analyzed for small non-coding RNA profiling and differential expression.

last: Martín

first: Jorke

last: Kamstra

first: Selma

last: Hurem

first: Leif

middle: C

last: Lindeman

first: Vidar

last: Berg

first: Dag

last: Brede

first: Hans

last: Teien

first: Ole

last: Lind

first: Håvard

last: Aanes

first: Igor

last: Babiak

first: Amilcar

last: Arenal

first: Brit

last: Salbu

first: Jan

last: Lyche

first: Peter

last: Aleström


title: Epigenetic silencing of miR-144/451a cluster contributes to HCC progression via paracrine HGF/MIF-mediated macrophage remodeling [mRNA]

first: Li

last: chen

summary: TAMs of tumor-bearing mice were isolated via FACS, and RNA was extracted and sequencing was performed at Genergy Co., Ltd.

overall_design: TAMs from mice bearing orthotopic HCC were next sorted for RNA-seq to detect if the anti-tumor cytokines or molecules were increased upon miR-144 or miR-451a overexpression in HCC cells. For Functional analysis of the cluster further indicated that pathways of immune system process and inflammatory response were altered remarkably when miR-144 or miR-451a was overexpressed

first: Huichen

last: Li

first: Lei

last: Liu


title: RNA sequencing of Wild-Type MA-10 cells and STAR Knockout MA-10 cells

city: Los Angeles

first: Melanie

last: Galano

state: California

address: 1985 Zonal Ave

institute: University of Southern California

summary: The purpose of this study was to identify differentially-expressed genes between WT MA-10 mouse tumor Leydig cells and MA-10 cells in which the steroidogenic acute regulatory protein (STAR) is knocked out.

overall_design: Gene expression profile of MA-10 and STAR KO MA-10 mouse tumor Leydig cells

first: Yuchang

first: Lu

first: Chantal

last: Sottas

first: Vassilios

last: Papadopoulos


title: Mesenchymal Stem Cells (MSCs) Alleviate Experimental Immune-mediated Liver Injury via Chitinase 3-like protein 1-mediated T cell suppression

city: Guangzhou

first: Yan

last: Xu

address: No. 600 Tianhe Road

department: Biotherapy Center

institute: The Third Affiliated Hospital of Sun Yat-Sen University

summary: RNA-seq for MSCs from human bone marrow (BM-MSCs), olfactory mucosa (OM-MSCs), and umbilical cord (UC-MSCs) (2 donors for each). RNA-sequencing for human naïve CD3+ T cells, CD3+ T cells activated with PHA (2.5 μg/mL) for 48 h， and CD3+ T cells co-cultured with human UC-MSCs in the presence of PHA for 48 h.

overall_design: MSCs from bone marrow (BM-MSCs), olfactory mucosa (OM-MSCs), and umbilical cord (UC-MSCs) (2 donors for each) were collected and sequenced to identify the differently expressed genes and related pathways. FACS sorted human naïve CD3+ T cells, CD3+ T cells activated with PHA (2.5 μg/mL) for 48 h, and CD3+ T cells co-cultured with human UC-MSCs in the presence of PHA for 48 h were collected and sequenced to identify the differently expressed genes and related pathways.

first: Qi

last: Zhang

first: Andy

middle: P

last: Xiang

first: Qiuli


title: Expression data from mouse skin fibroblasts in homeostasis, inflammation and cancer

city: Zwijnaarde

first: VIB

last: Single Cell Core

address: Technologiepark-Zwijnaarde 71

department: VIB Single cell core

country: Belgium

institute: VIB

summary: Fibroblasts are highly heterogenous and can exhibit distinct phenotypes depending on their activation state. To evaluate the specific phenotype of fibroblasts involved in inflammation versus wound-induced skin tumorigenesis, a genome-wide expression study was performed comparing gene expression profiles of ‘normal’, ‘inflammatory’ and ‘papilloma-associated’ fibroblasts.

overall_design: There are 12 samples, consisting of 3 conditions (normal skin, inflamed skin, tumor-associated skin) in 4 replicates, where one of the conditions is a control.


title: Genome-wide analysis of genes regulated by AhR

city: Foster City

first: Luhua

middle: Hedberg

state: CA

address: 746 Pinta Ln

institute: Stanford University

summary: Analysis of gene expression changes due to lack of AhR in NK cells.  Cytokine activated NK cells upregulate expression of AhR and display homeostatic and  functional defects.  Goal of this study was to identify gene expression changes associated with NK cell activity.

overall_design: Total RNA obtained from IL-2 stimulated mouse splenic NK cells from AhR+/+ and AhR-/- mice.

first: John

last: Sunwoo


title: DNA hypomethylating agents increase activation and cytolytic activity of CD8+ T-cells

city: Toronto

first: Daniel

last: De Carvalho

state: Ontario

address: 101 College St

department: Princess Margaret Cancer Centre

country: Canada

institute: UHN

summary: DNA hypomethylating agents (HMAs) induce Type I/III interferon signaling through dsRNA-mediated viral mimicry in cancer cells. Yet, the direct effects of HMAs in immune cells remains less clear. Here, we demonstrate that HMA treatments can directly modulate the anti-tumor response and effector function of CD8+ T-cells. In vivo HMA treatment promotes CD8+ T-cell tumor infiltration and supresses tumor growth via CD8+ T-cell dependent activity. HMAs enhances primary human CD8+ T-cells activation markers, effector cytokine production, and anti-tumor cytolytic activity. Epigenomic and transcriptomic profiling shows that HMAs vastly regulate T-cell activation related transcriptional networks, culminating with over-activation of NFATc1 short-isoforms. Mechanistically, demethylation of an intragenic CpG Island immediately downstream to the 3'UTR of the short isoform was associated with anti-sense transcription and alternative polyadenylation of NFATc1 short-isoforms. High-dimensional single-cell mass cytometry (CyTOF) analyses reveal a selective effect of HMAs on a subset of human CD8+ T-cell subpopulations, resulting in an increase in both number and abundance of a granzymeBhigh, perforinhigh effector subpopulation. Overall, our findings support the use of HMAs as a therapeutic strategy to boost anti-tumor immune response.

overall_design: ATAC-seq profiling of primary human CD8+ T-cells under the following conditions: unstimulated; stimulated with α-CD3/CD28; stimulated with α-CD3/CD28 and treated with 300 nM Decitabine.

first: Emma

last: Bell

first: Helen

last: Loo

first: Ankur

last: Chakravarthy

middle: D


title: Assessing the influence of DNMTi on human CD8+ T cells on a global level using methylome and transcriptome analyses.

state: ON

institute: Princess Margaret Cancer Centre

summary: RRBS (Reduced Representation Bisulfite Sequencing) and RNA-seq were performed on human CD8+ T cells from peripheral blood of three independent healthy donors to study the influence of DNMTi on CD8+ T cells on a global level.

overall_design: The experiments were performed on unstimulated or resting CD8+ T cells (Day 0), CD8+ T cells stimulated with anti-CD3 and anti-CD28 ex vivo in the absence of 5-AZA-CdR (Day 5 Stimulated) or in the presence of 300nM of 5-AZA-CdR (Day 5 Stimulated + AZA).

first: Rajat

last: Singhania

last: Yau

first: Roxana

last: Shen


title: Proximity-dependent mapping of the Androgen Receptor identifies Kruppel-Like Factor 4 as a functional partner

city: Quebec

first: Steve

last: Bilodeau

state: Quebec

address: 2260 boul. Henri-Bourassa

institute: Centre de recherche du CHU de Québec-Université Laval

summary: Prostate cancer (PCa) is the most frequently diagnosed cancer in men and the third cause of cancer mortality. PCa initiation and growth is driven by the androgen receptor (AR). The AR is activated by androgens such as testosterone and controls prostatic cell proliferation and survival. Here, we report an AR signalling network generated using BioID proximity labeling proteomics in androgen-dependent LAPC4 cells. We identified 31 AR associated proteins in non-stimulated cells. Strikingly, the AR signalling network increased to 182 and 200 proteins, upon 24h or 72h of androgenic stimulation, respectively, for a total of 267 total non-redundant AR-associated candidates. Among the latter group, we identified 213 proteins that were not previously reported in databases. Many of these new AR-associated proteins are involved in DNA metabolism, RNA processing and RNA polymerase II transcription. Moreover, we identified 44 transcription factors, including the Krüppel-like factor 4 (KLF4), which were found interacting in androgen-stimulated cells. Interestingly, KLF4 repressed the well-characterized AR-dependent transcription of the KLK3 (PSA) gene; AR and KLF4 also colocalized genome-wide. Taken together, our data report an expanded high-confidence proximity network for AR, which will be instrumental to further dissect the molecular mechanisms underlying androgen signalling in PCa cells.

overall_design: Genome-wide binding of KLF4 and AR transcription factors in control and DHT-stimulated LAPC4 cells

first: Lauriane

last: Vélot

first: Frédéric

last: Lessard

first: Félix-Antoine

last: Bérubé-Simard

first: Christophe

last: Tav

first: Bertrand

last: Neveu

first: Valentine

last: Teyssier

first: Imène

last: Boudaoud

first: Ugo

last: Dionne

last: Pouliot

first: Nicolas

last: Bisson


title: TET2 is a component of the ER complex and controls 5mC to 5hmC conversion at ER cis-regulatory regions [RNA-Seq]

city: Cambridge

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

institute: Cancer Research UK, Cambridge Institute

summary: Estrogen receptor-a (ER) drives tumour development and metastasis in ER positive (ER+) breast cancer. GATA3 is a transcription factor that has been closely linked to ER function, but the role of GATA3 in ER transcriptional activity is not clear. We sought to identify the contribution of GATA3 to the ER complex by conducting quantitative multiplexed rapid immunoprecipitation mass spectrometry of endogenous proteins (qPLEX-RIME) to assess changes to the ER complex in response to GATA3 depletion. Unexpectedly, very few proteins were dissociated from the ER complex in the absence of GATA3, with the only major change being depletion of TET2 from the ER complex. In breast cancer cells and Patient-Derived Xenograft (PDX) tissue, TET2 binding events were shown to constitute a near-total subset of ER binding events, and loss of TET2 was functionally associated with reduced activation of proliferative pathways. To investigate the TET2-ER relationship, the role of TET2 in regulating DNA modifications in ER+ breast cancer cells was examined. TET2 knockdown did not appear to result in changes to global DNA methylation, however, oxidation of methylated DNA to 5-hydroxymethylcytosine (5hmC) was significantly reduced after TET2 depletion and these events occurred at ER enhancers. These findings implicate TET2 in the production and maintenance of 5hmC at ER sites, providing a potential mechanism for TET2-mediated regulation of ER target genes.

overall_design: RNA-seq in human breast cancer cell line MCF7 in response to siRNA-mediated knockdown of ER, GATA3 or TET2.

first: Rebecca

last: Broome

first: Igor

last: Chernukin


title: DDX41 inhibits cancer cell proliferation and regulates immune response expression

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: DDX41, a member of the DEXDc family of helicases and an innate immune protein, senses cytosolic DNA and bacterial secondary messengers and initiates signaling via the adaptor STING to induce type 1 interferon (IFN) response in dendritic cells. However, DDX41 function in tumor progression is poorly understood. Here we found that the DDX41 inhibited proliferation and promoted apoptosis, reported the whole transcriptome profiling in HeLa cells. RNA-seq analyses revealed that the overexpression of DDX41 resulted in 959 genes being differentially expressed (504 up-regulated and 455 down-regulated) compared to the control in HeLa cells. Interestingly, functional clustering pathway enrichment analysis of transcription identified antigen processing and presentation pathways were significantly activated in DDX41 overexpression samples, but alternative splicing enriched in the epidermal growth factor receptor signaling pathway and fibroblast growth factor receptor signaling pathway. The five antigen processing and processing genes, which could regulate cross-presentation of antigens and protective antitumor immune responses, were significantly upregulated, suggesting DDX41 is the key player in tumor immunity. In conclusion, our RNA-seq data identified molecules and pathways involved in the mechanisms of DDX41 that adds to the understanding of critical DDX41 tumorigenesis functions.

overall_design: transcrptional analysis of DDX41 overexpression and control in Hela cells

first: Juan

last: Wang


title: Inflammatory cell-derived CXCL3 promotes pancreatic cancer metastasis through a novel myofibroblast-hijacked cancer escape mechanism

status: Public on Feb 06 2021

city: shanghai

first: XIAOTING

last: SUN

state: SHANGHAI

address: 1200 cailun Road

department: shuguang hospital

institute: shanghai university of TCM

summary:
Objective: Pancreatic ductal adenocarcinoma (PDAC) is the most lethal malignancy and lacks effective treatment. We aimed to understand molecular mechanisms of the intertwined interactions between tumor stromal components in metastasis and to provide a new paradigm for PDAC therapy.
Design:Two unselected cohorts of 154 and 20 PDAC patients were subjected to correlation between IL-33 and CXCL3 levels and survivals. Unbiased expression profiling, and genetic and pharmacological gain- and loss-of-function approaches were employed to identify molecular signaling in TAMs and myoCAFs. The role of the IL-33-ST2-CXCL3-CXCR2 axis in PDAC metastasis was evaluated in 3 clinically relevant mouse PDAC models and in a zebrafish model.
Results: IL-33 was specifically elevated in human PDACs and positively correlated with tumor inflammation in human PDAC patients. CXCL3 was highly upregulated in IL-33-stimulated macrophages that were the primary source of CXCL3. CXCL3 was correlated with poor survival in human PDAC patients. Mechanistically, activation of the IL-33-ST2-Myc pathway attributed to high CXCL3 production. The highest level of CXCL3 was found in PDAC relative to other cancer types and its receptor CXCR2 was almost exclusively expressed in CAFs. Activation of CXCR2 by CXCL3 induced a CAF-to-myoCAF transition and a-SMA was uniquely upregulated by the CXCL3-CXCR2 signaling. Type III collagen was identified as the CXCL3-CXCR2-targeted adhesive molecule responsible for myoCAF-driven PDAC metastasis.
Conclusions: Our work provides novel mechanistic insights into understanding PDAC23 metastasis by the TAM-CAF interaction and targeting each of these signaling components would provide an attractive and new paradigm for treating pancreatic cancer.

overall_design: Primary fibroblast treated with CXCL3 or Control for 48h (n=3 samples/group)

first: Xiaoting

last: Sun

first: Yunlong

last: Yang

first: Qi

last: Li

first: Yihai

last: Cao


title: Transcriptional profiling of DNA damage tolerant (DDT) lymphomas after treatment either with Albendazole, Ethidium bromide or DMSO as a control

status: Public on Feb 05 2021

city: Amsterdam

first: Heinz

last: jacobs

address: Plesmanlaan 121

institute: NKI

summary: We studied the role of Albendazole in inducing loss of heterozygosity. Here, we generated RNA-seq data from DDT lymphomas after 12 hours of treatment either with Albendazole (400nM), Ethidium bromode (400 nM) or DMSO as a control.

overall_design: Transcriptional changes in DDT lymphomas after 12 hrs of treatment either with Albendazole (400nM), Ethoidium bromode (400 nM) or DMSO as a control were compared. Three biological replicates were analysed for each treatment for differential gene expression.

first: Mir

middle: F

last: Alemdehy

first: Muhammad

middle: A

last: Aslam


title: Stress-induced nuclear condensation of NELF drives global transcriptional downregulation

city: Freiburg

first: Barbara

last: Hummel

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: In response to stress, human cells actively downregulate ongoing gene expression programs. Translational downregulation is accompanied by the assembly of stress granules which are cytosolic condensates containing ribosomes and mRNA. Transcriptional downregulation is caused by an increased recruitment of Negative Elongation Factors (NELF) to promoters, inhibiting RNA Pol II elongation. We report here that NELF forms nuclear condensates upon stress which can be recapitulated by liquid-liquid phase separation of recombinant NELF in vitro. Stress leads to rapid dephosphorylation and SUMOylation of NELF in cells facilitating condensate formation driven by intrinsically disordered domains of NELFA and NELFE subunits. Using NELF mutants that do not form condensates we provide evidence that condensation is required for increased recruitment of NELF to downregulated promoters and cellular survival in stress. Thus, our study has uncovered a novel nuclear condensate that is conceptually similar to cytosolic stress granule in downregulating gene expression during stressful conditions.

overall_design:
Effect of SUMOylation to chromatin binding of RNA polymerase II was studied in UBE2I silenced (siRNA for UBE2I) and control (non-targeting siRNA transfected, siNON) VCaP cells (non-stressed or heat shocked (30 min at 43C)). All samples were done as biological replicates.

Slam-seq analysis pf HeLa cells to identify the effect of NELF condensates on transcription.

first: Prashant

last: Rawat

first: Ritwick

last: Sawarkar


title: miR-99 overexpression modulates neutrophil migration

city: West Lafayette

first: Qing

last: Deng

state: Indiana

address: 915 W. State Street

department: Department of Biological Sciences

institute: Purdue University

summary: We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils, and RNAseq for identification of mRNA targets of  miRNA-99 in neutrophils

overall_design:
For miR-99 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR1-99 or vector control

**Please note that the duplicated vector* sample records (of GSE127174 samples) have been created as the samples have been re-used in the current study and for the convenient retrieval of the complete raw data from SRA.

first: Alan

middle: Y

last: Hsu

first: Sheng

last: Liu

first: Jun

last: Wan


title: Epigenetic silencing of miR-144/451a cluster contributes to HCC progression via paracrine HGF/MIF-mediated macrophage remodeling

city: Xi'an

first: Li

last: chen

address: No.169 Changlexi Road

institute: Fourth Military Medical University

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: The human ApoE4 variant reduces functional recovery and neuronal sprouting after incomplete spinal injury in male mice

city: New York

first: Jens

last: Hansen

state: NY

address: 1425 Madison Ave

department: Department of Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Patients carrying one or two ApoE4 alleles suffer from worse functional recovery after spinal cord injury. Using transgenic mice expression human ApoE3 or ApoE4 we investigated potential cellular mechanisms of reduced recovery after spinal cord injury. Bulk RNA sequencing of the spinal cord lesion site followed by pathway enrichment analysis predicts that ApoE4 mice have a higher inflammatory and extracellular matrix remodeling activity 7 days after spinal cord injury. Contrary, higher activities for neuronal projection and action potential patways were predicted in the ApoE3 mice at 21 days after injury.

overall_design: Examination of differentially expressed genes at the lesion site at 7 and 21 days after spinal cord injury between ApoE4 and ApoE3 mice

first: Carlos

last: Toro

first: Mustafa

last: Siddiq

first: Kaitlin

last: Johnson

first: Wei

last: Zhao

first: Daniella

last: Azulai

first: Dibash

middle: K

last: Das

first: William

last: Bauman

first: Robert

last: Sebra

first: Dongming

last: Cai

first: Ravi

last: Iyengar

first: Christopher

last: Cardozo


title: The effects of selective inhibition of histone deacetylase 1 and 3 in Huntington’s disease mice

status: Public on Feb 04 2021

city: Berlin

first: Katharina

last: Hecklau

address: Charitéplatz 1, Virchowweg 6

institute: Charité-Universitätsmedizin Berlin

summary: Huntington’s disease (HD) is an autosomal dominant neurodegenerative disease characterized by a late clinical onset of psychiatric, cognitive, and motor symptoms. Transcriptional dysregulation is an early and central disease mechanism which is accompanied by epigenetic alterations in HD. Previous studies demonstrated that targeting transcriptional changes by inhibition of histone deacetylases (HDACs), especially the class I HDACs, provides therapeutic effects. Yet, their exact mechanisms of action and the features of HD pathology, on which these inhibitors act remain to be elucidated. Here, using transcriptional profiling, we found that selective inhibition of HDAC1 and HDAC3 by RGFP109 alleviated transcriptional dysregulation of a number of genes, including the transcription factor genes Neurod2 and Nr4a2, and gene sets and programs, especially those that are associated to insulin-like growth factor pathway, in the striatum of R6/1 mice. RGFP109 treatment led to a modest improvement of the motor skill learning and coordination deficit on the RotaRod test, while it did not alter the locomotor and anxiety-like phenotypes in R6/1 animals.  We also found, by volumetric MRI, a widespread brain atrophy in the R6/1 mice at the symptomatic disease stage, on which RGFP109 showed no significant effects. Collectively, our combined work suggests that specific HDAC1 and HDAC3 inhibition may offer benefits for alleviating the motor phenotypic deficits and transcriptional dysregulation in HD.

overall_design: RNA-seq in striatum of R6/1 and wild type (WT) mice (14-17 weeks of age).

first: Ferah

last: Yildirim


title: A bladder cancer patient-derived xenograft reflects aggressive growth dynamics in vivo and in organoids

status: Public on Feb 03 2021

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

summary: A MIBC patient with aggressive disease course was selected for ex vivo model establishment and growth dynamic studies. After standard neoadjuvant treatment with gemcitabine and cisplatin, cystectomy was performed, and excised urothelial carcinoma tissue was implanted subcutaneously into male SCID mice to generate CoCaB1 PDXs.  Established PDXs were passaged subcutaneously in SCID mice to generate early and late passage models for functional and molecular characterization.  Representative early and late passage PDXs were collected for organoid establishment.

overall_design: Bladder cancer is among the most prevalent cancers worldwide, but few well-characterized and representative laboratory models exist for use in therapy development. Here, we establish and molecularly characterize CoCaB1, a muscle-invasive bladder cancer patient-derived xenograft (PDX) and companion organoid system. PDX and organoids demonstrate concordant acceleration in growth upon serial passaging, suggesting the expansion of aggressive subclones. Transcriptome analysis revealed progression towards an increasingly proliferative and stem-like expression profile. Gene expression differences between organoid and PDX models reflected expected differences in cellular composition. Despite transcriptional changes, our models successfully maintained the histological identity and mutational heterogeneity of their parental tumor. These studies establish the CoCaB1 PDX and organoid system as companion representative tumor models for the development of novel bladder cancer therapies.

first: Elise

first: Andrew

last: Hsieh

first: Hung-Ming

last: Lam


title: Ly6C monocyte subsets transcriptome analysis from wild type and hyperhomocysteinemic mice

status: Public on Feb 02 2021

city: Philadelphia

first: Hong

last: Wang

state: PA

address: 3500 N Broad St. MERB1060

department: CMDR

institute: Temple University Lewis Katz School of Medicine

summary: Murine monocytes (MC) are classified into Ly6Chigh and Ly6Clow MC. Ly6Chigh MC is the pro-inflammatory subset and the counterpart of human CD14++CD16+ intermediate MC which contributes to systemic and tissue inflammation in various metabolic disorders, including hyperhomocysteinemia (HHcy). This study aims to explore molecule signaling mediating MC subset differentiation in HHcy and control mice.Mouse white blood cell were prepared from peripheral blood and stained with antibody against CD11b, Ly6G and Ly6C and subjected for flow cytometry cell sorting. CD11b+Ly6G- cells were selected as MC. MC subsets (CD11b+Ly6G-Ly6Chigh, and CD11b+Ly6G-Ly6Clow) were sorted based on Ly6C levels. The quantification of MC was used flow cytometry analysis for Ly6Chigh and Ly6Clow MC in CT and Cbs-/-. Then, 100 ng mRNA were obtained from 100,000 sorted cells of CT and Cbs-/- (HHcy) mice. Around 30 million reads were achived and 16,487 normalized genes per sample by mRNA-Seq analysis.

overall_design: Examination of 2 different monocyte in wild type and hyperhomocysteinemic mice

first: Pingping

last: Yang

first: Liu

last: Lu

first: Lizhe

last: Sun

first: Pu

last: Fang

first: Qinghua

last: Wu

first: Xiaofeng


title: RNA-seq of human pediatric cornea presenting with CCO

city: Sewickley

first: Bharesh

middle: Kumar

last: Chauhan

address: 400 45th St., Faculty Pavilion, Suite 5111

department: Ophthalmology

institute: University of Pittsburgh

summary:
The underlying mechanism for CCO is poorly understood
We sought to obtain key players and a potential pathway in disease causation through comparative transcriptome (via RNA-Seq) analyses between cornea with CCO from patient with Fanconi anemia and age-matched normal donor cornea

overall_design: Transcriptome of pediatric patient and normal donor corneas were generated by RNA-seq technology using Illumina HiSeq 2500.


title: GAS7 Deficiency Promotes Metastasis of MYCN-driven Neuroblastoma

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

summary: Neuroblastoma (NB), the most common extracranial solid tumor in children, often metastasizes at a high rate. Here, we demonstrate that loss of function of the growth arrest-specific 7 gene (GAS7), located on Chr17p13.1, a deleted region in a subset of high-risk NB, accelerates dissemination of MYCN-overexpressing tumor cells in both zebrafish and xenografted mice models. Transcriptomic analysis of neuroblasotma tumors isolated from transgenic zebrafish overexpressing MYCN oncogene alone or MYCN with knockout  of gas7 gene revealed that gene signitures affecting tumor cell-cell or cell-extracellular matrix interactions are significantly downregulated in tumors with gas7 loss of function. Our results provide the first genetic evidence that loss of function of a gene located in the Chr17p region contributes significantly to NB metastasis.

overall_design: Examination of the transcriptomic profiles of neuroblastomas arose from transgenic fish overexpressing MYCN alone or MYCN with knockout of gas7.

first: Shizhen

last: Zhu


title: The yeast ISW1b ATP-dependent chromatin remodeler is critical for nucleosome spacing and dinucleosome resolution

city: Bethesda

first: Peter

last: Eriksson

state: Maryland

address: 9000 Rockville Pike, Bldg.6A/2A14

department: NICHD

institute: National Institutes of Health

summary: We addressed the roles of primarily two remodeling complexes, ISW1a and ISW1b, in affecting the chromatin organization in the yeast Saccharomyces cerevisiae.

overall_design: Comparison of budding yeast nucleosome positions obtained using micrococcal nuclease digestion followed by paired-end sequencing (MNase-seq). We sequenced nucleosomes from isogenic strains with the isw1Δ, ioc2∆, ioc3∆, ioc4∆, chd1Δ, set1∆, set2∆ mutations in different combinations. We also examine a histone H4 N-terminal deletion mutation.

middle: R

first: David

middle: J

last: Clark


title: p300/CBP mediated activation of MHCI machinery and IFNg receptor loci controls chemoimmunotherapy

status: Public on Feb 01 2021

city: Buffalo

first: Mark

last: Long

address: Elm & Carlton Streets

department: Bioinformatics & Biostatistics

institute: Roswell Park Comprehensive Cancer Center

summary: Certain chemotherapeutic drugs potentiate responses to immune checkpoint inhibitors (ICI), including PD-(L)1 antibodies, but the mechanisms underlying this synergism are poorly understood.  Many cancers evade immune rejection by suppressing MHC-I antigen processing and presentation (AgPP). We show that two classes of DNA damaging drugs, platinoids (e.g. oxaliplatin) and topoisomerase inhibitors (e.g. mitoxanthrone), induce NF-kB activation, nuclear translocation of the histone and lysine acetyl transferases p300/CBP, interferon (IFN) regulatory factors and IFNg receptor 2 (IFNgR2). This results in transcriptional activation of loci coding for the MHC-I transactivator NLRC5 and components of the MHC-I AgPP machinery. Accordingly, p300 inactivation prevents drug-induced upregulation of MHC-I antigen presentation leading to impaired recognition of cancer cells by effector CD8+ T cells, whose tumor rejecting activity is IFNgR2-dependent. Correspondingly, EP300 loss in human cancers correlates with reduced expression of MHC-I related genes and/or changes in neoantigen amount and expression, suggesting that p300 is an immune-directed oncosuppressor.

overall_design: To investigate Oxali’s effects on CD8+ T cells, we sorted tumor-infiltrating CD8+ T cells (TI-CD8+) from subcutaneous (s.c.) Myc-CaP tumors, which were treated weekly with either Oxali, aPD-L1, both (combo) or left untreated (Ctrl) and performed scRNA-seq. Droplet-based 3’ end massively parallel single-cell RNA sequencing was performed by encapsulating sorted live TI-CD8+ into droplets and libraries prepared using Chromium Single Cell 30 Reagent Kits V3 according to manufacturer’s protocol (10x Genomics).

first: Shabnam

last: Shalapour

first: Michael

last: Karin

first: Yixuan

last: Zhou

first: Ingmar

middle: B

last: Bastian

first: Michelle

last: Dow


title: Hypothalamic estrogen receptor alpha mediates key side effects of tamoxifen therapy in mice

city: Los Angeles

first: John

middle: Edward

last: van Veen

address: 610 Charles E young Dr

department: Integrative Biology and Physiology

institute: UCLA

summary: Adjuvant tamoxifen therapy for invasive breast cancer improves patient survival but comes with side effects that impact health and quality of life. Partly due to a lack of proven animal models, the tissues and cells that mediate these negative side effects are largely unknown. Here we show that mice undergoing a 28-day course of tamoxifen treatment experience dysregulation of core and skin temperature, changes in bone density, and decreased physical activity, recapitulating several aspects of the human response. Single cell RNA sequencing reveals that tamoxifen induces widespread gene expression changes in the hypothalamus, particularly in neurons and ependymal cells. These effects are largely dependent on estrogen receptor alpha (ERα), as conditional ERα knockout ablated or reversed tamoxifen-induced changes in gene expression, thermoregulation, bone, and movement. These findings provide mechanistic insights into the effects of tamoxifen on the hypothalamus and suggest that hypothalamic ERα mediates several side effects of tamoxifen therapy.

overall_design: A total of sixteen hypothalami were analyzed. Group sizes are as follows: Wild-type, control injections n = 3; Wild-type, tamoxifen injections n = 5; Esr1cKO, control injections n = 4, Esr1cKO tamoxifen injections n = 4

first: Zhi

last: Zhang

first: Jae

middle: W

last: Park

first: In

middle: S

last: Ahn

first: Graciel

last: Diamante

first: Nilla

last: Sivakumar

first: Douglas

middle: V

last: Arneson

first: Xia

middle: E

first: Stephanie

middle: M

last: Correa


title: The H2BE76K mutation drives breast cancer development by enhancing the transcription of ADAM19

city: Hong Kong

first: Ming

middle: Kui

last: Chan

address: Tat Chee Avenue

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

summary: Study was conducted to understand the effect of the cancer associated H2BE76K mutation. Using CRISPR/Cas9 Knock-in cell lines expressing FLAG-tagged WT and E76K mutant H2B, we conducted gene expression profiling experiments and studied the effect of the H2BE76K mutation on H2B occupancy using CUT&RUN sequencing.

overall_design: CRISPR/Cas9 cell lines expressing FLAG tagged Wildtype (WT) H2B and H2BE76K were generated to study the H2BE76K mutation in breast invasive carcinoma. Two WT and two mutant E76K cell lines as well as the Parental MDA-MB-231 cell lines were used for experiments. Gene expression of WT and E76K mutant lines was profiled by RNA-seq. Genomic localization of FLAG-tagged WT and E76K H2B proteins were profiled by CUT&RUN sequencing. ATAC-seq was performed to detect any difference of chromosomal accessibility between H2BE76K and WT.

first: Tze

middle: Z

last: Kang

first: Lina

last: Zhu

first: Kui


title: Gene expression alternations in Qishen Yiqi Dripping Pill-treated rats kidney

city: Beijing

first: Qian

address: No. 1 Shuaifuyuan, Dongcheng District

institute: Peking Union Medical College Hospital

summary:
Diabetic rats changes gene exprssion in Qishen Yiqi Dripping Pill-treated rats kidney
Diabetic nephropathy (DN) is a severe microvascular complication of diabetes. Qishen Yiqi Dripping Pill (QYDP) has been reported to be a renal protective drug. However, the mechanisms remain not certain. This study was performed to investigate the mechanisms of the extract. In this study, Sprague Dawley SD rats were fed with a high-fat diet, and injected with streptozotocin (STZ) to generate a diabetic model. Diabetic rats were administered QYDP.

overall_design: We performed microarray analyses of Qishen Yiqi Dripping Pill-treated rats kidney

first: Xinhua

last: Xiao

first: Jia

last: Zheng

last: Li

first: Miao

last: Yu

first: Fan

last: Ping

first: Zhixin

last: Wang

first: Cuijuan

last: Qi

first: Tong

first: Xiaojing


title: Platinoid drugs augment immunotherapy via histone acetylation of MHCI machinery genes [CCO19-MC]

city: Houston

first: Shabnam

last: Shalapour

state: TX

address: 1881 East Road

department: Cancer Biology

institute: MD Anderson Cancer Center

summary: Here we show that low dose Oxali, and to a lesser extent other platinoids, can uniquely activate the transcriptional program that controls MHCI antigen processing and presentation. Activation of this program correlates with induction of histone acetylation and enhanced chromatin accessibility. Oxaliplatin also induces NF-kB dependent IFNg receptor 2 (IFNgR2) thereby augmenting the tumor response to exogenous IFNg produced by reinvigorated effector CD8+ T cells.

overall_design: RNA were isolated after 48h treatment of prostate cancer cell line Myc-Cap with Oxaliplatin (2uM), IFNg (200pg or 2000pg), or a combination of Oxaliplatin (2uM) + IFNg (200pg or 2000pg).

first: Michael

last: Karin


title: Platinoid drugs augment immunotherapy via histone acetylation of MHCI machinery genes [AT_MC]

overall_design: Nuclei/DNA were isolated after 48h treatment of prostate cancer cell line Myc-Cap with Oxaliplatin (2uM), Cisplatin (2uM), IFNg (1000pg), or a combination of Oxali (2uM) + IFNg (1000pg).


title: A combinatorial attack strategy uncovers a molecular rationale for treating inflammatory cardiomyopathy

status: Public on Jan 31 2021

city: Oxford

first: Shoumo

last: Bhattacharya

address: Roosevelt Drive

department: RDM Cardiovascular Medicine

institute: Wellcome Centre For Human Genetics, University of Oxford

summary: Here we show how the cardiac transcriptome evolves during murine myocarditis revealing early and persistent activation of cytokine and chemokine-signalling pathways together with innate immune, antigen-presentation, complement  and cell-adhesion pathway activation. We identified a 50-gene subnetwork based on expression importance and quantified network tolerance to combinatorial node removal to determine target-specific therapeutic potential. Combinatorial attack of Traf2, Nfkb1, Rac1 and Vav1 causes 80% subnetwork disconnection. NFKB1 and RAC1 are targeted by prednisolone and azathioprine, creating 56% network disconnection, establishing a molecular rationale for immunosuppressive therapy. Additional combinatorial attack of BTK and PIK3CD with approved therapeutics causes 72% network disconnection, suggesting that they could be re-purposed to treat inflammatory cardiomyopathy. We propose that the combinatorial attack strategy developed here could be applied to other immune-mediated diseases.

overall_design: Analyzing evolution of cardiac transcriptome during development of autoimmune myocarditis

first: Kamayani

last: Singh

first: Hai

last: Fang

first: Graham

last: Davies

first: Benjamin

last: Wright

first: Helen

last: Lockstone

first: Richard

last: Williams

first: Daniela

last: Cihakova

first: Julian

middle: C

last: Knight


title: Platinoid drugs augment immunotherapy via histone acetylation of MHCI machinery genes [Myc_CaP]

overall_design: RNA were isolated after 24h treatment of prostate cancer cell lines Myc-Cap and TRAMP-C2 with Oxaliplatin and Cisplatin at 2uM or 20uM dosages.


title: DNA hydroxy-methylation data of tumor and non-tumor liver (NTL) tissues from Peruvian patients with hepatocellular carcinoma (HCC)

city: Toulouse

first: Juan Pablo

last: Cerapio

address: Av 2 Hubert Curien

institute: CRCT

summary:
A large fraction of HCC in Peru arises in younger, non-cirrhotic patients. Global DNA hydroxy-methylation analysis of the HCC and NTL tissues demonstrate that hydroxy-methylation conversion interplays with gene expression to enact cell fate determination and cancer cell reprogramming.
We used microarrays to identify hydroxy-methylated CpGs by comparison to Gene Expression Omnibus (GEO) series GSE136319 and GSE136380.

overall_design: HCC patients were treated by anatomic liver resection. Non-tumor liver tissues were obtained from tumour-free margins of resected surgical pieces. Total DNA was isolated from flash-frozen samples for hybridization on Illumina microarrays.

first: Juan

middle: P

first: Pascal

last: Pineau


title: DNA methylation data of tumor and non-tumor liver tissues from Peruvian patients with hepatocellular carcinoma (HCC)

type: Methylation profiling by genome tiling array

summary:
A large fraction of HCC in Peru arises in younger, non-cirrhotic patients. Global DNA methylation analysis of the HCC and non-tumor liver (NTL) tissues demostrate a profound overhaul of the developmental DNA methylation programme culminating in an global hyper-methylated pattern in HCC.
We used microarrays to compare global DNA methylation between tumor and non-tumor liver tissues and identified CpGs and ontologies that are distinctively differentially methylated between subsets.

overall_design: HCC patients were treated by anatomic liver resection. Non-tumor liver tissues were obtained from tumor-free margins of resected surgical pieces. Total DNA was isolated from flash-frozen samples for hybridization on Illumina microarrays.


title: DNA methylation data of tumor and non-tumor liver (NTL) tissues from Peruvian patients with hepatocellular carcinoma (HCC).

summary:
A large fraction of HCC in Peru arises in younger, non-cirrhotic patients. Global DNA methylation analysis of the HCC and non-tumor liver (NTL) tissues demostrate a profound overhaul of the developmental DNA methylation programme culminating in an  global hyper-methylated pattern in HCC.
We used microarrays to compare global DNA methylation between tumor and non-tumor liver tissues and identified CpGs and ontologies that are distinctively differentially methylated between subsets.


title: Platinoid drugs augment immunotherapy via histone acetylation of MHCI machinery genes

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

overall_design: Refer to individual Series


title: Silver Nanoparticles Induce a Triclosan-Like Antibacterial Action Mechanism in Multi-Drug Resistant Klebsiella pneumoniae

city: Columbia

first: Sathesh

last: Sivasankaran

state: MO

address: Bond Life Sciences Center Suite 106, 1201 Rollins Street

institute: University of Missouri

summary: Infections associated with antimicrobial-resistant bacteria now represent a significant threat to human health using conventional therapy, necessitating the development of alternate and more effective antibacterial compounds. Silver nanoparticles (Ag NPs) have been proposed as potential antimicrobial agents to combat infections. A complete understanding of their antimicrobial activity is required before these molecules can be used in therapy. Lysozyme coated Ag NPs were synthesized and characterized by TEMEDS, XRD, UV-vis, FTIR spectroscopy, zeta potential, and oxidative potential assay. Biochemical assays and deep level transcriptional analysis using RNA sequencing were used to decipher how Ag NPs exert their antibacterial action against multi-drug resistant Klebsiella pneumoniae MGH78578. RNAseq data revealed that Ag NPs induced a triclosan-like bactericidal mechanism responsible for the inhibition of the type II fatty acid biosynthesis. Additionally, released AgC generated oxidative stress both extra and intracellularly in K. pneumoniae. The data showed that triclosan-like activity and oxidative stress cumulatively underpinned the antibacterial activity of Ag NPs. This result was confirmed by the analysis of the bactericidal effect of Ag NPs against the isogenic K. pneumoniae MGH78578 1soxS mutant, which exhibits a compromised oxidative stress response compared to the wild type. Silver nanoparticles induce a triclosan like antibacterial action mechanism in multi-drug resistant K. pneumoniae. This study extends our understanding of anti-Klebsiella mechanisms associated with exposure to Ag NPs. This allowed us to model how bacteria might develop resistance against silver nanoparticles, should the latter be used in therapy.

overall_design: RNA sequencing was carried out for Klebsiella pneumoniae MGH78578 (ATCC™700721) exposing it to the MIC75 concentration of L-Ag NPs for 5 and 30 min., duplicate samples were sequenced for each stage.

first: Vikram

last: Pareek

first: Stephanie

last: Devineau

first: Arpit

last: Bhargava

first: Jitendra

last: Panwar

first: Shabarinath

last: Srikumar

first: Séamus

last: Fanning


title: Effects of IL-4 conditioning on human umbilical cord blood-derived mast cells

status: Public on Jan 30 2021

city: Boston

first: Daniel

last: Dwyer

state: MA

address: 60 Fenwood Road

institute: Brigham and Women's Hospital

summary: This study evaluates the effects of 96h stimulus with Interleukin 4 (100 ng/mL) on the transcriptome of human umbilical cord blood derived mast cells. Through this approach, we identify upregulation of key intraepithelial mast cell-associated transcripts and downregulation of subepithelial mast cell-associated transcripts. Replicates are technical duplicates. Samples were sequenced on an Illumina NextSeq 500.

overall_design: RNA-seq analysis of human umbilical cord blood-derived mast cells grown in SCF (100 ng/mL), IL-6 (50 ng/mL) and IL-10 (10 ng/mL) and stimulated in media containing SCF with saline or IL-4 (10 ng/mL) for 96 hours

first: Joshua

last: Boyce


title: Lasting consequences of psyllid (Bactericera cockerelli L.) infestation on tomato defense, gene expression, and growth

city: Lincoln

first: Kyle

last: Harrison

state: Nebraska

address: 1700 E Campus Mall

department: Entomology

institute: USDA-ARS

summary: BACKGROUND: The tomato psyllid, Bactericera cockerelli Šulc (Hemiptera: Triozidae), is a pest of solanaceous crops such as tomato (Solanum lycopersicum L.) in the U.S. and vectors the disease-causing pathogen ‘Candidatus Liberibacter solanacearum’. Currently, the only effective strategies for controlling the diseases associated with this pathogen involve regular pesticide applications to manage psyllid population density. However, such practices are unsustainable and will eventually lead to widespread pesticide resistance in psyllids. Therefore, new control strategies must be developed to increase host-plant resistance to insect vectors. For example, expression of constitutive and inducible plant defenses can be improved through selection. Currently, it is still unknown whether psyllid infestation has any lasting consequences on tomato plant defense or tomato plant gene expression in general. RESULTS: To characterize the genes putatively involved in tomato defense against psyllid infestation, RNA was extracted from psyllid-infested and uninfested tomato leaves (Moneymaker) three weeks post-infestation. Transcriptome analysis identified 362 differentially expressed genes. These differentially expressed genes were primarily associated with defense responses to abiotic/biotic stress, transcription/translation, cellular signaling/transport, and photosynthesis. These gene expression changes suggested that tomato plants underwent a reduction in plant growth/health in exchange for improved defense against stress that was observable three weeks after psyllid infestation. Consistent with these observations, tomato plant growth experiments determined that the plants were shorter three weeks after psyllid infestation. Furthermore, psyllid nymphs had lower survival rates on tomato plants that had been previously psyllid infested. CONCLUSION: These results suggested that psyllid infestation has lasting consequences for tomato gene expression, defense, and growth.

overall_design: Comparison of transcript counts between uninfested and psyllid-infested tomato plants three weeks after treatment

first: Azucena

last: Mendoza-Herrera

first: Julien

middle: G

last: Levy

first: Cecilia

last: Tamborindeguy