title: Gene expression profiling of newly diagnosed multiple myeloma patients included in the HOVON131 clinical trial

summary:
This gene expression set contains data from patients included in the HOVON131 clinical trial. Using this data the relation between circulating tumor cells and gene expression patterns was studied in newly diagnosed multiple myeloma patients.
Circulating tumor cells are a known prognostic factor in multiple myeloma. However, the causes of high circulating tumor cells have been insufficiently characterised. This study aimed to identify factors involved in high circulating tumor cell count, using a model to correct for important contributing factors to this phenotype, which is closely associated with aggressive disease.

overall_design: 109 samples were analysed, which were taken from 109 individual patients. Samples were derived from bone marrow aspirates, which were subjected to enrichment of MM cells using CD138 specific beads.  RNA sample workup was performed according to the instructions for use of the MMprofilers at the SkylineDx reference lab (SkylineDx, Rotterdam, The Netherlands). Samples were hybridized to Affymetrix HG-U133 plus2 chips, using Affymetrix Inc. (Santa Clara, CA)  3' IVT PLUS reagents. All samples passed wet lab and data QC acceptance criteria. Gene expressions were MAS5.0 normalized (values below 30 were truncated) with a target value of 1500. The MMprofiler CE IVD assay was used to obtain SKY92 scores, classifying a patient as high risk or standard risk.

first: Erik

last: Valent


title: The splicing factor HNRNPM promotes hepatocellular carcinoma by decreasing TRIM7 expression through the alternative splicing of lncRNA-TRIM7-AS

status: Public on Jun 01 2022

city: shanghai

first: Gui-Qi

last: zhu

address: shanghai

country: China

institute: zhongshan hospital

type: Expression profiling by high throughput sequencing

summary: Understanding the roles of splicing factors and splicing events during tumorigenesis would open new avenues for targeted therapies. Here we identify an oncofetal splicing factor, heterogeneous nuclear ribonucleoprotein M (HNRNPM), which promotes tumorigenesis and predicts poor prognosis of hepatocellular carcinoma (HCC) patients. HNRNPM knockdown almost completely abolishes HCC tumorigenesis. Transcriptomic analysis combined with RNA-immunoprecipatation sequencing revealed that HNRNPM induces lncRNA-TRIM7-AS exon 2 inclusion. The transcript containing exon 2 binds to coding sequences of TRIM7 mRNA, causes dissociation of translation elongation factors from TRIM7 mRNA, and thereby inhibits TRIM7 mRNA translation. In contrast, the transcript including exon 3 preferentially binds to the 3’ untranslated region of TRIM7 mRNA, protects TRIM7 mRNA from microRNA-145-5p induced degradation, and thereby increases TRIM7 expression. Through inducing exon 2 inclusion, HNRNPM downregulates TRIM7 protein expression, which mediates the pro-tumorigenic roles of HNRNPM. Collectively, these data demonstrate detailed mechanistic links between an oncofetal splicing factor, a splicing event and tumorigenesis, and establish splicing factors and splicing events as potential therapeutic targets.

overall_design: Examination of alternative splicing genes regulated by splicing factor HNRNPM

first: Gui-qi

last: Zhu

first: Yi

last: Wang

first: Biao

first: Zhi

last: Dai


title: Differentially expressed genes (DEGs) analysis in control and hsa_circ_0004287 knockdown THP1-derived macrophages

city: Guangzhou

first: Lan

last: Yang

state: Guangdong

address: 1838 North Guangzhou Street

department: Department of Plastic and Aesthetic Surgery

institute: Nanfang Hospital of Southern Medical University

summary: To explore the detailed mechanism by which hsa_circ_0004287 inhibits M1 macrophage activation, we performed RNA-seq in control and hsa_circ_0004287 knockdown THP1-derived macrophages, and identified 43 upregulated and 35 downregulated genes with the criterion of |FC|≥2 and p≤0.05.

overall_design: We prepared 3 replicates for control and hsa_circ_0004287 knockdown group, respectively, to perform the RNA-seq analysis.

first: Yufeng

last: Zhou


title: Gene expression profiling of newly diagnosed multiple myeloma patients included in the HOVON95 clinical trial

city: Rotterdam

first: Mark

last: van Duin

address: Wytemaweg 80

country: Netherlands

institute: Erasmus MC

summary:
This gene expression set contains data from patients included in the HOVON95 clinical trial. Using this data the relation between a signature identifying patients with aggressive biology and clinical parameters was studied in newly diagnosed multiple myeloma patients.
This dataset was used to identify the relationship between a signature for aggressive disease and clinical parameters.

overall_design: 240 samples were analysed, which were taken from 240 individual patients. Samples were derived from bone marrow aspirates, which were subjected to enrichment of MM cells using CD138 specific beads.  RNA sample workup was performed according to the instructions for use of the MMprofilers at the SkylineDx reference lab (SkylineDx, Rotterdam, The Netherlands). Samples were hybridized to Affymetrix HG-U133 plus2 chips, using Affymetrix Inc. (Santa Clara, CA) GPR reagent for samples obtained in 2014 or earlier, and Affymetrix 3' IVT PLUS reagents for samples obtained after 2014. All samples passed wet lab and data QC acceptance criteria. Gene expressions were MAS5.0 normalized (values below 30 were truncated) with a target value of 1500. The MMprofiler CE IVD assay was used to obtain SKY92 scores, classifying a patient as high risk or standard risk.

first: Rowan

last: Kuiper

first: Davine

last: Hofste op Bruinink

first: Tom

last: Cupedo

first: Annemiek

last: Broijl

first: Pieter

last: Sonneveld


title: RNA profiling of cervical cancer exosomes using next- generation sequencing.

city: Delhi

first: Alok

middle: Chandra

last: Bharti

state: New Delhi

address: North campus, Chhatra Marg

department: Zoology Department

country: India

institute: University of Delhi

summary: In the preset study we isolated and characterized exosomes from both HPV positive and negative cervical cancer cell lines and identified a subset of mRNA’s enriched specifically in HPV positive exosomes through deep sequencing methods. Potential target prediction gene ontology, KEGG pathway analysis revealed possible functions associated with differentially expressed genes of CaCx exosomes. Profiling of these exosomes also revealed the export of HPV 16 associated transcripts (E1,E2, E5, and L2) within SiHa exosomes, however no such export was observed for major oncogenic transcripts (E6 and E7). Our Reverse transcription PCR experiments could validate our deep sequencing results for the absence of E6, E7 transcripts in exosomes. Interestingly, PCR could amplify a truncated version of E6 transcript in HeLa exosomes, which was not detectable in our sequencing results.

overall_design: To study the differentially expressed genes in HPV-positive and negative cervical cancer cell lines exosomes

last: Chandra Bharti

first: Anjali

last: Bhat

first: Joni

last: Yadav


title: Targeting Aberrant Replication and DNA Repair Events for Treating Breast Cancers

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

country: USA

institute: UT Health Science Center at San Antonio

summary: We aimed to determine carbazole blue's (CB) targets by gene expression microarray. Our results show that CB inhibits the expression of pro-tumorigenic genes that promote unchecked replication and aberrant DNA repair that cancer cells get addicted to survive.

overall_design: Samples collected from CB treated at 2 different doses are comparied to control group for target identifiation. 2 replicates were performed.

first: Subapriya

last: Rajamanickam

first: Manjeet

middle: K

last: Rao


title: A Transcriptional State Driven by Yin Yang 1 Confers a Therapeutic Vulnerability in Glioblastoma Stem Cells

city: Shanghai

first: Zhixin

last: Qiu

address: Dongan Road

institute: Fudan University

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: RNAseq of Oesophageal Adenocarcinoma Cell Lines

city: Cambridge

first: David

last: Shorthouse

address: Hutchison/MRC Research Centre

country: United Kingdom

institute: MRC Cancer Unit

summary: rna sequencing of Oesophageal Adenocarcinoma Cell lines: OACP4, OE19, FLO-1, SK-GT-4, ESO26, OE33, ESO51, OACM5.1 C, JH-EsoAd1

overall_design: 3 x technical replicates of each cell line performed under normal conditions

first: Benjamin

middle: A

last: Hall

first: Rebecca

middle: C

last: Fitzgerald


title: RNA-seq of YY1 knockdown and alvocidib treatment in glioblastoma stem cells

overall_design: 1) RNA-seq analysis of YY1 knockdown in different glioblastoma stem cells (GSC23, GSC1517 and GSC3028). 2) RNA-seq analysis of alvocidib treatment in glioblastoma stem cell GSC1517.

first: Jeremy

last: Rich


title: ChIP-seq of YY1 in glioblastoma stem cells

overall_design: ChIP-seq analysis of YY1 binding in glioblastoma stem cells.


title: Expression data of human follicular lymphoma (FL) B cells purifed from bone marrow samples (BM)

city: RENNES

first: Celine

last: Pangault

address: 2, avenue du Léon Bernard

department: Medical School of Rennes

country: France

institute: Rennes University Hospital

summary: GEP on Affymetrix U133+2.0 microarrays was performed on ex vivo cell-sorted FL B cells from infiltrated human BM samples, according to the CD20hiCD44loCD38posIgDnegCD138negCD34neg  phenotype.

overall_design: GEP was performed on 5 FL BM samples

first: Karin

last: Tarte

first: Thierry

last: Fest


title: Bridge Linker-Hi-C (BL-Hi-C) analysis after YY1 knockdown in glioblastoma stem cells

overall_design: Bridge Linker-Hi-C (BL-Hi-C) analysis of chromatin interactions after YY1 knockdown in one glioblastoma stem cell (GSC1517)


title: KLF7 ChIP-seq in human keratinocytes HaCaT cell line

first: Jun

last: Liu

address: No.2 Lujing Road

department: Dermatology Hospital

institute: Southern Medical University

summary: KLF7, a member of the KLF family, is an evolutionarily conserved zinc finger-containing transcription factor. Previous studies demonstrated that KLF7 possesses diverse regulatory functions related to embryogenesis, cell growth, proliferation, and differentiation. Our results reveal that there was an increased abundance of KLF7 in OSM-treated HaCaT cells. Mechanistically, our results showed that OSM induces epidermal keratinocyte differentiation through phosphorylation of STAT5, which binds to the promoter and activates KLF7 transcription.

overall_design: Examination of KLF7 bingding sites in Keratinocyte HaCaT cells.

first: Zhili

last: Rong


title: insulin resistant duodenum vs. non-insulin resistant duodenum

city: Malaga

first: Eduardo

last: García-Fuentes

state: Malaga

address: Plaza del Hospital Civil s/n

country: Spain

institute: Instituto de Investigación Biomédica de Málaga (IBIMA)/Hospital Regional Universitario, Málaga, Spain.

summary: Transcriptional profiling of duodenum from non-obese patients and patients with morbid obesity comparing non-insulin resistance vs. insulin resistande. Goal was to determine the involvement of the duodenum in the development of insulin resistance and the possible influence of obesity.

overall_design: Four-condition experiment: non-obese patients with low insulin resistance (n=6), non-obese patients with high insulin resistance (n=7), patients with morbid obesity and low insulin resistance (n=7) and patients with morbid obesity and high insulin resistance (n=8).

first: Ailec

last: Ho-Plagaro

first: Concepción

last: Santiago-Fernandez

first: Cristina

last: Rodríguez-Díaz

first: Carlos

last: Lopez-Gómez

first: Sara

last: Garcia-Serrano

first: Francisca

last: Rodríguez-Pacheco

first: Sergio

last: Valdes

first: Alberto

last: Rodríguez-Cañete

first: Guillermo

last: Alcaín-Martínez

first: Natalia

last: Ruiz-Santana

first: Luis

last: Vázquez-Pedreño


title: Deficient LEF1 expression is associated with lithium resistance and hyperexcitability in neurons derived from bipolar disorder patients

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

summary: Bipolar disorder (BD) is a psychiatric condition characterized by depressive and manic episodes that affect 2% of the world population. The first-line long-term treatment for mood stabilization is lithium (Li). Induced pluripotent stem cell modeling of BD using hippocampal dentate gyrus-like neurons derived from Li responsive (LR) and Li non-responsive (NR) patients previously showed neuronal hyperexcitability. Li treatment reversed hyperexcitability only on LR neurons. In this study we searched for specific targets of Li resistance in NR neurons and found that the activity of Wnt/β-catenin signaling pathway was severely affected, with a significant decrease in expression of LEF1. Li targets the Wnt/β-catenin signaling pathway by inhibiting GSK-3β and releasing β-catenin that forms a nuclear complex with TCF/LEF1, activating the Wnt/β-catenin transcription program. Therefore, we propose that downregulation of LEF1 may account for Li resistance in NR neurons. Our results show that valproic acid (VPA), a drug used to treat NR patients that also acts downstream of GSK-3β, upregulated LEF1 and Wnt/β-catenin gene targets, increased transcriptional activity of complex β-catenin/TCF/LEF1 and reduced excitability in NR neurons. Additionally, decreasing LEF1 expression in control neurons using shLEF1 caused hyperexcitability, confirming that the impact of VPA on excitability in NR neurons was connected to changes in LEF1 and in the Wnt/β-catenin pathway. Our results suggest that LEF1 may be a useful target for the discovery of new drugs for BD treatment.

overall_design: Comparison of neurons by RNA-Seq across differentiation time and with treatment.

first: Renata

last: Santos

middle: B

last: Linker

first: Shani

last: Stern

first: Ana

middle: P

last: Mendes

first: Maxim

middle: N

last: Shokhirev

first: Galina

last: Erikson

first: Lynne

last: Randolph-Moore

first: Vipula

last: Racha

first: Yeni

last: Kim

first: John

middle: R

last: Kelsoe

first: Anne

middle: G

last: Bang

first: Maria

last: Marchetto

first: Fred

middle: H

last: Gage


title: Effects of Minocycline and EE in CUMS as a MDD model: transcriptomic profiles and synaptic plasticity of microglia

city: Warsaw

first: Adria-Jaume

last: Roura

address: Ludwika Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology, Polish Academy of Sciences

summary: Two independent differential expression analyses were performed in mice subjected to chronic unpredictable mild stress (CUMS): one consisted of microglia (Cd11b+ cells) from the prefrontal cortex (PFC) and the other from the hippocampus (HC). After the CUMS protocol, minocycline, a wide spectrum antibiotic with anti-inflammatory properties, was delivered (CUMS_M group) in the drinking water/saccharine solution during 21 days. Transcriptomic profiling for a vehicle group (VEH), who spent 3 weeks in the cage with the same drinking solutions (Water/ saccharine 0.1%) and for a environmental enrichment (EE) group, that also spent 3 more weeks in the cage where enrichment materials were provided, were performed as well.

overall_design: All bulk mRNA expression profiles were acquired from isolated PFC and HC areas. CD11b+ cells were sorted using the purity precision mode on FACS Aria. RNA was isolated following the protocol described in RNeasy kit manual and RNA concentration was immediately determined using a spectrophotometer (NanoDrop2000 ThermoScientific). Quality and integrity of total RNA was assessed with Agilent 2100 Bioanalyzer and strand-specific polyA enriched RNA libraries were prepared using the KAPA Stranded mRNA Sample Preparation Kit. Then, libraries were run in the rapid run flow cell -paired-end sequenced (2x76bp) - on HiSeq 1500. RNA sequencing analysis revealed several differentially expressed genes between groups in both PFC and HC.

last: Banqueri

first: Anna

last: Kiryk

first: Adria

middle: J

first: Bartek

last: Gielnielski

first: Bozena

last: Kaminska


title: RNAseq to profile transcriptomes of  murine common dendritic cell progenitors (CDPs)

city: Beijing

first: Yujie

last: Tian

address: No.1 Tsinghua Park

institute: Tsinghua University

summary: We performed the transcriptomic analysis of RNA-seq of CDPs isolated from the bone marrow of wildtype C57BL/6 mice

overall_design: Three CDP subsets were sorted by flow cytometer and lysed. RNA was extracted, polyA enriched and prepared for sequencing libraries.


title: Genome wide RNA-seq of wild-type Hela transfected with SAFA-ADAR1cd upon HSV-1 infection

first: Shengde

last: Liu

address: 38 Xueyuan Rd , Haidian District

institute: Peking University Health Science Center

summary: Genome wide RNA-Seq screen was did to detect gene expression of  HSV-1 and Hela . We constructed a HeLa cell line that stably expresses the plasmids of SAFA or SAFA-ADAR1 catalytic domain(SAFA-ADAR1cd) or SAFA-ADAR1 catalytic domain E488Q(SAFA-ADAR1cd E488Q) . The RNAs were harvested followed by RNA sequencing to identify the edited RNA.

sample_organism:
Homo sapiens
Human alphaherpesvirus 1

platform_organism:
Homo sapiens
Human alphaherpesvirus 1

overall_design: Hela were infected with HSV-1 for 20 hours,and then did genome wide RNA-Seq screen to detect the edited RNA.

first: Fuping

last: You


title: Transcriptome analysis of Escherichia coli K-12 MG1655 under toxoflavin and troplone conditions

city: Busan

first: Jungwook

last: Park

address: Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea

department: Microbiology

country: South Korea

institute: Pusan National University

summary: RNA-seq based transcriptome analysis was employed to understand the genome-wide expression patterns under the phytotoxin treatment. To identify differentially expressed genes, we compared phytotoxins (toxoflavin and tropolone) transcriptome to methanol transcriptome as the solvent of phytotoxins. The expression of 2327 and 830 genes was differentially changed by toxoflavin and tropolone, respectively.

overall_design: Nine libraries constructed: Each three replicates of toxoflavin, tropolone, methanol conditions in Escherichia coli K-12 MG1655

first: Hyun-Hee

last: Lee

first: Hyejung

last: Jung

first: Young-Su

last: Seo


title: Genomic profile of human plasmacytoid dendritic cells exposed to oxidized LDL at baseline or after activation with CpG-A

city: Maastricht

first: Han

last: Jin

address: P. Debyelaan 25

institute: Maastricht University

summary: Maturation and activation of plasmacytoid dendritic cells (pDCs), induced by the interaction of pathogens or trauma-derived danger signals, with pattern-recognition receptors, is a pivotal step in pDC innate and adaptive immune activation. Exposure to metabolites present in the pDC microenvironment may well influence critical signaling pathways in their function, and thereby tune host immune responses against endogenous, bacterial and viral pathogens. In this experiment, we have addressed the impact of hyperlipidemia on human pDCs at baseline and after  activation. We show that exposure to pro-atherogenic (oxidized) low density lipoproteins led to pDC lipid accumulation, which in turn ablated Toll-like receptor (TLR) 7 and 9 dependent up-regulation of pDC maturation markers CD40, CD83, CD86 and HLA-DR. Transcriptional profiling and in vitro cell experiments  revealed that, oxLDL exposure dampened TLR9 activation induced production of pro-inflammatory cytokines in a NUR77/IRF7 dependent manner and impaired the capacity of pDCs to prime and polarize CD4+ T helper (Th) cells. These results highlight the marked impact of hyperlipidemia on pDC responses to pathogen-derived signals.

overall_design: PDC were bead-isolated from human blood at >90% purity; pre-incubated with oxLDL or mock medium and then challenged with CpG, after which cells were lysed and total RNA was isolated.

first: A

last: Christ

first: Pieter

last: Goossens

first: Erik

last: Biessen


title: Effect of plasma from western diet fed mice on bone marrow derived macrophages (BMDM)

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

country: Germany

institute: University Heidelberg

summary:
Due to their ligand profiles, it can be hypothesized that Stab1 and Stab2 may be involved in atherosclerosis. We treated bone marrow derived macrophages (BMDM) with plasma from Stabilin-deficient and Wildtype mice to account for gene changes.
We used microarrays to detail the global programme of gene expression in BMDM during different plasma treatments. We identified distinct classes of up- and down-regulated genes in response to the treatment.

overall_design: Mouse femurs were dissected and flushed with PBS containing 10% FCS and filtered through a 70 μm Nylon cell strainer. The bone marrow was collected in a 50 ml tube. The bone marrow was pipetted up and down and centrifuged for 5 minutes with 400g. Supernatant was discarded and the cell pellet was resuspended in 10 ml red blood cell lysis buffer for 30 s. Immediately afterwards, 20 mL DMEM (Dulbecco's Modified Eagle Medium; Gibco) was added and cells were again centrifuged for 5 minutes with 400g. Supernatant was discarded and the cell pellet was resuspended in DMEM containing 10% FCS; 0,5% Penicillin; 0,5% Streptavidin and MCSF 30 ng/ml (Peprotech; cat. no. 315-02). At day four after BMDM isolation, the initial medium was replaced with DMEM containing 10% plasma of Wildtype (WT), ApoE-KO (ApoE), ApoE-Stab1-KO (AS1) and ApoE-Stab2-KO (AS2) mice after 8 weeks of Western Diet treatment. The RNA was isolated 48 hours after cultivation with the corresponding plasma.

first: Cyrill

last: Géraud


title: Comparison of normal and KCNQ3 overexpressing HEK293T cells

first: David

last: Shorthouse

summary: KCNQ3 (KQT-like potassium channel member 3) was overexpressed in HEK293T cells and compared to control

overall_design: KCNQ3 overexpression vs normal HEK293T, 4 biological replicates for each condition

first: Benjamin

last: Hall


title: Synthetic amorphous magnesium-substituted calcium phosphate: silent constructs that trap macromolecules for intracellular delivery

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: Amorphous magnesium-substituted calcium phosphate (AMCP) nanoparticles form constitutively in large numbers in the gastrointestinal tract. Collective evidence indicates that they trap luminal macromolecules, such as bacterial and dietary protein antigen, delivering this cargo to mucosal antigen presenting cells. Here using a precise synthetic mimetic of the AMCP nanomineral, we studied whether trapping of macromolecules by AMCP modulates signalling of the macromolecule itself. Based upon whole genome transcriptomic analyses and using peptidoglycan as a macromolecule, we showed that neither AMCP nanomineral itself regulated any gene, nor did it modify any gene regulation by peptidoglycan. We conclude that synthetic AMCP nanomineral can deliver macromolecular cargo intracellularly without affecting gene transcription.

overall_design: Peripheral blood mononuclear cells (PBMC) were isolated from 7 subjects and further enriched for monocytes by Percoll density gradient centrifugation. Protein-containing (bovine serum albumin at 500 µg/ml), synthetic amorphous magnesium-substituted calcium phosphate nanoparticles were prepared in the absence (AMCP) or presence (AMCP/sPg) of 50 µg/ml soluble, purified peptidoglycan from Escherichia coli. Monocyte-enriched PBMC were stimulated for 3 hr with synthetic AMCP or AMCP/sPg nanoparticles (both diluted 1:9 in tissue culture medium) or with 4 µg/ml soluble peptidoglycan (sPg) or with vehicle control. Cells were subsequently recovered and subjected to genome-wide gene expression analysis.

first: Carolin

middle: T

last: Haas

first: Mark

middle: V

last: Boekschoten

first: Laetitia

last: Pele

first: Jonathan

last: Powell


title: PIWIL3 forms a complex with TDRKH in mammalian oocytes

city: Mainz

last: Rosenkranz

address: Anselm-Franz-von-Bentzel-Weg 7

department: Institute of Anthropology

institute: Johannes Gutenberg-University Mainz

type: Non-coding RNA profiling by high throughput sequencing

summary: PIWIs are crucial guardians of genome integrity, particularly in germ cells. While mammalian PIWIs have been primarily studied in mouse and rat, a homologue for the human PIWIL3 geneis absent in the Muridae family, and hence the unique function of PIWIL3 in germ cells cannot be effectively modeled by mouse knockouts. Herein, we investigated the expression,distribution and interaction of PIWIL3 in bovine oocytes. We localized PIWIL3 to mitochondria, and demonstrated that PIWIL3 expression is stringently controlled both spatially and temporally before and after fertilization. Moreover, we identified PIWIL3 in a mitochondrial-recruited three-membered complex with TDRKH and PNLDC1, and demonstrated by mutagenesis that PIWIL3 N-terminal arginine modifications are required for complex assembly. Finally we sequenced the piRNAs bound to PIWIL3-TDRKH-PNLDC1 and report here that about 50% of these piRNAs map to transposable elements, recapitulating the important role of PIWIL3 in maintaining genome integrity in mammalian oocytes.

overall_design: Small RNA sequencing from GV stage bovine oocytes (Tdrkh co-Immunoprecipitation vs. Input)

first: Minjie

last: Tan

first: Helena

last: van Tol

first: Elke

middle: F

last: Roovers

first: Mirjam

last: Damen

first: Tom

last: Stout

first: Wei

last: Wu

first: Bernard

last: Roelen


title: Transcriptome analysis using RNA sequencing of the neurospheres from EGFL7-/- versus wildtype mice

city: Frankfurt

first: Irmgard

last: Tegeder

state: Hessen

address: Theodor Stern Kai 7

department: Clinical Pharmacology

institute: Goethe University Frankfurt

summary: We assessed the effect of a deletion of epidermal growth factor like 7 (EGFL7) on neurogenesis. Here, we assessed differential gene expression in neuropheres of EGFL7-/- versus wildtype mice using RNA-sequencing. EGFL7 deficiency increases the rate of proliferation of neural stemm cells (NSC), and increases the velocity of maturation and integration of adult born mature neurons into existing networks. Hence, EGFL7 pushes NSCs towards quiescence and neural progenitors towards differentiation. Differential genes expression was used to assess underlying mechanisms. The experiment was done in two sequential analyses, experiment-1 comprised 6 sample per genotype (single end reads), and experiment-2 had 4 samples per genotype (paired end reads). The final analysis was done with a pooled dataset. A total number of 19709 genes was reliably detected in >8 valid samples out of 20 in total. GSEA gene set enrichment analysis was used for gene ranking and identication of top up- and downregulated genes and evaluation of their functions. VENN diagrams were used to assess the agrement of Exp1 and Exp2 and the combined analysis.

overall_design: RNA from neurospheres from the subventricular zone (d3) and the hippocampus (d5) was analyzed by RNA sequencing of 10 biological replicates per genotype (EGFL7 versus wildytpe) using an Illumina Novaseq600 system.

first: Mirko

last: Schmidt


title: MiR-26a targets EphA2 to resist intracellular Listeria monocytogenes in macrophages

city: ChongQing

first: Jiangbei

last: Yuan

state: Please select

address: School of Pharmaceutical Sciences,Huxi Campus, Chongqing University

institute: Chongqing University

summary: We performed transcriptome analyses of miR-26a-overexpressing RAW264.7 cells (RAW264.7.miR-26a.OE) and NC-plasmid-transfected RAW264.7 cells (RAW264.7.NC), using RNA-seq . We identified 121 genes that were downregulated in RAW264.7.miR-26a.OE cells compared with RAW264.7.NC cells. Among the downregulated genes, we identified four putative target genes, using TargetScan (www.targetscan.org), including EphA2, Map3k9, Nhsl1, and Otud1, which all contain a putative miR-26a seed sequence.

overall_design: We detect RNA expression level of miR-26a-overexpressing RAW264.7 cells (RAW264.7.miR-26a.OE) and NC-plasmid-transfected RAW264.7 cells (RAW264.7.NC) upon  L.m infection 5h.

first: Ying

last: Wan


title: Late transcriptional changes in blood, neural, and colon tissues in rat stress alone and comorbid pain model compared with naïve have regulatory roles in neurological disease

status: Public on May 31 2022

city: Baltimore

first: Evelina

last: Mocci

state: MD

address: 655 W Lombard S

department: PTSS

institute: SON

summary:
Purpose: Irritable bowel syndrome (IBS) and temporomandibular disorder (TMD) are two chronic pain conditions that frequently occur in the same individuals, most commonly women. Stress is the main risk factors associated; however, the mechanisms underlying IBS-TMD co-morbidity are mostly unknown
Methods: Twenty-four female rats were randomly assigned to one of three experimental groups: naïve, stress-induced visceral hypersensitivity (SIH), and CPH (orofacial pain plus stress). RNA was extracted from blood, colon, spinal cord, and dorsal root ganglion after 1 or 7 weeks from the induction of stress. We combined differential gene expression and co-expression network analyses to define both SIH and CPH expression profiles across tissues and time
Results: The transcriptomic profile in blood and colon showed increased expression of genes enriched in inflammatory and neurological biological processes in CPH compared to SIH rats, both at 1 and 7 weeks after stress. In lumbosacral spinal tissue, both SIH and CPH rats compared to naïve revealed decreased expression of genes related to synaptic activity and increased expression of genes enriched in “angiogenesis”, “Neurotrophin” and “PI3K-Akt” pathways. In DRG, CPH rats showed decreased expression of immune response genes at week1 and inhibition of nerve myelination genes at 7 weeks compared to naïve.   For all tissues we observed higher expression of genes involved in ATP production in SIH compared to CPH at one week and this was reversed at seven weeks after the induction of stress.  Compared to SIH, CPH rats showed increased expression of angiogenesis-related genes one week after exposure to stress, while 7 weeks post stress the expression of these genes was higher in SIH rats
Conclusions: Our study highlights an increased inflammatory response in CPH compared to SIH rats in the blood and colon. DRG and spinal transcriptomic profiles of both CPH and SIH rats showed inhibition of synaptic activity along with activation of angiogenesis. Targeting these biological processes may lead to more profound understanding of the mechanisms underlying IBS-TMD comorbidities and new diagnostic and therapeutic strategies

overall_design:
Differential gene expression and co-expression network analyses:
RNA-seq bulk
Twenty-four female rats were randomly assigned to one of three experimental groups: naïve, stress-induced visceral hypersensitivity (SIH), and CPH (orofacial pain plus stress). RNA was extracted from blood, colon, spinal cord, and dorsal root ganglion after 1 or 7 weeks from the induction of stress. We combined differential gene expression and co-expression network analyses to define both SIH and CPH expression profiles across tissues and time

first: Richard

last: Traub

first: Susan

last: Dorsey


title: Interferon alpha-inducible protein 27 (IFI27) expression is linked to disease severity in chronic infection of both HIV-1 and HIV-2

city: Lund

first: Angelica

last: Palm

address: Baravägen 18

country: Sweden

institute: Lund University

summary: To explore if specific host responses are linked to HIV disease severity, we here investigated blood gene expression profiles comparing different progressor groups, including those with HIV-1, HIV-2 or HIV-1/HIV-2 dual infection and HIV seronegative individuals. We found interferon alpha-inducible protein 27 (IFI27) to be the most strongly, and significantly, upregulated gene in HIV infected, compared with HIV seronegative, individuals. The expression of IFI27 was higher in HIV-1, compared with HIV-2, infected individuals and correlated with both plasma viral load (pVL) and CD4% levels.

overall_design: Whole blood was collected in PAXgene Blood RNA tubes from individuals with mono HIV-1 or HIV-2, or dual HIV-1 and HIV-2 infection, and from HIV seronegative controls. Samples from 8 individuals in each group (7 individuals for HIV-2) were analyzed.

first: A

first: S

last: Veerla

first: J

last: Lindman

first: P

middle: E

last: Isberg

first: E

last: Johansson

last: Biague

first: F

last: Månsson

first: H

last: Norrgren

last: Esbjörnsson

last: Medstrand

first: M

last: Jansson


title: Enhancing PD-L1 Degradation by ITCH during MAPK Inhibitor Therapy Suppresses Acquired Resistance

city: LOS ANGELES

first: Sixue

last: Liu

address: 10833 Le Conte Avenue

department: Medicine

institute: UCLA

summary: MAPK inhibitor (MAPKi) therapy in melanoma leads to accumulation of tumor-surface PD-L1/2, which may evade antitumor immunity and accelerate acquired resistance. Here, we discover that the E3 ligase ITCH binds, ubiquitinates, and down-regulates tumor-surface PD-L1/L2 in MAPKi-treated human melanoma cells, thereby modulating activation of co-cultured T cells. During MAPKi therapy in vivo, tumor cell-intrinsic ITCH knockdown in murine melanoma induced tumor-surface PD-L1, reduced intratumoral cytolytic CD8+ T cells, and accelerated acquired resistance only in immune-proficient mice. Conversely, tumor cell-intrinsic ITCH over-expression reduced MAPKi-elicited PD-L1 accumulation, augmented cytolytic CD8+ T-cell infiltration, and suppressed acquired resistance in BrafMUT, NrasMUT, and Nf1MUT murine melanoma and KrasMUT pancreatic cancer models. CD8+ T-cell depletion and tumor cell-intrinsic PD-L1 over-expression nullified the ability of ITCH over-expression to suppress MAPKi-resistance, supporting in vivo the ITCH–PD-L1–T-cell regulatory axis demonstrated in human cancer cell lines. Moreover, we identified a small-molecular ITCH activator which suppressed acquired MAPKi-resistance in vivo. Thus, MAPKi-elicited tumor-surface PD-L1 accelerates acquired-resistance, and degrading PD-L1 by activating ITCH may be a combinatorial approach to promote antitumor T-cell immunity and durable responses.

overall_design: This dataset contains the scRNAseq and scTCR-seq data of intratumoral CD45+ cells in murine melanoma model  (NILER1-4, Nras mutant) under MEKi treatment and scRNAseq data of dissociated tumors in BRAFmut murine melanoma model (YUMMER1.7) under MEKi treatment

first: Zhentao

last: Yang

first: Yan

last: Wang

first: Weixian

last: Deng

first: Shirley

last: Lomeli

first: Gatien

last: Moriceau

first: James

last: Wohlschlegel

first: Marco

last: Piva

first: Roger

middle: S

last: Lo


title: Transcriptomic profile in in vitro produced bovine morulae treated with MAT2A inhibitor

city: Kyoto

first: Shuntaro

last: Ikeda

address: Kitashirakawa Oiwake-cho, Sakyo-ku

department: Graduate School of Agriculture

country: Japan

institute: Kyoto University

summary: We obtained transcriptomic profiles in bovine morulae which had been in vitro treated with a methionine adenosyltransferase 2A (MAT2A) inhibitor from the 8-16 cell stage.

overall_design: In vitro produced bovine morulae were processed to RNA-Seq. The experiments were triplicated using three single morula per group.

first: Airi

last: Ota

first: Akihisa

last: Shinozawa

first: Hisataka

last: Iwata

first: Miki

last: Sugimoto

first: Naojiro

last: Minami

first: Takeshi

last: Ohta


title: Effect of plasma from western diet fed mice on mouse aorta endothelial cells (MAOEC)

first: Carolina

last: Delatorre

summary:
Due to their ligand profiles, it can be hypothesized that Stab1 and Stab2 may be involved in atherosclerosis. We treated mouse aorta endothelial cells (MAOEC) with plasma from Stabilin-deficient and Wildtype mice to account for gene changes.
We used microarrays to detail the global programme of gene expression in MAOEC during different plasma treatments. We identified distinct classes of up- and down-regulated genes in response to the treatment.

overall_design: Primary mouse aorta endothelial cells (MAOEC) (Pelo Biotech; cat. no. C57-6052) were grown to confluence in 6-well plates supplied with Endothelial Cell Medium (Pelo Biotech) containing 10% FCS. Subsequently, the Endothelial Cell Medium was supplemented with 10% plasma of ApoE-KO, ApoE-Stab1-KO and ApoE-Stab2-KO mice after 8 weeks of Western Diet treatment instead of FCS. After 48 hours of incubation, the RNA of the MAOEC was isolated.

first: Cyrill

last: Géraud


title: De novo construction of T cell compartment in humanized mice engrafted with iPSC-derived thymus organoids

city: Pittsburgh

first: Yong

last: Fan

state: Pennsylvania

address: 320 E North Ave

department: Institute of Cellular Therapeutics

institute: Allegheny Health Network

summary: Hematopoietic humanized (hu) mice are powerful tools for modeling the action of human immune system and are widely used for preclinical studies and drug discovery. However, generating a functional human T cell compartment in hu mice remains challenging, primarily due to the species-related differences between human and mouse thymus. While engrafting human fetal thymic tissues can support robust T cell development in hu mice, tissue scarcity and ethical concerns limit their wide use. Here, we describe the tissue engineering of human thymus organoids from inducible pluripotent stem cells (iPSC-thymus) that can support the de novo generation of a diverse population of functional human T cells. T cells of iPSC-thymus engrafted hu mice could mediate both cellular and humoral immune responses, including mounting robust proinflammatory responses upon TCR engagement, inhibiting the growth of allogeneic tumor grafts and facilitating efficient Ig class switching. Our findings suggest that hu mice engrafted with iPSC-thymus can serve as a novel animal model to study human T cell-mediated immunity and accelerate the translation of animal studies into the clinic.

overall_design: Cells used in this study were thymic epithelial cells (TECs) derived from iPSCs and then grown in different culture conditions. One set of samples is TECs grown in a 2-dimensional cell culture environment, while the other is a set of TECs grown in a 3-dimensional alginate capsule. No replicates or controls were used. Reference samples were taken from the publically available datasets generated by Campinoti et al. (2020) and Zeng et al. (2019).

first: Ann

last: Zeleniak

first: Catherine

last: McCormick

first: Connor

last: Wiegand

first: Wen

last: Liu

first: Amir

last: Alavi

first: Ravi

last: Krishnamurthy

first: Haonan

last: Guan

first: Suzanne

last: Bertera

first: Robert

last: Lakomy

first: Asako

last: Tajima

first: Henry

last: Cohen

first: Stephanie

last: Wong

first: Lame

last: Balikani

first: Benjamin

last: Mizerak

first: Ziv

last: Bar-Joseph

first: Massimo

last: Trucco

first: Ipsita

last: Banerjee


title: Genome-wide H3K27me3 profile in in vitro produced bovine morula treated with MAT2A inhibitor

first: Shuntaro

last: Ikeda

summary: We obtained genome-wide profiles of histone H3 lysine 27 trimethylation (H3K27me3) in bovine morula which had been in vitro treated with a methionine adenosyltransferase 2A (MAT2A) inhibitor from the 8-16 cell stage.  Sequencing center: NODAI Genome Research Center, Tokyo University of Agriculture

overall_design: In vitro produced bovine morulae were processed to ChIP-Seq using H3K27me3 antibody. The experiments were duplicated using two biological replicates.

first: Airi

last: Ota

first: Akihisa

last: Shinozawa

first: Hisataka

last: Iwata

first: Miki

last: Sugimoto

first: Naojiro

last: Minami

first: Takeshi

last: Ohta


title: Intratumoral TFR cells curtail anti-PD-1 treatment efficacy

city: La Jolla

first: Pandurangan

last: Vijayanand

address: 9420 Athena Circle

department: Division of Vaccine Discovery

institute: La Jolla Institute for Allergy and Immunology

summary: Follicular regulatory T cells (TFR cells) and their functional role in cancer have been completely disregarded so far. Our data identify that as a critical oversight, as these cells account for a substantial proportion of tumor-infiltrating CD4+ T cells

overall_design: Assessment of the transcriptomic profile of tumor-infiltrating TREG and TFR cells

first: Simon

last: Eschweiler

first: James

last: Clarke

first: Ciro

last: Suastegui

first: Bharat

last: Panwar

first: Ariel

last: Madrigal

first: Serena

last: Chee

first: Edwin

last: Woo

first: Aiman

last: Alzetani

first: Peter

last: Friedmann

first: Tilman

last: Sanchez-Elsner

first: Ferhat

last: Ay

first: Christian

last: Ottensmeier


title: Patient iPSCs with NEUROG3 mutation reveal pancreatic insufficiency

city: Chicago

first: Cambrian

middle: Yangshao

last: Liu

state: IL

address: 5841 S Maryland Ave

department: Department of Medicine

institute: The University of Chicago

summary: Patients with NEUROGENIN3 mutations have enteric endocrinopathy and diabetes mellitus. We generated pluripotent stem cells from a patient’s fibroblasts to investigate if gene editing restores endocrine differentiation. Corrected cell lines differentiated into all pancreatic lineages while native cell lines failed to activate pancreatic progenitor and lineage determination genes, suggesting that the mutation disrupts pancreatic organogenesis and results in endocrine and exocrine dysfunction. Clinical testing revealed the patient has exocrine pancreatic insufficiency. These results expose a novel role for NEUROGENIN3 in human pancreatic differentiation and illustrates how patient-specific stem cells can be used to interrogate disease etiology and affect patient care.

overall_design: 14 samples were analyzed for bulk RNA sequencing. We sequenced two biological replicates for NGN3-NULL at stages 3, 4, and 5. We sequenced two biological replicates for NGN3-CORR at stages 4 & 5, and one biological replicate at stage 3. We used the H1 line as a control at stages 3, 4, and 5.

first: Katelyn

last: Millette

middle: Y

first: Senta

last: Georgia


title: RNA-seq of detecting the effect of CDK4&6 inhibitor Abemaciclib and VSV-M51 in glioma

city: Shenzhen

first: Ping

last: Li

address: Gongchang Road

department: School of Medicine

institute: Sun Yat-sen University

summary: The RNA-seq data provided evidence that CDK4&6 inhibitor Abemaciclib and VSV-M51 increase the oncolytic effect in glioma

overall_design: Setting three groups, control, VSV-M51, CDK4&6 inhibitor Abemaciclib and VSV-M51. CDK4&6 inhibitor Abemaciclib pretreat the T98 human glioma cells, then using the VSV-M51 oncolytic virus infect the T98 cells for 24 hours. Collected the three groups cells by trizol.

first: Xiao

last: Jingshu


title: Genome-wide maps of chromatin state in human adipose derived stem cells isolated from abdominal (ABD) and gluteofemoral (GF) subcutaneous adipose tissue

city: orlando

first: Adeline

last: Divoux

state: FL

address: 301 E. Princeton St

department: Translational Research Institute

institute: Adventhealth

summary: Human adipose serived stem cells (ASC) isolated from A and GF adipose tissue obtained from premenopausal women were used to perform assess accessible chromatin regions by ATAC-seq, chromatin marks, CTCF and RNAPII identification by chIP-seq

overall_design: Chromatin state in human adipose derived stem cells isolated from abdominal (ABD) and gluteofemoral (GF) subcutaneous adipose tissue

first: T

last: Osborne

first: S

last: Smith


title: Single-cell multi-omics dataset of hepatocellular carcinoma cell lines

city: shenzhen

first: CNSA

last: CNGB

address: BGI

institute: BGI

summary: We interrogated single-cell transcriptomes, proteomes and epigenetic information revealing metastasis potential heterogeneity in 5 HCC cell lines across metastasis capacity.

overall_design: We performed CITE-seq, scATAC-seq and scRNA-seq on five HCC cell lines which have diverse metastatic abilities and six markers of liver cancer stem cell (LCSC) were measured,including CD44, EPCAM, CD133, CD24, CD90, and CD54.

first: Shanshan

last: Wang

first: Jiarui

last: Xie

first: Xuanxuan

last: Zou

first: Qichao

last: Yu


title: The impact of protein quantity during energy restriction on genome-wide gene expression analysis in human adipose tissue

first: Guido

last: Hooiveld

summary: Overweight is a growing health problem worldwide. The most effective strategy to reduce weight is energy restriction (ER): restriction of food intake without malnutrition. ER has been shown to be beneficial in disease prevention, healthy aging, and inflammation. Recent studies suggest that reducing the protein content of a diet contributes to the beneficial effects by ER. The first objective of our study was to assess the effect of energy restriction on changes in gene expression in adipose tissue. Secondly, the changes in gene expression were compared between a high protein diet and a normal protein diet during energy restriction. In a parallel double-blinded study, overweight older subjects adhered to a 25% ER diet, either combined with high protein intake  (HP-ER, 1.7 g/kg per day), or with normal protein intake  (NP-ER, 0.9 g/kg per day) for 12 weeks. From 10 HP-ER subjects and 12 NP-ER subjects subcutaneous adipose tissue biopsies were collected before and after the diet. Adipose tissue was used to isolate total RNA and to evaluate whole genome gene expression changes upon a HP-ER and NP-ER diet. Upon 25% ER, clusters of gene sets in energy metabolism, such as lipid metabolism and PPARα targets, NRF2 targets, glucose metabolism, and TCA cycle, as well as gene sets in oxidative phosphorylation, adaptive immune response, immune cell infiltration, and cell cycle were decreased, and RNA translation and processing gene sets were increased. A different gene expression response between HP-ER and NP-ER was observed for 530 genes. Pathway analysis revealed that after NP-ER a downregulation in expression of genes involved in adaptive immune response was present. HP-ER resulted in an upregulation of pathways involved in cell cycle, GPCR signalling, olfactory signalling and nitrogen metabolism. Based on the gene expression changes, we concluded that HP seems to be less beneficial for ER’s effect on immune-related gene expression in adipose tissue.

overall_design: In a parallel double-blinded study, overweight middle-aged subjects adhered to a 25% ER diet, either combined with high protein (HP-ER, 1.5 g/kg-bw/d), or with standard protein (SP-ER, 0.8 g/kg-bw/d) for 12 weeks. From 10 HP-ER subjects and 12 SP-ER subjects subcutaneous adipose tissue biopsies were collected before and after the diet. Adipose tissue was used to isolate total RNA and to evaluate whole genome gene expression changes upon a HP-ER and SP-ER diet.

first: Inge

last: van Bussel

first: E

middle: M

last: Backx

first: C

last: de Groot

middle: A

last: Tieland

first: Lydia

last: Afman


title: Effects of siRNA-mediated knockdownof RUNX1 expression in breast cancer cells

city: Houston

first: Chin-Yo

last: Lin

state: TX

address: 3517 Cullen Blvd, Rm 3018

department: Biology and Biochemistry

institute: University of Houston

summary: Previous studies have identified an interaction between RUNX1 and estrogen receptor alpha and its potential role in estrogen signaling in breast cancer. To determine the transcriptomic actions of RUNX1, we knocked down its expression by using siRNAs, both in the absence and presence of estradiol (E2).

overall_design: MCF-7 cells were either transfected with control (NT) or RUNX1 targeting siRNA in the absence of estrogen (ETOH vehicle) or in the presence of estradiol dissolved in ethanol).

first: Nicholes

last: Candelaria


title: NR1H3 (LXRα) IS ASSOCIATED WITH PRO-INFLAMMATORY MACROPHAGES, PREDICTS SURVIVAL AND PROVIDES RATIONALE FOR NEW IMMUNOMODULATION IN DIFFUSE LARGE B-CELL LYMPHOMA

city: Bari

first: Maria Carmela

last: Vegliante

address: Viale Orazio Flacco,65

department: Hematology and Cell Therapy Unit

country: Italy

institute: IRCCS-Istituto tumori "Giovanni Paolo II"

summary:
The role of macrophages (Mo) and their prognostic impact in diffuse large B-cell lymphomas (DLBCL) remain controversial. By regulating the lipid metabolism, Liver-X-receptors (LXRs) control Mo polarization/inflammatory response, and their pharmacological modulation is under clinical investigation to treat human cancers, including lymphomas. Herein, we surveyed the role of LXRs in DLBCL for potential prognostic and therapeutic purposes. By comparing bulk tumors with purified malignant and normal B-cells, we found an intriguing association of NR1H3, encoding for the LXR-α isoform, with the tumor microenvironment (TME). CIBERSORTx-based purification on large DLBCL datasets revealed a high expression of the receptor in M1-like pro-inflammatory Mo. By determining an expression cut-off of NR1H3, we used digital-expression to validate its prognostic capacity on two large independent on-trial and real-world cohorts. Independently of classical prognosticators, NR1H3high patients displayed longer survival compared to NR1H3low cases and, a high-resolution Mo GEP dissection suggested a remarkable transcriptional divergence between subgroups. Finally, treating in vitro generated M2 Mo, that display basal low NR1H3, with a new oral LXR agonist, we observed significant upregulation of NR1H3 along with inflammatory genes. Overall, our findings indicate NR1H3 as a biomarker of Mo in DLBCL, useful to identify patients at different risk and heterogenous TME who could benefit from Mo-directed immunomodulation in DLBCL.
Expression data from in vitro generated macrophages from ThP1 treated either with DMSO or RGX104

overall_design: In this experiment we analized the effect of RGX104 treatment on transcriptome of M2 generated in vitro from ThP1 cell lines. ThP1 were polarized toward M2  with PMA (320nM) fron six hours and IL-4 and IL-13 (20ng/µl each) for the last 18 hours. Then, cells were eicther treated with DMSO (control) and RGX104 (2μM) for 24 hours in a 3D cell culture system (Alvetex). RNA was extracted and gene expresion profiling performed.

first: Maria

middle: C

first: Stefano

last: Pileri

first: Sabino

last: Ciavarella


title: RNA Polymerase I activity prevents terminal differentiation and growth arrest in colorectal cancer and induce vulnerability for senolytics

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

summary: Loss of the tumor suppressor APC, which constitutes the initiating event in the adenoma carcinoma sequence for colorectal cancer (CRC), induces expression of RNA polymerase I (RNAPOL1) transcription machinery and subsequently upregulates rDNA transcription. Targeting RNAPOL1 with a specific inhibitor, CX5461, disrupts nucleolar integrity and induces a disbalance of ribosomal proteins. CX5461-induced growth arrest is irreversible, and exhibits features of senescence as well as terminal differentiation. Mechanistically, CX5461 promotes differentiation in a MIZ1- and Rb-dependent manner. In addition, inhibition of RNAPOL1 renders CRC cells vulnerable towards senolytic agents.

overall_design: RNA-seq of LS174T cells treated with CX5461

first: Armin

last: Wiegering

first: Christoph

last: Otto

first: Carolin

last: Kastner

first: Stefanie

last: Schmidt

first: Konstantin

last: Uttinger

first: Apoorva

last: Baluapuri

first: Sarah

last: Denk

first: T

last: Rosenfeldt

first: Andreas

last: Rosenwald

first: Florian

last: Röhrig

first: Carsten

last: Ade

first: Christina

last: Schülein-Völk

first: Markus

last: Diefenbacher

first: Christoph-Thomas

last: Germer

first: Elmar

last: Wolf


title: Sputum microRNA‐screening reveals Prostaglandin EP3 receptor as selective target in allergen‐specific immunotherapy

city: Munich

first: Ulrich

last: Zissler

address: Biedersteiner Str. 29

department: Center of Allergy & Environment (ZAUM)

institute: Technical University of Munich & Helmholtz Center Munich

summary:
Several microRNAs (miRs) have been described as potential biomarkers in liquid biopsies and in the context of allergic asthma, while therapeutic effects on the airway expression of miRs remain elusive. In this study, we investigated epigenetic miR-associated mechanisms in the sputum of grass pollen allergic patients with and without allergen specific immunotherapy (AIT). Induced sputum samples of healthy controls (HC), AIT treated and untreated grass pollen allergic rhinitis patients with (AA) and without asthma (AR) were profiled using miR microarray and transcriptome microarray analysis of the same samples. miR targets were predicted in silico and used to identify inverse regulation. Local PGE2 levels were measured using ELISA.
Two Hundred and fifty nine miRs were upregulated in the sputum of AA patients compared with HC, while only one was downregulated. The inverse picture was observed in induced sputum of AIT-treated patients: while 21 miRs were downregulated, only 4 miRs were upregulated in asthmatics upon AIT. Of these 4 miRs, miR3935 stood out, as its predicted target PTGER3, the prostaglandin EP3 receptor, was downregulated in treated AA patients compared with untreated. The levels of its ligand PGE2 in the sputum supernatants of these samples were increased in allergic patients, especially asthmatics, and downregulated after AIT. Finally, local PGE2 levels correlated with ILC2 frequencies, secreted sputum IL13 levels, inflammatory cell load, sputum eosinophils and symptom burden.While profiling the sputum of allergic patients for novel miR expression patterns, we uncovered an association between miR3935 and its predicted target gene, the prostaglandin E3 receptor, which might mediate AIT effects through suppression of the PGE2-PTGER3 axis.

overall_design: Induced sputa were performed in healthy controls, allergic rhinitis with and without concomittant asthma in grass pollen season. Some of the patients received allergen-specific immunotherapy (AIT).

first: C

last: Jakwerth

first: A

last: Chaker

first: F

last: Guerth

first: M

last: Oelsner

first: L

last: Pechtold

last: zur Bonsen

first: J

last: Ullmann

first: S

last: Krauss-Etschmann

last: Erb

last: Kau

last: Plaschke

last: Winkler

last: Kurz

last: Kloss

last: Esser-von

middle: B

last: Schmidt-Weber

first: U


title: Expression profiles of placenta and umbilical cord blood with or without gestational diabetes mellitus (GDM)

city: Shanghai

first: Jiahao

last: Wang

state: Shanghai

address: Yueyang road

department: Bioinformatisc core

institute: Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences

summary: Objective: To explore the characteristics and underlying molecular mechanisms of genome-scale expression profiles of women with- or without- GDM and their offspring.  Materials and Methods: We recruited a group of 21 pregnant women with GDM and 20 healthy pregnant women as controls. For each pregnant women, RNA-seq were performed using the placenta and paired neonatal umbilical cord blood specimens. Differentially expressed genes (DEGs) were identified with BMI of pregnant women as covariates. Then, functional enrichment analysis was performed separately or interactively in placenta and umbilical cord blood.  Results: Through the comparison of GDM and healthy samples, 1442 and 488 DEGs were identified from placenta and umbilical cord blood, respectively. Functional enrichment analysis showed that the placenta expression profiles of GDM women mirrored the molecular characteristics of type II diabetes and insulin resistance patients. DEGs illustrated significant overlaps among placenta and umbilical cord blood samples, and the overlapping DEGs were associated with endocrine resistance and insulin resistance.  Conclusions: Our research demonstrated the transcriptomic alternations of GDM mothers and offspring. Our findings emphasized the importance of epigenetic modifications in the communication between pregnant women with GDM and offspring, and provided reference for the prevention, control, treatment, and intervention of perinatal deleterious events of GDM and neonatal complications.

overall_design: RNA-seq of placenta and paired umbilical cord blood from 21 pregnant women with GDM and 20 healthy pregnant women

first: Sha

last: Lu

first: Jiantao

last: Shi

first: Wensheng

last: Hu


title: IG-MYC rearrangement defines a high-risk subgroup of B-cell precursor acute lymphoblastic leukaemia

city: Newcastle upon Tyne

first: Ed

last: Schwalbe

address: Ellison Place

department: Applied Sciences

institute: Northumbria University

type: Methylation profiling by genome tiling array

summary: We assessed the molecular relationship of IG-MYC rearranged ALL with other ALL subtypes and Burkitt’s lymphoma and describe the genetic and clinical outcomes of IG-MYC rearranged ALL

overall_design: We assessed 17 IG-MYC rearranged ALL and integrated with previously published DNA methylation datasets

first: Edward

first: Lisa

last: Russell


title: Reduced representation bisulfite sequencing (RRBS) methylation profiles of placenta and umbilical cord blood with or without gestational diabetes mellitus (GDM)

type: Methylation profiling by high throughput sequencing

summary: Objective: To explore the characteristics and underlying molecular mechanisms of genome-scale expression profiles of women with- or without- gestational diabetes mellitus and their offspring.  Materials and Methods: We recruited a group of 21 pregnant women with gestational diabetes mellitus (GDM) and 20 healthy pregnant women as controls. For each pregnant women, RRBS were performed using the placenta and paired neonatal umbilical cord blood specimens. Differentially methylated regions (DMRs) were identified. Then, functional enrichment analysis was performed to differential methylated genes (DMGs) separately or interactively in placenta and umbilical cord blood.  Results: Through the comparison of GDM and healthy samples, 2779  and 141 DMRs were identified from placenta and umbilical cord blood, respectively. Functional enrichment analysis showed that the placenta methylation and expression profiles of GDM women mirrored the molecular characteristics of “type II diabetes” and “insulin resistance”. Methylation-altered genes in umbilical cord blood were associated with pathways “type II diabetes” and “cholesterol metabolism”. DMGs illustrated significant overlaps among placenta and umbilical cord blood samples, and the overlapping DMGs were associated with cholesterol metabolism.  Conclusions: Our research demonstrated the epigenomic alternations of GDM mothers and offspring. Our findings emphasized the importance of epigenetic modifications in the communication between pregnant women with GDM and offspring, and provided reference for the prevention, control, treatment, and intervention of perinatal deleterious events of GDM and neonatal complications.

overall_design: RRBS methylation profiles of placenta and paired umbilical cord blood from 21 pregnant women with gestational diabetes mellitus (GDM) and 20 healthy pregnant women


title: Short-chain fatty acid-induced changes in colonic gene expression depend on dietary fat content in mice

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: Background: Acetate, propionate, and butyrate are the main short-chain fatty acids (SCFA) produced in the colon as a result of microbial fermentation of dietary fibers. An increasing amount of evidence suggests that these SCFA have major health benefits. The composition of the microbiota is altered by dietary fat, and this is believed to impact SCFA production. Currently it is unknown whether host gene expression responses to SCFA are modulated by fat content of the diet. The aim of this study was to compare the changes in colonic gene expression profiles after acetate, propionate and butyrate infusions between a low fat and high fat diet. Methods: Male C57BL/6J mice were fed semi-synthetic low fat (10 energy%) or high fat (45 E%) diets starting 2 weeks before the SCFA treatment period. During treatment, mice received a rectal infusion of either an acetate, propionate, butyrate, or a saline (control) solution for 6 consecutive days, after which colon was subjected to gene expression profiling. Unsupervised visualization of the dataset was performed using Independent Principal Component Analysis. For each SCFA, similarities of its effects on a low fat and a high fat diet were assessed using Rank-Rank Hypergeometric Overlap. In addition, differentially expressed genes were identified, and gene set enrichment analysis was performed to determine functional implications of the regulated genes. Results: Taking into account the complete dataset, we observed that more variation in gene expression profiles was explained by fat content of the diet than by SCFA treatment. Gene expression responses to acetate and butyrate were similar on the low fat versus high fat diet, but were opposite for propionate. Functionally the expression changes reflected differential modulation of several metabolic processes; genes involved in oxidative phosphorylation, lipid catabolism, lipoprotein metabolism and cholesterol transport were suppressed by acetate and butyrate treatment, whereas propionate treatment resulted in changes in fatty acid and sterol biosynthesis, and in amino acid and carbohydrate metabolism. Conclusions: We demonstrated that dietary fat content impacts the colonic gene expression response to propionate, and to a lesser extent to acetate and butyrate. The study demonstrates that knowledge on diet composition is essential when studying effects of SCFAs on metabolism.

overall_design: Mice were rectally infused with either one of the three main short chain fatty acids or control solution for 6 consecutive days.  4 hrs after the last infusion, colons were removed, scraped and RNA samples were subjected to gene expression profiling.

first: Danielle

last: Haenen

first: Katja

last: Lange

first: Shohreh

last: Keshtkar

first: Michael

last: Müller


title: Genome-wide mapping of hnRNPA2B1 binding in human adipose derived stem cells isolated from gluteofemoral (GF) subcutaneous adipose tissue

first: Adeline

last: Divoux

summary: NOT PROVIDED; REQUESTED

overall_design: Human adipose serived stem cells (ASC) isolated from  GF adipose tissue obtained from premenopausal women were used to perform assess hnRNPA2B1 binding by ChIP-seq

first: T

last: Osborne

last: Smith


title: The effect of Asari Radix et Rhizoma on hematopoietic stem cells in C57BL/6 mouse.

status: Public on May 30 2022

city: Daejeon

first: Da Yeon

last: Kim

state: Daejoen (30)

address: 141, Gajeong-ro, Yuseong-gu,

department: Genetic & Epigenetic Toxicology Research Group

institute: Korea Institute of Toxicology

summary: To investigate the toxicity of long-term treatment with Asari Radix et Rhizoma on hematopoietic cells, we have performed the 28 days gavage administration of AR in C57BL/6 mouse. Then, we have harvested the RBC lysed bone marrow cells, and analyzed the RNA-seq. analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for vehicle control (sterile water) or Asari Radix et Rhizoma.

first: Da

first: Seng-Min

last: Back

first: Su-Min

last: Bak

first: Na-Young

last: Jeung

first: Nan-Young

first: Sohee

first: Yong-Bum

first: Byoung-Seok

last: Lee

first: Seong-Hoon

last: Park


title: Profilig the Atopic Dermatitis Epidermal Transcriptome by Tape Stripping and BRB-seq

city: Copenhagen

first: Tu

last: Hu

address: 5 Artillerivej

department: Infectious Disease Immunology

country: Denmark

institute: Statens Serum Institut

summary: Tape stripping has recently gained use for the study of the transcriptome of atopic dermatitis (AD), a common inflammatory skin disorder characterized by a defective epidermal barrier and perturbated immune response. Here, we performed BRB-seq (a low cost, multiplex-based, transcriptomic profiling technique) to study the epidermal transcriptome of AD patients and healthy controls from tape stripped skin samples.

overall_design:
30 AD patients and 30 age and gender matched healthy controls (HC) were recruited from the outpatient clinic at Gentofte Hospital between April 2018 and November 2019.
Tape stripped skin samples were obtained by attaching adhesive tape strips (diameter 22 mm, Disc D-Squame, Monaderm, Monaco, France) to the skin for 10 seconds with a standardized pressure (225 g cm−2) using the D-Squame pressurizer D500 (CuDerm, Dallas, TX, USA).
Each sample consisted of 8 consecutive D-squame tapes, where the 5th to 8th tapes were proceed for transcriptomics analysis.
A subpopulation of patients with AD and HC continued in a longitudinal study, where tape stripped skin samples were taken at 3, 6, 9 and 12 months after the baseline visit. In total, and after quality control, 132 samples were included for transcriptomic profiling.

first: Thomas

last: Litman


title: Profile in in vitro produced bovine morulae treated with MAT2A inhibitor

first: Shuntaro

last: Ikeda

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

overall_design: Refer to individual Series


title: Mapping cis-regulatory elements in human excitatory and inhibitory neurons links psychiatric disease heritability and activity-regulated transcriptional programs [ATAC-seq]

city: New York

last: Yan

email: linda.lee2@mssm.edu, nan.yang1@mssm.edu

state: NY

address: 1425 Madison Ave

department: Neuroscience

institute: Mount Sinai

summary: Genome-wide association studies (GWAS) have identified hundreds of loci associated with psychiatric diseases, yet there is a lack of understanding of disease pathophysiology. Common risk variants can shed light on the molecular mechanisms underlying these diseases; however, identifying specific causal variants remains challenging. An added complication is that most common risk variants are in non-coding regions. Their impact is likely to be restricted to particular cell types, developmental stages, or cell states. Here, we comprehensively mapped cis-regulatory elements in two defined populations of human excitatory and inhibitory neurons derived from pluripotent stem cells.

overall_design: We performed  bulk ATAC-seq to identify open, accessible chromatin regions in human induced glutamatergic (Glu) and GABAergic (GABA) neurons derived from human pluripotent stem cells (ES and iPSCs). We exposed neurons to an elevated level of potassium chloride (KCl) to study activity-induced responses, and profiled chromatin accessiblity at various timepoints after depolarization.

first: Carlos

last: Sanchez-Priego

first: Ruiqi

first: Linda

last: Boshans

first: Matthew

last: Lalli

last: Yang


title: High-throughput characterization of hematopoietic stem cell engraftment after intravenous and intracerebroventricular dosing

city: London

first: Luca

last: Biasco

address: 30 Guilford St, Holborn

institute: UCL

summary: Hematopoietic stem/progenitor cell gene therapy (HSPC-GT) has shown clear neurological benefit in rare diseases, which is achieved through the engraftment of genetically modified microglia-like cells (MLCs) in the brain. Still, the engraftment dynamics and the nature of engineered MLCs, as well as their potential use in common neurogenerative diseases have remained largely unexplored. Here, we firstly comprehensively characterized how different routes of administration affect the biodistribution of genetically engineered MLCs and other HSPC-derivatives in mice. We then generated a high-resolution single cell transcriptional map of MLCs and discovered that they could clearly be distinguished from macrophages as well as from resident microglia by the expression of a specific gene signature which is reflective of their HSPC ontogeny and irrespective of their long-term engraftment history. Lastly, using murine models of Parkinson’s disease and frontotemporal dementia, we demonstrated that MLCs can deliver therapeutically relevant levels of protein to the brain, thereby opening avenues for the clinical translation of HSPC-GT to the treatment of major neurological diseases.

overall_design: We combined cell sorting with high-throughput single-cell RNA (scRNA) sequencing to characterize long-term engrafted Microglia-Like Cells (MLCs) and endogenous microglia from the same animals. We isolated endogenous microglia (GFP-negative) and MLCs (GFP-positive) from enzymatically dissociated whole brains by FACS based on the expression of cell surface markers (CD45+, CD11b+, CX3CR1+) from one male and one female mouse 12-13 months after either IV or ICV administration of hematopoietic stem/progenitor cells (HSPCs). We also generated comparator datasets from a 12-week-old, treatment naïve C57BL/6J animal for several cell populations: microglia (CD45+, CD11b+, CX3XCR1+), neurons (CD45-, Thy1+, ACSA2+), astrocytes (CD45-, Thy1-, ACSA2+) and peripheral blood mononuclear cells (PBMCs)


title: Transcriptomic response of Pseudomonas aeruginosa Z154 planktonic cultures to N-acetylcysteine exposure.

city: Siena

first: Felice

last: Valzano

state: Siena

address: Viale Mario Bracci, 16

department: Medical Biotechnologies

institute: University of Siena

summary: N-acetylcysteine (NAC) is a mucolytic agent commonly administered together with antibiotics for the treatment of lower respiratory tract infections, which has been demonstrated to exert also an antimicrobial and antibiofilm activity against relevant respiratory pathogens. We analysed the transcriptomic response of P. aeruginosa planktonic cultures to NAC exposure (at concentration achievable by the inhalation route of administration).

overall_design: A representative P. aeurginosa mucoid strain from CF (Z154 strain) was analyzed. There is one tested condition (i.e., NAC 8000 mg/L) compared to control at one time point (i.e., 30 minutes). Two biological replicates were performed.

first: Selene Rebecca

last: Boncompagni

first: Maria

last: Micieli

first: Tiziana

last: Di Maggio

first: Vincenzo

last: Di Pilato

first: Lorenzo

last: Colombini

first: Francesco

last: Santoro

first: Gianni

last: Pozzi

first: Gian Maria

last: Rossolini

first: Lucia

last: Pallecchi


title: The effect of dietary fibre exposure on gene expression profiles of THP-1 macrophages

first: Coen

last: Govers

address: Bornse Weilanden 9

institute: Wageningen Food & Biobased Research

summary: Background: Macrophages represent an important part of the immune system in the intestine and are crucial for maintaining homeostasis. As part of research investigating the effect of dietary fibres on the intestinal immune barrier THP-1 macrophages were used as model system. Methods: THP-1 monocytes were stimulated for 48 hours with 100 ng/ml PMA and 48 hours rested in medium. Subsequently, they were stimulated with 500 ug/ml dietary fibres and the maximal observed LPS contamination to serve as background control. After 6 hours, total RNA was extracted and Affymterix Human Gene 1.1 ST arrays were used to analyze the gene expression profiles. To identify dietary fibre induced gene expression profiles in dietary fibre gene responses were compared to medium samples. Furthermore, to analyse differentiatlly affected pathways Ingenuite Pathway Analysis was employed. Results: There was a clear difference in significantly differentially expressed genes (gene cut-off p<0.05) with beta-glucan oat medium viscosity and GOS changing transcription of a relative small amount of genes and Sugar beet pectin and Resistant starch a relative large amount of genes. These latter two were also the only dietary fibres to demonstrate an increase in Fc-receptor-related pathway activation. Alternatively, beta-glucan oat medium viscosity and GOS were the only dietary fibres to activate pathways related to cellular movement and the only two to not activate the Ahr-signaling pathway (p<0.05). Conclusion: our data indicate that the in vitro THP-1 macrophage model can be used to differentiate in immunomodulatory potential of dietary fibres and provide hypotheses for functional differentiation.

overall_design: Microarray analysis was performed on THP-1 macrophages incubated with dietary fibres  for 6 hours. This experiment was performed three times, so three independent biological replicates per treatment were included in the microarray analysis.

first: Jurriaan

last: Mes

first: Mark

last: Boekschoten

first: Paul

last: de Vos


title: The effect of dietary fibre exposure on gene expression profiles in intestinal Caco-2 cells

summary: Background: Human intestinal tissue samples are barely accessible to study potential health benefits of nutritional compounds. Dietary fibres have been descirbed to be beneficial for intestinal health. Therefore, in this study we explored the applicability of an in vitro model, namely human intestinal Caco-2 cells, to study the effect of dietary fibres on intestinal health. Transcriptomics was applied to obtain more insight into their mode of actions in the intestinal cells. Methods: Caco-2 cells were stimulated with 500 ug/ml dietary fibres and the maximal observed LPS contamination to serve as background control for 6 hours, total RNA was extracted and Affymterix Human Gene 1.1 ST arrays were used to analyze the gene expression profiles. To identify dietary fibre induced gene expression profiles in dietary fibre gene responses were compared to medium samples. Furthermore, to analyse differentiatlly affected pathways Ingenuite Pathway Analysis was employed. Results: Pathway analysis revealed a distinct separation between the dietary fibres. GOS and beta-glucan oat medium viscosity affected transcription of a lower amount of genes (gene cut-off p<0.05) and gen transcription changes suggest an increase in vesicle transport and altered cholesterol regulation. On the other hand, the other dietary fibres differentially regulated a larger numbers of genes (gene cut-off p<0.05) and all appeared related to immune responses. We observed an increase in intracellular and extracellular anti-bacterial pathways and production of cytokines specifically aimed at communication with the adaptive immune system. Conclusion: GOS and beta-glucan oat medium viscosity appeared to induce intestinal epithelial communication with the body, whereas the other dietary fibres appeared recognized as PAMP and induce epithelial cells to interact with the immune system.

overall_design: Microarray analysis was performed on 21-days differentiated Caco-2 cells incubated with dietary fibres and LPS and medium control for 6 hours. This experiment was performed three times, so three independent biological replicates per treatment were included in the microarray analysis.


title: Molecularly defined circuits for cardiovascular and cardiopulmonary control

status: Public on May 28 2022

city: Stanford

first: Avin

last: Veerakumar

state: CA

address: 279 Campus Drive, Beckman Center B400

institute: Stanford University

summary: The sympathetic and parasympathetic nervous systems regulate the activities of internal organs, but the molecular and functional diversity of their constituent neurons and circuits remains largely unknown. Here we use retrograde neuronal tracing, single-cell RNA sequencing, optogenetics and physiological experiments to dissect the cardiac parasympathetic control circuit in mice. We show that cardiac-innervating neurons in the brainstem nucleus ambiguus (Amb) are comprised of two molecularly, anatomically and functionally distinct subtypes. The first, which we call ambiguus cardiovascular (ACV) neurons (approximately 35 neurons per Amb), define the classical cardiac parasympathetic circuit. They selectively innervate a subset of cardiac parasympathetic ganglion neurons and mediate the baroreceptor reflex, slowing heart rate and atrioventricular node conduction in response to increased blood pressure. The other, ambiguus cardiopulmonary (ACP) neurons (approximately 15 neurons per Amb) innervate cardiac ganglion neurons intermingled with and functionally indistinguishable from those innervated by ACV neurons. ACP neurons also innervate most or all lung parasympathetic ganglion neurons—clonal labelling shows that individual ACP neurons innervate both organs. ACP neurons mediate the dive reflex, the simultaneous bradycardia and bronchoconstriction that follows water immersion. Thus, parasympathetic control of the heart is organized into two parallel circuits, one that selectively controls cardiac function (ACV circuit) and another that coordinates cardiac and pulmonary function (ACP circuit). This new understanding of cardiac control has implications for treating cardiac and pulmonary diseases and for elucidating the control and coordination circuits of other organs.

overall_design: Single cell mRNA profiles were generated from mouse nucleus ambiguus neurons that were retrogradely labeled from the heart or larynx. Mice were postnatal day 2 to 4 at time of sequencing. cDNA was generated using the Smart-seq2 protocol.

first: A

last: Yung

first: Y

last: Liu

first: M

last: Krasnow


title: Single-cell TCR-RNA-seq of splenic Tregs

city: Minneapolis

first: Rebecca

last: LaRue

state: MN

address: 117 Pleasant St SE

department: Department of Lab medicine and Pathology

institute: University of Minnesota

summary: A single-cell TCR-RNA-seq dataset comprised of CD4+ Tregs from the spleen.

overall_design: Pooled splenocytes from 4 female TCliB x TCRa+/- x Foxp3-RFP mice (5 weeks old) were used to sort CD4+Dump(B220/CD8a/Ter119/Live-Dead)-TCRVα2+Foxp3+ cells for single-cell RNA-seq and VDJ repertoire analysis.

first: Louisa

last: Sjaastad

first: David

middle: L

last: Owen

first: Michael

last: Farrar


title: Directional capacity of human mesenchymal stem cells to support hematopoietic stem cell proliferation in vitro

city: Tehran

first: Pooria

last: Safarzadeh Kozani

state: Tehran

address: Jalaal st.

department: Medical Biotechnology

country: Iran

institute: Tarbiat Modares University

summary:
Objectives: Hematopoietic stem cells (HSCs) reside in a specialised microenvironment in the bone marrow, which is majorly composed of mesenchymal stem cells (MSCs) and its' derivatives. This study aimed to investigate the regulatory role of MSCs to decipher the cellular and humoral communications on HSCs' proliferation, self-renewal, and differentiation at the transcriptomic level.

Materials and methods: Microarray assay was employed to analyse the gene expression profile of HSCs that imparted by MSCs during co-culture.

Results: The proliferation of human umbilical cord blood-derived HSCs (hUC-HSCs) markedly propagated when MSCs were used as the feeder layer, without disturbing the undifferentiated state of HSCs, and reduced the cell death of HSCs. Upon co-culture with MSCs, the global microarray analysis of HSCs disclosed 712 differentially expressed genes (DEGs) (561 up-regulated and 151 down-regulated). The dysregulations of various transcripts were enriched for cellular functions such as cell cycle (including CCND1), apoptosis (including TNF), and genes related to signalling pathways governing self-renewal, as well as WNT5A from the Wnt signalling pathway, MAPK, Hedgehog, FGF2 from FGF, Jak-STAT, and PITX2 from the TGF-β signalling pathway. To concur this, real-time quantitative PCR (RT-qPCR) was utilised for corroborating the microarray results from five of the most dysregulated genes.

Conclusion: This study elucidates the underlying mechanisms of the mitogenic influences of MSCs on the propagation of HSCs. The exploitation of such mechanisms provides a potential means for achieving larger quantities of HSCs in vitro, thus obviating the need for manipulating their differentiation potential for clinical application.

overall_design: 8 samples for micro array/12 samples for QC

first: Mohadese

last: Hashem Boroojerdi

first: Pouya

first: King-Hwa

last: Ling

first: Rajesh

last: Ramasamy


title: Microarray analysis of transcriptional changes in MeJA-treated tobacco leaves

city: Qingdao

first: Hongbo

last: Zhang

state: Shandong

address: No.11 Keyuan Rd.

institute: Tobacco Research Institute, Chinese Academy of Agricultural Sciences

summary: Using this microarray data, we identified 19898 probes (717 upregulated and 1512 downregulated in the mock- and MeJA-treated leaf samples at ‘1wk’ and ‘2wk’ stages; 17669 with differential expression in these samples), compared with the mock-treated sample at ‘0wk’ stage. This work aims to identify the genes related to MeJA-induced senescence of tobacco whole-plant, and found several genes differentially expressed between the mock- and MeJA-treated samples at the same stage.

overall_design: Differential expression analysis between mock- and MeJA-treated tobacco leaves under normal light condition, sample mixture of 3 different replicates was used for each treatment.

first: C

last: Wang

first: X

last: Zhao

first: W

middle: P

last: Timko

first: Z

first: H


title: Whole transcriptome sequencing from covid-19 and control lung biopsies

city: Karimnagar

first: Abhilash

last: Dasari

state: Telangana

address: H.No:8-4-652/3/1/1, Hanuman Nagar, Karimnagar

department: Biochemical engineering and biotechnology

institute: IIT Delhi

summary: Whole transcriptome analysis performed on lung samples from dead covid-19 patients and healthy non-covid-19 individuals of multiple age groups.

overall_design: We examined the lung samples from dead covid-19 patients and healthy non-covid-19 individuals

first: Ishaan

last: Gupta

first: Deepali

last: Jain

first: Atish

last: Gheware

first: Anshul

last: Budhraja

first: Anubhav

last: Basu

first: Dasari

last: Abhilash


title: Gene expression in radio-sensitive or -resistant breast cancer cells [MCF-7]

city: Gyeongju

first: soyoung

last: Kim

address: Dongdae-ro 123

department: Department of Pharmacology

institute: Dongguk university

summary:
During radiotherapy most cancer cells are removed, but some cells are not. These remained cancer cells become resistant to radiotherapy and lead to cancer recurrence. Radioresistnat cancer cells show different gene expression profile than radiosensitive tumor cells. Among the genes distinctly up or down-changed in expression level, some are associated with development of radioresistance.
We used microarrays to select multiple genes showing distinct change in expression level for seeking genes that contribute to the develpoment of radioresistance in breast cancer cells during radiotherapy.

overall_design: We selected 2 kinds of cell lines with different radiosensitivity for RNA extraction and hybridization on Affymetrix microarrays. To that end, parental MCF-7 cells were irradiated with 5 Gy twice a week and then cultured until survived cells recovered. The same cycle of irradiation were repeated until cells exhited distinct radioresistance. We tested cells' sensitivity to radiation by colony forming assay. Finally, MCF-7 and MR cells were selected as radiosensitive and radioresistant cells, respectively.

first: Yun-Suk

last: Kwon

first: Min-Gu

last: Lee

first: Hyunsoo

last: Jang

first: Soyoung


title: RNA-sequencing of  SKBR3 cells with and without NTN4 overexpression

status: Public on May 27 2022

city: Beijing

first: Han

last: Yang

state: Beijing

address: 38 xueyuan road

institute: Peking University Health Science Center

summary: Low NTN4 expression is correlated with breast cancer proliferation and metastasis, while the molecular mechanism of NTN4 has not been fully explored. Here, the breast cancer cells SKBR3 stably expressing dCas9-VP64 and MS-P65-HSG1 were generated by transducing a lentiviral plasmid containing lenti-dCAS-VP64-Blast (Addgene plasmid # 61425) and lenti-EF1a-MS2–p65–HSF1-2A-Hygro-WPRE (Addgene plasmid # 89308), followed by selection and maintained using 10 μg/mL of blasticidin and 200 μg/mL of hygromycin. SKBR3-dCas9-VP64-MPH cells were further transduced with a doxycycline (Dox)-induced expressing sgRNA targeting NTN4 promoter. The successfully transfected cells were selected and maintained with puromycin at a concentration of 0.5 μg/mL for SKBR3-dCas9-VP64-MPH. SKBR3-dCas9-VP64-MPH-AC-sgRNA cells were treated with or without 50 ng/μL Dox (three biological repeats for both groups) to induce NTN4 overexpressing. Total RNA was extracted using TRIzol according to the manufacturer’s instructions. The quality of RNA samples was examined by Agilent BioAnalyser 2100. The samples were subjected to RNA-sequencing analysis on the BGISEQ-500 system by Beijing Genomics Institute (BGI, China). The clean-tag reads were aligned to the reference genome and reference genes using HISAT2 and Bowtie2. The matched reads were calculated and then normalized using RSEM software. Differential gene expression was analyzed using DESeq2 and was carried out further to explore the mechanism of NTN4 in breast cancer.

overall_design: Examination of with or without Dox-induced overexpression of endogenous NTN4 in triplicates. In total, 6 samples were analyzed with RNA sequencing.

first: Xin-xia

last: Tian


title: SMCHD1 variants induce variegated expression in Facio Scapulo Humeral Dystophy and Bosma Arhinia and microphtalmia syndrome.

city: Marseille

first: Frederique

last: Magdinier

address: 27 Bvd Jean Moulin, Aix-Marseille Université. Faculté de Médecine. Campus La Timone

institute: Aix-Marseille Université - Marseille Medical Genetics


title: De novo transcriptome assembly based RNA-Seq and dynamic expression of key enzyme genes in baicalin biosynthetic pathway of Scutellaria baicalensis Georgi

city: Xi'an

first: Bo

last: Cao

state: Shaanxi

address: 620 West Chang'an Road, Changan District

institute: Shaanxi Normal University

summary: Scutellaria baicalensis Georgi, a perennial herb, is an important medicinal plant that possesses broad pharmacological actions and contains flavonoids with good bioactivities such as anti-inflammation, anti-bacteria and anti-tumor. However, little is known on the molecular processes responsible for the medical properties of this species, owing to the absence of genomic resources such as available sequences of key enzyme genes in biosynthetic pathways. In this study, the RNA sequencing data of S. baicalensis were first generated and used for transcriptome analysis.

overall_design: Root mRNA profiles of Scutellaria baicalensis Georgi collected in October were generated by deep sequencing, in a mixture of three samples, using Illumina® Hiseq 2000 platform. qRT–PCR validation was performed using SYBR Green assays.

first: Bai

last: Chengke

first: Li

last: Xia

first: Cao

last: Bo

first: Duan

last: Chongyang

first: Xu

last: Jun

last: Guishuang


title: Herpesvirus-encoded microRNA dysregulate M1 and M2 macrophage miRNA profiles

city: Chicago

first: Afsar

last: Naqvi

address: 801 S Paulina, Room 561B

department: Periodontics

institute: University of Illinois at Chicago

summary:
Primary human M1 and M2 macrophages were transfected with different human herpesvirus-derived viral miRNA and the impact on the cellular microRNAs was profiled using microarray.
Viral miRNA-mediated impact was assessed on the host cellular microRNA profiles by miRNA microarray analysis. Five different viral miRNA representing 4 different human herpesviruses were overexpressed in M1 and M2 macrophages and the changes in cellular miRNA compared to control mimic were examined. Viral miRNA exhibit unique impact on M1 and M2 miRNA profiles.

overall_design: Human macrophages were differentiated to M1 and M2 phenotype using CD14+ monocytes in presence of GM-CSF and M-CSF, respectively. At Day 7, cells were transfected with viral miRNA or control mimics (50 nM final concentration). After four hours, media was replaced with complete media containing IFNγ+LPS and IL4+IL-13 for M1 and M2 macrophages, respectively. Total RNA was isolated after 48 hours and cellular microRNA profiles was analyzed by microarray.

first: A

middle: R


title: Whole-transcriptome profiling of laser-capture microdissected striatal neurons at single-cell resolution using retrograde tracing

first: Michael

middle: Lawrence

last: Miller

address: One Gustave L. Levy Place

department: Fishberg Department of Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Pathway-specific striatal transcripts were identified in a neuroanatomically defined manner using retrograde tracing, laser capture micodissection and whole-transcriptome sequencing.

overall_design: Fluorescent retrograde tracers were stereotaxically infused into striatal terminal fields and laser capture microdissection was used to isolate striatomesencephalic and striatipallidal neurons at single-cell resolution.

first: Yasmin

last: Hurd


title: Inflammatory Gene Expression Associates with Hepatitis B Virus cccDNA- but Not Integrant-Derived Transcripts in HBeAg Negative Disease

city: Oxford

first: Andrea

last: Magri

address: Old Road Campus, Roosevelt Dr, Headington

institute: University of Oxford

summary: 26 chronic hepatis B patients and 8 non-viral control liver biopsies were analysed to study differential gene expression profiles to determine host factors associated with viral transcription.

overall_design: In this study we analysed 26 treatment-naïve HBeAg negative chronically HBV infected liver biopsies and 8 non-viral related controls. Gene expression of 249 inflammation-related genes was performed with Nanostring.

first: James

last: Harris

first: Rosalba

last: Minisini

first: Peter

last: Balfe

first: Mario

last: Pirisi

first: Jane

last: McKeating


title: LncRNA and circRNA expression profiles of Aβ25-35-induced AD mice hippocampus treated with Tripterygium Glycoside

city: Changsha

first: Liang

last: Tang

address: No 1501, Leifeng road

institute: Changsha Medical University

summary: Tripterygium glycosides (TG) was reported to have effect of ameliorating Alzheimer's disease (AD). However, the mechanism is not clear. We aimed to investigate the lncRNAs and circRNAs expression profiles of AD treated with TG by using microarray. LncRNAs, mRNA and circRNA in 3 AD mice and 3 AD+TG mice hippocampal were detected by microarray. The most differentially expressed lncRNAs, mRNA and circRNA in AD+TG group were screened. The differentially expressed lncRNAs and circRNAs were analyzed for GO enrichment and KEGG pathway. Co-expression analysis of lncRNAs and mRNA was performed by calculating correlation coefficients. Protein-protein interaction (PPI) network analysis was performed on mRNAs using STRING. LncRNA-target-TFs network were analyzed by Network software. CircRNA-mirNA network were conducted by Cytoscape software. A total of differentially expressed 661 lncRNAs, 64 circRNAs and 503 mRNAs were detected in AD mice treated with TG. The Pou4f1, Egr2, Mag, and Nr4a1 were the hub genes in the PPI network. The KEGG results showed the mRNAs that co-expressed with lncRNAs were enriched in TNF, PI3K-Akt, and Wnt signaling pathway. lncRNA-target-TFs network analysis indicated the TFs including Cebpa, Zic2, and Rxra were the most likely to regulate the detected lncRNAs. The circRNA-miRNA interaction network indicated 275 miRNAs may bind to the 64 circRNAs. In conclusion, the findings supplied a novel perspective for AD pathogenesis. And the detected lncRNAs, mRNAs, and circRNAs might be novel therapeutics targets for AD.

overall_design: AD mice treated with TG and AD mice treated with NS

first: Yan

last: Wang

first: Qin

last: Xiang

first: Ju

first: Dawei

last: Yang

last: Zhang


title: Methylation profiling (RRBS) and expression profiling (RNA-seq) of placenta and umbilical cord blood with gestational diabetes mellitus (GDM)

city: Shanghai

first: Jiahao

address: Yueyang road

institute: Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences

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

overall_design: Refer to individual Series


title: Mapping cis-regulatory elements in human excitatory and inhibitory neurons links psychiatric disease heritability and activity-regulated transcriptional programs [RNA-seq]

last: Yan

address: 1425 Madison Ave

institute: Mount Sinai

summary: Genome-wide association studies (GWAS) have identified hundreds of loci associated with psychiatric diseases, yet there is a lack of understanding of disease pathophysiology. Common risk variants can shed light on the molecular mechanisms underlying these diseases; however, identifying specific causal variants remains challenging. An added complication is that most common risk variants are in non-coding regions. Their impact is likely to be restricted to particular cell types, developmental stages, or cell states. Here, we comprehensively mapped cis-regulatory elements in two defined populations of human excitatory and inhibitory neurons derived from pluripotent stem cells.

overall_design: We performed  bulk RNA-seq to measure transcriptomic profiles in human induced glutamatergic (Glu) and GABAergic (GABA) neurons derived from human pluripotent stem cells (ES and iPSCs). We exposed neurons to an elevated level of potassium chloride (KCl) to study activity-induced responses, and profiled gene expression at various timepoints after depolarization.

first: Carlos

last: Sanchez-Priego

first: Ruiqi

last: Hu

first: Linda

last: Boshans

first: Matthew

last: Lalli


title: Mouse SINE B2 elements function as IFN-inducible enhancer elements [CUT&Tag]

city: Boulder

first: Edward

last: Chuong

state: Colorado

address: 3415 Colorado Ave. JSC Biotech Bldg

department: Molecular, Cellular and Developmental Biology

institute: BioFrontiers Institute at University of Colorado Boulder

summary: B2_Mm2 acts as a STAT1 binding site and interferon inducible enhancer of the nearbby interferon-stimulated gene Dicer1 during an innate immune response (IFNG stimulated). J774 knockouts deficient of B2_Mm2 were also found to have downregulated expression of Serpina3f and Serpina3g, indicating that B2_Mm2 acts as an enhancer on these nearby genes likely due to its capability as a CTCF-binding site.

overall_design: Chromatin profiling (CUTnTag) of wildtype mouse cell lines (J774) that were stimulated with 100 ng/mL interferon gamma (IFNG) for 4h. CUTnTag is also provided from clonal B2 knockout J774 lines that were modified using CRISPR Cas9 and a pair of gRNAs targetting the B2_Mma2 element in the first intron of Dicer1 on chr12.

first: Horton

last: Isabella

first: Kelly

last: Conor

first: Simpson

last: David


title: Whole transcriptome RNAseq analysis of germ cells in Inhba and Inha fetal testis

status: Public on May 26 2022

city: Giessen

first: Daniela

last: Fietz

address: Frankfurter Straße 98

department: Institute for Veterinary Anatomy,  Histology and Embryology

institute: Justus Liebig University Giessen

summary: We performed bulk RNA-Seq on male fetal germ cells isolated from E13.5 and E15.5 testes from activin A-deficient mice (Inhba KO), and from E13.5 testes from mice with greater activin A bioactivity (Inha KO). The aim of this expereiment was to determine how chronic altered activin A bioactivity altered the germline transcriptome.

overall_design: Germ cells were isolated from embryonic E13.5 and E15.5 Inhba x Oct4-Gfp WT and KO testes, and E13.5 Inha x Oct4-Gfp WT and KO testes via FACS. Cells were collected from n=3-4  (Inhba) and n=2 (littermate pairs; Inha) animals/age/genotype.

first: S

last: Moody

first: P

last: Whiley

first: PS

last: Western

first: K

last: Loveland


title: Human endometrium and epithelial organoids

city: RTP

first: Franco

last: Demayo

state: NC

address: 111 TW Alexander Drive

institute: NIEHS


title: Mapping cis-regulatory elements in human excitatory and inhibitory neurons links psychiatric disease heritability and activity-regulated transcriptional programs

city: New York