title: 14-3-3 epsilon is an intracellular component of TNFR2 receptor complex and its activation protects against osteoarthritis

city: NEW YORK

first: WENHUO

last: HU

email: huwenhuo@gmail.com, huw@mskcc.org

state: NEW YORK

address: 1275 YORK AVENUE

department: HOPP

institute: MEMORIAL SLOAN KETTERING CANCER CENTER

summary: In an effort to identify novel differentially-expressed genes in OA, we performed RNA-seq analysis using cartilage isolated from nonarthritic and OA patients. Total RNA was isolated from 3 samples of nonarthritic cartilage and 4 samples of OA cartilage (Kellgren-Lawrence Grade 3 or 4). Genes (900 total, 600 up-regulated, 300 down-regulated) were differentially expressed in OA vs. normal (fold change > 2, FDR < 0.00001, adjusted p < 0.05). Gene set enrichment analysis (GSEA) indicated altered gene expression pattern in OA cartilage compared with nonarthritic cartilage. Specifically, pathways known to be implicated in OA pathogenesis, including inflammatory response, interferon alpha and gamma response, apoptosis, and oxidative phosphorylation, were up-regulated in OA cartilage compared with nonarthritic cartilage.

overall_design: mRNA frofiles of cartilage isolated from nonarthritic and OA patients

first: Wenyu

last: Fu

first: Aubryanna

last: Hettinghouse

first: Wenhuo

last: Hu

first: Chuan-ju

last: Liu


title: Long RNA in endothelial cells treated with GW4869

status: Public on Mar 10 2022

city: New Orleans

first: Tina

middle: M

last: O'Grady

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

country: USA

institute: Tulane Health Sciences Center

type: Expression profiling by high throughput sequencing

summary: RNA was harvested from endothelial cells treated with GW4869, an inhibitor of extracellular vesicle biogenesis

overall_design: 3 replicates each of HUVECs treated with GW4869 or DMSO

first: Makon-Sébastien

last: Njock

first: Ingrid

last: Struman

first: Franck

last: Dequiedt


title: Single-cell mRNA sequencing of embryonic and extra-embryonic mesoderm  and extra-embryonic structures in mouse embryo during gastrulation.

city: Brussels

first: Wallis

last: Migeotte

address: route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

summary: We performed scRNAseq on embryonic and extra-embryonic mesoderm cells from mouse embryo at Mid/Late Streak stage (Embryonic day 7.25) as well as on Late Bud stage (Embryonic day 7.75) microdissected amnion, chorion and allantois. We used transgenic embryos (Brachyury-Cre; mTmG) in which all mesoderm cells are converted to membrane-GFP upon Cre-mediated recombination and the rest express membrane Tomato. For all the samples, we identified clusters related to the localization in the tissue or the structures. Those results provide an atlas of early stages of morphogenesis of the maternal-fetal interface.

overall_design: Cells enriched from embryonic mesoderm, extra-embryonic mesoderm, amnion, chorion and allantois from mouse Tcre-mTmG embryos. One replicate for each, except amnion, which has two replicates.

first: Isabelle

last: Nahaboo


title: Systems genetics of single nucleotide substitutions at the Drosophila Obp56h locus

city: Greenwood

first: Heather

last: Flanagan-Steet

state: SC

address: 101 Gregor Mendel circle

institute: Greenwood Genetic Center

summary: Individual variation in complex traits results from allelic variants of multiple segregating genes, which are expressed as coregulated ensembles that are modulated by the environment. Coregulated transcriptional networks around focal genes, defined as their ‘transcriptional niches’, are sensitive to genetic and environmental perturbations. Understanding how single base pair substitutions affect this complex genotype-phenotype relationship by perturbing transcriptional niches is possible in Drosophila, which allows precise control of both the genetic background and the environment. We used a two-step CRISPR-Cas9 mediated gene deletion and reinsertion strategy to generate in a common genetic background five single nucleotide substitutions in the D. melanogaster Obp56h gene that correspond to naturally occurring allelic variants. Changes in single base pairs give rise to differential, sexually dimorphic effects on a plethora of fitness traits, including viability, sex ratio, feeding behavior, starvation resistance, recovery from a chill-induced coma, response to heat shock, activity, and sleep traits. These pleiotropic effects are accompanied by sexually dimorphic shifts in the transcriptional niche of Obp56h. Pairwise comparisons between the lines show common coregulated genes along with varying numbers of transcripts unique to one or few Obp56h alleles. Gene ontology enrichment analyses indicate that fundamental cellular processes for each sex underlie the phenotypic pleiotropy revealed by the Obp56h allelic series. Furthermore, different Obp56h alleles in a common genetic background give rise to allele-specific, sexually dimorphic microenvironmental variation. The reverse genetic engineering strategy, illustrated here, can be generally applied to other genes to dissect variation in the genotype-phenotype relationship at single base pair resolution.

overall_design: RNA seq profiles (post rRNA depletion) of heads of CSB, Obp56h knockout and 5 allelic variants in both sexes.

first: Sneha

last: Mokashi

first: Vijay

last: Shankar

first: Joel

last: Johnstun

first: Trudy

middle: C

last: Mackay

first: Robert

middle: H

last: Anholt


title: DeepLoop enables robust mapping of DNA loops from low-depth single cell or allele-resolved Hi-C data at high resolution

status: Public on Mar 14 2022

city: Cleveland

first: Shanshan

last: Zhang

state: OH

address: 10900 Euclid Avenue

department: Department of Genome and Genetics

institute: Case Western Reserve University

type:
Other
Third-party reanalysis

summary: High-resolution mapping of the gene regulatory chromatin interactions from noisy Hi-C contact heatmaps remains a major challenge in 3D genome research due to the complex bias structure and severe data sparsity. Here we present DeepLoop, which addresses this problem by combining a rigorous bias correction strategy (HiCorr) and deep learning-based signal enhancement techniques. We demonstrated that DeepLoop can robustly identify high-resolution chromatin interactions from low-depth and single cell Hi-C data. With DeepLoop, we for the first-time mapped the genetic and epigenetic determinants of human homolog-specific chromatin loops in GM12878 cells at 5kb-resolution. We nominated two new imprinting loci with unbalanced DNA folding in additional to the well-known H19/IGF2 locus. Interestingly, we also found that the sub-TAD loops at the DXZ4 “megadomain” boundary escapes X-inactivation, but the loops at the FIRRE “superloop” locus do not escape. Unexpectedly, DeepLoop detected four previously unknown Mb-sized heterozygous structure variants in the GM12878 genome, including two large inversions causing allele-specific gene expression via enhancer rewiring. Finally, DeepLoop also pinpointed dozens of loop regulatory SNPs that often have transcriptional consequences. Taken together, DeepLoop expands the use of Hi-C to provide genome-wide insights into the genetics of 3D genome at loop resolution.

sample_organism:
Homo sapiens
Mus musculus

overall_design: DeepLoop robustly identify high-resolution chromatin loops regardless of noise and depth. Each text file (300K) contains a chromatin loop calling list from Hi-C data for one cell type.

first: Dylan

last: Plummer

first: Leina

last: Lu

first: Jian

last: Cui

first: Fulai

last: Jin

first: Jing

last: Li


title: Tn-seq of desiccated Acinetobacter baumannii

status: Public on Mar 09 2022

city: Nashville

first: Erin

middle: R

last: Green

state: TN

address: 1161 21st Ave South

department: Pathology, Microbiology, and Immunology

institute: Vanderbilt University Medical Center

summary: A major reservoir for spread of the emerging pathogen Acinetobacter baumannii is hopsital surfaces, where bacteria persist in a desiccated state. To identify gene products influencing desiccation survival, a transposon sequencing (Tn-seq) screen was performed. Using this approach, we identified genes both positively and negatively impacting the desiccation tolerance of A. baumannii.

overall_design: A transposon library containing 90,000 insertions in A. baumannii was desiccated for 2 days or 14 days and the frequency of insertion mutants following desiccation was then compared to control input libraries to identify genes either promoting or inhibiting desiccation tolerance.

first: Joseph

middle: N

last: Fakhoury

first: Andrew

middle: J

last: Monteith

first: Hualiang

last: Pi

first: David

middle: P

last: Giedroc

first: Eric

last: Skaar


title: Novel miRNAs of Podophyllum hexandrum

city: Kolkata

first: Sharmila

last: Chattopadhyay

state: West Bengal

address: 4, Raja S.C. Mullick Road,

country: India

institute: CSIR-Indian Institute of Chemical Biology, Kolkata

type: Non-coding RNA profiling by high throughput sequencing

summary: Novel miRNAs of P.hexandrum

overall_design: small RNAs were sequenced and analysed to identify the novel miRNAs


title: Long RNA in endothelial cells and EVs cultured alone or with tumor cells

first: Tina

last: O'Grady

summary: RNA was harvested from endothelial cells cultured alone or with tumor cells and the associated endothelial extracellular vesicles.

overall_design: 3-4 replicates each of HUVECs cocultured with tumor cells and their EVs, HUVECs cultured alone and their EVs

first: Makon-Sébastien

last: Njock

first: Ingrid

last: Struman

first: Franck

last: Dequiedt


title: Identification of stress responsive miRNAs in Arabidopsis under altered GSH condition

summary: Identification of miRNAs in GSH mediated plant defense.


title: NanoSTRING nCounter Human tumor Signaling 360 Panel for xenograft tumor tissue

city: Seoul

first: Dong Young

last: Kim

address: 75 Nowon-ro

country: South Korea

institute: KIRAMS

summary: Whether Wnt signaling-targeted genes and co-receptors were downregulated in STP1002 (TNKSi)-treated tumor tissues,

overall_design: Three mice were randomly selected from eight mice in each group. Control 3 mice, STP1002 5 mpk 3 mice, STP1002 10 mpk 3 mice

first: Jae-Sung

first: Dong

middle: Y


title: Pre-clinical validation of an RNA-based precision oncology platform for patient-therapy alignment in a diverse set of human malignancies resistant to standard treatments

city: New York

first: Prabhjot

middle: Singh

last: Mundi

state: NY

address: 1130 St. Nicholas Avenue

summary:
We use a Master Regular-based precision cancer medicine framework to perform joint analysis of transcriptomic profiles from patients with distinct treatment refractory cancer and drug perturbation transcriptional profiles in cognate cell lines, to predict drug sensitivity.
Validation of predictions was performed in patient-derived xenograft (PDX) mice. Pharmacodynamic samples were obtained from PDX mice after the third dose for RNASeq and downstream analysis.

overall_design: RNASeq profiles of patient tumors and their respective xenografts for which drugs were predicted using the PCM tools OncoTarget and OncoTreat; RNASeq profiles of cognate cell line models; drug perturbational (DMSO controls and post-perturbation) profiles in these cell lines; RNASeq of on-treatment pharmacodynamic PDX samples; RNAseq profiles of 103 meningioma patient tumors sequenced at Columbia University Irving Medical Center and used to derive a meningioma gene regulatory network (interactome).

middle: S

first: Mariano

last: Alvarez

first: Andrea

last: Califano


title: Genome-wide association studies identify novel genetic loci for epigenetic age acceleration among survivors of childhood cancer [Metadata_SJLIFE_controls_282]

city: Memphis

first: Zhaoming

last: Wang

address: 262 Danny Thomas Place

department: Epidemiology & Cancer Control

institute: St. Jude Children's Research Hospital

type: Methylation profiling by genome tiling array

summary: Background: Increased epigenetic age acceleration (EAA) in survivors of childhood cancer is associated with specific treatment exposures, unfavorable health behaviors, and presence of certain chronic health conditions. To better understand inter-individual variability, we investigated the genetic basis underlying EAA.  Methods: Genome-wide association studies of EAA based on multiple epigenetic clocks (Hannum, Horvath, PhenoAge, and GrimAge) were performed. MethylationEPIC BeadChip array and whole-genome sequencing data were generated with blood-derived DNA from participants in the St. Jude Lifetime Cohort Study (discovery: 2,138 pre-existing and 502 newly generated data, all survivors; exploratory: 282 community controls). Linear regression models were fit for each epigenetic age against allelic dose of each genetic variant, adjusting for age at sampling, sex, and cancer treatment exposures. Fixed-effects meta-analysis was used to combine summary statistics from two discovery data sets. LD (Linkage disequilibrium) score regression was used to estimate single-nucleotide polymorphism (SNP)-based heritability.  Results:  For EAA-Horvath, a genome-wide significant association was mapped to SELP gene with the strongest SNP rs732314 (meta-GWAS: β=0.57, P=3.30×10-11). Moreover, the stratified analysis of the association between rs732314 and EAA-Horvath showed substantial heterogeneity between children and adults (meta-GWAS: β=0.97 vs. 0.51, I2=73.1%) as well as between survivors with and without chest/abdominal/pelvic-RT exposure (β=0.64 vs. 0.31, I2=66.3%). For EAA-Hannum, an association was mapped to HLA locus with the strongest SNP rs28366133 (meta-GWAS: β=0.78, P=3.78×10-11). There was no genome-wide significant hit for EAA-PhenoAge or EAA-GrimAge. Interestingly, among community controls, rs732314 was associated with EAA-Horvath (β=1.09, P=5.43×10-5), whereas rs28366133 was not associated with EAA-Hannum (β=0.21, P=0.49). The estimated heritability was 0.33 (SE=0.20) for EAA-Horvath and 0.17 (SE=0.23) for EAA-Hannum, but close to zero for EAA-PhenoAge and EAA-GrimAge.  Conclusions: We identified novel genetic variants in SELP gene and HLA region associated with EAA-Horvath and EAA-Hannum, respectively, among survivors of childhood cancer. The new genetic variants in combination with other replicated known variants can facilitate identification of survivors at higher risk in developing accelerated aging, and potentially inform drug targets for future intervention strategies among vulnerable survivors.

overall_design: We included (1) SJLIFE1: 2,138 survivors (median age at DNA sampling 31.8 years); (2) SJLIFE2: 502 survivors (median age at DNA sampling 16.5 years); (3) SJLIFE_controls: 282 non-cancer controls (median age at DNA sampling 35.0 years of European ancestry from the St. Jude Lifetime Cohort Study, a retrospective hospital-based study with prospective clinical follow-up. Cumulative doses of chemotherapy and region-specific radiation were abstracted from medical records. DNAm profile was measured using MethylationEPIC BeadChip with blood-derived DNA.

first: Qian

last: Dong

last: Song

last: Qin

first: Cheng

last: Chen

first: Zhenghong

first: Xiaojun

last: Sun

first: John

last: Easton

first: Heather

last: Mulder

first: Emily

last: Plyler

first: Geoffrey

last: Neale

last: Walker

first: Xiaotu

last: Ma

first: Xiang

first: I-Chan

last: Huang

first: Yutaka

last: Yasui

first: Kirsten

middle: K

last: Ness

first: Jinghui

last: Zhang

first: Melissa

last: Hudson

first: Leslie

middle: L

last: Robison


title: Genome-wide association studies identify novel genetic loci for epigenetic age acceleration among survivors of childhood cancer [Metadata_SJLIFE2_502]

first: Zhaoming

last: Wang

last: Dong

last: Li


title: Preterm Birth Buccal Cell Epigenetic Biomarkers to Facilitate Preventative Medicine

city: Pullman

first: Michael

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

type: Methylation profiling by high throughput sequencing

summary: Preterm birth is the major cause of newborn and infant mortality affecting nearly one in every ten live births. This study was designed to develop an epigenetic biomarker for susceptibility of preterm birth using buccal cells from the mother, father, and child (triads). MeDIP-seq was used to identify differential DNA methylation regions (DMRs) using a comparison of control term birth versus preterm birth triads. Epigenetic DMR associations with preterm birth were identified for both the mother and father that were distinct and suggest potential epigenetic contributions from both parents. The mother (165 DMRs) and female child (136 DMRs) at p<1e-04 had the highest number of DMRs and were highly similar suggesting potential epigenetic inheritance of the epimutations. The male child had negligible DMR associations. The DMR associated genes for each group involve previously identified preterm birth associated genes.

overall_design: Buccal cells were collected from the mother, father, and newborn child (triads) to assess differences in methylation in each group separately. The full term (FT) birth controls had 21 triad participants and the pre-term birth (PTB) cases had 19 triad participants. DNA was isolated from the buccal cell collections and analyzed with a methylated DNA immunoprecipitation (MeDIP) procedure to obtain methylated DNA for subsequent sequencing (Seq) for an MeDIP-Seq protocol. Differential DNA methylation regions (DMRs) were identified by comparing the control and PTB case samples for each mother, father, or child triad.

first: Paul

last: Winchester

first: Eric

last: Nilsson

first: Daniel

last: Beck


title: The dynamic change of immune responses between acute and recrudescence stages of rodent malaria infection

city: Chongqing

first: taiping

last: Liu

address: Gaotanyan zhengjie 30, Shapingba district, Chongqing

country: China

institute: Department of Pathogenic Biology, Army Medical University (Third Military Medical University)

summary: Malaria infections are persistent as frequent recrudescence of the disease may occur following the acute infection stage, but the different immune responses that control the acute and recrudescence stages are still largely unknown. Using single-cell RNA sequencing (scRNA-seq), we showed that the number of Th1 and plasma cells in the spleen was significantly reduced during the recurrence stage compared to the acute stage of Plasmodium chabaudi chabaudi AS (P. chabaudi) infection. Additionally, the ability of both CD4+ T cell responses and B cells to control P. chabaudi recurrence was significantly reduced compared to their roles in the control of acute infection. In contrast, the number of innate immune cells, including red pulp macrophages (RPMs), gamma delta (γδ) T cells, Dendritic cells (DCs), and neutrophils were significantly increased during the recurrence stage and demonstrated to be critical for P. chabaudi infection recurrence control. Thus, our data strongly suggest the complementary role of innate immune responses in controlling malaria recrudescence when adaptive immune responses are suppressed. These findings shed new light on the development of immune interventions against malaria.

overall_design: sc-RNASeq analysis of splenocytes isolated from  P. chabaudi-infected mice at Day0, Day8 and Day16 post-infection.

first: Wenyue

last: Xu

first: Taiping

first: Jian

last: Zhou


title: Whole-genome bisulfite sequencing anaysis of PSCs

city: Stanford

first: Kent

last: Imaizumi

state: CA

address: 318 Campus Drive

institute: Stanford University

summary: Human ESCs [KhES1] under feeder-free [StemFit] cultures with or without  FGF inhibitor [100 nM PD173074] were analyzed.

overall_design: 1 samples for each condition.

first: Hirosato

last: Ideno

first: Hideyki

last: Okano


title: Gene expression of matched treatment-naive versus FOLFIRINOX-treated PDAC patient-derived organoids

city: Munich

first: Hans

middle: Carlo

last: Maurer

state: Bavaria

address: Ismaninger Str. 22

department: II. Medizinische Klinik

country: Germany

institute: Klinikum rechts der Isar

summary: In our study, we aimed to investigate adaptive processes of tumors under treatment and therefore, generated PDAC patient-derived organoids (PDOs) and 2D cell lines before and after chemotherapy. We enrolled a patient with borderline resectable PDAC who received neoadjuvant FOLFIRINOX. Endoscopic fine needle (pre-FFX) and surgical biopsies (post-FFX) were used to generate PDOs and 2D cells. Whole exome sequencing (WES) and RNA sequencing data of the pre-FFX and post-FFX organoids were compared in order to evaluate the genetic landscape and PDAC subtypes. Although transcriptional subtyping classified both PDOs as classical PDAC, gene set enrichment analysis (GSEA) revealed a reduced pathway activation linked to the basal-like phenotype such as KRAS signaling in the post-FFX organoids. WES did not show major differences in the genetic landscape of the tumor pre- and post-FFX induction suggesting a plasticity process rather than a clonal selection during chemotherapy. 2D cells were subjected to an unbiased automated drug screening of 415 compounds to investigate FFX-induced vulnerabilities. Top targets such as MEK inhibitors were validated manually in the 2D cells and organoids and an increased sensitivity was observed in the post-FFX cells. Thus, integrating functional layers into personalized medicine allows to identify chemotherapy-induced vulnerabilities as potent targeted therapy options in PDAC.

overall_design: Bulk gene expression data are presented for matching treatment-naive and FOLFIRINOX-treated patient-derived organoids of pancreatic ductal adenocarcinoma.

first: Katja

last: Peschke

first: H

first: Maximilian

last: Reichert


title: Remodeling of the tumor microenvironment via blockade of LAIR-1 and TGF-β signaling [bulk RNA-seq]

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

summary: Collagens in the extracellular matrix (ECM) provide a physical barrier to tumor immune infiltration, while also acting as a ligand for immune inhibitory receptors. Transforming growth factor-β (TGF-β) is a key contributor to shaping the ECM by stimulating the production and remodeling of collagens. TGF-β-activation signatures and collagen-rich environments have both been associated with T-cell exclusion and lack of responses to immunotherapy. Here we describe the effect of targeting collagens that signal through the LAIR-1 inhibitory receptor in combination with blockade of TGF-β and programmed cell death ligand 1 (PD-L1). This approach remodeled the tumor collagenous matrix, enhanced tumor infiltration and activation of CD8+ T cells, and repolarized suppressive macrophage populations resulting in high cure rates and long-term tumor-specific protection across murine models of colon and mammary carcinoma. The results highlight the advantage of direct targeting of ECM components in combination with immune checkpoint blockade therapy.

overall_design: Bulk RNA sequencing of M2 polarized human macrophages derived in vitro from monocytes, left untreated or treated with immunotherapy agents.

first: Lucas

middle: A

last: Horn

last: Chariou

first: Sofia

last: Gameiro

first: Haiyan

last: Qin

first: Masafumi

last: Iida

first: Kristin

last: Fousek

first: Margaret

last: Cam

first: Dallas

last: Flies

first: Soloman

last: Langermann

first: Jeffrey

last: Schlom

first: Claudia

last: Palena


title: Remodeling of the tumor microenvironment via blockade of LAIR-1 and TGF-β signaling [single cell RNA-seq]

overall_design: Analysis of tumor infiltrating immune cells from control or immunotherapy treated tumor bearing mice.

first: Paul


title: Brewer’s spent dry yeast modulates immunity in gilthead sea bream (Sparus aurata)

city: Bodø

first: Ioannis

last: Konstantinidis

state: Nordland

address: Universitetsalléen 11

department: Faculty of Biosciences and Aquaculture

country: Norway

institute: Nord University

summary: We report a comparison of tissue-specific (head kidney, intestine and liver) gene expression profiles from gilthead sea bream fed with control and Brewer's spent dry yeast (SDY) diets.The inclusion of SDY at 30% in the experimental diet (40% crude protein, 16% crude lipid) resulted in a reduction in FM (10%) and PP (31.4%) contents. 218 differentially expressed genes (DEGs) were identified among all tissues, out of which, 141 were up- and 77 down-regulated. The enrichment analysis of DEGs revealed that SDY had a modulatory effect on several processes related to host’s immunity, oxygen’s carrier capacity, sexual differentiation, metabolism, and digestion. This study supports the notion that brewery’s by-products like SDY are suitable for aquafeeds of carnivorous fish species such as the gilthead sea bream, and promotes a circular bioeconomy model that reuses, recovers and recycles resources instead of producing wastes

overall_design: Gene expression analysis in head kidney, intestine and liver using RNA-seq, between gilthead sea bream group fed a control diet and an experimental Brewer's spent dry yeast (SDY) diet at 30% inclusion, replacing 10% fish meal and 31.4% plant proteins.

first: Joana

last: Firmino

first: Alberto

last: Ruiz

first: Bruno

last: Iñarra

first: David

last: San Martin

first: Alicia

last: Estévez

first: Jorge

last: Fernandes

first: Enric

last: Gisbert


title: Phenotyping of BM TpMos and Mature Ly6Chi monocytes in steady state and during sepsis

city: Singapore

first: Nicholas

last: Ang

address: 8a Biomedical Grove, Singapore 138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

summary: Circulating monocytes are crucial for tissue resident macrophage (TRM) replenishment. While a temporary loss of TRMs does not impose immediate danger to the host in sterile conditions, the niche comprising of dying macrophages in the presence of pathogenic bacteria predisposes the host to increased morbidity if these cells are not effectively replaced. Importantly, monocytes have been shown to be susceptible to cell death after executing effector functions such as phagocytosis. Hence, the demands and contribution of monocytes in pathogen clearance and macrophage differentiation is perplexing. Interestingly, we show that proliferating transitional pre-monocytes (TpMos), an immediate precursor of mature Ly6Chi monocytes (MatMos), were mobilized into the periphery in response to acute bacterial infection and sepsis. Since TpMos are absent in the circulation in the steady state, we aim to understand how TpMo recruitment into the periphery may result in differing functions from MatMos during sepsis.

overall_design: Mice were subjected to cecal ligation and punture (CLP) to induce sepsis. Age- and gender-matched sham-operated mice were included as control. BM TpMos and mature Ly6Chi monocytes were sorted 6 days post-surgery for RNA isolation.

first: Ye

last: Teh

first: Ming

last: Chooi

first: Immanuel

last: Kwok

first: Keith

last: Leong

first: Ka

last: Liong

first: Leonard

last: Tan


title: Phenotyping of macrophages derived from TpMos and Mature Ly6Chi monocytes

summary: Monocytes are integral cells of the innate immune system that play important roles in host defence and tissue repair. It is well established that monocytes are derived from the common monocyte progenitor (cMoP) in the bone marrow (BM) before giving rise to Ly6Chi mature monocytes that enter the circulation. However, our lab has discovered that BM Ly6Chi monocytes are not homogenous, and consist of two subpopulations (CXCR4hi and CXCR4lo) in both mice and humans. In particular, the CXCR4hi subset (termed transitional pre-monocyte (TpMo) population) actively proliferates in the BM and matures into the CXCR4lo subset, which represents mature Ly6Chi monocytes. Nevertheless, how this TpMo population may behave beyond their precursor role in the BM remains undefined. While TpMos have been shown to be strictly immobilized in the BM in the steady state, our preliminary data revealed the mobilization of TpMos into the circulation during sepsis. Furthermore, TpMos were found to give rise to more macrophages than mature Ly6Chi monocytes. Our data hence suggests a critical peripheral role for TpMos that may implicate the outcome of sepsis and possible potential implications in future therapies associated with monocytes. Based on our preliminary findings, we aim to have a better understanding of these monocyte subsets and how they are transcriptionally distinct when they have become macrophages. In particular, we would like to determine if TpMo-derived macrophages are less inflammatory compared to mature monocyte-derived macrophages.

overall_design: BM TpMos and Mature Ly6Chi monocytes were sorted and cultured for 7 days. TpMo-derived and Ly6Chi-derived macrophages were then harvested for RNA isolation for sequencing.


title: Zeb1-induced metabolic reprogramming of glycolysis is essential for macrophage polarization in breast cancer

city: Tian jin

first: Huimin

last: Jiang

address: weijin rode

institute: nankai

summary: Aerobic glycolysis (the Warburg effect) has been demonstrated to facilitate tumor progression by producing lactate, which has important roles as a proinflammatory and immunosuppressive mediator. However, how aerobic glycolysis is directly regulated is largely unknown. Here, we show that ectopic Zeb1 directly increases the transcriptional expression of HK2, PFKP and PKM2, which are glycolytic rate-determining enzymes, thus promoting the Warburg effect and breast cancer proliferation, migration, and chemoresistance in vitro and in vivo. In addition, Zeb1 exerts its biological effects to induce glycolytic activity in response to hypoxia via the PI3K/Akt/HIF-1α signaling axis, which contributes to fostering an immunosuppressive tumor microenvironment (TME). Mechanistically, breast cancer cells with ectopic Zeb1 expression produce lactate in the acidic tumor milieu to induce the alternatively activated macrophage M2-like phenotype through stimulation of the PKA/CREB signaling pathway. Clinically, the expression of Zeb1 is positively correlated with dysregulation of aerobic glycolysis, accumulation of M2-like tumor-associated macrophages (TAMs) and a poor prognosis in patients with breast cancer. In conclusion, these findings identify a Zeb1-dependent mechanism as a driver of breast cancer progression that acts by stimulating tumor-macrophage interplay, which could be a viable therapeutic target for the treatment of advanced human cancers.

overall_design: mRNA profiles of THP1 MΦ-Hcl and THP1 MΦ-Lactate

last: Wei

first: Shuang

last: Yang


title: Enhanced safety and efficacy of protease-regulated CAR-T cell receptors

first: Louai

last: Labanieh

address: 265 Campus Drive, Room G2105

department: Stanford Cancer Institute

summary: Regulatable CAR platforms could circumvent toxicities associated with CAR-T therapy, but existing systems have shortcomings including leakiness and attenuated activity. Here, we present SNIP-CARs, a novel protease-based platform for regulating CAR activity using an FDA-approved small molecule. Design iterations yielded CAR-T cells that manifest full functional capacity with drug and no leaky activity in the absence of drug. In numerous models, SNIP CAR-T cells were more potent than constitutive CAR-T cells and showed diminished T cell exhaustion and greater stemness. In a ROR1-based CAR lethality model, drug cessation following toxicity onset reversed toxicity, thereby credentialling the platform as a safety switch. In the same model, reduced drug dosing opened a therapeutic window that resulted in tumor eradication in the absence of toxicity. SNIP-CARs enable remote tuning of CAR activity, which provides solutions to safety and efficacy barriers currently limiting progress in using CAR T cells to treat solid tumors.

overall_design: Bulk RNA-seq of in vitro D10 constitutive vs SNIP CAR-T cells and single-cell RNA profiling of  CAR TILs.


title: Identification of long noncoding RNAs involved in clinicopathological features of papillary thyroid carcinoma complicated with Hashimoto's thyroiditis

city: Hangzhou

first: Kai-ning

last: Lu

state: Zhejiang

address: No.238 Huansha Road, Shangcheng District

institute: Hangzhou First People's Hospital

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

summary: Long noncoding RNAs (lncRNAs) have been shown to play a significant role in cancer biology. The aim of this study was to determine roles of lncRNAs in differences of clinical features related to the of papillary thyroid carcinoma (PTC) patients with or without Hashimoto's thyroiditis (HT). In the present study, we detected the differentially expressed lncRNAs in tumor tissues of PTC with or without HT by lncRNA microarrays. qRT-PCR, cell viability assay, cell cycle analysis and bioinformatics tools were used to verify and analyze the data. We found that 1031 lncRNAs and 1338 mRNAs were abnormally expressed in 10 tissue samples of PTC complicated with HT compared to pure PTC. Gene Ontology and pathway analyses of the mRNAs suggested that several biological processes and pathways, especially immune system processes, were promoted in PTC complicated with HT. Twenty lncRNAs were verified in 31 PTC complicated with HT and 64 pure PTC specimens using qRT-PCR, and the results were consistent with the microarrays data. Specifically, ENST00000452578, a down-regulated lncRNA in PTC complicated with HT, was negatively correlated with tumor size. Cell viability assay revealed that ENST00000452578 could inhibit cell proliferation. Co-expression analysis revealed that PPM1H, an mRNA regulated by ENST00000452578, may play an important role in cell cycle arrest. Our results indicate that lncRNAs and mRNAs plays an important role in the different clinical characteristics of PTC patients with or without HT, which might provide new insight from the perspective of RNA into the understanding of the cancers.

overall_design: Ten samples (5 for each group) were selected for microarray analysis of lncRNAs.

first: Yu

last: Zhang

first: Jin-wang

last: Ding

first: You

last: Peng

first: Gang

last: Pan

first: Ding-cun

last: Luo


title: Hdac4 regulates proliferation of neural crest-derived osteoblasts during murine craniofacial development

city: Shanghai

first: Nayoung

last: Ha

address: 639 Zhizaoju road

institute: Shanghai People's Ninth Hospital

summary: Craniofacial development involves regulation of a compendium of transcription factors, signaling molecules and epigenetic regulators. Histone deacetylases (HDACs) are involved in the regulation of cell proliferation, differentiation and homeostasis across a wide range of tissues, such as brain, cardiovascular system, muscular system, and skeletal system. However, functional role of Hdac4 during craniofacial development is still unclear. In this study, we investigated the effects of Hdac4 knockout in craniofacial skeletal development by conditionally disrupting the Hdac4 gene in cranial neural crest cells (CNCCs) using Cre-mediated recombination. Mice deficient in Hdac4 in CNCCs-derived osteoblasts demonstrated a dramatic decrease in bone formation in frontal bone. In vitro pre-osteoblasts (MC3T3-E1 cells) lacking Hdac4 exhibited reduced proliferation activity in association with dysregulation of cell cycle-related genes. These findings suggest that Hdac4 acts partially as a regulator of craniofacial skeletal development by positively regulating proliferation of CNCCs-derived osteoblasts.

overall_design: Bulk RNA sequencing of Scramble control MC3T3 and Hdac4-knockdown MC3T3. Three biological replicates per group

first: Jian

last: Sun

first: Qian

last: Bian

first: Dandan

last: Wu

first: Xudong

last: Wang


title: Quantitative Analysis of Wild Type and Pich-KO fetal liver LSK Transcriptomes

first: Xinwei

last: Geng

address: 866 Yuhangtang Rd., Zijingang Campus, Zhejiang University, Hangzhou, China

institute: Zhejiang University School of Medicine

summary: mRNA profiles of embryonic day 14.5 wild-type (WT) and Pich-KO mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.


title: Genome-wide association studies identify novel genetic loci for epigenetic age acceleration among survivors of childhood cancer [Metadata_SJLIFE1_2138]

first: Zhaoming

last: Dong

last: Song

last: Qin

first: Cheng

last: Chen

first: Zhenghong

last: Li

first: Xiaojun

first: John

last: Easton

first: Heather

last: Mulder

first: Emily

last: Plyler

first: Geoffrey

last: Neale

last: Walker

first: Xiaotu

last: Ma

first: Xiang

first: I-Chan

last: Huang

first: Yutaka

last: Yasui

first: Kirsten

last: Ness

first: Jinghui

first: Melissa

last: Hudson

first: Leslie

last: Robison


title: Transcriptional changes underlying progression from islet autoantibody positivity to type 1 diabetes

city: Parkville

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: Type 1 diabetes (T1D) usually has a preclinical phase identified by the presence of circulating autoantibodies to pancreatic islet antigens, and most young children who have multiple autoantibodies progress to diabetes within 10 years. While autoantibodies denote underlying islet autoimmunity, how this process is initiated and then progresses to clinical diabetes on a background of genetic susceptibility is not clearly understood. We analysed gene expression by RNA-seq in four types of immune cells from five genetically at-risk children with islet autoantibodies who progressed to diabetes in ≤ 3 years (‘progressors’) and in five at-risk children matched for sex, age and HLA who had not progressed to diabetes (‘non-progressors’).

overall_design:
RNA-seq analysis was performed for CD4+ T cells, CD8+ T cells, NK cells and B cells in a screening cohort of 10 genetically at-risk children. All children had autoantibodies to two or more islet antigens, five of whom progressed to clinical T1D within 36 months. Sampling was performed 36 months before and at diabetes onset in the progressors. Progressors and non-progressors were matched for age, sex and HLA genotype. The data for the CD4+ Tcells was generated separately to all other cell types, and that there are multiple sequencing runs within each data set. Autoantibodies measured were as follows:  insulin autoantibodies (IAA), glutamic acid decarboxylase 65 autoantibodies (GADA),  tyrosine phosphatase-like insulinoma antigen autoantibodies (IA2A) and transporter 8 (COOH R/W dimer) (ZnT8A) autoantibodies. Positive cut-offs  for these antibodies were defined as IAA ≥ 0.7 mU/L, GADA > 5.0 U/mL, IA2A > 3.0 U/mL and ZnT8A ≥ 3.1U/mL, respectively.

Note: This deposition provides genewise read counts, from which our analyses can be reproduced, but the raw sequence data files cannot be made publicly available because of privacy issues with human samples. The raw sequence data will be made available for appropriate research projects upon application to the WEHI Data Access Committee (dataaccess@wehi.edu.au).

first: Alexandra

last: Garnham

first: Naiara

middle: G

last: Bediaga

first: Leonard

last: Harrison


title: Genome-wide association studies identify novel genetic loci for epigenetic age acceleration among survivors of childhood cancer

first: Zhaoming

last: Wang

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

overall_design: Refer to individual Series


title: H3K27me3 and H3K4me3 ChIP-seq on DMSO or MAK683 treated cancer cell

first: Wei

last: Qi

state: Shanghai

address: B514, L Building

department: School of Life Science and Technology

institute: ShanghaiTech University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The methyltransferase Polycomb Repressive Complex 2 (PRC2), composed of EZH2, SUZ12, and EED subunits, is associated with transcriptional repression via tri-methylation of histone H3 on lysine 27 residue (H3K27me3). PRC2 is a validated drug target, as the EZH2 gain-of-function mutations identified in patient samples drive tumorigenesis. PRC2 inhibitors have been discovered and demonstrated anti-cancer efficacy in clinic. However, their pharmacological mechanisms are poorly understood. MAK683 is a potent EED inhibitor in clinical development. The overall goal of our study is to understand the molecular events leading to tumor regression after PRC2 inhibition. Our study revealed that multiple senescence-associated secretory phenotype (SASP) genes, such as Gata4, Mmp2/10, Itga2 and Gbp1, are derepressed upon PRC2 inhibition and contribute to decreased Ki67+, ECM reorganization, inflammation and tumor regression even in Cdkn2a/p16 knockout tumor.

overall_design: We performed RNA-seq, ATAC-seq, whole genome bisulfide sequencing (WGBS) and H3K27me3 and H3K4me3 ChIP-seq with spike-in on MAK683-sensitive cancer cells G401 treated with DMSO or PRC2 inhibitor MAK683 at 3  μM. Two other MAK683-sensitive cells G402 and A2780 were also included in the cellular RNA-seq study. To reveal the p16-independent transcriptome change, we also constructed p16 KO G401 cell clone, build G401 and p16 KO cell-derived xenograft models in mice, and obtained the expression profiles of G401-derived xenograft tissues (WT or p16 knock out) after treatment with vehicle or 100 mg/kg MAK683 for 46 days.

first: Liping

last: Chu

first: Yuxiu

last: Qu

first: Yang

last: An


title: Genome-wide chromatin accessibility change after PRC2 inhibition by MAK683 treatment


title: Activation of p63 initiates quality control programs in oocytes

city: Greifswald

first: Stefan

last: Simm

address: Walter-Rathenau-Straße 48

institute: University Medicine Greifswald

summary: Specialized surveillance mechanisms are essential to maintain the genetic integrity of germ cells, which are not only the source of all somatic cells but also of the germ cells of the next generation. DNA damage and chromosomal aberrations are, therefore,

overall_design: For differential expression analysis RNA-Seq experiments of mouse were used containing five different points of time (0h, 1h, 2h30min., 4h, 6h) after irradiation wth 0.5 and 0.2 Gy respectively. 30bp single-end reads of RNA-Seq samples on illumina HiSeq.

first: Niclas

last: Fester

first: Elisabeth

last: Zielonka

first: Laura

last: Luh

first: Jakob

last: Goldmann

first: Christian

last: Osterburg

first: Ann-Sophie

last: Frombach

first: Gregor

last: Deutsch

first: Marcel

last: Tuppi

first: Uta

last: Müller-Kuller

first: Enrico

last: Schleiff

first: Bernd

last: Klaus

first: Krishnaraj

last: Rajalingam

first: Huiqing

last: Zhou

first: Volker

last: Dötsch


title: Chromatin accessibility changes underlying progression from islet autoantibody positivity to type 1 diabetes

first: Gordon

last: Smyth

summary: Type 1 diabetes (T1D) usually has a preclinical phase identified by the presence of circulating autoantibodies to pancreatic islet antigens, and most young children who have multiple autoantibodies progress to diabetes within 10 years. While autoantibodies denote underlying islet autoimmunity, how this process is initiated and then progresses to clinical diabetes on a background of genetic susceptibility is not clearly understood. Only one study has thus far reported changes in gene expression in isolated immune cells associated with progression to islet autoimmunity. We analysed chromatin accessibility by ATAC-seq in CD4+ T cells in four genetically at-risk children with islet autoantibodies who progressed to diabetes in ≤ 3 years (‘progressors’), compared to five at-risk children matched for sex, age and HLA who had not progressed (‘non-progressors). From ATAC-seq data, we generated the first map of chromatin accessibility in T cells of islet autoantibody-positive children. Progression was associated with a subtle reconfiguration of regulatory chromatin regions, and some of the chromatin conformation changes could be linked to progression associated expression changes at cytotoxic genes.

overall_design:
ATAC-seq analysis was performed on CD4+ T cells sorted from PBMC samples of 9 genetically at-risk children with autoantibodies to two or more islet antigens, four of whom progressed to T1D. Autoantibodies measured were as follows:  insulin autoantibodies (IAA), glutamic acid decarboxylase 65 autoantibodies (GADA),  tyrosine phosphatase-like insulinoma antigen autoantibodies (IA2A) and transporter 8 (COOH R/W dimer) (ZnT8A) autoantibodies. Positive cut-offs  for these antibodies were defined as IAA ≥ 0.7 mU/L, GADA > 5.0 U/mL, IA2A > 3.0 U/mL and ZnT8A ≥ 3.1U/mL, respectively.

Note: This deposition provides read counts for each peak in each sample, from which our analyses can be reproduced, but the raw sequence data files cannot be made publicly available because of privacy issues with human samples. The raw sequence data will be made available for appropriate research projects upon application to the WEHI Data Access Committee (dataaccess@wehi.edu.au).

first: Naiara

last: Bediaga

first: Alexandra

last: Garnham

first: Leonard

last: Harrison


title: Transcriptional and chromatin accessibility changes underlying progression from islet autoantibody positivity to type 1 diabetes


title: RNA-seq on DMSO or MAK683 treated cancer cells and xenograft tumor samples

first: Wei

last: Qi

first: Liping

last: Chu

first: Yuxiu

last: Qu

first: Yang

last: An


title: RBBP4 modulates gene activity through acetylation and methylation of histone H3 lysine 27

city: Chapel Hill

first: Weipeng

last: Mu

state: MA

address: 120 Mason Farm Road

department: Genetics

institute: UNC at Chapel Hill


title: Melatonin signaling pathways implicated in metabolic processes in human granulosa cells (KGN)

city: Québec

first: Asma

last: Arjoune

state: Québec

address: 3326,rue de la monnerie, Appertement 1

department: Animal sciences

country: Canada

institute: Laval University

summary: Female reproduction depends on the metabolic status especially during the period of folliculogenesis. Even though it is believed that melatonin can improve oocyte competence, there is still limited knowledge of how it can modulate metabolic processes during folliculogenesis, and of which signaling pathways are involved in regulating gene expression. To investigate the effects of melatonin on metabolic signals during the antral stage of follicular development, human granulosa-like tumour cells (KGN) were treated with melatonin or forskolin and gene expression was analyzed with RNA seq technology. Following appropriate normalization and the application of a fold change cut-off of 1.5 (FC 1.5, P ≤ 0.05), 1,009 and 922 genes were identified as differentially expressed in response to melatonin and forskolin, respectively. Analysis of major upstream regulators suggested that melatonin may activate PKB/mTOR signaling pathways to program the metabolism of KGN cells to support slower growth and differentiation and to prevent follicular atresia. Similarly, PKA activation through stimulation of cAMP synthesis with FSK seemed to exert the same effects as melatonin in reducing follicular growth and regulating differentiation. This study suggests that it is possible that melatonin acts through PKA and PKB simultaneously in human granulosa cells to prevent follicular atresia and early luteinisation at the antral stage.

overall_design: Granulosa cells treated with melatonin or FSK to activate signaling pathways with gene functional analysis. RNA was pooled from four replicates per sample condition.

first: A

first: M

last: Sirard


title: PRC2


title: Continuous ZnO nanoparticle exposure induces melanoma-like skin lesions in epidermal barrier dysfunction model mice through anti-apoptotic effects mediated by the oxidative stress–activated NF-κB pathway

city: Guangzhou

first: Ping

last: Wang

state: Guangdong

address: No. 1023-1063, Shatai South Road, Baiyun District, Guangzhou city

institute: Southern Medical University

summary: Increasing interest in the hazardous properties of zinc oxide nanoparticles (ZnO NPs), commonly used as ultraviolet filters in sunscreen, has driven efforts to study the percutaneous application of ZnO NPs to diseased skin; however, in-depth studies for epidermal barrier dysfunction remain lacking. Our epidermal barrier dysfunction model develops large gaps between keratinocytes due to keratinocyte-specific Cdc42 knockout, allowing ZnO NPs entry to the stratum basale of the epidermis, impacting melanocytes. ZnO NP application for 14 and 49 consecutive days induced melanoma-like skin lesions, dysregulated melanoma-associated gene expression, increased oxidative injury, inhibited apoptosis, and increased nuclear factor kappa B (NF-κB) p65 and Bcl-2 expression in melanocytes. Exposure to 5.0 µg·mL−1 ZnO NPs for 72 h increased cell viability, decreased apoptosis, and increased Fkbp51 expression in melanocytes, consistent with histological observations. The oxidative stress–mediated mechanism underlying the induction of anti-apoptotic effects was verified using the reactive oxygen species scavenger N-acetylcysteine. The entry of ZnO NPs into the stratum basale of skin with epidermal barrier dysfunction resulted in melanoma-like skin lesions and an anti-apoptotic effect induced by oxidative stress, activating the NF-κB pathway in melanocytes. These findings suggest that ZnO NPs are potentially carcinogenic for skin with a damaged barrier function.

overall_design: Skin mRNA profiles of WT and Cdc42 KO mice in the negative control group (no ZnO NP exposure) and WT and Cdc42 KO mice continuously treated with ZnO NPs for 14 days were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Yinghua

last: Chen


title: RBBP4 modulates gene activity through acetylation and methylation of histone H3 lysine 27 [ChIP-Seq]

summary: ChIPseq analysis profiled changes in genomic landscape of H3K27me3, H3K27ac, SUZ12 , RBBP4, and HDAC1 in Rbbp4 mutant ESCs

overall_design: Two E14 ESC lines as controls, two Rbbp4 mutant, and two Rbbp7 knockout ESC lines were included for the assay.

first: Noel

last: Murcia

first: Keriayn

last: Smith

first: Debashish

middle: U

last: Menon

first: Della

last: Yee

first: Terry

last: Magnuson


title: Transcriptional response of Arabidopsis seedlings to light

city: riverside

first: Peter

last: Quail

address: 7774 Kingdom Dr

department: PMB

institute: UC Berkeley

summary: We report the transcriptomic response of Arabidopsis thaliana seedlings grown in continuous white light, darkness or darkness and 1 hour of red light

overall_design: Plants were germinated in true-dark conditions as described in (Leivar et al., 2008). Briefly, seeds were sterilized, plated in MS medium without sucrose, irradiated for 3h with white light to induce germination, followed by a saturating far-red light pulse during 5 min before being stratified for 4 days at 4ºC in darkness. They were grown in the dark at 21ºC for 2 days before being collected (D samples) or grown in the dark for 47 hours and treated with 10 μE⋅m−2⋅s−1 red light for 1 hour (R1 samples). White-light grown samples (WLc) were grown under continuous white-light (100 μE⋅m−2⋅s−1 PAR) after stratification for 2 days.

first: Eduardo

last: Gonzalez-Grandio

first: Zhang

last: Yu

first: Quail

last: Peter


title: Remodeling of the tumor microenvironment via blockade of LAIR-1 and TGF-β signaling

first: Thomas

last: Meyer

platform_organism:
Homo sapiens
Mus musculus


title: miRNA sequencing in liver of rats exposed to glyphosate, MON 52276, and a mixture of pesticides

city: London

first: Robin

last: Mesnage

address: Guy's Hospital, 8th Floor, Tower Wing

country: United Kingdom

institute: Kings College London

summary: Small RNAs have emerged as a promising new type of biomarker to monitor health status and track the development of diseases. Here we report changes in the levels of small RNAs in the liver of rats exposed to a mixture (MIX) of six pesticides frequently detected in foodstuffs (azoxystrobin, boscalid, chlorpyrifos, glyphosate, imidacloprid and thiabendazole), and glyphosate (G50) (50 mg/kg bw/day), or its representative EU commercial herbicide formulation Roundup MON 52276 (R50) at the same glyphosate equivalent doses in comparison to a control group (CON).

overall_design: The pesticides were administered to female Sprague-Dawley rats for 90 days in drinking water

first: Charles

last: Mein


title: Oncogenic lncRNAs alter epigenetic memory at a fragile chromosomal site in human cancer cells [ChIP-seq]

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

summary: Chromosome instability is a key event in cancer progression. The essential histone H3 variant CENP-A plays a fundamental role in defining centromere identity, structure, and function, but is innately overexpressed in several types of solid cancers. In the cancer background, excess CENP-A is deposited ectopically on chromosome arms, including at the 8q24/cMYC locus, by invading transcription-coupled H3.3 chaperone pathways. Intriguingly, in many cancers, transcription of lncRNAs is upregulated and correlates with poor prognosis, therapeutic resistance, and cancer recurrence in patients. Here, we report that the transcription of chromosome 8q24-derived oncogenic lncRNAs plays an unanticipated role in altering the chromatin landscape of the 8q24 locus. We report that transcription of oncogenic ncRNAs and associated R-loop formation at the 8q24 genomic locus results in the recruitment of H3.3 chaperone-CENP-A histone variant complexes to 8q24. Finally, we demonstrate that a transgene cassette which encodes a specific oncogenic lncRNA from the 8q24 region integrated into a naïve chromosome locus, recruits CENP-A to the new location specifically in a cis-acting manner. These data provide a plausible mechanistic link between locus-specific oncogenic lncRNAs, aberrant local chromatin structure, and the generation of new epigenetic memory in human cancer cells.

overall_design: ChIP-seq of human SW480 colon cancer wild cells and SW480 colon cancer cells knocked-in with PCAT2 gene array (3x) under CMV promoter in replicates. Anti-CENP-A antibody was used to ChIP the bound DNA. ChIP DNA sample was RNase I treated. ChIP samples and Inputs are in replicates.

first: Arun Kumar

last: Ganesan

first: David

last: Sturgill

first: Minh

last: Bui

first: Yamini

last: Dalal


title: Changs in Histone 3 Lysine 9 Acetylation (H3K9ac) in Arabidopsis seedlings in response to light

summary: We report the changes in H3K9ac in Arabidopsis thaliana seedlings grown in continuous white light, darkness or darkness and 1 hour of red light

overall_design: Plants were germinated in true-dark conditions as described in (Leivar et al., 2008). Briefly, seeds were sterilized, plated in MS medium without sucrose, irradiated for 3h with white light to induce germination, followed by a saturating far-red light pulse during 5 min before being stratified for 4 days at 4ºC in darkness. They were grown in the dark at 21ºC for 2 days before being collected (D samples) or grown in the dark for 47 hours and treated with 10 μE⋅m−2⋅s−1 red light for 1 hour (R1 samples). White-light grown samples (WLc) were grown under continuous white-light (100 μE⋅m−2⋅s−1 PAR) after stratification for 2 days. pif1pif3pif4pif5 (pifq) line is described in (Leivar et al., 2008).


title: Oncogenic lncRNAs alter epigenetic memory at a fragile chromosomal site in human cancer cells [RNA-seq]

overall_design: RNA-seq of human SW480 colon cancer cells and SW480 knocked-in with PCAT2 gene array (3x) under CMV promoter in replicates.


title: Oncogenic lncRNAs alter epigenetic memory at a fragile chromosomal site in human cancer cells


title: Affymetrix SNP array data for two parents and their 326 progenies and other 143 registered tea cultivars

first: Liu-Bin

last: Wang

address: 9 South Meiling road

department: Tea Research Institute

institute: Chinese Academy of Agricultural Sciences

summary: For developing the more SNPs and new high-density genetic linkage map of tea plant, two parents and their 326 progenies and 147 registered tea cultivars was sequencing by newly developed Affymetrix Axiom genotyping technology

overall_design: Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from tea plant samples.

first: Li-Yuan

first: Kang

last: Wei


title: Transcriptomic analysis of B73 and zmte1 responding to auxin.

city: Qingdao

first: Fengxia

address: Number 72, Binhai Road

institute: Shandong University School of Life Science

summary: The goal of this study is to clarify the function of ZmTE1 in auxin signal pathway and regulting cell cycle related genes. We isolated total RNA from the three nodes together with internodes of 28-day-old B73 and ZmTE1 seedlings. New genes act downstream of ZmTE1 at the nodes, are discovered.

overall_design: We isolated total RNA from three nodes together with internodes of 28-day-old B73 and zmte1 seedlings.

first: ZhaoJun

last: Ding


title: Repertoires of small RNAs in Botrytis cinerea strains isolated from tomato or grapevine.

city: Palaiseau

first: Adeline

last: SIMON

address: 22 place de l'agronomie

country: France

institute: INRAE

summary: Sets of small RNAs from strains of Botrytis cinerea isolated from tomato or grapevine were compared to determine whether some small RNAs were specific to a population. The small RNAs were mapped to the retrotransposons identified in Sl3, Vv3 or B05.10 genomes.

overall_design: Sixteen Botrytis cinerea strains, i.e., the referent strain B0510, seven strains isolated from tomato (T population), eight strains isolated from grapevine (five from G1 and three from G2 population) were grown in vitro. The small RNAs were extracted and sequenced.

last: Simon

first: Muriel

last: Viaud

first: Anne-Sophie

last: Walker


title: RBBP4 modulates gene activity through acetylation and methylation of histone H3 lysine 27 [RNA-Seq]

first: Weipeng

last: Mu

summary: RNAseq anaysis detected dramatic changes in transcriptome due to Rbbp4 disruption

overall_design: mRNA profiles of E14 embryonic stem cells as controls, and two Rbbp4 mutant cell lines. Each cell line has triplicate.

first: Noel

last: Murcia

first: Keriayn

last: Smith

first: Debashish

last: Menon

first: Della

last: Yee

first: Terry

last: Magnuson


title: Transcriptome analysis of liver from  subjects with normal glucose tolerance and steatosis<1  compared  to subjects with impaired glucose metabolism and steatosis >3

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

country: Italy

institute: European Brain Research Institute

summary: Liver transcriptome profile  in subjects with impaired glucose metabolism and steatosis >3 revealed differences compared with subjects with steatosis <1 and normal glucose tolerance. Several well-characterized markers of non-alcoholic fatty liver disease (NAFLD) were identified as differentially expressed between the two groups.

overall_design: Hepatic transcriptome from subjects with normal glucose tolerance and histological steatosis grade 0-1 (n=3) were compared with subjects with impaired glucose metabolism and steatosis grade >3 (n=3).

first: Massimo

last: Federici

first: Rossella

last: Menghini

first: Marina

last: Cardellini


title: Glomerular Transcriptome from Experimental Nephrotic Syndrome Model and Treatment with PPARgamma Agonists

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

summary: Nephropathy was induced with puromycin amino-nucleoside (PAN) in Wistar rats and treated with daily treatments of Pioglitazone (Pio) and GQ-16. Total glomerular RNA was isolated, and mRNA libraries were generated and subjected to sequencing using NovaSeq6000 SP. Injury with PAN resulted in 1089 DEGs compared to controls, and 26 of these DEGs were restored by both Pio and GQ-16 treatments, whereas 106 unique GQ-16 regulated DEGs and 17 unique Pio-regulated DEGs were identified (Fig. 4A). Overall, Pio and GQ-16 treatment resulted in 75 and 173 DEGs compared to PAN injury, which included 29 common and 190 distinct genes (Fig. 4A). Of the 29 common DEGs, 28 DEGs were down-regulated by both Pio and GQ-16 and only 1 DEG upregulated by both treatments, when compared to PAN (Fig. 4B).  Of the 190 distinct DEGs identified between Pio and GQ-16 treatments, 41 were down-regulated and 5 up-regulated by Pio and 124 down-regulated and 20 up-regulated by GQ-16 treatment.

overall_design: 4 groups each with 4 replicates sequenced over 2 lanes

first: Shipra

last: Agrawal

last: Webb

first: Claire

last: Burton


title: Analysis of RA vs 4-oxo-RA gene expression regulation in Xenopus laevis

city: New York

first: Ziyan

last: Lin

department: Applied Bioinformatics Laboratories

institute: NYU Grossman School of Medicine

summary: We analyzed anterior halves of NF stage 15 embryos that were treated with 10uM DMSO (control), or 1uM RA and 10uM 4-oxo-RA (experimental) for changes in gene expression induced by the two mophogens. RNA-sequencing revealed significant overlap in genes upregulated by both RA and 4-oxo-RA, and to a lesser extent, those downregulated by them. We report all Zic-1 targets described in accompanying manuscript to be regulated by both RA and 4-oxo-RA.

overall_design: Examination of gene expression changes induced by RA and 4-oxo-RA in anterior regions of neurulating NF stage 15 Xenopus laevis embryos

first: Aditi

last: Dubey

first: Jean-Pierre

last: Saint-Jeannet

first: Paul

last: Zappile


title: Oncogenic lncRNAs alter epigenetic memory at a fragile chromosomal site in human cancer cells [WGS]

city: Bethesda

first: Songjoon

last: Baek

overall_design: Whole Genome Sequencing of human SW480 colon cancer cells knocked-in with PCAT2 gene array (3x) under CMV promoter in replicates. gDNA was isolated with PCI method. The samples quality was assessed by BioAnalyzer.

first: Arun Kumar

last: Ganesan

first: David

last: Sturgill

first: Minh

last: Bui

first: Yamini

last: Dalal


title: Hepatocellular carcinoma Huh7: siHINT1 vs. siControl

city: KUNMING City

first: Cheng

last: Zhang

state: Yunnan Province

address: No. 374 Kunrui Road

department: Department of hepatobiliary surgery

institute: The Second Affiliated Hospital of Kunming Medical University

summary: LncRNA and mRNA expression profiling of Hepatocellular carcinoma Huh7 when HINT1 knockdown. HINT1 is a novel tumor suppressor gene, which can regulate the transcription of a variety of cancer-related genes, and its regulation networks is poorly understood in hepatocellular carcinoma. We used the total RNA from siControl and siHINT1 Huh7 cells to analyze the differentially expressed lncRNA and mRNA which were regulated by HINT1, and further explored the ceRNA network that HINT1 may involved.

overall_design: Two-condition experiment, siHINT1 vs. siControl Huh7 cells. Biological replicates: 3 siHINT1 Huh7 cells, 3 siControl Huh7 cells.

first: Yang

last: Ke

first: Xin

last: Liu

first: Xinghong

last: Wang

first: Tianhao

last: Bao

first: Lin


title: Selective Kinin Receptor B2 Antagonist Icatibant Reduces SARS-CoV-2 Replication in Primary Bronchial Epithelium Early

city: Munich

first: Ulrich

middle: M

last: Zissler

address: Biedersteiner Str. 29

department: Center of Allergy & Environment (ZAUM)

institute: Technical University of Munich & Helmholtz Center Munich

summary: We provide evidence that the licensed drug icatibant, a selective antagonist of kinin B2 receptor interfering with the kinin-kallikrein system, has protective effects on primary airway epithelial cells (NHBE) during SARS-CoV-2 infection. Icatibant suppresses gene expression broadly, thereby reducing the expression of SARS-CoV-2 entry receptor ACE2 in vitro and in a murine airway inflammation model in vivo. Icatibant further impedes SARS-CoV-2 replication in NHBE and the release of infectious particles into supernatants.

overall_design: Primary normal bronchial epithelial cells (NHBEs) were incubated with SARS-CoV-2 and Icatibant (1nM) or Hydrocortisone (10µM).

first: C

last: Jakwerth

first: M

last: Feuerherd

first: F

last: Guerth

last: Oelsner

first: L

last: Schellhammer

last: Mogler

first: B

last: Haller

first: A

last: Erb

last: Wollenberg

middle: D

last: Spinner

first: T

last: Buch

first: U

last: Protzer

middle: B

last: Schmidt-Weber

last: Chaker


title: Phospho-RNA sequencing with CircAID-p-seq

city: Trento

first: Alessia

last: Del Piano

state: Trento

address: Via Sommarive 18

institute: IMMAGINA BioTECHNOLOGY

summary: Accurate positional information concerning ribosomes and RNA binding proteins with respect to their transcripts is important to understand the global regulatory network underlying protein and RNA fate in living cells. Most footprinting approaches generate RNA fragments bearing a phosphate or cyclic phosphate groups at their 3′ end. Unfortunately, all current protocols for library preparation rely only on the presence of a 3′ hydroxyl group. Here, we developed circAID-p-seq, a PCR-free library preparation for 3′ phospho-RNA sequencing. We applied circAID-p-seq to ribosome profiling, which produces fragments protected by ribosomes after endonuclease digestion. CircAID-p-seq, combined with the dedicated computational pipeline circAidMe, facilitates accurate, fast, highly efficient and low-cost sequencing of phospho-RNA fragments from eukaryotic cells and tissues. While assessing circAID-p-seq to portray ribosomes engaged with transcripts, we provide a versatile tool to unravel any 3′-phospho RNA molecules.

overall_design: we design and validate a new library preparation for sequencing of 3'P or 2'/3' cP smallRNA fragments, using Oxford Nanopore platform

first: Tea

last: Kecman

first: Michael

last: Schmid

first: Ruggero

last: Barbieri

first: Luciano

last: Brocchieri

first: Silvia

last: Tornaletti

first: Claudia

last: Firrito

first: Luca

last: Minati

first: Paola

last: Bernabò

first: Ilaria

last: Signoria

first: Fabio

last: Lauria

first: Thomas

middle: H

last: Gillingwater

first: Gabrilla

last: Viero

first: Massimiliano

last: Clamer


title: Discovery and functional interrogation of the virus and host RNA interactome of SARS-CoV-2 proteins

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

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

sample_organism:
Homo sapiens
Chlorocebus sabaeus

platform_organism:
Homo sapiens
Chlorocebus sabaeus

overall_design: Refer to individual Series


title: High-density genetic map and genome-wide associaation studies of floral color traits in Phalaenopsis orchids

city: Tainan City

first: Shu-Yun

last: Chen

address: No. 1 University Road

country: Taiwan

institute: NCKU

summary: The F1 population of Phalaenopsis Intermedia, which established from the cross between P. equestris and P. aphrodite was applied to build a high-density genetic map based on SSRs and SNPs from GBS methodology, with the digestion of by Hinp1 I and Hae III. In addition, another GBS was performed with enzymes ApeK I and Hae II to increase the SNP number for the GWAS analysis. We identified 10 SNPs highly associated with floral aesthetic trait, and among them, 4 were associated with flower color related. Genes with function related to anthocyanin biosynthesis were identified as the candidate genes. In addition, the flowering time-related gene SOC1 may contribute to flower color regulation in our discovery.

overall_design: A cross between P. equestris and P. aphrodite gave rise to F1 population for two different GBS sequencings.

first: Chia-Chi

last: Hsu


title: Fusobacterium nucleatum promotes colorectal cancer cells adhesion to endothelial cells and facilitates extravasation and metastasis by inducing ALPK1/NF-κB/ICAM1 axis

city: Hangzhou

first: zhang

last: ying

address: Kaixuan Road, Jianggan District

institute: Zhejiang University

summary: Fusobacterium nucleatum-treated HCT116 cells reported an increased adhesion to endothelial cells compared with PBS control. To understand the underlying mechanisms of Fusobacterium nucleatum-induced intercellular adhesion ability of CRC cells, we performed RNA-sequencing in HCT116 cells with or without Fusobacterium nucleatum treatment with three independent biological replicates.

overall_design: Examination of  gene expression variation in HCT116 cells treated with or without Fusobacterium nucleatum (MOI of 100:1)

first: Wei

last: Zhuo

first: Ying

last: Zhang


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and terfa-/- zebrafish embryos

city: Shanghai

first: Yilin

last: YING

address: Ruijin No.2 road 197, building11-1110

institute: Ruijin Hospital Shanghai China

summary:
The goals of this study are to compare NGS in 3day post fertilized zebrafish embryo after knockout terfa (telomere repeats binding factor 2). In order to investigate the role of terfa in DDR, telomere protection and neuro-development.
Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the zebrafish genome (build zv10) and identify 8840 NGS in 'WT vs terfa-/-' group and 4137 NGS in 'WT vs terfa+/-' group.
Our results indicate that zebrafish terfa involved in 1. cell cycle dysregulation (e.g. senescence, p53, spliceosome, RNA transport, Ribosome, mRNA surveillance and cell cycles), including an increased expression of two p53-targeted genes, cdkn1a (p21) and gadd45; 2. inflammation (e.g. Salmonella and Herpes simplex infections, TOL-like receptor signaling and Cell Adhesion), including an increased expression of two pro-inflammatory genes, il6 and isg15. 3. neuronal dysfunction (e.g. Phototransduction, Calcium signaling and Neuroactive ligand-receptor interaction), including a signature of glial injury (gfap, ctsl, metrn, gcm2, clu and 5 members of the slc1a family (3, 4, 5, 7, 8)).

overall_design: mRNA profiles of 3 day post fertilised embryos in wild type (WT), terfa+/- and terfa-/- zebrafish embryos

first: Melanie

last: Pousse

first: Kehua

last: CHEN

first: Jing

last: YE

first: Eric

last: GILSON


title: RNAseq reveals differential gene expression contributing to Phytophthora nicotianae adaptation to partial resistance in tobacco

city: Raleigh

first: Howard

middle: David

last: Shew

state: NC

address: 112 Derieux Pl

department: Entomology and Plant Pathology

institute: North Carolina State University

summary: RNAseq was performed on two isolates of P. nicotianae (adapted to either the susceptible tobacco genotype Hicks or the partially resistant genotype K 326 Wz/Wz) to identify differentially expressed genes (DEGs) during their pathogenic interactions with K 326 Wz/Wz and Hicks.

sample_organism:
Nicotiana tabacum
Phytophthora nicotianae

overall_design: mRNA profiles of two P. nicotianae isolates and two tobacco genotypes during their interactions.

last: Jin

first: Rui

last: Shi

first: Ramsey

last: Lewis

first: H


title: Discovery and functional interrogation of the virus and host RNA interactome of SARS-CoV-2 proteins [RNA-Seq]

summary: The coronavirus disease 2019 (COVID-19) pandemic was caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). Understanding the molecular functions of SARS-CoV-2 proteins is thus imperative to developing effective antiviral treatments. Here, we use enhanced crosslinking and immunoprecipitation to investigate SARS-CoV-2 protein interactions with viral and host RNAs. SARS-CoV-2 proteins, NSP8 and NSP12, are found to specifically bind to untranslated regions of the RNA viral genome, with NSP12 additionally binding to all transcription regulatory sequences. This provides evidence for their central roles in replication and transcription. Moreover, we discovered a potential site of NSP12 mediated genome recombination, which could explain the genetic diversity found in coronaviruses. SARS-CoV-2 proteins exogenously expressed in human lung epithelial cells bind to 4,281 unique host RNAs. Nine SARS-CoV-2 proteins upregulate target gene expression, including NSP12 which upregulates mitochondrial electron transport and N-linked glycosylation proteins. Furthermore, siRNA knockdown of NSP12-targeted proteins in human lung organoid cells demonstrates substantial antiviral effects. Conversely, NSP9 inhibits host gene expression via blocking mRNA export and dampens antiviral inflammation response such as interleukin 1α (IL1α) production. Our extensive viral protein-RNA interactome provides a catalog of potential therapeutic targets and offers insight into the etiology of COVID-19 as a safeguard against future pandemics.

overall_design:
Vero E6 and A549-ACE2 cells were treated with 1µg/ml doxycyline and infected with SARS-CoV-2 at MOI 0.1 and MOI 3, respectively, for 48 hours before treating with Trizol.
BEAS-2B cells were treated with Trizol when 70-90% confluent.

first: Joy

last: Xiang

first: Jasmine

last: Mueller

first: En-Ching

last: Luo

first: Brian

last: Yee

first: Danielle

last: Schafer

first: Jonathan

last: Schmok

first: Frederick

last: Tan

first: Hsuan-Lin

last: Her

first: Chun-Yuan

first: Kristopher

last: Brannan

first: Krysten

last: Jones

first: Samuel

last: Park

first: Wenhao

first: Rachael

last: McVicar

first: Elizabeth

last: Kwong

first: Phuong

last: Le

first: Kofman

last: Eric

first: Anthony

last: Vu

first: Yanhua

last: Li

first: Kevin

last: Dong

first: Alexandra

last: Tankka

first: Yan

last: Song

last: Van Nostrand

first: Sandra

last: Leibel

middle: W


title: Lung genes modification in elastase-induced emphysema following in utero nicotine exposure

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School


title: Effect of in utero nicotine exposure and elastase instillation on transcriptomic profile at post-elastase day 21 in mice

summary:
Purpose: The goal of this study is to address if in utero and early life nicotine exposure can prime the offspring to be more succetible to develop emphysema in adulthood
Methods:  A mouse model of two hits: a prenatal hit and a later insult delivered in adulthood was used in this study. In brief, Nicotine (200 mg/L) was supplied immediately after mating and administered to the females in drinking water supplemented with 2% saccharin for the whole period of gestation and until the post-natal day 16 (nicotine group). As a control, we used drinking water with 2% saccharin (control group). Pups born from nicotine-exposed or control mothers were intranasally instilled with elastase or saline at the age of 11 weeks and sacrificed at post-elastase day (ped) 21. Lungs were collected at ped21 and laser dissected to separate the emphysematous and normal-looking tissue from elastase-instilled lungs. The RNA was then extracted and submited to RNAseq analysis. We had 6 different groups: two for saline instilled animals (normal_control_saline (C-S),  normal_nicotine-saline (N-S)), and for elastase-instilled animals we had 4 groups: 2 for emphysematous regions (emphysema_ControlElastase (eC-E) and emphysema_NicotineElastase(eN-E)) and 2 for normal regions (normal_ControlElastase(nC-E) and normal_NicotineElastase(nN-E)).
Results: Nicotine upregulated zero and 46 genes and downregulated 2 and 29 in saline and elastase instilled respectivelly. Elastase upregulated zero and 3 and downregulated 1 and 1 genes in controls and nicotine-pretreated samples respectively. Pathway analysis performed with differentially expressed genes due to nicotine-pretreatment in elastase instilled animals with MetaCore software (https://portal.genego.com/) (fold change of 2 or more and p<0.05) revealed downregulation of the several immune system related pathways, gamma-secretase proteolitic pathway, ubiquitin-proteasomal pathway, notch signaling pathway and others.
Conclusions: Our results identify the the early nicotine exposure as an important insult that affects the proteomic signature at ped21

overall_design: Lung mRNA profiles of wild type (WT) C57BL/6J mouse lungs were generated using single-end reads with Illumina HiSeq

first: Sanja

last: Blaskovic

first: Yves

last: Donati

first: Isabelle

last: Ruchonnet-Metrailler

first: Yannick

last: Avila

first: Johannes

middle: C

last: Schittny

first: Constance

last: Barazzone-Argiroffo


title: Effect of in utero nicotine exposure and elastase instillation on transcriptomic profile at post-elastase day 3 in mice

summary:
Purpose: The goal of this study is to address if in utero and early life nicotine exposure can affect genetic profile in early ephysema
Methods:  A mouse model of two hits: a prenatal hit and a later insult delivered in adulthood was used in this study. In brief, Nicotine (200 mg/L) was supplied immediately after mating and administered to the females in drinking water supplemented with 2% saccharin for the whole period of gestation and until the post-natal day 16 (nicotine group). As a control, we used drinking water with 2% saccharin (control group). Pups born from nicotine-exposed or control mothers were intranasally instilled with elastase or saline at the age of 11 weeks and sacrificed at post-elastase day (ped) 3. Whole lung were collected at ped3 and total RNA was sequenced. We had 4 different groups: control_saline (C-S), control_elastase (C-E), nicotine_saline (N-S) and nicotine_elastase (N-E). ALl the groups had 3 replicas, except N-E group that had 5 different replicas.
Results: At ped3 nicotine upregulated 219 and 2 and downregulated 2 and 109 genes in saline and elastase-instilled samples respectively. Elastase upregulated 723 and 439 and downregulated 116 and 77 genes in controls and nicotine-pretreated samples respectively. Pathway analysis performed with MetaCore software (https://portal.genego.com/) (fold change of 2 or more and p<0.05) revealed many identical pathway activated by elastase instillation in both controls and nicotine-pretreated samples such as the cell cycle, DNA damage and cell adhesion, but also revieled the main difference in activation of the immune system between the controls and nicotine-pretreated samples.
Conclusions: Our results identify the the early nicotine exposure as an important insult that affects the proteomic signature at ped3


title: ZRSR1 cooperates with ZRSR2 in regulating splicing of U12-type introns in murine hematopoietic cells I

city: Singapore

first: Pushkar

last: Dakle

address: 14 Medical Dr

institute: Cancer Science Institute of Singapore

summary: Recurrent loss-of-function mutations of spliceosome gene, ZRSR2, occur in myelodysplastic syndromes (MDS).  Mutation/loss of ZRSR2 in human myeloid cells primarily causes impaired splicing of the U12-type introns. To investigate further the role of this splice factor in splicing and hematopoietic development, we generated mice lacking ZRSR2. Unexpectedly, Zrsr2-deficient mice developed normal hematopoiesis with no abnormalities in myeloid differentiation evident in either young or ≥1-year old knockout mice. Repopulation ability of Zrsr2-deficient hematopoietic stem cells was also unaffected in reconstitution assays. Myeloid progenitors lacking ZRSR2 exhibited mis-splicing of U12-type introns, however, this phenotype was moderate compared to the ZRSR2-deficient human cells. Our investigations revealed that a closely related homolog, Zrsr1, expressed in the murine hematopoietic cells, but not human, contributes to splicing of U12-type introns. Depletion of Zrsr1 in Zrsr2 KO myeloid cells exacerbated retention of the U12-type introns, thus highlighting a collective role of ZRSR1 and ZRSR2 in murine U12-spliceosome. We also demonstrate that aberrant retention of U12-type introns of MAPK9 and MAPK14 leads to their reduced protein expression. Overall, our findings highlight that both ZRSR1 and ZRSR2 are functional components of the murine U12-spliceosome, and depletion of both proteins is required to model accurately ZRSR2-mutant MDS in mice.

overall_design: K562 cells transduced wih either shRNAs targeting ZRSR2 or control shRNA

first: Vikas

last: Madan

first: Zeya

last: Cao

first: Weoi

last: Teoh

first: Lin

last: Han

first: Pavithra

last: Shyamsunder

first: Siqin

last: Zhou

first: Jia

first: Hazimah-Binte

last: Nordin

first: Shi

last: Jizhong

first: Yu

last: Shuizhou

first: Henry

last: Yang

first: Md

middle: Z

last: Hossain

first: Wee

middle: J

last: Chng

first: H.

middle: P

last: Koeffler


title: Gene expression analysis of hematopoietic stem cells based on Syndecan-2 surface expression

city: Los Angeles

first: John

last: Chute

address: 615 Charles E Young Dr S

institute: UCLA

summary: Analysis of how Syndecan-2 expression identifies hematopoietic stem cells with unique gene expression profiles. We tested the hypothesis that Syndecan-2 expression enriches for hematopoietic stem cell gene expression programs. The results provide important insight into how Syndecan-2 can be used to isolate hematopoietic stem cells with distinct hematopoietic properties.

overall_design: Total RNA was obtained from sorted adult mouse (C57BL/6.J, mixed gender) hematopoietic stem cells isolated using fluorescence activated cell sorting (FACS). The cell populations analyzed are c-Kit+/Sca-1+/Lineage- (KSL) CD34-, KSL CD34- Syndecan-2- (Sdc2m) and KSL CD34- Syndecan-2+ (Sdc2p).

first: Christina

last: Termini


title: Indentification of differentially expressed genes  on tumor tissues of CT-26 cells after swimming

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

summary: Swimming signficantly attenuates tumor growth of CT-26 cells in vivo, and up-regulated 715 transcripts expression, while down-regulated 629 transcripts, comparing to Control group.

overall_design: The CT-26 cells were injected into right flank area of mice and were divided into Control and Swimming groups. The mice in Swimming group were subjected to physical training for swimming in water for total 3 weeks. RNA sequencing was performed to detect the differentially expressed genes on tumor tissues of CT-26 cells with or without swimming.

first: Jiapeng

last: Li

first: Aling

last: Shen

first: Liya

last: Liu

first: Zhiqing

first: Meizhu

last: Wu


title: Hydrostatic pressure controls angiogenesis through endothelial YAP1 during lung regeneration

city: Milwaukee

first: Akiko

last: Mammoto

state: WI

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

summary: Pulmonary artery (PA) pressure increases during lung growth after unilateral pneumonectomy (PNX). Mechanosensitive transcriptional co-activator, yes-associated protein (YAP1), in endothelial cells (ECs) is necessary for angiogenesis during post-PNX lung growth. We investigate whether increases in PA pressure following PNX controls angiogenesis through YAP1. When hydrostatic pressure is applied to human pulmonary arterial ECs (HPAECs), the expression of YAP1, transcription factor TEAD1, and angiogenic factor receptor Tie2 increases, while these effects are inhibited when HPAECs are treated with YAP1 siRNA or YAP1S94A mutant that fails to bind to TEAD1. Hydrostatic pressure also stimulates DNA synthesis and cell migration in HPAECs, while YAP1 knockdown or YAP1S94A mutant inhibits the effects. Gene enrichment analysis reveals that the levels of extracellular matrix (ECM) or cell adhesion molecules are altered in post-PNX mouse lung ECs, which interact with YAP1. Exosomes are known to promote tissue regeneration. Proteomics analysis reveals that exosomes isolated from conditioned media of post-PNX mouse lung ECs contain the higher levels of ECM and cell-adhesion proteins compared to those from sham-operated mouse lung ECs. Recruitment of host lung ECs and blood vessel formation are stimulated in the fibrin gel containing exosomes isolated from post-PNX mouse lung ECs or pressurized ECs, while YAP1 knockdown inhibits the effects. These results suggest that increases in PA pressure stimulate angiogenesis through YAP1 during regenerative lung growth.

overall_design: Mouse lung endothelial cells were isolated from C57Bl6J mouse lungs (8 week old male mice) 7 days after PNX and sham-operated mouse lungs (n=2 per group, each n was pooled from 2 male mice) using anti-CD31 conjugated magnetic beads for transcriptome analysis.

first: Tadanori

first: Kathryn

last: Hendee


title: P53 and rH2AX enrichment in overexpressed SNCA on SHSY5Y

city: seoul

first: Jueng Soo

last: You

address: 120 Neungdong-ro

institute: Konkuk University

summary: This study was designed to determine P53 and rH2AX regulated genes after a-synuclein expression. Our results showed that many genes involved in apoptosis and cellular senescence are directly regulatd by P53. rH2AX binding was more complex in that a-synuclein expression showed a change from random binding to specific bindings in certain promoters.

overall_design: To determine P53 and rH2AX enrichment after ectopic expression SNCA

first: H

last: Lee

first: J

middle: S


title: Transcriptome analysis of overexpressed SNCA in differentiated SH-SY5Y neuroblastoma cells

summary: The goal of this study is to compare NGS-derived transcriptome profiling (RNA-seq) of alpha-synuclein expressing Sh-SY5Y cells vs. lacZ control protein and find characteristic changes that may be related to alpha-synucleinopathies. Our results showed the enrichments of p53 pathways, DNA damage responses, and cellular senescence. Further studies validated genes involved in such pathways.

overall_design: To obtain transcriptome profiling after ectopic SNCA expression.


title: Overexpressed SNCA in differentiated SH-SY5Y neuroblastoma cells


title: Higher-order chromatin organization defines PR and PAX2 binding to regulate endometrial cancer cell gene expression (Hi-C)

city: buenos aires

first: Patricia

last: Saragüeta

state: CABA

address: Vuelta de Obligado 2490

country: Argentina

institute: IByME

summary: Estrogen (E2) and Progesterone (Pg) via their specific receptors, ER and PR respectively, are major determinants in the development and progression of endometrial malignancies. We have studied how E2 and the synthetic progestin R5020 affect genomic function in Ishikawa endometrial cancer cells. Using ChIPseq in cells exposed to the corresponding hormones, we identified cell specific binding sites for ER (ERbs) and PR (PRbs), mostly binding to independent sites and both adjacent to PAXbs. Long-range interactions (HiC) showed enrichment of PRbs and PAXbs, which we call progestin control regions (PgCRs) inside TADs with differentially progestin-regulated genes. Effects of hormone treatments on gene expression were detected by RNAseq. PgCRs correlate with open chromatin independently of hormonal stimuli. In summary, endometrial response to progestins in differentiated endometrial tumor cells results in part from binding of PR to compartmentalized PgCRs in hormone-independent open chromatin, which include binding of partner transcription factors, in particular PAX2.

overall_design: Endometrial adenocarcinoma Ishikawa cells were treated with R5020 10nM or E2 10nM for different times and submitted to Hi-C.

first: Alejandro

last: La Greca


title: ZRSR1 cooperates with ZRSR2 in regulating splicing of U12-type introns in murine hematopoietic cells

first: Pushkar

last: Dakle

overall_design: RNA-seq of sorted common myeloid precursors (CMP), granulocyte monocyte precursors (GMP) and megakaryocyte erythroid precursors (MEP) from three WT and three ZRSR2 KO male littermates; and murine embryonic fibroblasts (MEF) prepared from three WT and three ZRSR2 KO male embryos. RNA-seq of Lin-Kit+ murine bone marrow cells from either WT or ZRSR2 KO mice transduced with shRNA targeting murine ZRSR1 (sh1 or sh10) or control shRNA; experiment performed in duplicate.

first: Vikas

last: Madan

first: Zeya

last: Cao

first: Weoi

last: Teoh

first: Lin

last: Han

first: Pavithra

last: Shyamsunder

first: Siqin

last: Zhou

first: Jia

first: Hazimah

last: Nordin

first: Shi

last: Jizhong

first: Yu

last: Shuizhou

first: Henry

last: Yang

first: Md

first: Wee


title: Small RNA-seq analysis of human liver cancer cell lines and human liver tissues

city: Seoul

first: HEE

last: CHO

address: 50 YONSEI-RO, SEODAEMUN-GU

institute: Yonsei University

summary: We applied small RNA sequencing technology to identify precursor tRNA derived small RNA expression in human cancer cell lines and human liver tissues.

overall_design: Small RNA-seq of human liver cancer cell lines Huh7 (n=2), normal liver samples (n=2), and liver samples from HCV patients (n=3)

first: Hee

last: Cho

first: Jong-Won

last: Oh


title: Higher-order chromatin organization defines PR and PAX2 binding to regulate endometrial cancer cell gene expression (RNAseq)

first: Patricia

overall_design: Endometrial adenocarcinoma Ishikawa cells were treated with R5020 10nM or E2 10nM for 12h and polyA-enriched RNA was submitted to high-throughput sequencing.

first: Alejandro

middle: E


title: Higher-order chromatin organization defines PR and PAX2 binding to regulate endometrial cancer cell gene expression

overall_design: Refer to individual Series


title: Physiological traits assessment and RNAseq data analysis revealed a high vulnerability of Setaria viridis to salt compared to its close relative Spartina alterniflora

city: shanghai

first: Ming

middle: Ju

last: Lu

state: shanghai

address: 320 Yueyang Road, Xuhui Area, Shanghai, China

department: Partner Institute for Computational Biology, Shanghai Institutes for Biologic Sciences, CAS

institute: Shanghai Institutes for Biological Sciences, CAS

summary: Our recently published results demonstrated a crucial role for plastid terminal oxidase (PTOX) as an alternative electron pathway in the halophyte Spartina alterniflora (S. alterniflora) under salt stress but not for the glycophyte Setaria viridis (S. viridis). Herein, the effect of salt on the photosynthetic electron transport and RNA-seq analysis was probed in Setaria and its salt-tolerant close relative S. alterniflora. Initially, plants were grown at soil then were salt-treated under hydroponic conditions for two weeks. Setaria shows high vulnerability to salt compared to Spartina; while, Setaria was unable to survive exposure to greater than 100 mM, Spartina could tolerate salt concentrations as high as 550 mM with merely negligible effect on gas exchange and conductance of electrons transport chain (gETC). After exposure to salt, the prompt fluorescence (OJIP-curves) reveals an increase in the O- and J-steps in Setaria and very less or no change for SA. This suggests a higher QA over-reduction in Setaria than in Spartina. Following salt treatment, a dramatic decline in PSII primary photochemistry for Setaria was observed, as displayed by the drastic drop in Fv/Fm, Fv/Fo and ΦPSII. However, no substantial change was recorded regarding these parameters for Spartina under NaCl treatment. Interestingly, we report an improvement in primary PSII photochemistry (ΦPSII) for Spartina with increasing either salt concentration or duration. Besides, the magnitude of NPQ dynamics was strongly enhanced for Setaria even at low NaCl level (50 mM); however, it remains unchangeable or slightly increased for Spartina at high NaCl concentrations (above 400 mM). For plants endured salt, we notice an increase in both the proportion of oxidized P700 and the amount of active P700 in Setaria and almost no change for Spartina. The slowdown of electrons flow through PSII was accompanied by a dramatic decline in gETC. Under salt, CO2 assimilation (A) and stomatal conductance (gs) evaluations demonstrate that A decreases earlier, even after one week exposure to only 50 mM NaCl for Setaria; however, the effect of salt was negligible in Spartina regarding these two parameters even after exposure for two weeks to high salt levels (400 and 550 mM). For Setaria exposed for 12 d to salt, the use of 2,000 μmol m-2 s-1 external CO2 was not sufficient to fully restore A to the control level as assessed by A-Ci curves, even for 50 mM salt. The A at all NaCl levels, except 550 mM, was able to completely recover to initial level before stress in Spartina. RNAseq analysis shows a stimulation of oxido-reduction reactions in Setaria. Gene onthology (GO) enrichment emphasizes differentially expressed genes (DEGs) and some transcription factors (TFs) under salt. The up-regulated genes in Setaria are related to three metabolic processes; C4, photorespiration and the oxidation/reduction pathways. Some other specifically highly up-regulated genes in Setaria are mostly related to TFs including DNA-binding transcription factor activity, stress marker genes such as peroxidase and senescence-related genes such as flavonol synthase.

sample_organism:
Setaria viridis
Sporobolus alterniflorus

overall_design: Seeds of Spartina (thereafter S. alterniflora) were collected from San-San Lake in South East Shanghai city at november end (2016 and 2017). The cleaned spikelets were stored in wet tissue in sealed plastic in the refrigerator at 4°C. S. alterniflora seeds require between two and three months after ripening in cold, wet storage (stratification) to break dormancy (Garbisch and McIninch, 1992) and they remain viable for about one year. Setaria viridis (thereafter S. viridis) grass seeds were stored in a dry place. Seeds of Spartina were rinsed several times with tap water outdoors to reduce odors that come out then transfer them to Petri-dishes and covered with water till germinate then transfer them to potted soil. When the young seedlings of Spartina are about 2 cm in length and started turning green, they then removed from the glass petri dishes and seeds. Trays containing Spartina seedlings were kept indoor at a temperature controlled room of (25-27°C), under fluorescent grow light (80 - 120 μmol m-2 s-1) on a photoperiod of 16/8 hour (light/dark) photoperiod. Then two-month old healthy plants with large expanded leaves where transferred to hydroponic for salt treatment.

first: Jemaa

last: Essemine

first: Ming-Ju

last: Lyu

first: Xin-Guang

last: Zhu


title: Higher-order chromatin organization defines PR and PAX2 binding to regulate endometrial cancer cell gene expression (ChIPseq PAX2)

last: Saragüeta

overall_design: Endometrial adenocarcinoma Ishikawa cells were treated with R5020 10nM or E2 10nM for different times and submitted to ChIPseq using PR and ERalfa antibodies for immunoprecipitation.

last: La Greca


title: Gene expression profiles of MCF7 cells treated with NB001

status: Public on Mar 08 2022

city: 上海

first: Xueting

last: Wu

state: 上海

address: Fenglin Road 300, Xuhui District

institute: CAS China

summary:
Type 1 adenylyl cyclase (ADCY1) is a main enzyme to produce cyclic AMP (cAMP) upon activation of G-protein coupled receptors and increase of intracellular calcium. It regulates cAMP signaling and in turn affects physiological functions including neural plasticity, cognition, motor function, cell survival, and neuropathic pain.
We used microarrays to determine the effect of a known ADCY1 inhibitor NB001 on gene transcription.

overall_design: We produced the gene expression profiles of MCF7 cells to NB001 and vehicle control (DMSO). Two biological replicates for each group and the data set includes profiles for 4 samples.

first: Xuan

last: Li


title: Lysophosphatidic acid Shifts Metabolic and Transcriptional Landscapes to Induce a Novel Cellular State in Human Embryonic Stem Cells

city: Macau

first: Guokai

last: Chen

address: University of Macau Avenida da Universidade Taipa, Macau, China

institute: University of Macau

summary: Pluripotent stem cells can be maintained in a continuum of cellular states with distinct features. Exogenous lipid supplements are commonly utilized to shift the balance of global metabolism relieving the dependence on de novo lipogenesis. However, it is largely unexplored how specific lipid components regulate metabolism and pluripotency state. In this study, we investigate the impact of lipid supplements on human embryonic stem cells (hESCs), and report that signaling lipid lysophosphatidic acid (LPA) is the key component to shift the metabolic landscape in lipid supplement AlbuMAX. Although the maintenance of ERK phosphorylation and primed pluripotency is independent of exogenous lipids, LPA increases ERK phosphorylation, especially upon niche disintegration. We further demonstrate that LPA leads to distinctive transcriptome profile that is not associated with de novo lipogenesis. We also show that LPA causes unique and reversible phenotypes in cell cycle, morphology and mitochondria. This study reveals an LPA -induced primed state that allow people to drastically alter cell physiology for basic research and stem cell applications with hESCs.

overall_design: Total RNA obtained from H1 hESC cultured in E8 medium and E8 medium supplemented with 1.6% AlbuMAX, 1 μM LPA, 2 μM S1P, 1% CDL, 1% CDL (without Tween-80), 0.001% hCDL, 0.01% hCDL, 1% Albumin,  1 μM LPA + 1% Albumin, and 1 μM LPA + 2 μM S1P + 1% Albumin. Samples were collected after 2 days. SAMPLE 1, 2, 3, 5, 8, 9, 10 are used in the paper.


title: Higher-order chromatin organization defines PR and PAX2 binding to regulate endometrial cancer cell gene expression (ChIPseq)