title: Differential expression of LncRNAs and mRNAs and their modulated network construction during the process of HIV transcription

city: Jilin city

first: Bing

last: Shao

state: Jilin province

address: Jilin street 5

institute: Jilin Medical University

summary:
Objective: Seek the differentially expressed mRNAs and long non-coding RNAs (LncRNAs) to construct the modulated network and seek for the hub LncRNAs during the process of human immunodeficiency virus (HIV) transcription.
Method: Blood samples from HIV-infections were collected. They were divided into transcription active group and relatively inactive group based on the quantitative detection results of total HIV DNA and cell-association RNA (CA-RNA) from peripheral blood mononuclear cells (PBMCs). Individuals within each group were matched by age and genders. Microarray chips detection technology were utilized to detect and find the differentially expressed LncRNAs and mRNAs by statistical method of paired T test, then underwent some bioinformatics analysis.
Result: 1240 differentially expressed genes (include 689 LncRNAs and 551 mRNAs) were found. Gene ontology analysis showed the differentially expressed mRNAs mainly enriched in positive or negative gene expression, immune cell formation or epigenetic regulation in the biological process; nucleosome, nucleolus, cytoplasm, nuclear chromatin in the cell component; RNA polymerase II regulatory region sequence-specific DNA binding, DNA, histone, and nucleic acid binding, transcription factor activity in molecular function. Pathway analysis showed the differentially expressed mRNAs enriched in the biological pathways such as systemic lupus erythematosus, alcoholism, cytokine-cytokine receptor interaction, RNA transport, mRNA surveillance pathway, Pathways in cancer, etc. Cis and trans analysis to the differentially expressed LncRNAs searching its targeted genes and then made intersection for the differentially expressed mRNAs, then constructed the modulated network between LncRNAs and mRNAs. Based on this modulated network, four hub transcripts were excavated and validated by quantitative real-time PCR to confirm the veracity of microarray analysis findings. Two hub transcripts of lnc-CCNYL1-1:2 and ZNF793 were found directly interacted in the modulated network and their level of expression transformed parallelly.
Conclusion: Quantitative detection results of cellular levels of total HIV DNA and RNA can distinguish whether HIV is in the state of active transcription. During process of HIV transcription, the differentially expressed LncRNAs involve the biological process of gene expression regulation, the hub genes excavated form the modulated network may become the potential candidate targets for HIV antiviral treatment.

overall_design: 6 samples from HIV-infections were selected, 3 of them were detected in transcriptional activity as the experimental group, the other 3 were detected in transcriptional inactivity as the control group. Individuals of each group were matched by age and genders.

first: QingHai

last: Li

first: Juan

first: Shiyan

last: Feng

first: Yuanlong

last: Lin

first: Siyu

first: Zheng

first: Yuou

first: Xubo

first: Fuxiang

last: Wang

first: Bo


title: Analysis of Listeria monocytogenes

status: Public on Jan 23 2022

city: Paris

first: Pascale

last: Cossart

address: 25 rue du Dr Roux

country: France

institute: Institut Pasteur

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: RNA sequencing of young and old lung ILC2 cells

city: New Brunswick

first: Qi

last: Yang

state: NJ

address: 89 French St

country: USA

institute: Rutgers RWJMS

summary: ILC2 cells from young and old mouse lungs were analysed and revealed altered transcriptome of old ILC2 compared to the young.

overall_design: ILC2 from lungs of young (8 weeks) and old (20 months) female C57BL/6 mice were harvested. ILC2 were sorted

first: Qic

first: Shanti

middle: S

last: D'Souza


title: Analysis of Listeria monocytogenes VirR regulon

summary: by comparing WT strain vs a delta-VirR strain, we complete the analysis of VirR regulon, and we show that virR induces the expression of a small RNA

overall_design: WT EGDe Lmo grown in BHI vs delta-virR EGDe Lmo grown BHI

first: Yulia

last: Redko

first: Mikael

last: Koutero


title: The m6A reader YTHDC2 is essential for escape from KSHV SOX-induced RNA decay

city: Amherst

first: Daniel

last: MacVeigh-Fierro

state: MA

address: 639 N Pleasant St, Morrill Iv North

department: Microbiology

institute: UMass Amherst

summary: Here we used m6A-eCLIP to enrich for m6A in RNA samples from latent and lytic KHSV infected mammalian cells. Through this highthroughput method we were able to not only indentify differences of m6A clusters between KSHV states, but through the use of the PureCLIP porgram identify m6A sites with single nucelotide resolution. From there were able to identify m6A sites on an SRE containing transcript, IL-6.

overall_design: m6A-eCLIP RNA sequencing data

first: Ashley

last: Cadorette

first: Vasudha

last: Sharma

first: Angleina

last: Cicerchia

first: Mandy

last: Muller


title: Analysis of Listeria monocytogenes response to bacitracin

summary: we report that bacitracin is the signal that triggers the induction of VirR, its operon and its regulon

overall_design: WT EGDe Lmo grown in BHI vs WT EGDe Lmo grown BHI + bacitracin (50 μg/ml)


title: Gene expression profile of PMM2_CDG (Congenital Disorder of Glycosylation) B lymphoblastoid cell lines (B-LCL)

status: Public on Jan 22 2022

city: Murcia

first: Antonio

last: Parrado

address: Ctra. Madrid-Cartagena, s/n

country: Spain

institute: Hospital Clinico Universitario Virgen de la Arrixaca

summary: Glycosylation of proteins is an important post-translational modification that comprises two major stages: synthesis and attachment of glycans in the endoplasmic reticulum (ER), and glycan remodeling in the ER and Golgi apparatus (GA). Genetic disorders impairing a step of this process give rise to a group of pathologies named congenital disorders of glycosylation (CDG). The most common CDG type is PMM2-CDG, caused by mutations on PMM2 (phosphomannomutase 2) genes. PMM2-CDG clinical presentation vary among affected individuals. CDG condition is considered a form of chronic ER stress. Inhibition of glycosylation results in the accumulation of misfolded proteins in the ER, which induces a complex protective reaction known as the unfolded protein response (UPR), which includes translational repression, transcriptional activation of ER chaperones, and ER-associated degradation of unfolded proteins. In search for CDG biomarkers, EBV-transformed CDG B-lymphoblastoid cell lines (B-LCL) were used as cellular models due to two main advantages: first, B-LCL are secretory cells that are forced to continuously synthetize proteins such as immunoglobulins, cytokines or other cell to cell communication molecules, so their ER is chronically stressed; second, as immune system cells, they express common genes and share common regulatory mechanisms with nervous system cells such as neurons (affected cell in most CDG patients). In this work we generated a collection of 7 EBV-transformed PMM2-CDG B-LCL by culture of patients' purified blood B lymphocytes with supernatants of the marmoset EBV-leukocyte cell line B95-8, and compared their transcriptome with that of 7 EBV-transformed healthy B-LCL. Our analysis revealed 348 significantly up-regulated and 106 down-regulated protein-coding genes compared to non-CDG cell lines, which included response to stress, transcription factors, glycosylation, motility and cell junction, development and cell (neuron) differentiation and synapse genes. Gene Set Enrichment Analysis (GSEA) identified biological consequences associated to gene expression changes in PMM2-CDG cells related to the unfolded protein response (UPR), RNA metabolism and the endoplasmic reticulum, Golgi apparatus and mitochondria components. Dysregulated important genes were MAN1A1, MGAT2, CHST4, LARGE, ADAM23, SEMA4D, UNC13C, AUTS2, CA2, SMN1, EXOSC2 expressed not only in the immune system but in other tissues including the nervous system that were compatible with CDG pathophysiology. Our results confirm PMM2-CDG EBV-transformed B-LCL as a suitable cell model that expands both our knowledge and tools to study CDG pathology at the cellular level, useful for functional characteristics and potential therapeutic drugs testing.

overall_design: EBV-transformed PMM2-CDG and healthy B-LCL cell lines were cultured in IMDM supplemented with 10 % FCS, 50 U/ml penicillin, 50 U/ml streptomycin, and 2 mM L-glutamine. Cells growing at exponential phase were pelleted and preserved in RNAlater solution until RNA isolation. Total RNA was isolated using the miRNeasy Mini Kit (Qiagen). A pooled sample composed of equimolar amounts of RNA from 4 control B-LCL cells and 4 control NK cells was used as reference. For microarray analysis, reference and test RNA samples were labeled using Agilent Two Color (cyanine-3-CTP (Cy3) and cyanine-5-CTP (Cy5), respectively) Quick Amp Labeling and RNA Spike-In kits, according to the manufacturer's protocol. Microarray experiments were designated as PMM2-CDG (N = 7) or CTRL (N = 7), and were performed using SurePrint G3 Human Gene Expression v3 Microarray Kit targeting 26083 Entrez genes and 30606 lncRNA transcripts. The labeled cRNAs were mixed together and hybridized onto the microarray slides using the Agilent Gene Expression Hybridization kit. After hybridization, the microarray slides were washed and scanned in an Agilent G2565CA DNA Microarray Scanner. Datasets, expressed as log10 ratios for test vs reference, were computed from images by the Agilent Feature Extraction software, using normalization by linear and Lowess methods.

first: Natalia

last: Ruiz-Lafuente

first: Trinidad

last: Hernández-Caselles


title: RNA-Seq of IL-2-KO follicular CD8 T cells and IL-2-KO follicular CD4 T cells

city: Livermore

first: Dina

last: Weilhammer

state: California

address: 7000 East Ave

institute: Lawrence Livermore National Laboratory

summary: Follicular CXCR5+ PD-1+ CD8 T cells (CD8 Tfc) arise in multiple models of systemic autoimmunity yet their functional contribution to disease remains in debate. Here we define the follicular localization and functional interactions of CD8 Tfc with B cells during autoimmune disease. The absence of functional T regulatory cells in autoimmunity allows for CD8 Tfc development that then expands with lymphoproliferation. CD8 Tfc are identifiable within the lymph nodes and spleen during systemic autoimmunity, but not during tissue-restricted autoimmune disease. Autoimmune CD8 Tfc cells are polyfunctional, producing helper cytokines IL-21, IL-4, and IFNγ while maintaining cytolytic proteins CD107a, granzyme B, and TNF. During autoimmune disease, IL-2-KO CD8 T cells infiltrate the B cell follicle and germinal center, including the dark zone, to induce AID in vitro in naïve B cells via IL-4 secretion. CD8 Tfc represent a unique CD8 T cell population with a diverse effector cytokine repertoire that can contribute to pathogenic autoimmune B cell response.

overall_design: 4 samples sequenced, 2 biological replicates. Pooled 15-16 day old IL-2-KO CD4+ CXCR5+PD-1hi, Pooled 15-16 day old IL-2-KO CD8+ CXCR5+PD-1hi

first: K

middle: M

last: Valentine

first: G

last: Mullins

first: O

middle: A

last: Davalos

first: L

last: Seow

middle: K

last: Hoyer


title: Single cell RNA-seq data comparing in vitro macrophages with M-CSF and M-CSF/Squalene

city: Los Angeles

first: Tran

middle: Hue

last: Do

state: CA

address: 615 Charles E Young Dr

institute: David Geffen School of Medicine

summary: We performed single-cell RNA seq analysis on in vitro M-CSF-derived macrophages

overall_design: Examine the transcriptomics differences in acne lesional and non-lesional skin

middle: H

first: Rosane

last: Teles

first: Chanyue

last: Hu

first: Matteo

last: Pellegrini

first: Robert

middle: L

last: Modlin


title: Exploring differentially expressed genes related to metabolism by RNA-Seq in porcine embryonic fibroblast after insulin treatment

city: Harbin

first: YingJuan

last: Liang

address: 600 Changjiang Road

country: China

institute: Northeast Agricultural University

summary:
Purpose: In this study,RNA-Seq technology was used to analyse the effects of insulin on glucose and lipid metabolism of fibroblasts in pigs. We focus mainly on the cellular mechanisms of insulin signalling and on new insights into pathways of primary relevance to insulin’s metabolic effects.
Methods: porcine embryonic fibroblast(PEF) mRNA profiles of control group and insulin treated group were generated by deep sequencing, in triplicate,using Illumina HiSeq 2000. Paired-end clean reads were aligned to the reference genome using Hisat2. Featurecounts was used to count the read numbers mapped to each gene. Then, the expected number of fragments per kilobase of transcript sequence per million base pairs sequenced (FPKM) was calculated for each gene based on the length of the gene and the read counts mapped to the gene. qRT–PCR validation was performed using TB Green assays.
Results: A total of 439,950,662 clean reads filtered from 458,016,778 paired-end raw reads were identified, Of these sequence reads, 94.89%–97.20% was successfully aligned with the Sus scrofa. After insulin treated, a total of 801 and 1176 genes were differentially expressed after 48 and 72 h, respectively. Of these, 272 up-regulated genes and 264 down-regulated genes were common to both time points. The functions of the differentially expressed genes were annotated by a GO analysis, the biological processes related lipid metabolism and cell cycle were dominant. Via KEGG enrichment analysis, we found the DEGs were significantly enriched in  IL-17 signaling pathway, PI3K-Akt signaling pathway, pyruvate metabolism, and others pathway related to lipid metabolism. These results elucidate the transcriptomic response to insulin in PEF.
Conclusions: Our data support a role of the insulin on lipid and glucose metabolism, show an association among insulin, glycolipid metabolism and cell cycle in PEF . Our study identified some important genes associated with metabolic and these genes can be used to increase our understanding of the mechanism of relieving the metabolic disturbance induced by insulin. Additionally, PEF treated with insulin would provides a useful cell model for glycolipid metabolism disorder such as diabetes.

overall_design: Prior to add insulin,PEF lines were thawed and cultured,The cells were collected at 48 hours and 72 hours after the addition of insulin. The control samples were taken at 0 hours and three biological replicates were collected at each time point. Then the PEF mRNA profiles of control samples and insulin treated were generated by deep sequencing.

first: Yingjuan

first: Jingpeng

last: Wang

first: Shuang

last: Wu

first: Chaoqian

last: Jiang

first: Yue

first: Xuechun

last: Li

first: Zhonghua

last: Liu

first: Yanshuang

last: Mu


title: Senescence-associated metabolomic phenotype in primary and iPSC-derived mesenchymal stromal cells

city: Odense

first: Eduardo

last: Fernandez-Rebollo

address: Campusvej 55

department: Functional Genomics and Metabolism

country: Denmark

institute: University of Southern Denmark

summary: Long-term culture of primary cells is reflected by functional and secretory changes, which ultimately result in replicative senescence. In contrast, induced pluripotent stem cells (iPSCs) do not show any signs of cellular aging while in the pluripotency state, whereas little is known how they senesce upon differentiation. Furthermore, it is largely unclear how the metabolome of cells changes during replicative senescence and if such changes are consistent across different cell types. In this study, we have directly compared culture expansion of primary mesenchymal stromal cells (MSCs) and iPSC-derived MSCs (iMSCs) until they reached growth arrest after a mean of 21 and 17 cumulative population doublings, respectively. Both cell types acquired similar changes in morphology, in vitro differentiation potential, up-regulation of senescence-associated beta-galactosidase, and senescence-associated DNA methylation changes. Furthermore, MSCs and iMSCs revealed overlapping gene expression changes during culture expansion, particularly in functional categories related to metabolic processes. We subsequently compared the metabolome of MSCs and iMSCs at early and senescent passages and observed various significant and overlapping senescence-associated changes in both cell types, including down-regulation of nicotinamide ribonucleotide and up-regulation of orotic acid. Replicative senescence of both cell types was consistently reflected by the metabolic switch from oxidative to glycolytic pathways. Taken together, long-term culture of iPSC-derived MSCs evokes very similar molecular and functional changes as observed in primary MSCs. Replicative senescence is associated with a highly reproducible senescence-associated metabolomics phenotype, which may be used to monitor the state of cellular aging.

overall_design: Bone marrow mesenchymal stromal cells were cultured until reach senescence, reprogrammed to induced pluripotent stem cells and finally differentiated back to induced mesenchymal stromal cells.

first: Julia

last: Franzen

first: Jonathan

last: Hollmann

first: Alina

last: Ostrowska

last: Oliverio

first: Torsten

last: Sieben

first: Björn

last: Rath

first: Jan

middle: W

last: Kornfeld

first: Wolfgang

last: Wagner


title: Differential expression of microRNAs is associated with myogenic-lineage differentiation in mouse embryonic stem cells

city: Daejeon

first: Lee

last: Sunwoo

address: #211, Next2Vill, 278-2, Jangdae-dong, Yuseong-gu

country: South Korea

institute: GenomicWorks

summary: Establish the microRNA expression profile between normoxic- and hypoxic-culture during differentiation of mouse embryonic stem cells

overall_design: Total RNA from cultures exposed to three experimental conditions (mESCs cultured for 16 h under normoxia, EBs cultured for 16 h under normoxia, EBs cultured for 16 h under hypoxia) was prepared

first: Seo-Yeon

last: Lee

first: Jimin

last: Yang

first: Hyo-Soo

last: Kim


title: Identification of regulatory factors promoting embryogenic callus formation in barley through transcriptome analysis

city: Hangzhou

first: Suo

middle: jing

last: qi

state: Zhejiang

address: 866 Yuhangtang Rd

department: college of life sciences

institute: Zhejiang university

summary: The aim of this study was to uncover the differential transcription regulation pathways between immature embryo (IME)- and mature embryo (ME)-derived callus formation through transcriptome sequencing. We showed that incubation of embryos on auxin-rich medium caused dramatic changes in gene expression profiles within 48 h. A total of 9330 and 11318 differentially expressed genes (DEGs) were found in the IME and ME systems, respectively. 3880 DEGs were found specific to IME_0h/IME_48h, and protein phosphorylation, regulation of transcription, and oxidative-reduction process were the most common gene ontology categories of this group. Twenty-three IAA, 14 ARF, 8 SAUR, 3 YUC, and 4 PIN genes were found to be differentially expressed during callus formation. The effect of callus-inducing medium (CIM) on IAA genes was broader in the IME system than in the ME system, indicating that auxin response in regulating cell reprogramming during callus formation. BBM, LEC1 and PLT2 exhibited a significant increase in expression level during IME system but were not activated in the ME system, WUS showed a more substantial growth trend in the IME system than in the ME system, suggesting that these embryonic, shoot, and root meristems genes play crucial roles in determining the acquisition of competency. In addition, epigenetic regulators—including SUVH3A, SUVH2A, HDA19B/703—exhibited differential expression patterns between the two induction systems, indicating that epigenetic reprogramming might contribute to gene expression activation/suppression in this process.

overall_design: The immature embryo samples were harvested at 0 h, 24 h, and 48 h after culture in CIM. The mature embryos were harvested at 0 h and 24 h after culture in CIM.

middle: j

first: Zhou

middle: c

last: lu

first: Zeng

middle: z

last: hui

first: lI

middle: x

last: pu

first: Han

last: ning


title: Gene expression profiles in the cultured dorsal root ganglia (DRG) neurons treated with PBS or oncomodulin (ONCM)

status: Public on Jan 21 2022

city: Su-won

first: Min Jung

last: Kwon

address: 206, World cup-ro

institute: Ajou University

summary: Preconditioning nerve injury drives pro-regenerative perineuronal macrophage activation in dorsal root ganglia (DRG). The present study reports that oncomodulin (ONCM) is produced from the regeneration-associated macrophages (RAMs) and strongly influences regeneration of DRG sensory axons. ONCM in macrophages was necessary to produce RAMs in the in vitro model of neuron-macrophage interaction and played an essential role in for preconditioning-induced neurite outgrowth. In order to gain insight on potential mechanisms downstream of ONCM for potent neurite outgrowth activity, we performed RNA-seq using cultured DRG neurons treated with ONCM.

overall_design: Cultured DRGs neurons from WT mouse and treated with PBS or 100 ng/ml of recombinant ONCM for 12 hr.

first: Min

middle: J

first: Yeojin

last: Seo

first: Hana

last: Cho

first: Hyung

first: Young

last: Oh

first: Minjae

first: Hee

last: Park

first: Eun-Hye

last: Joe

first: Myung-Hee

middle: C

last: Kang

first: Byung

middle: G


title: circRNA profiles of diabetic retinopathy

city: Ningbo

first: Mengyun

last: Liu

address: Baizhang East Road

institute: the affiliated People's hospital of Ningbo University

summary: To compare the circRNA expression profile of diabetic retinopathy with that of diabetes mellitus and controls, peripheral blood mononuclear cell samples were obtained and extracted from healthy controls and diabetes mellitus patients (with or without diabetic retinopathy). CircRNA Capital Bio Technology Human CircRNA Array v2 was performed to detect circRNA expression profiles. To further check differentiate circRNA, qRT_PCR assay was performed to detect the level of 5 candidates.

overall_design: CicrRNAS expression profiles in Peripheral blood mononuclear cells (PBMCs) of 4 diabetes mellitus patients, 4 diabetic retinopathy patients and 4  healthy individuals .

first: Hengqian

last: He

first: Qinkang

last: Lu


title: Transcriptional profiling of early haematopoietic mesoderm and endoderm in differentiating human pluripotent stem cells.

city: St. Lucia

first: Othmar

last: Korn

state: Queensland

address: University of Queensland

country: Australia

institute: Australian Institute for Bioengineering and Nanotechnology

summary: The aim of this project was to compare the transcriptional profiles of populations of cells derived from human pluripotent stem cells under haematopoietic and endoderm differentiation conditions. We used a reporter line (denoted SOX-RUNX) that carries mCHERRY inserted into the SOX17 locus and GFP inserted into the RUNX1C locus to mark haematopoietic progenitors (Ng et al., Nature Biotechnology, Nov 2016). SOX17 marks both endothelium and early endoderm. SOX17 is absolutely required at all stages of endoderm formation and the gene is also required for normal endothelial formation and subsequent haematopoieisis. We have also shown that RUNX1 is required for all definitive blood cell formation (Bruveris et al., manuscript submitted).

overall_design: (i) Haematopoietic mesoderm differentiation and analysis. This compared the parental SOX-RUNX reporter line and on a derivative in which the DNA binding domain of the RUNX1 gene was deleted using CRISPR mediated gene editing (RUNX KO). These experiments will demonstrate key transcriptional changes occurring during the course of differentiation and will identify RUNX1 dependent transcripts. Samples differentiated for 0, 2, 4, 7 and 12 days were collected from each cell line. The protocol used biased differentiation towards an intra embryonic, AGM-like fate. The samples at d0, d2 and d4 were not flow sorted, but samples at d7 and d12 are sorted into 2 and 3 fractions respectively. Samples from d7 time points represent SOX17 expressing and non expressing CD34+CD43- endothelial cells and the d12 time points have been sorted on SOX17, CD34 and CD43 to generate endothelial and haematopoietic fractions. (ii) Endoderm differentiation. These samples provided comparison with mesodermal differentiation of the SOX-RUNX line for days 0, 2, 4 and 7 of differentiation. Given that the phenotype by day 7 is virtually 100% SOX17+EPCAM+CXCR4+KIT+ endoderm, there was no need to sort cells.

first: Andrew

last: Elefanty

first: Ed

last: Stanley

first: Elizabeth

last: Ng

first: Freya

last: Bruveris

first: Katherine

last: Lim

first: Jasna

last: Kaur

first: Christine

last: Wells

first: Tyrone

last: Chen


title: Exosomal RNA expression profiles and their prediction performance in gestational diabetes mellitus patients with macrosomia

city: Nanjing

first: Juan

last: Wen

address: Tianfei Xiang 123#

institute: Women’s Hospital of Nanjing Medical University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Exosomal RNAs in cord blood may allow intercellular communication between  maternal and fetus. We aimed to establish exosomal RNA expression profiles in cord blood exosomes from gestational diabetes mellitus (GDM) patients with macrosomia.We used microarray technology to establish the differential mRNA, lncRNA and circRNA expression profiles in cord blood exosomes from GDM patients with macrosomia compared with normal controls. A total of 98 mRNAs, 372 lncRNAs and 452 circRNAs were differentially expressed in cord blood exosomes from GDM patients with macrosomia. Pathway analysis showed the differential genes were associated with PI3K-Akt signaling pathway, JAK-STAT signaling pathway, TGF-beta signaling pathway, insulin resistance, glycerolipid metabolism, fatty acid degradation and mTOR signaling pathway. These results showed that exosomal RNAs are aberrantly expressed in the cord blood of GDM patients with macrosomia.

overall_design: 6 human cord blood samples were collected for microarray profiling, including 3 GDM-macrosomia samples and 3 control samples


title: RNA sequencing data of 2102EP cells treated with epigenetic agents Quisinostat, JIB-04, Chaetocin, MZ-1, LP99, PRT4165 and GSK343 and DMSO as solvent control

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Moorenstr. 5

department: Dep. of Urology

country: Germany

institute: Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University

summary: Single end 3' RNA sequencing of embryonal carcinoma cell line 2102EP treated with epigenetic agents Quisinostat, JIB-04, Chaetocin, Mz-1, LP99, PRT4165 and GSK343. DMSO was used as solvent control. Cells were treated with the epi-drugs for 16 h.

overall_design: cells were treated with corresponding EC50 values of each epi-drug for 16 h


title: Whole blood transcriptomics in RSV infected children

city: Beerse

first: Kim

last: Thys

state: Antwerpen

address: Turnhoutseweg 30

department: Infectious Diseases

country: Belgium

institute: Janssen

summary:
The objective of this study was to identify gene expression markers of disease severity in a cohort of RSV infected children
Respiratory syncytial virus (RSV) is the number one pathogen causing lower respiratory tract infection that leads to hospitalization in young children. Despite growing insights in the disease pathogenesis, the clinical presentation in these children is highly variable and heterogeneous, and reliable markers predictive of disease progression are lacking.   We characterized the host response to acute RSV infection to identify biomarkers associated with RSV disease and disease severity.  Whole genome transcriptome was analysed early on the disease course in blood samples from otherwise healthy children <2 years of age, who were either hospitalized (n = 110) or evaluated as outpatients (n = 37) due to RSV infection. Age-matched non-RSV-infected healthy children (n = 51) were analysed in parallel.   A clustering approach on the transcriptome data revealed biologically meaningful biomarkers associated with progression to severe RSV disease. Overall, the whole blood transcriptome pointed to alterations in frequency of specific immune cell types (neutrophils, T- and B-lymphocytes, NK cells, monocytes) in RSV-infected children. In addition, a cluster enriched for neutrophil degranulation genes, was highly correlated with clinical disease severity. The driver genes of this cluster (OLFM4, ELANE, MMP8, BPI, CEACAM8, LCN2, LTF and MPO) were selected and validated in independent existing transcriptomics datasets.   We identified a set of genes involved in neutrophil degranulation as markers for RSV disease severity. Additional prospective studies using these markers are required to further confirm their value as predictive tool in routine clinical care.

overall_design: Blood samples for transcriptome analysis were collected at presentation from 37 outpatients and 110 inpatients. Follow-up blood samples were collected 30 and 180 days later from 86 and 69 of the patients, respectively. In addition, a cohort of 51 healthy children were enrolled and a blood sample was collected.

first: Asuncion

last: Mejias

first: Marjolein

last: Crabbe

first: Cristina

last: Garcia-Maurino

first: Lisa

last: Jaramillo

first: Gabriela

last: Ispas

first: Jacques

last: Bollekens

first: Octavio

last: Ramilo

first: Jeroen

last: Aerssens


title: b-globin enhancers regulate bistable gene expression states

city: Dallas

first: Jeremiah

last: Herbert

state: Texas

address: 5323 Harry Hines Blvd., MC 8511

department: Green Center for Reproductive Biology

institute: University of Texas Southwestern Medical Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Multiple enhancers can coordinately regulate a target gene to ensure robust expression. Under the failure rate model, each redundant enhancer contributes a probability of target gene expression in the cell, and genetic deletion will cause single-cell expression phenotypes. However, this model has been challenging to test in human cells. To examine the role of the human β-globin enhancers in controlling single-cell expression phenotypes, we engineered a haploid locus in K562 cells that fluorescently reports the expression of HBG1. We isolated combinatorial enhancer deletion clones having single-cell expression phenotypes. Genetic and epigenetic analysis shows that deletion of HS3 or HS4 yields clonal cells having bimodal expression of HBG1. Time course analysis indicates that clonal cells can transition between bimodal expression states, and that GFP+ cells have more open chromatin at the HBG1 promoter than GFP- cells. Finally, we derive failure rate contributions for several enhancers. Thus, β-globin enhancers regulate bistable gene expression states, supporting the failure rate model of enhancer redundancy in human cells.

overall_design: Multiple cell lines were sequenced with the goal of finding beta globin (bgl) enhancer deletions for downstream analysis. Prospective knockouts were prepared in duplicate for ATAC-seq, with several samples sequenced multiple times for increased coverage.


title: effects of water temperature stress in the adductor muscle of Argopecten irradians concentricus by transcriptomics

city: Qingdao

first: JunLin

last: Song

address: Changcheng Road

institute: JunLin Song

summary: Both high and low water temperature stresses are major environmental threats of growth and productivity in aquatic animals. However, the mechanism of response to temperature stress of scallop remains unclear. In this study, Argopecten irradians concentricus treated with high and cold temperature stress were analysed with the transcriptomes, metabolomes and integrated network analysis. Transcriptomic analyses revealed that there were many differentially expressed genes enriched calcium ion, kinase activity, phosphatase activity, and lipid related pathways between high temperature stress group and the control group. Although similar results were found in the low temperature stress group versus the control group, the genes enriched in these pathways were different. Moreover, much more genes were enriched in transcription factor activity in the low temperature stress group versus the control group

overall_design: Total mRNA profiles of the control group under normal temperature，high temperature and cold temperature were generated by deep sequencing, in triplicate.

first: Junlin


title: 3D chromatin topography of LSK cells with hyperactivated Notch1 and/or Tcf7 knock-out [HiC-seq]

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

summary: NOTCH1 is a well-established lineage specifier for T cells and amongst the most frequently mutated genes throughout all subclasses of T cell acute lymphoblastic leukemia (T-ALL). How oncogenic NOTCH1 signaling launches a leukemia-prone chromatin landscape during T-ALL initiation is unknown. Here we demonstrate an essential role for the high-mobility-group transcription factor Tcf1 in orchestrating chromatin accessibility and topology allowing for aberrant Notch1 signaling to convey its oncogenic function. Although essential, Tcf1 is not sufficient to initiate leukemia. The formation of a leukemia-prone landscape at the distal Notch1-regulated Myc enhancer, which is fundamental to this disease, is Tcf1-dependent and occurs within the earliest progenitor stage even before cells adopt a T lymphocyte or leukemic fate. Moreover, we discovered an additional evolutionarily conserved Tcf1-regulated enhancer element, in the distal Myc-enhancer, which is important for the transition of pre-leukemic cells to full-blown disease.

overall_design:
Chromatine conformation comparisons of sorted LSK derived from C57BL/6J; Sv/129 compound mice with Notch1 induced or Tcf1 knocked-down.

Please note that the following files were generated per each condition and are linked to the corresponding replicate 1 sample records:
Contact matrices hic files: 2 different resolutions (i.e. 2 per condition)
TADs: bedpe files labeled like _5000_blocks.bedpe contain the TADs at resolution 5000Kb, one per contition
Chromatin loops: bedpe files labeled  _postprocessed_pixels_XXXX.bedpe  where XXXX is the resolutions 2500Kb and there every 1000Kb from 5000 to 25000 (i.e. 22 per contition)

first: Mateusz

last: Antoszewski

last: Zangger

first: Freddy

last: Radtke


title: Systems analysis of interaction between p38/MAPK pathway and SARS-CoV-2

city: New York

first: Jeffrey

last: Johnson

state: NY

address: 1 Gustave L. Levy Pl

institute: Icahn School of Medicine at Mount Sinai

summary: SARS-CoV-2, the causative agent of the COVID-19 pandemic, drastically modifies the cells that it infects. One such effect is the activation of the host p38 mitogen-activated protein kinase (MAPK) pathway, which plays a major role in inflammation pathways that are dysregulated in severe COVID-19 cases. Inhibition of p38/MAPK activity in SARS-CoV-2-infected cells reduces both cytokine production and viral replication. Here, we applied a systems biology approach to better understand interactions between the p38/MAPK pathway and SARS-CoV-2 in human lung epithelial cells. We found several components of the p38/MAPK pathway positively and negatively impact SARS-CoV-2 infection and that p38ß is a required host factor for SARS-CoV-2 that acts by promoting viral protein translation in a manner that prevents innate immune sensing. Furthermore, we combined chemical and genetic perturbations of p38ß with quantitative phosphoproteomics to identify novel, putative p38ß substrates in an unbiased manner, with broad relevance beyond SARS-CoV-2 biology.

overall_design: Bulk mRNA-Seq of three biological replicates of each condition in A549-ACE2 cells: mock-infected/control transfected, SARS-CoV-2 infected/siNTC transfected, SARS-CoV-2 infected/sip38MAPK11-transfected

first: Higgins

last: Christina

first: Johnson

last: Jeffrey

first: tenOever

last: Benjamin


title: Tcf1 is essential for initiation of oncogenic Notch1-driven chromatin topology.

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Chromatin accessibility analysis of human cord blood cells with hyperactivated Notch1 [ATAC-seq_human]

overall_design: ATAC chromatin profile comparisons of human cord blood cells with Notch1 induced GoF


title: Metabolic Adjustments of Blood-Stage Plasmodium falciparum in Response to Sublethal Pyrazoleamide Exposure

city: Frederick

first: Shivendra

last: Tewari

state: MD

address: 2405 Whittier Drive, Suite 200

institute: Biotechnology HPC Software Applications Institute

summary: Due to the recurring loss of antimalarial drugs to resistance, there is a need for novel targets, drugs, and combination therapies to ensure the availability of current and future countermeasures. Pyrazoleamides belong to a novel class of antimalarial drugs that disrupt sodium ion homeostasis, although the exact consequences of this disruption in Plasmodium falciparum remain under investigation. In vitro experiments demonstrated that parasites carrying mutations in the metabolic enzyme PfATP4 develop resistance to pyrazoleamide compounds. However, the underlying mechanisms that allow mutant parasites to evade pyrazoleamide treatment are unclear. Here, we first performed experiments to identify the sublethal dose of a pyrazoleamide compound (PA21A092) that caused an approximately 50% reduction in growth over one intraerythrocytic developmental cycle (IDC). At this drug concentration, we collected transcriptomic and metabolomic data at multiple time points during the IDC to quantify gene- and metabolite-level alterations in the treated parasites. To probe the effects of pyrazoleamide treatment on parasite metabolism, we coupled the time-resolved omics data with a metabolic network model of P. falciparum. We found that the drug-treated parasites adjusted carbohydrate metabolism to enhance synthesis of myoinositol—a precursor for phosphatidylinositol biosynthesis. This metabolic adaptation caused a decrease in metabolite flux through the pentose phosphate pathway, causing a decreased rate of RNA synthesis and an increase in oxidative stress. Our model analyses suggest that downstream consequences of enhanced myoinositol synthesis may underlie adjustments that could lead to resistance emergence in P. falciparum exposed to a sublethal dose of a pyrazoleamide drug.

overall_design: PfDd2 parasites were cultured for 48 hours in the absence and presence of sublethal dose of a pyrazoleamide drug, PA21A092, with samples taken every eight hours for transcriptomics and processed in quadruplicate. Note that the samples from the treated cultures for Time 24 and 32 of Rep 2 were lost during the hybridization process. Also, for the treated cultures, the Time 48 of Rep 2 was collected in duplicate.

first: Bobby

last: Kwan

first: Rubayet

last: Elahi

first: Krithika

last: Rajaram

first: Amanda

last: Dziedzic

first: Anne

middle: E

last: Jedlicka

first: Jaques

last: Reifman

first: Sean

middle: T

last: Prigge

first: Akhil

middle: B

last: Vaidya

first: Anders

last: Wallqvist


title: Chromatin accessibility profiling of LSK cells with hyperactivated Notch1 and/or Tcf7 knock-out [ATAC-seq_mouse]

first: Nadine

last: Fournier

overall_design: ATAC chromatin profile comparisons of sorted LSK derived from C57BL/6J; Sv/129 compound mice with Notch1 induced or Tcf1 knocked-down or NDME…

last: Antoszewski


title: Gene expression profiling of LSK cells with hyperactivated Notch1 and/or Tcf7 knock-out [RNA-seq]

overall_design: Expression profile comparisons of sorted LSK derived from C57BL/6J; Sv/129 compound mice with Notch1 induced or Tcf1 knocked-down

first: Mateusz

last: Zangger

last: Radtke


title: Landscape of cell populations and communication in normal and aging inflammatory dental pulp

city: Wuhan

first: Wei

last: Yin

address: 237 Luoyu road

institute: Wuhan Unuversity

summary: We profiled the cell populations in dental pulp from two normal premolars and one aging inflammatory molar through single-cell RNA sequencing.

overall_design:
Cells in dental pulp from two normal premolars and one aging inflammatory molar were sequenced.
*** Raw data not provided due to patient privacy concerns ***

first: Gaoxia

last: Liu

first: Jinhong

last: Li

first: Zhuan

last: Bian


title: Disrupting the adult-globin promoter alleviates promoter competition and reactivates foetal-globin gene expression

status: Public on Jan 20 2022

city: Guangzhou

first: Peng

last: Huang

state: Guangdong

address: Xinzao, Panyu District

department: GMU-GIBH Joint School of Life Sciences

institute: Guangzhou Medical University

summary: The benign condition Hereditary Persistence of Foetal Haemoglobin (HPFH) is known to ameliorate symptoms when co-inherited with beta-haemoglobinopathies, such as sickle cell disease and beta-thalassaemia. The condition is sometimes associated with point mutations in the foetal globin promoters that disrupt the binding of the repressors BCL11A or ZBTB7A/LRF, which have been extensively studied. HPFH is also associated with a range of deletions within the beta-globin locus that all reside downstream of the foetal HBG2 gene. These deletional forms of HPFH are poorly understood and are the focus of this study. Numerous different mechanisms have been proposed to explain how downstream deletions can boost the expression of the foetal globin genes, including the deletion of silencer elements, of genes encoding non-coding RNA, and bringing downstream enhancer elements into proximity with the foetal globin gene promoters. Here we systematically analyse the deletions associated with both HPFH and a related condition known as beta-thalassaemia and propose a unifying mechanism. In all cases where foetal globin is up-regulated, the proximal adult beta-globin (HBB) promoter is deleted. We use CRISPR gene editing to delete or disrupt elements within the promoter and find that virtually all mutations that reduce promoter activity, result in elevated foetal globin expression. These results fit with previous models where the foetal and adult globin genes compete for the distal Locus Control Region and suggest that targeting the promoter might be explored to elevate foetal globin and reduce sickle globin expression as a treatment for beta-haemoglobinopathies.

overall_design: We performed Capture-C on WT control, HBB promoter deletion and TATA deletion clones. Two replicates were performed for each condition.

first: Merlin

last: Crossley


title: Genome-wide histone mark and CTCF profiling of LSK cells with hyperactivated Notch1 and/or Tcf7 knock-out [ChIP-seq]

overall_design: Histone marks and CTCF ChIP comparisons of sorted LSK derived from C57BL/6J; Sv/129 compound mice with Notch1 induced or Tcf1 knocked-down.

first: Freddy


title: CRISPR-Cas13d induces efficient mRNA knock-down in animal embryos

city: Kansas City

first: Huzaifa

last: Hassan

state: MO

institute: Stowers Institute for Medical Research

summary: Early embryonic development is driven by maternal gene products deposited into the oocyte. Due to the lack of reliable knockdown strategies, maternal mRNA functions have remained elusive. CRISPR-Cas13 systems have recently been employed to induce RNA degradation in yeast, plants and mammalian cell lines. However, no systematic study of the potential of Cas13 has been carried out in an animal model system. Here, we show that CRISPR-Cas13d is an effective and precise system to deplete specific mRNA transcripts in zebrafish embryos. We demonstrate that both zygotically-expressed and maternally-provided transcripts are efficiently targeted, resulting in an 85% average decrease in transcript level and the recapitulation of well-known embryonic phenotypes. Moreover, we show that this system can be used in medaka, killifish, sea anemone and mouse embryos. All together our results demonstrate that CRISPR-Cas13d is an efficient knockdown platform to understand gene function in animal embryos.

overall_design: Zebrafish embryos were injected with the indicated mRNA and/or guideRNAs and after 6 hours post injection.There are two biological replicates per treatment.

first: Ariel

middle: A

last: Bazzini

first: Miguel

last: Moreno-Mateos


title: 3D chromosome structure reveals unique signatures involved in mouse female germline stem cells and their development II

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

summary: We use RNA-seq to report the gene expression of FGSCs and shCTCF FGSCs

overall_design: Examination of the gene expression in FGSCs

first: Geng

last: Tian


title: Comparison of transcriptomic  between human amniotic epithelial stem cells and keratinocytes

city: Zhenjiang

first: Liping

state: Jiangsu

address: No.438 Jiefang Road

department: Department of Dermatology

institute: Affiliated Hospital of Jiangsu University

summary: Amniotic epithelial stem cells (AESCs) are considered potential alternatives for keratinocytes (KCs) in tissue-engineered skin substitutes. However, their clinical application to skin regeneration is hindered as AESCs and KCs are not identical. Herein, transcriptomics analysis were used to understand the commonalities and differences between human AESCs and KCs. RNA-sequencing revealed that AESCs are involved in multiple epidermis-associated biological processes, which are shared by KCs, and show more similarity to early-stage immature KCs than adult KCs. However, AESCs were heterogeneous, and some possessed hybrid mesenchymal and epithelial features distinct from KCs.  Thus, although AESCs and KCs are highly similar, their differences need to be addressed to modulate the cell fate of human AESCs to be applicable in skin regeneration.

overall_design: RNA sequencing of human AESCs, KCs, and fibroblasts.

first: Li-Ping

first: Dong-Xu

last: Zheng

first: Yun-Wen

first: Yu-Mei


title: Polysome profiling of Arabidopsis translatome upon hypertonic stress

city: Shenzhen

first: Bosheng

address: SUStech Huiyuan #1 406

department: MCDB

institute: SUSTC (current, may different with previous institution )

summary: We examined the possible effects of hypertonic stress on Arabidopsis translatome using polysome profiling. We found that the translatome is partly and rapidly reprogrammed in response to hypertonic stress, and such translatome reprogramming is DCP5-dependent.

overall_design: High-throughput sequencing of polysome-bound mRNA from Col-0 and dcp5-1 Arabidopsis seedlings with or without 15 min 150 mM NaCl-mediated hypertonic stress

first: Zhenyu

last: Wang


title: High-speed fluorescence image-enabled cell sorting

city: Heidelberg

first: Benedikt

last: Rauscher

address: Meyerhofstr. 1

institute: EMBL

summary: Fast and selective isolation of single cells with unique spatial and morphological traits remains a technical challenge. We address this by establishing high speed image-enabled cell sorting (ICS), which records multicolor fluorescence images, and sorts cells based on measurements from image data at speeds up to 15,000 events per second. We combine ICS with CRISPR-pooled screens to identify novel regulators of the NF-κB pathway, enabling the completion of genome-wide image- based screens in around nine hours of run-time.

overall_design: Pooled CRISPR-Cas9 screens for regulators of NFkB signaling with a novel sorting technology using a genome-wide and a focused gRNA library in HeLa cells.

first: Daniel

last: Schraivogel

first: Lars

last: Steinmetz


title: Promoter Identification and Optimization for the Response of Lactobacillus plantarum WCFS1 to the Gram-negative pathogen-associated molecule N-3-oxododecanoyl homoserine lactone

city: Washington

first: Joseph

last: Spangler

state: DC

address: 4555 Overlook Ave SW

institute: US Naval Research Lab

summary: Quorum sensing (QS) in bacteria has been a well studied cellular communication phenomenon for decades. In recent years, such systems have been repurposed for the use of biosensors in both cellular and cell-free contexts as well as for inducible protein expression in non-traditional chassis organisms. Such biosensors are particularly intriguing when considering the association between the pathogenesis of some bacteria and the QS signaling intermediates. Considering this relationship, and considering the recent demonstration of the species L. plantarum WCFS1 as both a synthetic biology chassis and an organism capable of detecting a pathogen-associated QS molecule, we wanted to develop this organism as a QS sentinel. Using an approach combining techniques from both systems and synthetic biology, we identified a number of native QS response genes and altered associated promoter activity to tune the output of L. plantarum cultures exposed to N-3-oxododecanoyl homoserine lactone. The resulting engineered QS sentinel reinforces the potential of modified Lactic Acid Bacteria for use in human health promoting applications, and also demonstrates a simple rational workflow to engineer sentinel organisms to respond to any environmental or chemical stimuli.

overall_design: L. plantarum was treated with 3OC12 at OD600 of 0.5 and RNA was extracted after one doubling for transcriptomic analysis.

middle: R

first: Denver

middle: N

last: Cooper

first: Anthony

middle: P

last: Malanoski

first: Scott

last: Walper


title: Gene Regulatory Network inference in long-lived C. elegans reveals modular properties that are predictive of novel ageing genes

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

summary: We design a “wisdom-of-the-crowds” GRN inference pipeline, and couple it to network analyses, to understand the organisational principles governing gene regulation in long-lived glp-1/Notch C. elegans. The GRN has three layers (input, core, output) and is topologically equivalent to bow-tie/hourglass structures prevalent among metabolic networks. To assess functional importance of structural layers, we screened 80% of the regulators and discovered 50 new ageing genes, 86% with human orthologues and 56% further extending the long life of glp-1. Genes essential for longevity—including ones involved in insulin-like signalling (ILS)—are at the core, indicating that GRN’s structure is predictive of functionality. Using in vivo reporters, we found an intricate relationship between fat accumulation, SOD enzymes, and lifespan. We queried 5,497 genetic interactions (https://s-andrews.github.io/wormgrn/qpcr/), and identified modulators that phenocopy ILS genes and share identical targets. We present a framework with predictive power that can accelerate discovery in C. elegans and potentially humans.

overall_design: Total of 115 samples were analyzed including replicates. Treatments were indicated for each sample accordingly. Please see Figure S1 in the manuscript for details of the design. 2 samples are not included in the network inference, but were used as GLP-GS (set-15 RNAi datasets).

first: Manusnan

last: Suriyalaksh

first: Celia

last: Raimondi

first: Abraham

last: Mains

first: Anne

last: Segonds-Pichon

first: Sheikh

last: Mukhtar

first: Sharlene

last: Murdoch

first: Rebecca

last: Aldunate

first: Roger

last: Guimera

first: Simon

last: Andrews

first: Marta

last: Sales-Pardo

first: Olivia

last: Casanueva


title: HMCES safeguards genome integrity and long-term self-renewal of hematopoietic stem cells during stress responses

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

summary: Hematopoietic stress drives quiescent hematopoietic stem cells (HSCs) to proliferate, generating reactive oxygen species and oxidative DNA damage including abasic sites. The coupling between abasic site generation and DNA replication during HSC stress responses, however, presents a challenge to accurately repair these abasic sites in the single-stranded DNA (ssDNA) generated during replication, leading to strand breaks and mutations. Here, we show in mice that HMCES, an evolutionarily conserved sensor and shield of ssDNA abasic sites, plays a pivotal role in overcoming this challenge. Hmces-deficient HSCs exhibited compromised long-term self-renewal capacity and elevated DNA damage in vivo in response to various hematopoietic stress, as well as broad attenuation of DNA damage response and repair pathways. Loss of HMCES also rendered HSCs hypersensitive to alcohol-derived acetaldehyde and might associate with increased susceptibility of leukemia. Collectively, our findings highlighted HMCES as a novel protector of HSCs and shed light on its physiological roles in regeneration and tumorigenesis.

overall_design: LT-HSCs of WT and Hmces knockout for duplicates are performed RNA sequencing.

first: Yinghao

last: Pan

first: Hongna

last: Zuo

first: Zhenyu

last: Ju

first: Hu

last: Wang


title: Regulation of RNA translation after TUFM knockout

city: Chicago

first: Zhe

last: Ji

state: ILLINOIS

address: 303 E Superior St, Lurie 6-107

institute: Northwestern University

summary: We performed RNase footprinting and RNA-seq to examine the regulation of RNA translation after TUFM knockout in HeLa cells

overall_design: RNase footprinting and RNA-seq in TUFM knockout and control cells.

first: Qianru

last: Li

first: Haiwang

last: Yang


title: Regulation of RNA translation among human primary immune cells

summary: We performed RNase footprinting and RNA-seq to examine the regulation of RNA translation comparing human primary immune cell types, including T-cells, B-cells, monocytes.

overall_design: RNase footprinting and RNA-seq of T-cells, B-cells, monocytes, and Peripheral blood mononuclear cells (PBMCs).


title: The RNA helicase DDX39B activates FOXP3 RNA splicing to control T regulatory cell fate

city: Galveston

first: Steven

last: Widen

address: 301 University Blvd

department: BMB

institute: University of Texas Medical Branch

summary: Autoimmune disease is caused by environmental and genetic factors. Genetic factors associated with increased susceptibility to multiple sclerosis (MS), an autoimmune disease of the central nervous system, have been identified, but their mechanisms of action are incompletely understood.(Briggs, 2019) We previously established that the association between MS risk and the interleukin-7 receptor-a gene (IL7R) is mediated by alternative splicing of IL7R transcripts.(Gregory et al., 2007) This splicing is regulated by the RNA helicase DEAD Box Polypeptide 39B (DDX39B), which shows genetic and functional epistasis with IL7R in enhancing MS risk (Galarza-Munoz et al., 2017). Here we discover that DDX39B, which is also known by immunologists as BAT1 (Spies et al., 1989), impacts the expression of many genes likely to play roles in autoimmunity.(Allcock et al., 2001; Degli-Esposti et al., 1992) We show that DDX39B controls expression of Forkhead Box P3 (FOXP3), a master regulator of the development, maintenance and function of CD4+/CD25+ T regulatory cells(Georgiev et al., 2019; Josefowicz et al., 2012) and repressor of autoimmunity (Bennett et al., 2001; Brunkow et al., 2001; Chatila et al., 2000; Wildin et al., 2001). Splicing of FOXP3 introns, which belong to a new subclass of introns with C-rich polypyrimidine tracts, was exquisitely sensitive to DDX39B levels, making FOXP3 expression highly sensitive to the levels of this RNA helicase. Low DDX39B levels in primary human T regulatory cells lead to loss of regulatory gene expression and cytokine signatures and gain of effector ones. Given the importance of FOXP3 in autoimmunity, this work cements DDX39B as a critically important guardian of immune tolerance that can reduce autoimmune disease risk by regulating IL7R splicing and upregulating FOXP3.

overall_design: Primary human CD4 positive T cells from two donors were activated with anti-CD3 and anti-CD28. After two days the cells were transduced with with lentiviruses coding non-targeting control or DDX39B (Sh3 or Sh5) shRNAs for 3 days. After 4 more days of selection with puromycin and one day without drug, RNA was isolated for analysis.

first: Gaddiel

last: Galarza-Muñoz

first: Minato

last: Hirano

first: W

middle: S

last: Fagg

first: Geraldine

last: Schott

first: Liuyang

first: Alejandro

middle: L

last: Antonia

first: Jain

last: Vaibhav

first: Jason

last: Gibson

first: Xiaxing

last: Yu

first: Farren

last: Briggs

first: Dennis

last: Ko

last: Gregory

first: Shelton

last: Bradrick

first: Mariano

last: Garcia-Blanco


title: Examine RNA translation of fresh frozen tumor and spleen tissues from the 4T1 mouse model

first: Zhe

last: Ji

summary: We performed RNase footprinting and RNA-seq to examine the regulation of RNA translation of fresh frozen tumor and spleen tissues from the 4T1 mouse model

overall_design: RNase footprinting and RNA-seq of 4T1 tumor and spleen tissues


title: Identification of Potential Gene targets and Pathways Shared by Diabetes and Atherosclerosis

city: Beijing

first: Rongrong

last: Hua

state: China

address: Beijing

department: Department of Radiology

institute: the Third Medical Centre, Chinese People’s Liberation Army General Hospital

summary: We analyzed the microarray gene expression datasets of DM and AS in Ba-Ma mini pigs models using different combinations of high cholesterol (HC) diet, high lipo (HL)-diet, and streptozotocin (STZ) injection. Common differentially expressed genes (DEGs) were identified between DM and AS comparing with the control group, which further underwent Gene Ontology (GO), KEGG pathway, and protein–protein interactions (PPI) analyses to screen the significant molecular pathways and hub proteins common to DM and AS.

overall_design: Peripheral blood serum mRNA profiles of pigs models, including Control (n=4), HC+STZ (n=4), STZ+HC (n=3), HL+STZ (n=4), and STZ+HL (n=5) were generated ,in duplicate, using Illumina.

first: Guisheng

last: Wang

first: Xiaoxia

last: Chen


title: Low-input RNase footprinting to profile RNA translation

summary: We treated HEK293T cells with different doses of RNase and sequence RNA fragements after the treatments. Furthermore, we developed a low-input RNase footprinting approach to quantify genome-wide RNA translation using 50,000 and 1,000 HEK293T and K562 cells. The ribosome profiling and RNA-seq data were used as the control.

overall_design: 1. HEK293T cells were treated with 3 different doses of RNase (i.e. low, medium, high) and RNA fragments were isolated for sequencing. 2. Low-input RNase footprinting for 50,000 and 1,000 HEK293T and K562 cells. 3. Ribosome profiling and RNA-seq data for HEK293T and K562 cells were used for comparisons.

first: Qianru

last: Li

first: Haiwang

last: Yang


title: 3D chromosome structure reveals unique signatures involved in mouse female germline stem cells and their development

first: Ji

last: Wu

summary: We use in situ Hi-C to report the female germline cell development

overall_design: Examination of the chromatin architecture in GV stage oocytes

first: Geng

last: Tian


title: 3D Chromosome Structure Can Reveal Stem Cell Signatures (RNA-Seq)

summary: We use in situ Hi-C to report the most comprehensive survey to date of chromatin organization in stem cells

overall_design: 2 cell types


title: 3D Chromosome Structure Can Reveal Stem Cell Signatures (Hi-C)

overall_design: Examination of the chromatin architecture in 5 cell types.


title: 3D Chromosome Structure Can Reveal Stem Cell Signatures

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

overall_design: Refer to individual Series


title: Increased CD44 expression in low-dose chemotherapeutic treated colon cancer cells is controlled by ELF3

city: shiyan

first: Xueyan

last: Xi

state: Hubei Province

address: Renmin Nanlu #30

institute: Hubei University of Medicine

summary:
Background: It has been considered that long-term exposure to chemotherapeutic drugs would cause the development of resistance in colorectal cancer (CRC) patients. Though the detailed mechanism for this process is varied under different circumstances, the existence of cancer stem cells (CSCs) in CRC tissues has been proposed to be one of the reasons.
Methods: In this study, low dose of fluorouracil (IC10 of 5-FU) treatment against colon cancer cells had been used to mimic the situation occurred in vivo when the cancer patients were received chemotherapy.

overall_design: RNA-seq analysis were then performed in IC10 of 5-FU treated HCT-8 cells.

first: Fen

last: Qiu

first: Xu

last: Fan

first: Boyu

last: Du


title: 3D Chromosome Structure Can Reveal Stem Cell Signatures (ChIP-Seq)

overall_design: 1 cell type


title: Differentially expressed genes between YY1 knockdown and control cells, transfected in colorectal cancer cell line SW48

status: Public on Jan 19 2022

city: Chiba city

first: Nami

last: Sato

state: Chiba purefecture

address: Chuo-ku, Inohana 1-8-1

department: General Surgery

country: Japan

institute: Chiba university

summary:
Yin Yang 1 (YY1) is a multifunctional transcription factor with critical roles in carcinogenesis and metastasis. However, its biological role and clinical impact in colorectal cancer (CRC) remain unclear.
This study aimed to elucidate the oncological role of YY1 in CRC. To indentify the target genes of YY1, microarray analysis was performed on siYY1 and siControl transfected cells.

overall_design: SW48 was transfected with siControl and siYY1. After culturing for 3 days, total RNA was isolated from each cell. Differentially expressed genes in YY1 knockdown cells compared to siControl cells were analyzed.


title: Differentially expressed genes between YY1 knockdown and control cells, transfected in colorectal cancer cell line DLD-1

overall_design: DLD-1 was transfected with siControl and siYY1. After culturing for 3 days, total RNA was isolated from each cell. Differentially expressed genes in YY1 knockdown cells compared to siControl cells were analyzed.


title: RNA-seq Analysis of mouse SCLC cell lines with or without Kdm1a knock-out

first: yujuan

last: jin

address: Yueyang Road 320#

institute: Shanghai Institutes for Biological Sciences, CAS

summary:
Purpose: Histone demethylase Kdm1a affected mouse SCLC progression through many down-stream factors or pathways. RNA-seq of mouse SCLC cell lines with or without Kdm1a knock-out was used to find the most enriched pathways in Kdm1a knock-out cells
Methods: Total mRNA profiles of control (Crispr-V2) or Kdm1a knock-out mouse SCLC cell lines (Kdm1a-sg1, Kdm1a-sg2) were generated by deep sequencing, using Illumina Hiseq platform and 125 bp/150 bp paired-end reads. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9). Commonly differential expression after Kdm1a knock-out with two different single guide RNAs to control mouse SCLC cells were selected with a fold change ≥1.5.
Conclusions: Our data showed four Rest related pathways, including negative cell proliferation, negative cell differentiation, positive regulation of programmed cell death enriched, in commonly up-regulated genes after Kdm1a knock-out with twe different single guide RNAs. Meanwhile, the commonly down-regulated genes were mostly enriched in neron related pathways. These result illustrated the Kdm1a depletion inhibited mouse SCLC progression, defected its neuroendocrine phenotype through the up-regulation of Rest.

overall_design: Total mRNA profiles of mouse SCLC cell lines with or without Kdm1a knock-out with two different single guide RNAs (Kdm1a-sg1, Kdm1a-sg2) were generated by deep sequencing, an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated.

first: Yujuan

last: Jin

first: Hongbin

first: Yujiang

last: Shi


title: Vascular tumor spectrum in aP2-Cre mice

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

institute: Purdue University

summary:
The combined activation of KrasG12D and loss of Cdkn2a leads to aggressive angiosarcomas in aP2-Cre mice. Whereas, the conditional deletion of Tsc1 leads to vascular tumor formation that mimic human kaposiform hemangioendotheliomas.
We used Affymetrix microarrays to compare angiosarcoma tumors with the combined activation of KrasG12D and loss of Cdkn2a and the conditional deletion of Tsc1

overall_design: Comparison of angiosarcoma tumors from aP2-Cre;LSL-KrasG12D;Cdkn2aFl/Fl (AKC mice) and tumors from aP2-Cre;Tsc1Fl/Fl mice (AT mice).

first: Jason

last: Hanna

first: Annaleigh

last: Benton

first: Casey

last: Langdon

first: Matthew

last: Garcia

last: Lanman

first: David

last: Finkelstein

first: Jerold

last: Rehg

first: Mark

last: Hatley


title: CUT&Tag-seq for H3K27ac in hematopoietic stem cells in bone marrow after 5-FU administration

city: Kumamoto

first: Terumasa

last: Umemoto

address: 2-2-1, Honjo, Chuo-Ku

institute: Kumamoto University

summary: Purpose: The goals of this study are to elucidate the underlying mechanism for the regulation of HSC divisions.  Methods: Before or after wild type (WT) mice were treated with 5-fluorouracil (5-FU), 12500 cells of HSCs were sorted. These cells were subjected to CUT&Tag-seq to analyze H3K27ac profile by using Next-seq. The sequence reads that passed quality filters were analyzed by Trimmomatic.

overall_design: After 6 or 10 days from 5-FU administration, HSCs (CD150+ CD48- EPCR+ Lineage-) or HPC  (CD150+ CD48+ EPCR+ Lineage-) were sorted were sorted, and subsequently CUT&Tag peaks for H3K27ac were generated by deep sequencing using Next-seq.


title: RNA sequencing analysis after syngeneic graft of B16F10 tumor.

city: Daejeon

first: HyunSeok

last: Kim

address: 291, Daehak-ro, Yuseong-gu

institute: Korea Advanced Institute of Science and Technology (KAIST)

summary: It is known that melanoma of foot surface occurs more frequently at points of mechanical stress on the plantar surface. However, the role of mechanical stress on acral melanoma is not well demonstrated. To investigate the effect of mechanical stress on gene regulation, we performed RNA sequencing analysis after performing syngeneic transplantation of B16F10 mouse melanoma cell into the flank and the hind footpad of the mice.

overall_design: Examination of transcriptiome difference between flank-injected B16F10 tumors and footpad-injected B16F10 tumors.

first: Jimyung

last: Seo

first: Joon


title: Metabolic control of adult neural stem cell self-renewal by the mitochondrial protease YME1L

city: Köln

first: Matteo

last: Bergami

address: Joseph Stelzmann Str 26

institute: CECAD Research Center

summary: The transition between quiescence and activation in neural stem and progenitor cells (NSPCs) is coupled to reversible changes in energy metabolism with key implications for life-long NSPC self-renewal and neurogenesis. How this metabolic plasticity is ensured between NSPC activity states is unclear. We find that a state-specific rewiring of the mitochondrial proteome by the i-AAA peptidase YME1L is required to preserve NSPC self-renewal. YME1L controls the abundance of numerous mitochondrial substrates in quiescent NSPCs, and its deletion activates a differentiation program characterized by broad metabolic changes causing the irreversible shift away from a fatty acid oxidation-dependent state. Conditional Yme1l deletion in adult NSPCs in vivo results in defective self-renewal and premature differentiation, ultimately leading to NSPC pool depletion. Our results disclose an important role for YME1L in coordinating the switch between metabolic states of NSPCs and suggest that NSPC fate is regulated by compartmentalized changes in protein network dynamics.

overall_design: Examination of two different comparisons between adult NSPC conditions: quiescent vs active; and wild-type vs Yme1lKO

first: Gulzar

last: Wani

first: Richard

last: Acton


title: Subfractions within hematopoietic stem cells in bone marrow


title: single ATAC-seq of subfractions within hematopoietic stem cells in bone marrow

summary: Purpose: The goals of this study are to elucidate the underlying mechanism for the regulation of HSC divisions.  Methods: One hundred thousand cells of subfractions within the HSC fraction were sorted. These cells were subjected to ATAC-sequence by using 10X Genomics Chromium Next GEM Single Cell ATAC Reagent Kits v1.1.  The sequence reads that passed quality filters were analyzed by FASTX-toolkit.

overall_design: EPCR+ or +++ fraction within the HSC fraction (CD150+ CD48- EPCR+ Lineage-) were sorted, and subsequently ATAC peaks were generated by deep sequencing using Hi-seq.


title: EXOSOMAL microRNAs AS POTENTIAL BIOMARKERS OF HEPATIC INJURY AND KIDNEY DISEASE IN GLYCOGEN STORAGE DISEASE TYPE IA PATIENTS.

city: Genova

first: Roberta

last: Resaz

address: via Gerolamo Gaslini 5

country: Italy

institute: IRCCS Istituto Giannina Gaslini

summary: Glycogen storage disease type Ia (GSDIa) is an inherited metabolic disorder caused by mutations in the enzyme glucose-6-phosphatase-α (G6Pase-α). Affected individuals develop renal and liver complications, including the development of hepatocellular adenoma/carcinoma and kidney failure. The purpose of this study was to identify potential biomarkers of the evolution of the disease in  GSDIa patients. To this end, we analyzed the expression of exosomal microRNAs (Exo-miRs) in the plasma exosomes of 45 patients aged 6 to 63 years. Plasma from age-matched  normal individuals were used as controls.   We found that the altered expression of several Exo-miRs correlates with the pathologic state of the patients and might help to monitor the progression of the disease and the development of late GSDIa-associated complications.

overall_design: Exo-miR were analyzed by the TaqMan Array Card Technology. Exo-miR were reverse transcribed with the TaqMan microRNA Reverse Transcription Kit, using the MegaplexTM RT primers Human Pool A (Thermo Fisher Scientific, Monza, MB, Italy). Pre-amplification of cDNA was performed with TaqMan PreAmp Master Mix and MegaplexTM  Pre-Amp primers Human Pool A. The pre-amplification product was diluted according to the manufacturer’s instructions and used to perform microRNA profiling on the ViiATM 7 Real-Time PCR System.

first: Alessandra

last: Eva


title: ATAC-seq of subfractions within hematopoietic stem cells in bone marrow

summary: Purpose: The goals of this study are to elucidate the underlying mechanism for the regulation of HSC divisions.  Methods: Fifteen thousand cells subfractions within the HSC fraction were sorted. These cells were subjected to ATAC-seq using Hi-seq. The sequence reads that passed quality filters were analyzed by FASTX-toolkit.


title: mRNA profiles of subfractions within hematopoietic stem cells in bone marrow

summary: Purpose: The goals of this study are to elucidate the underlying mechanism for the regulation of HSC divisions.  Methods: One hundred cells of subfractions within the HSC fraction were sorted. These cells were subjected to mRNA sequence using Next-seq. The sequence reads that passed quality filters were analyzed by CLC genomic workbench.

overall_design: EPCR+, ++ or +++ fraction within the HSC fraction (CD150+ CD48- EPCR+ Lineage-) were sorted, and subsequently mRNA profiles were generated by deep sequencing using Next-seq.


title: mRNA profiles of hematopoietic stem and progenitor cells in bone marrow

summary: Purpose: The goals of this study are to elucidate the underlying mechanism for the regulation of HSC divisions.  Methods: Five thousand cells of subfractions within the HSC fraction were sorted. These cells were subjected to mRNA sequence using Next-seq. The sequence reads that passed quality filters were analyzed by CLC genomic workbench.

overall_design: The HSC fraction (CD150+ CD34- Sca1+ c-Kit+ Lineage-) and HPC fraction (CD150+ CD34+ Sca1+ c-Kit+ Lineage-)were sorted, and subsequently mRNA profiles were generated by deep sequencing using Hi-seq.


title: Transcriptome profiling of murine cardiomyocytes after treatment with recombinant murine Leukemia inhibitory factor (mLIF), murine Oncostatin M (mOSM) and human-like Oncostatin M orthologue (hlOSM).

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: This study comparatively assesses downstream effects of exclusive activation of Leukemia inhibitory factor receptor (LIFR), Oncostatin M receptor (OSMR) and dual LIFR/OSMR signaling in murine, cultured cardiomyocytes upon administration of recombinant mLIF, mOSM and hlOSM that is capable to activate both receptors in murine cells.

overall_design: Cultures of murine, primary cardiomyocytes were treated with recombinant mLIF, mOSM and hlOSM for 24 hours under normoxic conditions. Addition of equivaltne volumes of steriles PBS (=solvent of proteins) was used as reference/control.

first: Holger

last: Lörchner

first: Juan

middle: M

last: Adrian-Segarra


title: Transcriptome of YTN16 tumor tissues after treatment with anti-PD-L1 or anti-CTLA-4

city: Osaka

first: Koji

last: Nagaoka

address: 377-2 Ohno-Higashi, Osaka-Sayama

department: Department of Immunology

institute: Kindai University Faculty of Medicine

summary: A murine gastric cancer YTN16  is sensitive to anti-CTLA-4, but resistant to anti-PD-L1. To investigate tumor microenvironments after treatment of these mAbs, we performed RNA-Seq analyses.

overall_design: C57BL/6 mice were inoculated with 5×106 YTN16 on day 0. Anti-PD-L1 (clone 10F9G2, 200 µg/mouse) or anti-CTLA4 (clone 9H10, 100 µg/mouse) antibodies were injected on days 0, 4 and 8. On days 7, 14 and 21, tumors were harvested and subjected to RNA-Seq.

first: Kazuhiro

last: Maejima

first: Hidewaki

last: Nakagawa

last: Kakimi


title: Fosfomycin and the intermediate metabolites PEP and GA-3P effect on Stenotrophomonas maltophilia transcriptome

city: Cantoblanco

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

institute: CNB, CSIC

summary: Transcriptomic analysis of S. maltophilia D457 after one-hour induction with the antibiotic fosfomycin, the intermediate metabolites phosphoenolpyruvate or glyceraldehyde-3-phosphate

overall_design: 4 transcritpomes (S. maltophilia D457 control, 16 μg/mL fosfomycin, 2.5 mM PEP and 0.5 mM GA-3P)  with 3 independent replicates

first: Teresa

last: Gil-Gil

first: José

last: Martínez


title: The splicing factor DHX38/PRP16 is required for ovarian clear cell carcinoma tumorigenesis, as revealed by a CRISPR-Cas9 screen

city: Yayoi, Bunkyo-ku

first: Tomoatsu

last: Hayashi

state: Tokyo

institute: The University of Tokyo

summary: Certain cancers, such as ovarian clear cell carcinoma (OCCC), display high levels of genetic variation between patients, confounding the development of effective therapies. In order to identify novel genes critical to OCCC growth, we employed the pooled genome-scale CRISPR Knock-Out (GeCKO) v2 CRISPR-Cas9 knockout screening system using the OCCC cell line JHOC5, as well as the T-antigen immortalized normal ovarian surface epithelium cell line OSE3 as a negative control.  We identified the gene encoding DHX38/PRP16, an ATP-dependent RNA helicase involved in splicing, as critical for the growth and tumorigenesis of OCCC; DHX38 knockdown in OCCC cells, but not normal cells, induces apoptosis and impairs OCCC tumorigenesis in a mouse model. Our results suggest that DHX38/PRP16 may play a role in OCCC tumorigenesis, and can be regarded as a promising therapeutic target.

overall_design: Genome-wide CRISPR/Cas9  screen of JHOC5 (ovarian cancer cell) and OSE3 (normal ovarian epithelial cell) using the GeCKO v2 pooled sgRNA library.

first: Brandon

last: Cona

first: Naoko

last: Yokota

first: Ryuichiro

last: Nakato

first: Tetsu

last: Akiyama


title: IL10RA signaling deficiency change the anti-inflammatory signature of Ccr2-independent resident macrophages

city: Boston

first: Izabel

last: Patik

state: Massachusetts

address: 300 Longwood Ave

department: Division of Gastroenterology, Hepatology, and Nutrition

institute: Boston Children's Hospital

summary: In adult mice the majority of intestinal macrophages exhibit a mature phenotype and are derived from blood monocytes. In the steady state replenishment of these cells is reduced in the absence of the chemokine receptor Ccr2.  Within the intestine of mice with colitis there is marked increase in the accumulation of immature macrophages that  demonstrate an inflammatory phenotype. However, whether Ccr2 is necessary for the accumulation of these immature macrophages and further for the development of colitis in susceptible mouse models is incompletely defined.  Here, we ask whether Ccr2 is necessary for the development of colitis in mice lacking the receptor for IL10. We compared the development of intestinal inflammation in mice lacking IL10RA or both IL10RA and Ccr2. The absence of Ccr2 interfered with the accumulation of immature macrophages in IL10R-deficien mice, including a novel population of rounded submucosal Iba1+ cells and reduced the severity of colitis in these mice. In contrast, the absence of Ccr2 did not reduce augmented inflammatory gene expression observed in mature intestinal macrophages isolated from mice lacking IL10RA. These data suggest that both newly recruited Ccr2-dependent immature macrophages and Ccr2-independent residual mature macrophages contribute to the development of intestinal inflammation observed in IL10R-deficient mice.

overall_design: colonic mRNA profile comparisons of 5 week-old wild type (WT), Il10ra -/- and Il10ra -/-, Ccr2 -/- mice

first: Shorouk

last: El Sayed

first: Konstantinos

last: Karagiannis

first: Bruce

last: Horwitz


title: A nuclear function for an oncogenic microRNA as a modulator of snRNA and splicing

first: Yanhong

last: Zhang

address: 60 Fenwood Road, Room 9006

institute: Brigham And Women's Hospital

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

overall_design: Refer to individual Series


title: A nuclear function for an oncogenic microRNA as a modulator of snRNA and splicing [CLEAR-CLIP]

summary: miRNAs are regulatory transcripts established as repressors of mRNA stability and translation. Here we demonstrate that an oncomiR-10b binds to U6 snRNA, a core component of the spliceosomal machinery. We provide evidence of direct binding between miR-10b and U6, in situ visualizations of miR-10b and U6 co-localization in glioma cells and tumor tissues, and biochemical co-isolation of miR-10b with the components of the spliceosome. We further demonstrate that miR-10b modulates U6 N-6-adenosine methylation and pseudouridylation, U6 binding to splicing factors SART3 and PRPF8, and regulates U6 stability, conformation, and levels. The effects on U6 result in splicing alterations, illustrated by the altered ratio of the isoforms of a small GTPase CDC42, reduced overall CDC42 levels, and downstream CDC42 -mediated effects on cell viability. We, therefore, present an unexpected intersection of the miRNA and splicing machineries and a new nuclear function for a cancer-associated miRNA.

overall_design: To investigate endogenous miR-10b targets, we employed the modified CLEAR- CLIP protocol in glioma cells (Moore et al., 2015). The technique relies on miRNA crosslinking with proximal transcripts, ligation, and sequencing of chimeras. Therefore, it provides an unbiased mapping of the miRNA-target interactions, independent of bioinformatic predictions.

first: Rachid

last: El Fatimy


title: Molecular signatures of aging and flu vaccine response in Healthy and HIV infected individuals

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

summary: Individuals living with chronic HIV experience similar immune impairments as HIV-negative elderly however they manifest symptoms (e.g. suboptimal responses to vaccination) at a younger age. Mechanisms underlying premature immune-senescence are unclear. In this study, we aimed to identify molecular signatures of aging and vaccine response in HIV infected (HIV) individuals as compared to age-matched healthy-control participants (HC). Using RNA-sequencing, we evaluated transcriptomic profiles in peripheral blood mononuclear cells in study participants before and 1-week after influenza vaccination. Despite that fewer differentially expressed genes between young (<40yrs) and old (>59yrs) were observed in HIV, metabolic and innate immune activation pathways were associated with increasing age in both HIV and HC. Age was also associated with pathways involved with T cell immune activation in HC, and with Interferon signaling pathways in HIV. Predictive and correlative models of vaccine response using gene expression were different in HC and HIV. In this study, molecular signatures were defined for aging and vaccine response in HC and HIV. We observed signs of precocious immune aging at the transcriptional level in HIV and described a transcriptional perturbation associated with innate immunity and glucose metabolism induced by aging in both HC and HIV in resting conditions.

overall_design: 48 individuals from the FLORAH cohort(13) were selected based on their HIV serostatus, age and response to influenza vaccination. 6 vaccine Responder and 6 vaccine Non-Responder were selected for each of the 4 groups in analysis, namely young HIV infected (YH), old HIV (OH), young healthy (YC) and old HC (OC). Samples were taken at pre-vaccination (T0) and 7 days post-vaccination (T1)

first: S

last: Rinaldi

last: Pallikkuth

first: L

last: De Armas

first: B

last: Richardson

last: Pan

first: R

last: Pahwa

last: Williams

first: M


title: miR204-containing exosome ameliorates GVHD-associated dry eye disease

city: Guangzhou

first: Tian

last: Zhou

address: NO.7 Jinsui Road

department: State Key Laboratory of Ophthalmology

institute: Zhongshan Ophthalmic Center

type: Non-coding RNA profiling by high throughput sequencing

summary: The graft-versus-host disease (GVHD) associated dry eye disease usually leads to refractory pain and visual impairment with limited treatments currently. Here we found exosome derived from mesenchymal stromal cell (MSC-exo) administered as eye drops significantly alleviates GVHD-associated dry eye disease in human and mouse models. To find out the essential elements during exosome treatment, we performed miRNA sequencing of exosomes derived from MSCs and L929 cells, and identified miR-204 in MSC-exo benefited the recovery of dry eye, which targeted IL-6/IL-6R/Stat3 signaling. Blockade of miR-204 abolished the therapeutic effect of MSC-exo while miR-204 overexpression from L929-exo markedly attenuates dry eye. Thus MSC-exo eye drops are efficacious in treating GVHD-associated dry eye and highlight miR-204 as a potential therapeutic agent.

overall_design: Examination of different miRNAs in exosomes derived from murine MSCs and fibroblasts

first: Chang

last: He

first: Peilong

last: Lai

first: Yan

last: Liu

first: Ziqi

last: Yang

first: Huiyi

last: Xu

first: Xiaojing

last: Lin

first: Biyan

last: Ni

first: Qiumin

last: Feng

first: Wei

last: Yi

first: Lingyi

last: Liang

first: Charles

last: Egwuagu

first: Duanqing

last: Pei

first: Xialin


title: Next-generation sequencing is useful for quantitative analysis of the transcriptome of RSL3@O2-ICG NBS combined with low-frequency ultrasound treated and untreated HCC cells

city: Harbin

first: Bolin

last: Wu

state: Heilongjiang Province

address: No.150, Haping Road, Nangang District

institute: Harbin Medical University Cancer Hospital

summary: Hepatocellular carcinoma has a hidden onset and is often found at an advanced stage clinically. Moreover, because it is insensitive to radiotherapy and chemotherapy, its treatment is often difficult. Therefore, we constructed a new type of ultrasound contrast agent RSL3@O2-ICG NBS, combined with low frequency ultrasound irradiation, to realize the integration of diagnosis and treatment of hepatocellular carcinoma. At the same time, next-generation high-throughput RNA sequencing (RNA-seq) was performed to accurately analyze the differential expression of mRNA and lncRNA targets after adding RSL3@O2-ICG NBS and using low-frequency ultrasound (LFU)

overall_design: The transcripts of two kinds of HCC cells before and after RSL3@O2-ICG NBS combined with low-frequency ultrasound were detected

first: Yichi

last: Chen

first: Haitao

last: Shang

first: Wen

last: Cheng


title: Neanderthal Adaptively Introgressed Genetic Variants Regulate Human Immune Genes In Vitro.

city: Cambridge

first: Terence

middle: D

last: Capellini

state: MA

address: 11 Divinity Avenue

department: Human Evolutionary Biology

institute: Harvard Univserity

summary: Some Neanderthal introgressed variation underwent selective sweeps, but little is known about their functional significance. We used a Massively Parallel Reporter Assay (MPRA) to test 5,353 high-frequency introgressed variants for evidence of being in active cis-regulatory elements (CREs) and modulating gene expression in immune cell lines. We identified 2,546 variants in CREs and 292 expression-modulating variants (emVars). These emVars are predicted to regulate genes that are enriched for function in innate immune pathways including interferon signaling, toll like receptor pathways, and anti-viral response; one such emVar is significantly associated with protection against severe COVID-19 response. Using CRISPR-Cas9, we deleted two CREs containing expression-modulation variants linked to immune function, rs11624425 and rs80317430, identifying their primary genic targets as ELMSAN1, and PAN2 and STAT2 respectively, three genes differentially expressed during influenza infection. Overall, we present the first database of directly identified expression-modulating Neanderthal-introgressed alleles contributing to potential immune response in modern humans.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: MPRA testing the regulatory potential of 5,353 putatively adaptively introgressed variants. Four replicates were performed in K562 cells and 2 replicates in Jurkat cells.

first: Evelyn

last: Jagoda

first: James

last: Xue

first: Steven

middle: K

last: Reilly

first: Michael

last: Dannemann

first: Fernando

last: Racimo

first: Emilia

last: Huerta-Sanchez

first: Sriram

last: Sankararaman

first: Janet

last: Kelso

first: Luca

last: Pagani

first: Pardis

last: Sabeti


title: Transcriptomic analysis of CD4+ Tcells from maternal immune activation (MIA) exposed offspring

first: Eunha

last: Kim

address: 77 Ave Louis Pasteur

department: Immunology

institute: Harvard Medical School

summary: We report differentially regulated transcriptome of CD4+ T cells in MIA offspring

overall_design: Congenically marked T cells, isolated from PBS and MIA offspring with CD45.1 and CD45.2, respectively, and transferred them at a 1 to 1 ratio into the same RAG1-deficient mice. Four weeks after the transfer, we retrieved T cells (TCR+, CD4+) in the MLNs, sorted based on CD45.1 and CD45.2 markers, and performed RNAseq analyses.

first: Jun

last: Huh


title: ATAC-seq of hematopoietic stem cells in bone marrow after 5-FU administration

first: Terumasa

last: Umemoto

summary: Purpose: The goals of this study are to elucidate the underlying mechanism for the regulation of HSC divisions.  Methods: Before or after wild type (WT) mice were treated with 5-fluorouracil (5-FU), 15000 cells of HSCs were sorted. These cells were subjected to ATAC-seq using Next-seq. The sequence reads that passed quality filters were analyzed by FASTX-toolkit.

overall_design: After 6 or 10 days from 5-FU administration, HSCs (CD150+ CD48- EPCR+ Lineage-) were sorted were sorted, and subsequently ATAC peaks were generated by deep sequencing using Next-seq.


title: mRNA profiles of hematopoietic stem or progenitor cells in bone marrow after 5-FU administration

summary:
Purpose: The goals of this study are to elucidate the underlying mechanism for the regulation of HSC divisions.
Methods: Before or after wild type (WT) mice were treated with 5-fluorouracil (5-FU), 100 cells of HSCs were sorted. Moreover, after HSCs were cultured for 1day, 100 cells of phenotypic HSCs were sorted. These cells were subjected to mRNA sequence using Next-seq. The sequence reads that passed quality filters were analyzed by CLC genomic workbench.

overall_design: After 6 or 10 days from 5-FU administration, HSCs (CD150+ CD48- EPCR+ Lineage-) or HPCs (CD150+ CD48+ EPCR+ Lineage-)  were sorted were sorted, and subsequently mRNA profiles were generated by deep sequencing using Next-seq.  After culturing HSCs (CD150+ CD48- EPCR+ Lineage-) derived from untreated mice for 1 day, mRNA profiles were generated by deep sequencing using Next-seq .


title: Hematopoietic stem cells in bone marrow after 5-FU administration


title: A nuclear function for an oncogenic microRNA as a modulator of snRNA and splicing [RNA-Seq]

first: Yanhong

last: Zhang

overall_design: Alternative splicing changes in treatments of GBM4 cells with miR-10b inhibitor (using miR-10b ASO for inhibition) or U6 inhibitor (using U6 ASO for inhibition) and their corresponding control.


title: Training-associated alterations in equine respiratory immunity using RNAseq

city: Edinburgh

first: Anna Eleonora

last: Karagianni

address: Easter Bush Campus

department: Veterinary Clinical Sciences

institute: The Roslin Institute and the Royal Dick School of Veterinary Studies

summary: Neutrophilic airway inflammation is highly prevalent in racehorses in training, with the term mild to moderate equine asthma (MMEA) being applied to the majority of such cases. The current study is largely derived from the strong association between MMEA in racehorses and their entry into a race training program; this has led to our primary aim of measuring the effect of race training on pulmonary immune cell function. The objectives of this study are to characterise the effect of training on the local pulmonary immune system and quantify the magnitude of effect by defining the gene expression of tracheal wash (TW) derived cells from Thoroughbred racehorses prior to (T0) and following commencement of race training (T1).   This study demonstrated TW samples to represent a rich source of airway cells and RNA to study airway immunity in the horse and highlighted the benefits of advanced-omic methodological approach to studying the dynamics of equine airway immunity. Intense training induced quantifiable alterations in both gene expression of airway derived cells consistent with deregulation of airway immunity and haemopoietic abnormalities. Respectively, these findings likely reflect the known associations between race training and both airway inflammation and bleeding, in particular offering further insight into the potential mechanisms which underpin training associated airway inflammation.

overall_design: Tracheal wash (TW) samples were obtained at both time points (T0, T1) from the same Thoroughbred horses (n=16).  Gene expression of TW derived cells was determined by RNAseq and analysed by DEseq2

first: Anna

first: Eugenio

last: Cillán-Garcia

first: Thomas

last: Wishart

first: R

last: Pirie


title: Potent, p53-independent induction of NOXA sensitizes MLL-rearranged B-cell acute lymphoblastic leukemia cells to venetoclax [ATAC-Seq]

city: Warsaw

first: Malgorzata

last: Firczuk

state: masovian

address: Nielubowicza 5 Street

country: Poland

institute: Medical University of Warsaw

summary: The prognosis for B cell precursor acute lymphoblastic leukemia patients with Mixed-Lineage Leukemia (MLL) gene rearrangements (MLLr BCP-ALL) is still extremely poor. Inhibition of anti-apoptotic protein BCL-2 with venetoclax emerged as a promising strategy for this subtype of BCP-ALL, however lack of sufficient responses in pre-clinical models and possibility of developing resistance exclude using venetoclax as monotherapy. Herein, we aimed to uncover potential mechanisms responsible for limited venetoclax activity in MLLr BCP-ALL and to identify drugs that could be used in combination therapy. Using RNA-seq, we observed that long-term exposure to venetoclax in vivo in patient derived xenograft model leads to downregulation of particular p53-related genes. Interestingly, addition of auranofin, a thioredoxin system inhibitor, sensitized MLLr BCP-ALL to venetoclax in various in vitro and in vivo models, independently on the p53 pathway functionality. Synergistic activity of these drugs resulted from auranofin-mediated upregulation of NOXA pro-apoptotic protein and potent induction of apoptotic cell death. More specifically, we observed that auranofin orchestrates upregulation of NOXA-encoding gene (PMAIP1) by chromatin remodeling and increased transcriptional accessibility. Altogether, these results present novel, promising drug combination that could be exploited for the treatment of MLLr BCP-ALL patients, including those with TP53 mutations.

overall_design: ATAC-seq

first: Nicholas

last: Crump

first: Klaudyna

last: Fidyt

last: Milne


title: Potent, p53-independent induction of NOXA sensitizes MLL-rearranged B-cell acute lymphoblastic leukemia cells to venetoclax [RNA-Seq]

overall_design: RNA-seq in MLL-AF4+ patient derived xenograft ALL cells isolated from control (n=3) and venetoclax-treated (n=3) NSG mice

first: Joe

last: Harman

first: Joanna

last: Madzio

first: Agata

last: Pastorczak


title: Potent, p53-independent induction of NOXA sensitizes MLL-rearranged B-cell acute lymphoblastic leukemia cells to venetoclax


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Ptprz1-/- lung microvascular endothelial cell (LMVEC) Transcriptomes

city: Patras

first: Evangelia

last: Papadimitriou

state: Achaia

address: Panepistimioupoli

department: Dept of Pharmacy

country: Greece

institute: University of Patras

summary:
Purpose: To compare NGS-derived  transcriptome profiling (RNA-seq) between Wild Type and Ptprz1-/- LMVEC and identify transcripts that may be linked to the phenotypic differences observed.
Methods: Total RNA from freshly cultured LMVEC was extracted using the NucleoSpin RNA Plus kit from Macherey-Nagel and the concentration and purity was assessed by Nanodrop and gel agarose 1% in TBE 0.5x. RNA from 3 independent fresh cell isolations from the Ptprz1+/+ and the Ptprz1-/- LMVEC was extracted and sent for RNAseq analysis. Novogene Co., Ltd performed the mRNA isolation, cDNA library synthesis and sequencing, and the bioinformatics analysis. Results: Pairwise comparison of gene expression of Ptprz1-/- RNA (3 samples) against Ptprz1+/+ RNA (3 samples) identified several transcripts as differentially expressed. Twenty-six genes were significantly changed (adj. p value <0.05), with 9 being upregulated and 17 downregulated. These genes are linked to angiogenesis and heart development and function. Conclusions: Our study represents the first transcriptomic analysis of Ptprz1-/- endothelial cells compared to the corresponding wild-type cells, generated by RNA-seq technology.

overall_design: mRNA profiles of LMVEC isolated from wild type (WT) and Ptprz1-/- (KO) mice

first: Pinelopi

last: Kastana

first: Constantinos

last: Mikelis


city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

department: Diagnostics

institute: Fraunhofer Institute for Cell Therapy and Immunology

summary: Differential expression analysis of human brain samples with Alzheimer disease versus healthy control samples using an Agilent custom expression microarray.

overall_design: Brain tissue of 19 AD patients and 21 healthy controls dying without any history of neurological or psychiatric illness was used. The diagnosis of AD was made on the basis of both clinical and neuropathological evidence according to the criteria of the International Working Group (IWG) for New Research Criteria for the diagnosis of AD in the revision of 2014 (IWG-2), the NIA-AA diagnostic criteria in the revision of 201117 and the NIA-AA guidelines for the neuropathological assessment of AD. Only cases with typical AD according to IWG-2 criteria were included. All cases underwent neuropsychological assessment within the last 6 months prior to their death.  Note, 4 arrays (2 AD, 2 control) were excluded from further processing due to quality issues of arrays.

first: Christian

last: Arnold

first: Jörg

last: Hackermüller

first: Friedemann

last: Horn

first: Peter

middle: F

last: Stadler

first: Uwe

last: Ueberham


title: Homo sapiens whole genome expression microarray of peripheral blood monocytes obtained from Control Smokers, Control Never Smokers, COPD Smokers and COPD ExSmokers.

city: New delhi

first: Anjana

last: Talwar

state: Delhi

address: Ansari Nagar

department: Physiology

country: India

institute: All India Institute of Medical Sciences

summary:
Differential profiles from whole genome human expression arrays on monocytes obtained from peripheral blood in COPD was studied and compared with controls. Monocytes were isolated from Controls (Group 1) which included Control Smokers (Group 1A) and Control Never Smokers (Group 1B) and COPD (Group 2) which included COPD Smokers (Group 2A) and COPD ExSmokers (Group 2B).
Differential transcriptomic expression associated with (i) Smoking, (ii) COPD, and (iii) cessation of smoking were identified.

overall_design: Whole genome expression arrays of peripheral blood monocytes using total RNA obtained from Control Smokers, Control Never Smokers, COPD Smokers and COPD ExSmokers.

first: A

last: Trivedi