title: Effect of IL13 on MPLW515L Megakaryocytes

city: Memphis

first: Shibiao

last: Wan

state: Tennessee

address: 262 DANNY THOMAS PLACE

department: Center for Applied Bioinformatics

institute: St. Jude Children's Research Hospital

summary: Myelofibrosis (MF) is a disease associated with high unmet medical needs since allogeneic stem cell transplantation is not an option for most patients and JAK inhibitors are generally effective for only 2-3 years and do not delay disease progression. MF is characterized by the presence of dysplastic megakaryocytic hyperplasia and progression to fulminant disease, which is associated with progressively increasing marrow fibrosis. Despite evidence of an inflammatory milieu in MF that contributes to disease progression, the specific factors that promote megakaryocyte growth are poorly understood. Here, we analyzed changes in the cytokine profiles of MF mouse models before and after development of fibrosis coupled with analysis of bone marrow populations by scRNA-seq. We found high IL-13 levels in the bone marrow of MF mice. IL-13 promoted the growth of mutant megakaryocytes and induced the surface expression of TGF- and collagen biosynthesis. Analysis of samples from patients with myelofibrosis similarly revealed elevated levels of IL-13 in plasma and increased IL-13 receptor expression by marrow megakaryocytes. In vivo, IL-13 overexpression promoted disease progression while reducing IL-13/IL-4 signaling reduced several features of the disease including fibrosis. Lastly, we found an increase in the numbers of marrow T cells and mast cells, which are known sources of IL-13. Together, our data demonstrate that IL-13 is involved in disease progression in MF and that inhibition of the IL-13/IL-4 signaling pathway might serve as a novel therapeutic target to treat MF.

overall_design: Cells transduced with MPLW515l retroviruses and cultured for 4 days in stemspan media in the presence or absence of murine IL-13

first: Johanna

last: Melo-Cardenas

first: John

last: Crispino


title: The unique establishment of histone H3 lysine 4 mono-methylation pattern on the promoter regions in early embryo development [ChIP-seq]

status: Public on Jul 10 2022

city: Shanghai

first: Shaorong

last: Gao

address: Siping Road

department: School of life science and technology

country: China

institute: Tongji University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Histone H3 lysine 4 methylation on promoter regions plays essential roles  in transcriptional regulation in mouse early embryo development. Here, we  presented the first genome-wide map of H3K4me1 in mouse pre-implantation  embryos and observed a unique establishment process of H3K4me1 pattern on  promoter regions, which is strongly correlated with active transcription  and the broad H3K4me3 domain formation. We further demonstrate that the  histone methyltransferase ASH2L contributes to forming the H3K4me1 DIP  pattern on the promoter regions in mouse pre-implantation embryos.

overall_design: ChIP-seq: Genome-wide mapping of H3K4me1 occupancy on mouse  pre-implantation embryos from 2-cell stage to morula stage, and the mouse  embryonic stem cells.

first: Sheng'en

last: Hu

first: Linfeng

last: Zhang

first: Jingyi

last: Li

first: Yawei


title: Expression profile of Human blood monocytes treated with bacterial lipids

city: Cambridge

first: Ramnik

last: Xavier

state: MA

address: 415 Main Street

country: USA

institute: Broad Institute of MIT and Harvard

type: Expression profiling by high throughput sequencing

summary: Multiple studies have established associations between human gut bacteria and host physiology but determining the molecular mechanisms underlying these associations has been challenging1–3. Akkermansia muciniphila has been robustly associated with positive systemic effects on host metabolism, favorable outcomes to checkpoint blockade in cancer immunotherapy, and homeostatic immunity4–7. Here we report the identification of a lipid from A. muciniphila’s cell membrane that recapitulates the immunomodulatory activity of A. muciniphila in cell-based assays8. The isolated immunogen, a diacyl phosphatidylethanolamine with two branched chains (a15:0-i15:0 PE), was characterized through both spectroscopic analysis and chemical synthesis. The immunogenic activity of a15:0-i15:0 PE has a highly restricted structure-activity relationship, and its immune signaling requires an unexpected toll-like receptor 2/1 heterodimer9,10. Certain features of the phospholipid’s activity are noteworthy: it is significantly less potent than known natural and synthetic toll-like receptor 2 agonists; it preferentially induces some inflammatory cytokines but not others; and at low doses (1% of EC50) it resets activation thresholds and responses for immune signaling. Identifying both the molecule and an equipotent synthetic analog, its non-canonical toll-like receptor 2/1 signaling pathway, its immunomodulatory selectivity, and its low dose immunoregulatory effects provides a molecular mechanism for a model of A. muciniphila’s ability to set immunological tone and its varied roles in health and disease.

overall_design:
Peripheral blood mononuclear cells (PBMCs) from two separate buffy coats were isolated and enriched for monocyte cells using RosetteSep™ Human Monocyte Enrichment Cocktail (Cat # 15028; Stemcells technologies) , then the cells were treated with the active PEs for 2h,6h and 12hr.  After each timepoint, cells were lysed in 50uL of lysis buffer and kept at -80 C for downstream RNA-seq analysis.
***Raw data not available due to patient privacy concerns***

first: Munhyung

last: Bae

first: Chelsi

middle: D

last: Cassilly

first: Xiaoxi

last: Liu

first: Sung-Moo

last: Park

first: Betsabeh

last: Khoramian Tusi

first: Xiangjun

last: Chen

first: Jaeyoung

last: Kwon

first: Pavel

last: Filipcik

first: Andrew

middle: S

last: Bolze

first: Zehua

first: Hera

last: Vlamakis

first: Daniel

middle: B

last: Graham

first: Sara

middle: J

last: Buhrlage

first: Jon

last: Clardy


title: OsFD4 promotes the rice floral transition via florigen activation complex formation in the shoot apical meristem

city: Piscataway

first: Andrea

last: Gallavotti

state: New Jersey

address: 190 Frelinghuysen Rd

department: Waksman Institute

institute: Rutgers University

summary: We used mutant analysis, protein–protein interaction assays and DNA affinity purification (DAP) sequencing coupled to in silico prediction of binding syntaxes to study several bZIP proteins that assemble into florigen activation/repressor complexes (FACs/FRCs).

overall_design: DAP-seq of OsBZIP42, OsBZIP69, and OsBZIP77

first: Martina

last: Cerise

first: Francesca

last: Giaume

first: Mary

last: Galli

first: Bahman

last: Khahani

first: Jérémy

last: Lucas

first: Federico

last: Podico

first: Elahe

last: Tavakol

first: François

last: Parcy

first: Vittoria

last: Brambilla

first: Fabio

last: Fornara


title: Endothelial Brg1-Notch Signaling Regulates Zebrafish Heart Regeneration

status: Public on Jul 09 2022

city: Beijing

first: Jun-jie

last: Hou

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

department: Institute of molecular medicine

institute: Peking University

summary: The goal of this study is to compare the NGS-derived heart transcriptome profiling (RNA-seq) between kdrl GFP positive endothelial cells of 4-HT induced Tg(ubi:loxp-DsRed-stop-loxp-DN-xBrg1; kdrl:CreER; kdrl:eGFP) (DNK) and Tg(ubi:loxp-DsRed-stop-loxp-DN-xBrg1; kdrl:eGFP) (CtrlK) injured hearts.

overall_design: Zebrafish cardiac endothelial cell mRNA profiles of both wild-type sibling (CtrlK) and endothelial-specific over-expression of dominant-negative Xenopus Brg1 zebrafish (DNK) at 7 days post heart amputation were carried out by using Illumina Hiseq2500

first: Ya-Bing

last: Song

first: Jian-Bin

last: Wang

first: Cheng-Lu

last: Xiao

first: Jun-Jie

first: Ji-Yuan

last: Zheng

first: Jing-Wei

last: Xiong


title: HeLa cells treated and untreated with Clinacanthus nutans DCM fraction

status: Public on Jul 08 2022

city: Kepala Batas

first: Kristine

middle: Sandra

last: Pey Adum

state: Pulau Pinang

address: Bertam

department: Advanced Medicine and Dental Institute

country: Malaysia

institute: Universiti Sains Malaysia

summary: To investigate the effects of C. nutans DCM fraction on HeLa cells using transcriptomic analysis. We then performed gene expression profiling analysis using data obtained from RNA-seq of two different condition at two replicates.

overall_design: Gene expression profiling analysis of RNA-seq data for HeLa cell line treated with C. nutans DCM fraction.

first: Pey

middle: A

last: Kristine Sandra

first: Haron

last: Nor Hasyimah

first: Arsad

last: Hasni


title: Acquired semi-squamalization during chemotherapy suggests a differentiation therapy for bladder cancer

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

summary: Cisplatin-based chemotherapy is the most common treatment for unresectable bladder cancers and also increasingly used as neoadjuvant treatments before or after surgery and radiotherapy. Unfortunately, though many patients respond to the treatment, most of them develop resistance quickly with unclear mechanisms and few further treatment options. Here, we report that semi-squamazation is acquired during chemo treatment in both mice and human. Multi-omics analyses show that cathepsin H (CTSH), a direct target of p63, is associated with chemoresistance and semi-squamation. Treatment with the cathepsin inhibitor E64 specifically restrains chemoresistant but not chemosensitive cancer. Mechanistically, cathepsin inhibition induces fully squamous differentiation of bladder cancer cells, which requires TNF receptor 1alpha and is associated with pyroptosis. Our study suggests that semi-squamazation would be a diagnosistic marker for chemoresistance and differentiation therapy by targeting CTSH might be a potential treatment for chemoresistant bladder cancer.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Bulk RNAseq, ATAC-seq and sc-RNAseq in chemotherapy- sensitive and resistant mouse bladder cancer; sc-RNAseq in  mouse chemo resistant tumors treated with vehicle or E64; Bulk RNAseq in chemotherapy-resistant mouse bladder cancer treated by E64 or vehicle; Bulk RNAseq and sc-RNAseq in chemotherapy-sensitive and resistant human bladder cancer.

first: Xuelan

last: Chen

first: Manli

first: Ping

last: Tan

first: Chong


title: Alterations of RNA Modification in Mouse Germ Cell-2 Spermatids Under Hypoxic Stress

first: Yunfang

last: Zhang

address: 1239 Siping Road

department: Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology

summary: Infertility is a major health problem worldwide due to its deleterious psychological and physical effects. Understanding the molecular mechanisms underlying its onset or occurrence is essential for the development of treatments or preventive measures. Studies have shown that RNA modifications, as novel post-transcriptional regulators, are involved in spermatogenesis, and hypoxia-induced alterations in RNA modification in testes and sperm cells may be associated with impaired permatogenesis in mice. However, the molecular mechanisms via which RNA modifications affect spermatogenesis under hypoxic stress conditions are unclear. This study evaluated the effects of alterations in RNA modifications in spermatids under hypoxic stress conditions, which might be responsible for changes in RNA stability and subsequent alterations in sncRNA expression profiles and the transcriptome. The findings of this study provide a basis for a better understanding of the pathophysiology of male infertility and could facilitate the development of preventive measures and treatment strategies for the condition

overall_design: Gene expression profiles of GC-2spd cell line that growth under hypoxic conditions (3 replicates) or normal conditions (3 replicates).

first: Tong

last: He

first: Huanping

last: Guo

first: Lin

last: Xia

first: Xipeng

last: Shen

first: Yun

last: Huang

first: Xiao

last: Wu

first: Xuelin

last: Jiang

first: Yinying

last: Xu

first: Yi

first: Dongmei


title: Overlap Between Pediatric Nodal Marginal Zone Lymphoma (PNMZL) and Pediatric-Type Follicular Lymphoma (PTFL) : Morphological and Molecular Analysis (OncoScan)

status: Public on Jul 11 2022

city: Barcelona

first: Itziar

last: Salaverria

address: Rossello 153

country: Spain

institute: Hospital Clínic

type: Genome variation profiling by genome tiling array

summary: Pediatric nodal marginal zone lymphoma (PNMZL) is an unusual and poorly understood primary B-cell nodal neoplasms. Patients are predominantly young males presenting with localized disease. The tumor shows overlapping morphological features with pediatric-type follicular lympgoma. The  alterations involved in the pathogenesis of PNMZL are not known.

platform_organism:
Homo sapiens
Capra hircus
Mus musculus
Cavia porcellus
Ignicoccus hospitalis

overall_design: The aim of this study was to perform a complete genetic characterization of PNMZL. Fifty-two cases (47 males and 5 females; mean age: 17.5 years, range 5-48) were analyzed by copy number (CN) array and next-generation sequencing analyses as whole-exome sequencing and targeted sequencing investigating the state of genes associated with close related entities like adult NMZL, pediatric-type and adult follicular lymphoma.

first: Julia

last: Salmeron-Villalobos

first: Leticia

last: Quintanilla-Martinez


title: Cyclin B1 expression as an independent prognostic factor for lung adenocarcinoma and its potential pathways

city: Zunyi

first: Qing

last: Luo

state: Guizhou

address: 149 Dalian Road, Huichuan District, Zunyi, Guizhou 563003, P. R. China

institute: Affiliated Hospital of Zunyi Medical University

summary: To investigate the functional mechanism of CCNB1 in lung adenocarcinoma, we knocked down CCNB1 in H1299 cell line and performed sequencing analysis.We then performed gene expression profiling analysis using data obtained from RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for H1299 cells and its shRNA(shCCNB1).

last: Li

first: Yuanxiu

last: Leng


title: Expression profiles of transfer RNA-derived small RNAs in esophageal cancer

city: Nanjing

first: Shanliang

last: Zhong

address: Baiziting 42

institute: The Affiliated Cancer Hospital of Nanjing Medical University

summary: We collected 4 paired esophageal cancer (EC) tissues and adjacent normal tissues. Total RNA was extracted from the tissues. Then total RNA was processed and transfer RNA-derived small RNAs (tsRNAs) were profiled using tsRNA sequencing technique. Raw read counts were filtered to remove the tsRNAs that were expressed in low levels. We only kept the tsRNAs with a nonzero raw read count in all 4 EC tissues or all 4 adjacent normal tissues, and normalized the remaining tsRNAs with DESeq2 in the statistical program R (version 4.0.1). Differentially expressed tsRNAs were screened using following criterions: fold change was larger than 2 and adjusted P value was less than 0.05.

overall_design: The tsRNA expression levels in esophageal cancer tissues were compared to those in adjacent normal tissues.

first: Xinnian

last: Yu


title: MSH1 disruption in plants triggers RdDM-mediated reprogramming of phenotypic plasticity (RNA-Seq)

city: University Park

first: Hardik

last: Kundariya

state: PA

address: 361 N. Frear

institute: The Pennsylvania State University

summary: To generate epi-lines, two third-generation msh1 T-DNA mutant (SAIL_877_F01) plants were used to pollinate Col-0 to generate two independent F1 populations. Derived F1 progenies were self-pollinated to generate F2 populations that were genotyped for the msh1 T-DNA mutation. MSH1 F2 plants were self-pollinated to produce F3 families that were used in the study.

overall_design: 3 plants from each of the epi populations and Col-0 WT control were sequenced.

first: Xiaodong

last: Yang

first: Sally

last: Mackenzie


title: Single-nucleus and single-cell RNA-sequencing of human pancreatic islets

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

summary: Transcriptomics is frequently used to interrogate alterations in cultured human islet cells using single-cell RNA-sequencing. We introduce single-nucleus RNA-sequencing as an alternative approach for investigating human islets.

overall_design: The Nuclei EZ protocol was used to obtain nuclear preparations from human islet cells. Such preparations were used to generate single-nucleus RNA-seq datasets and compared to single-cell RNA-seq output obtained from cells from the same donor.

first: Giorgio

last: Basile

first: Sevim

last: KahramanDirice

first: Rohit

last: Kulkarni


title: Novel azetidine-based Stat3 inhibitors induce misfolded protein response, endoplasmic reticulum stress and mitophagy, and inhibit breast tumor growth in vivo

status: Public on Jul 12 2022

city: Los Angeles

first: Peibin

last: Yue

state: CA

address: 8700 Beverly Blvd

institute: Cedars Sinai Medical Center

summary: To identify differentially expressed genes and pathways in human breast cancer cell line MDA-MB-231 cells that are treated with a novel Stat3 inhibitor or DMSO control.

overall_design: MDA-MB-231 cells were treated with DMSO (Control) or H182 at 2 µM for 2 hours. Total RNA was prepared and RNA-sequencing analysis was performed to determine differentially expressed genes as stated in the methods section in the manuscript.

first: Francisco

last: Lopez-Tapia

first: Yinsong

last: Zhu

first: Christine

last: Brotherton-Pleiss

first: Wenzhen

last: Fu

first: Nagendra

last: Verma

first: Jasmine

last: Chen

first: Kayo

last: Nakamura

first: Weiliang

first: Felix

last: Alonso-Valenteen

first: Simoun

last: Mikhael

first: Lali

last: Medina-Kauwe

first: Kathleen

middle: M

last: Kershaw

first: Maria

last: Celeridad

first: Allison

last: Limpert

first: Douglas

last: Sheffler

first: Nicholas

last: Cosford

first: Stephen

middle: L

last: Shiao

first: Marcus

last: Tius

first: James

last: Turkson


title: ChIP-seq and RNA-seq in breast cancer cell lines

city: Lexington

first: Yadi

last: Wu

state: KY

address: 741 S. Limestone

department: Department of Pharmaceutical Sciences

institute: the University of Kentucky

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

overall_design: Refer to individual Series


title: RNAseq in breast cancer cells with EBF1 knockdown

summary: Transcriptional analysis of MDA-MB-157 and MDA-MB-436 with EBF1 knockdown

overall_design: Breast cancer cells were transduced with EBF1 shRNA virus.


title: The role acclimatization, adaptation, and symbiosis in the acquisition of heat tolerance in reef-building corals

city: Auburn

first: Marie

middle: E

last: Strader

state: AL

address: 101 Rouse Life Sciences, Biological Sciences Department

department: Biological Sciences

institute: Auburn University

summary: Transcriptional responses to heat stress were assayed in early life-history stages of 11 crosses between and amongst Acropora tenuis colonies originating from reefs along the Great Barrier Reef. We identified a single nucleotide polymorphism outlier (Fst=0.89) between populations in the unannotated gene Acropora25324, which exhibited constitutively higher gene expression in populations with dams originating from Curd reef, a far north, warm adapted inshore reef, suggesting an important role of this gene in adaptation to warmer environments. Further, juveniles exposed to heat and in symbiosis with heat-evolved Symbiodiniaceae displayed intermediate transcriptional responses between its progenitor taxa (Cladocopium goreaui) and the more stress tolerant Durusdinium trenchii, indicating that the development of heat tolerance acquisition is potentially a conserved evolutionary process in Symbiodiniaceae. These findings reveal the underlying mechanisms, and for the first time, their relative contribution, of coral responses to climate change and provide a foundation for optimizing conservation methods like assistant gene flow.

overall_design: crosses were generated from gametes collected from 5 populations across the Great Barrier Reef. Larvae from these crosses were sampled prior to experimentation ("Pre") and then set up into two treatments ("Control temperature", and "Heat stress"). Following experimentation, pools of larvae were sampled for RNAseq from both treatments for each cross. Remaining larvae from each cross was settled to the juvenile phase and exposed to either control or ambient temperature conditions. Further, juveniles were exposed to one of four symbiont uptake treatments. Juveniles were sampled following the experiment for RNA-seq

first: Kate

last: Quigley


title: Type I Interferon Signaling Mediates Microglial Dysfunction and Senescence in Human-Mouse Chimeric Brain Models of Down Syndrome and Alzheimer’s Disease

first: Mengmeng

last: Jin

state: NJ

address: 604 Allison Rd


title: The unique establishment of histone H3 lysine 4 mono-methylation pattern on the promoter regions in early embryo development [RNA-seq]

first: Shaorong

last: Gao

overall_design: Genome-wide expression profiles on mouse pre-implantation embryos  in morula stage upon different siRNA knockdown treatments.

first: Sheng'en

last: Hu

first: Linfeng

last: Zhang

first: Jingyi

last: Li

first: Yawei


title: Next Generation Sequencing of human first trimester placental EVTs (pEVT), decidual interstitial EVTs (iEVT), and trophoblast organoid (TB-ORG)-derived extravillous trophoblasts (TB-ORG-EVTs).

city: Vienna

first: Martin

last: Knoefler

address: Waehringer Guertel 18-20

country: Austria

institute: Medical University of Vienna

summary: Aim of the study was to verify signaling pathway-provoked EVT specification in human first trimester placental and decidual tissue. We further provide improvement for in-vitro differentiated TB-ORG-EVTs to more closely mimic in-situ placental EVT geno- and phenotypes.

overall_design: In the first batch, in-situ placental, and decidual, and in-vitro-derived TB-ORG-EVTs from first trimester tissue (7 - 8th weeks of gestation) were isolated and generated, respectively, from the same single donors. In the second batch TB-ORG-EVTs were differentiated under three conditions: a) DIFF1: conventional, transforming growth factor beta (TGFb)-inhibiting condition, b) DIFF2: without TGFb inhibition; c) DIFF3: without TGFb inhibition and recombinant TGFb1

first: Sandra

last: Haider

last: Knöfler

first: Andreas

middle: I

last: Lackner


title: Gene expression profiles of diabetic kidney disease and neuropathy in eNOS knockout mice

city: Ann Arbor

first: Jennifer

last: Harder

state: Michigan

address: 1150 W. Medical Center Drive

department: Division of Nephrology

institute: The University of Michigan

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct


title: Insulin secretory granules release exosomal miR-503 to promote insulin resistance and β-cell senescence.

first: Yuncai

last: Zhou

state: Jiangsu

address: No. 818 Tianyuan East Road, Jiangning District

institute: Nanjing medical university

summary: Since β cell specific miR-503 transgenic (βTG) mice showed metabolic stress induced insulin resistance and β cell dysfunction, we applied single cell sequencing (scSeq) technology to distinguish different cell type in β TG islets and define different phases of β cell subtypes through pseudotime analysis. Islets were isolated and digested at 37℃for 5 min by 0.08 % trypsin containing 0.006 % EDTA to generate islet single cell, cell suspension was centrifuged and resuspended in cold PBS buffer with 0.4% of BSA at the concentration of ~1000/μl, which then was loaded onto the 10X Chromium Controller using Chromium Single Cell 3’ v2 reagents.  Sequencing library was prepared following the manufacturer’s instructions (10X Genomics), and sequenced via a Illumina HiSeq PE150 instrument. 8698 cells were detected from 10-week old wild type (WT, n = 4540 cells) and βTG (n = 4158 cells) mice islets, cells were split to 12 subtypes by using cell ranger software and k-means algorithm. According to specific gene profile we found that βTG islets was infiltrated with Ccr6/Ccr7 positive immune cells, and most β cells in βTG mice islets were defined senescent cells  by using GO enrichment and pseudotime analysis. Our study represents the analysis of islet single cell transcriptomes, the results showed that miR-503 highly expression in β cells promotes β cell senescence and diabetes onset.

overall_design: Single-cell RNA-sequencing (scSeq) profiles of 10-week old wild type (WT) and βTG  mice islets.

first: Kerong

last: Liu

first: Yi

last: Sun

first: Yan

first: Yangyang

first: Ying

last: Shi

first: Zhengjian

last: Yao

first: Yating

first: Rongjie

last: Bai

first: Rui

last: Liang

first: Peng

first: Xiaoai

last: Chang

first: Wei

last: Tang

first: Shusen

last: Wang

first: Yunxia

last: Zhu

first: Xiao

last: Han


title: Renin-angiotensin system inhibition reverses the altered triacylglycerol metabolic network in diabetic kidney disease

first: Jennifer

summary: Dyslipidemia is a significant risk factor for progression of diabetic kidney disease (DKD). To identify  individual lipids and lipid networks that may be involved in DKD progression, we performed untargeted  lipidomic analysis of kidney cortex tissue from diabetic db/db and db/db eNOS-/- mice along with nondiabetic  littermate controls. A subset of mice were treated with the renin-angiotensin system (RAS)  inhibitors, lisinopril and losartan, which improves the DKD phenotype in the db/db eNOS-/- mouse model.  Of the three independent variables in this study, diabetes had the largest impact on overall lipid levels in  the kidney cortex, while eNOS expression and RAS inhibition had smaller impacts on kidney lipid levels.  Kidney lipid network architecture, particularly of networks involving glycerolipids such as  triacylglycerols, was substantially disrupted by worsening kidney disease in the db/db eNOS-/- mice  compared to the db/db mice, a feature that was reversed with RAS inhibition. This was associated with  decreased expression of the stearoyl-CoA desaturases, Scd1 and Scd2, with RAS inhibition. In addition to  the known salutary effect of RAS inhibition on DKD progression, our results suggest a previously  unrecognized role for RAS inhibition on the kidney triacylglycerol lipid metabolic network.  Keywords:  Dyslipidemia is a significant risk factor for progression of diabetic kidney disease (DKD). To identify individual lipids and lipid networks that may be involved in DKD progression, we performed untargeted lipidomic analysis of kidney cortex tissue from diabetic db/db and db/db eNOS-/- mice along with non-diabetic littermate controls. A subset of mice were treated with the renin-angiotensin system (RAS) inhibitors, lisinopril and losartan, which improves the DKD phenotype in the db/db eNOS-/- mouse model. Of the three independent variables in this study, diabetes had the largest impact on overall lipid levels in the kidney cortex, while eNOS expression and RAS inhibition had smaller impacts on kidney lipid levels. Kidney lipid network architecture, particularly of networks involving glycerolipids such as triacylglycerols, was substantially disrupted by worsening kidney disease in the db/db eNOS-/- mice compared to the db/db mice, a feature that was reversed with RAS inhibition. This was associated with decreased expression of the stearoyl-CoA desaturases, Scd1 and Scd2, with RAS inhibition. In addition to the known salutary effect of RAS inhibition on DKD progression, our results suggest a previously unrecognized role for RAS inhibition on the kidney triacylglycerol lipid metabolic network.

overall_design: RNAseq of kidney tissue of db/db eNOS -/- mice treated with RAAS blocking drugs

first: Kelli

last: Sas

first: Jiahe

last: Lin

first: Hongyu

last: Zhang

first: Jharna

last: Saha

first: Thekkelnaycke

last: Rajendiran

first: Tanu

last: Soni

first: Viji

last: Nair

first: Felix

last: Eichinger

first: Matthias

last: Kretzler

first: Frank

middle: C

last: Brosius III

first: George

last: Michailidis

first: Subramaniam

last: Pennathur


title: MSH1 disruption in plants triggers RdDM-mediated reprogramming of phenotypic plasticity (Bisulfite-Seq II)

first: Hardik

last: Kundariya

type: Methylation profiling by high throughput sequencing

summary: To generate msh1 memory revertant population, msh1 memory plant was used to pollinate Col-0 to generate F1 population. Derived F1 progenies were self-pollinated to generate F2 populations. F2 plants were self-pollinated to produce F3 families that were segregationg for the msh1 memory phenotype (small dwarf plants with delayed flowering).

overall_design: 3 plants from msh1 memory revertant, 2 plants from non-reverant (full-sibs of reverant), and 3 msh1 memory control plants were sequenced.

first: Sally

last: Mackenzie


title: EBF1 and HIF1a ChIPseq in breast cancer cell lines [ChIP-seq]

first: Yadi

last: Wu

summary: EBF1 and HIF1a ChIPseq in MDA-MB-157 cells under normoxia and hypoxia

overall_design: Cells were culutre under normoxia or hypoxia for 24h, then fixed with 1% formaldehyde for 10 min at room temprature. Fixiation was quenched with 125 mM Glycine. Chromatin was fragmented by Micrococcal nuclease (MNase) digestion. Transcription factor bound chromatin was pulled down using specific antibodies and protein-G megnetic beads. Enriched chromatin then was further de-crosslinked and used for libraries construction.


title: LncRNA-ENST00000501520 promotes the proliferation of malignant-transformed BEAS-2B cells induced with coal tar pitch mediated by target genes

city: Zhengzhou

first: Zhongqiu

last: Li

state: Henan

address: 100 Kexue Avenue

department: Department of Toxicology

institute: Zhengzhou University

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

summary: Coal tar pitch (CTP) is a byproduct of cooking process which is used in making coatings, corrosion protection materials, and electrode. and it has been verified that Coal tar pitch extract (CTPE) constitutes polycyclic aromatic hydrocarbons (PAHs) (87.91%) and monocyclic aromatic hydrocarbons, heterocyclic compounds and alkenes (the remaining total is 12.09%) using gas chromatography/mass spectrometry (GC/MS). In this study, we determine the lncRNA expression profile in CTPE group and control group. The key lncRNAs were screen out by using microarray analysis in defferent group.

overall_design: The experiment is divided into three groups: BEAS-2B cells  as control group, BEAS-2B cells induced with CTPE and BEAS-2B cells induced with B(a)p. then perform lncRNAs chips by Arraystar Human lncRNAs chip (Arraystar).

first: Liya

last: Meng

first: Qiao


title: High intensity aerobic exercise suppresses cancer growth by regulating skeletal muscle-derived oncogenes and tumor suppressors (Lung)

status: Public on Jul 13 2022

city: Gyeongsan

first: Hyunseok

last: Jee

state: Gyeongbuk

address: 280, Daehak-ro, Gyeongsan, Gyeongbuk, 38541, Republic of Korea

country: South Korea

institute: Yeungnam University

summary: High intensity aerobic exercise (90% of the maximum heart rate) can effectively suppress cancer proliferation in vivo. However, the molecular effect of aerobic exercise and its relevance to cancer prevention remains uninvestigated. The mRNA-sequencing technique (mRNA-seq) can provide a genome-wide depiction of gene expression changes by aerobic exercise. Mice with colorectal cancer were subjected to high intensity aerobic exercise, and mRNA-seq analysis was performed on heart, lung, and skeletal muscle tissues to analyze the molecular effects of the exercise in a genome-wide manner. The skeletal muscle-derived genes with exercise-dependent differential expressions were further evaluated for their effects on colorectal cancer cell viability. Regular and high intensity aerobic physical activity in the mice produced positive results in comprehensive parameters (i.e., food intake, weight, and survival rate) compared to those in the control groups (healthy and cancer with no exercise). A heatmap of differentially expressed genes revealed markedly different expression patterns between these groups. RNA-seq analysis of 23,282 skeletal muscle-derived genes identified a number of anticancer effector genes. Knockdown and overexpression of selected anticancer genes significantly repressed CT26 proliferation by 20% (p<0.05). Our finding based on the aerobic exercise cancer mouses model suggest that the high intensity exercise resulted in a global change in gene expression patterns, particularly those that affect cancer cell viability.

overall_design:
Examination of 4 group (i.e., Blue, Green, Pink, and Yellow, each 10 samples of mice)
E - Exercise
T - Tumor

first: Yoosik

last: Kim


title: MSH1 disruption in plants triggers RdDM-mediated reprogramming of phenotypic plasticity (Bisulfite-Seq I)

overall_design: 3 plants from each of the 4 epi populations and Col-0 WT control were sequenced.


title: EFFECT OF ORAL UREA SUPPLEMENTATION ON THE ENDOMETRIAL TRANSCRIPTOME OF MARES

first: Barry

middle: A.

last: Ball

state: Kentucky

address: 108 Gluck Equine Research Center,

department: Veterinary Scinece

institute: University of Kentucky

summary: At ovulation detection (D0), oral treatment with urea was initiated and continued until D7. Mares received a treatment or control diet (n= 11 mares/group) in a crossover design. The treated group received urea (0.4 g/kg body weight) mixed with sweet feed and molasses, the control group received sweet feed and molasses alone. Blood samples were collected daily, one hour after feeding, for BUN determination. Uterine and vaginal pH were evaluated with an epoxy pH probe. Endometrial biopsies were taken transcervically one hour after the last feeding on D7. RNA sequencing of the endometrium of a subset of mares (n=6/group) was conducted.

overall_design: A uterine biopsy was collected from the base of the uterine horn seven days after the start of the treatment (n= 6 per treatment). Total cellular RNA was extracted from endometrial samples using a RNeasy Mini Kit (Qiagen, Gaithersburg, MD). A total of 1 μg of RNA was treated with DNase I (Ambion Inc., Austin, TX) for 30 minutes at 37℃ to remove genomic DNA according to manufacturer’s instructions. Paired-end reads with 150 nucleotides in length were produced. A TruSeq Stranded mRNA library prep kit (Illumina, San Diego, CA) was used to prepare libraries for mRNA sequencing. Libraries were loaded onto an Agilent DNA 1000 chip and validated on an Agilent 2100 Bioanalyzer (Agilent). Quantitation was performed with the Illumina Library Quantification Kit, ABI Prism qPCR Mix from Kapa Biosystems. Libraries were run on a NextSeq 500 v2 (Illumina) 300cycles High Output kit in a 2x150 base pairs with paired-end reads. The Fastq files were evaluated for read quality using FastQC 0.11.4. Subsequently, Trim Galore 0.4.1 was used for adapter and read quality trimming (Phred score threshold of 30). Reads were mapped to the Equus caballus reference genome (EquCab 3.0) using the software STAR 2.5.3a, then annotated with the equine reference annotation from NCBI using Cufflinks 2.2.1. Fragments per kilobase per million (FPKM) were used to determine the expression level of genes. Lastly, we used Cuffdiff 2.2.1 to calculate differentially expressed genes (DEG) between samples from the control and urea groups. Significance level was set at FDR-adjusted p-value of the test statistic < 0.1 using a Benjamini-Hochberg correction.

first: Yatta

last: Boakari

first: Hossam

last: El-Sheikh Ali

first: Pouya

last: Dini

first: Shavahn

last: Loux

first: Claudia

last: Fernandes

first: Kirsten

last: Scoggin

first: Alejandro

last: Esteller-Vico

first: Yamê

middle: F

last: Sancler-Silva

first: Laurie

last: Lawrence


title: Gene expression profiles of diabetic kidney disease and neuropathy in eNOS knockout mice: predictors of pathology and RAAS blockade effects

first: Jennifer

last: Harder

summary: Diabetic kidney disease (DKD) and diabetic peripheral neuropathy (DPN) are two common diabetic complications. However, their pathogenesis remains elusive and current therapies are only modestly effective. We evaluated genome-wide expression to identify pathways involved in DKD and DPN progression in db/db eNOS -/- mice receiving renin-angiotensin-aldosterone system (RAAS) blocking drugs to mimic the current standard of care for DKD patients. Diabetes and eNOS deletion worsened DKD, which improved with RAAS treatment. Diabetes also induced DPN, which was not affected by eNOS deletion or RAAS blockade. Given the multiple factors affecting DKD and the graded differences in disease severity across mouse groups, an automatic data-analysis method, SOM or self-organizing map was used to elucidate glomerular transcriptional changes associated with DKD, whereas pairwise bioinformatics analysis was used for DPN. These analyses revealed that enhanced gene expression in several pro-inflammatory networks and reduced expression of development genes correlated with worsening DKD. Although RAAS treatment ameliorated the nephropathy phenotype, it did not alter the more abnormal gene expression changes in kidney. Moreover, RAAS exacerbated expression of genes related to inflammation and oxidant generation in peripheral nerves. The graded increase in inflammatory gene expression and decrease in development gene expression with DKD progression underline the potentially important role of these pathways in DKD pathogenesis. Since RAAS blockers worsened this gene expression pattern in both DKD and DPN, it may partly explain the inadequate therapeutic efficacy of such blockers.

overall_design: Identification of transcriptional pathways involved in progression of db/db eNOS mice receiving RAAS blocking drugs

first: Stephanie

last: Eid

first: Lucy

last: Hinder

first: Hongyu

last: Zhang

first: Ridvan

last: Eksi

first: Viji

last: Nair

first: Sean

last: Eddy

first: Meeyoung

last: Park

first: Jharna

last: Saha

first: Felix

last: Eichinger

first: Celine

last: Berthier

first: Hosagrahar

middle: V

last: Jagadish

first: Yuanfang

last: Guan

first: Subramaniam

last: Pennathur

first: Junguk

last: Hur

first: Eva

last: Feldman

first: Matthias

last: Kretzler

first: Frank

last: Brosius


title: EFFECT OF ORAL UREA ADMINISTRATION ON THE TRANSCRIPTOME OF THE EQUINE EMBRYO

first: Barry

last: Ball

summary: The effects of a high BUN on blastocoele fluid urea concentrations and analyzed the transcriptome of day-14 equine embryos based upon RNA sequencing.

overall_design: When a 25 ± 3 mm follicle was detected, mares were randomly allocated to a urea (n=9) or control treatment (n=10). The urea treatment consisted of an oral supplementation of urea (0.4 g/kg of body weight), mixed with sweet feed and molasses. The control treatment was sweet feed and molasses alone. Blood samples were collected every other day for BUN analysis, one hour after feeding. Mares were artificially inseminated in the presence of a 35-mm follicle and ovulation was detected (D0). Ultrasonographic exams for pregnancy detection started at D11, and embryo collection was done at D14 (n=5 urea-treated embryos; n=7 control embryos). RNA was extracted from embryos for RNA sequencing.

first: Yatta

last: Boakari

first: Hossam

last: El-Sheikh Ali

first: Pouya

last: Dini

first: Shavahn

last: Loux

first: Claudia

last: Faernandes

first: Kirsten

last: Scoggin

first: Alejandro

last: Esteller-Vico

first: Laurie

last: Lawrence


title: EFFECT OF ORAL UREA ADMINISTRATION ON THE TRANSCRIPTOME OF THE EQUINE ENDOMETRIUM AND EMBRYO


title: Transcriptome changes of liver from mice overexpressing Chrna4

first: Jun

last: Liu

address: Longmiandadao

institute: CPU

summary: We injected adenovirus overexpressing Chrna4 as well as vehicle via tail vein (1× 10^9 pfu per mouse). Mice were fed with high-fat diet at the same time. After two weeks from virius injection, mice were sacrificed and samples were collected

overall_design: Mice were grouped and injected vehicle or Chrna4-overexpressing adenovirus together with high-fat diet fed for two weeks.

first: Lirui

last: Wang

first: Haiyang

last: Hu

first: Yingsheng

last: Gao


title: New Insights Into VDR Signaling In Mouse Intestinal Biology

first: Michael

middle: P

last: Verzi

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

summary: Female C57BL/6J mice were fed a vitamin D deficient diet (0.47% calcium, 0.3% phosphate; Teklad diet TD 89123, Envigo Teklad diets, Madison, Wisconsin)  2 -3  weeks prior to mating to a male C57BL/6J male mouse and during subsequent pregnancy and lactation.  Pups from these mice were maintained on this diet until 12-14 weeks of age.  For this study, mice were maintained in a virus and parasite-free barrier facility and exposed to a 12h-light, 12h-dark cycle.  Food and water were given ad libitum. All the animal experiments conducted were approved by the Rutgers, New Jersey Medical School Animal Care and Use Committee.  Mice were ordered from Charles River Laboratories. 12 – 14 week old vitamin D deficient mice were randomly separated and injected with either 0.1 ml vehicle (9:1 mix of propylene glycol and ethanol) or 1,25(OH)2D3 (from Cayman Chemical Company Ann Arbor, MI)  (ip 10ng/g body weight) and sacrificed 4h after the injection.  Intestinal tissues were harvested from mice. About 10-15 cm of the proximal half of small intestine were used for the duodenum crypts and villi samples, and the entire colon tissues from the terminal cecum to rectum were used for colon samples. After flushing with cold PBS, the intestines were cut opened longitudinally, cut into 1 cm pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. The solution was discarded and the tissues were incubated with fresh 3mM EDTA/PBS in rotator for 10 min at 4 0C. After shaking the tubes gently for 10 times, the intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS, rotated for 30 min at 4 0C, then were shaken 30 times. The supernatant containing the whole epithelium tissues (crypts and villi) were collected and spun down at 200 rcf for 3 min at 4 0C. The pellet was resuspended with cold PBS and villi separated from crypts with 70 µm filter. Colon tissue was scraped with a glass slide to remove the epithelial mucosa and washed with PBS. All samples were centrifuged tubes at 200 rcf for 3 mins at 4 0C and at 300 rcf for 30 seconds at 40C in order to remove any residual PBS. We then proceeded to RNA extraction. RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions. All nucleic acid extracts were gDNA Eliminator Solution for 15 s at 37 °C, in order to remove contaminating chromosomal DNA. Resulting RNA was analyzed for quantity and quality with a NanoDrop spectrophotometer ND-1000 (Isogen Life Science, Utrecht, The Netherlands).

overall_design: 38 Samples were analyzed, which included 18 Vitamin D deficient samples and 20 Vitamin D treated samples.

first: Joseph

last: Hur

first: Rohit

last: Aita

first: Shanshan

last: Li

first: Sylvia

last: Christakos


title: Chromosomal abnormalities and pregnancy outcomes for fetuses with gastrointestinal tract obstructions

status: Public on Jul 07 2022

city: Fuzhou

first: Xiaoqing

last: Wu

address: 18 daoshan road, Gulou district

institute: Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University

summary: Fetal gastrointestinal tract obstructions (GITO) is the most frequently encountered gastrointestinal defects in prenatal. This study aimed to investigate the genetic disorders and pregnancy outcomes of fetal GITO. We reviewed data from 70 pregnancies who were referred for invasive prenatal testing due to fetal GITO. According to the levels of obstruction, they were classified into esophageal atresia/stenosis, duodenal atresia/stenosis, jejunal or ileal atresia/stenosis, and anal atresia. Traditional karyotyping was performed on all 70 pregnancies, and chromosomal microarray analysis (CMA) was performed on 32 of them in parallel. Traditional karyotyping revealed twelve (17.1%) chromosomal abnormalities, including 11 cases of trisomy 21 (Down syndrome), and one case of a supernumerary marker chromosome related to Cat Eye Syndrome. According to the absence or presence of other ultrasound anomalies, they were categorized into isolated GITO (n = 36) and non-isolated GITO (n = 34). The rate of chromosomal abnormalities in non-isolated GITO pregnancies was significantly higher than that in isolated GITO pregnancies (29.4% vs. 5.5%, p < 0.05); the survival rate in isolated group was significantly higher than that in non-isolated group (67.6% vs. 34.4%, p<0.05). Among the 32 cases where CMA was performed, additional one (3.1%) copy number variants with clinical significance was noted in a fetus with normal karyotype. The microduplication on 7q12 was consider to be the genetic etiologies of duodenal stenosis, although it was inherited from a phenotypically normal mother. Our study supports the strong association between Down syndrome and fetal GITO, especially duodenal stenosis. Our findings suggested that the risk of chromosomal abnormalities increased when GITO was accompanied by other ultrasound anomalies, thus chromosomal abnormalities and fetal anatomy should be carefully evaluated for pregnancy management of fetal GITO.

overall_design:
Traditional karyotyping was performed on all 70 pregnancies, and SNP array was performed on 32 of them in parallel.
**Please note that raw data CEL files for 22 samples (out of total 32) have been lost and thus are not provided***

first: Liangpu

last: Xu


title: A novel CREB5/TOP1MT axis confers cisplatin resistance through inhibiting mitochondrial apoptosis in head and neck squamous cell carcinoma

city: Shanghai

first: tong

last: tong

address: 639 Zhizaoju Road

institute: Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

summary: Cisplatin resistance is one of the main causes of treatment failure and death of head and neck squamous cell carcinoma (HNSCC). In order to better understand the mechanism of cisplatin resistance and formulate effective treatment strategies, we identified differentially expressed genes related to cisplatin resistance by RNA sequencing, RT-PCR and immunoblotting. CREB5 was selected as the most significantly up-regulated gene in cisplatin resistant cells. Gain- and loss-of-function experiments were performed to detect the effect of CREB5 on cisplatin resistance and mitochondrial apoptosis in HNSCC. Chromatin immunoprecipitation (ChIP) assay, dual-luciferase reporter assay, and immunoblotting experiments were performed to explore the underlying mechanisms of CREB5.

overall_design: Four independent cell samples were analyzed. HN4 is the control group of HN4_CR, and HN30 is the control group of HN30_CR.

first: Tong

last: Tong


title: Analysis of   M229-Par and M229-Res cells by Illumina HiSeq instrument (4000 or equivalent)  seq analysis .

city: Birmimgham

first: Romi

last: Gupta

state: Alabama

address: 720, 20th street south

institute: University of Alabama at Birmingham

summary: Briefly,  Melanoma M229-Par and M229-Res  were analysed for transcriptional changes using RNA seq Analysis.

overall_design: RNA-seq analysis was done in  M229-Par and M229-Res

first: Praveen

last: Guruvaiah

first: Kiran

middle: K

last: Reddi


title: M229-Par and M229-Res cells

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

overall_design: Refer to individual Series


title: Transgenic soybeans (Glycine max) secreting Phosphoinositide-3-phosphate binding proteins show enhanced resistance to oomycete pathogen Phytophthora sojae

city: Corvallis

first: Emily

last: Helliwell

state: OR

address: Oregon State University

institute: Oregon State University

summary: We created stable transgenic soybean plants that express and secrete two different PI3P-binding proteins, GmPH1 and VAM7, in an effort to interfere with effector delivery and confer resistance. Soybean plants expressing the two PI3P-binding proteins exhibited reduced infection by the oomycete pathogen Phytophthora sojae compared to control lines. Measurements of nodulation by nitrogen-fixing mutualistic bacterium Bradyrhizobium japonicum, which does not produce PI3P, revealed that the two lines with the highest levels of GmPH1 transcripts exhibited reductions in nodulation and in benefits from nodulation. Transcriptome and plant hormone measurements were made of soybean lines with the highest transcript levels of GmPH1 and VAM7, as well as controls, following P. sojae- or mock-inoculation. The results revealed increased levels of infection-associated transcripts in the transgenic lines, compared to controls, even prior to P. sojae infection, suggesting that the plants were primed for increased defense.

overall_design: Examination of transcriptomic changes in transgenic vs control Glycine max lines with and without Phytophthora sojae inoculation

first: Brett

last: Tyler


title: Analysis of open chromatin structures in M229-Par and M229-Res cells by ATAC seq analysis .

summary: Briefly,  Melanoma M229-Par and M229-Res  were analysed for  open chromatin structures using ATAC seq Analysis.

overall_design: ATAC-seq analysis was done in  M229-Par and M229-Res


title: Supt3 mutant nascent RNA-seq

city: Illkirch

first: Stephane

last: VINCENT

address: 1 rue Laurent Fries

department: Development and Stem Cells

country: France

institute: IGBMC

summary: Coactivator complexes regulate chromatin accessibility and transcription. SAGA (Spt-Ada-Gcn5 Acetyltransferase) is an evolutionary conserved coactivator complex. The core module scaffolds the entire SAGA complex and adopts a histone octamer-like structure, which consists of six histone fold domain (HFD)-containing proteins forming three histone fold (HF) pairs, to which the double HFD-containing SUPT3H adds an HF pair. Spt3, the yeast ortholog of SUPT3H, interacts genetically and biochemically with the TATA binding protein (TBP) and contributes to global RNA polymerase II (Pol II) transcription. Here we demonstrate that i) SAGA purified from human U2OS or mouse embryonic stem cells (mESC) can assemble without SUPT3H; ii) SUPT3H is not essential for mESC survival, iii) SUPT3H is required for mESC growth and self-renewal, and iv) the loss of SUPT3H from mammalian cells affects the transcription of only a specific subset of genes. Accordingly, in the absence of SUPT3H no major change in TBP accumulation at gene promoters was observed. Thus, SUPT3H is not required for the assembly of SAGA, TBP recruitment, or overall Pol II transcription, but plays a role in mESC growth and self-renewal. Our data further suggest that yeast and mammalian SAGA complexes contribute to transcription regulation by distinct mechanisms.

overall_design: Our goal is to analyze the nascent transcriptome (TT-seq) of wt vs Supt3 mutant ES cells in LIF+serum conditions.

last: Vincent


title: Cell type-specific gene expression profiles in CNS of patients with DM1

city: Suita

first: Masayuki

last: Nakamori

state: Osaka

address: 2-2, D-4, Yamadaoka

department: Neurology

country: Japan

institute: Osaka University Graduate School of Medicine

summary: Myotonic dystrophy type 1 (DM1) is a multisystem genetic disorder involving the muscle, heart, and central nervous system (CNS). The pathogenesis of CNS symptoms prevalent in patients with DM1 remains unelucidated. To elucidate the CNS pathogenesis in DM1, we investigated cell type-specific abnormalities in cortical neurons, white matter glial cells, and spinal motor neurons of patients with DM1 via laser-capture microdissection(LCM).

overall_design: We analyzed of mRNA expression in cortical neurons, white matter glial cells, and spinal motor neurons from three patients with DM1 and three disease controls.

first: Yuhei

last: Hasuike

first: Kotaro

last: Ogawa


title: Characterization of the crosstalk between Notch signaling and hypoxia

city: Philadelphia

first: Tobias

last: Friedrich

state: Pennsylvania

address: 421 Curie Boulevard

institute: University of Pennsylvania

summary: The Notch signaling pathway regulates several differentiation and developmental processes. Reduction of oxygen availability, a condition referred to as hypoxia, impacts on the Notch response. Here we made use of RNA-Seq and ChIP-Seq analysis to investigate the Notch/hypoxia crosstalk at genomic level.

overall_design: Mouse pre-T cells (Beko) were treated with the DMOG or kept under low oxygen concentration to induce hypoxia. Effects on gene expression were investigated by RNA-Seq and RBPJ occupancy was analyzed by ChIP-Seq.

first: Marek

last: Bartkuhn

first: Benedetto

last: Giaimo

first: Francesca

last: Ferrante


title: ECT2 promotes proliferation and metastasis of esophageal squamous cell carcinoma（ESCC） via Rho-ERK-VEGF/MMP9 signaling pathway

city: Luzhou

first: Muhan

last: Lv

address: Third Section of Zhongshan Road

institute: Southwest medical university

summary: In order to analyze the difference in the whole gene expression profile of ESCC(esophageal squamous cell carcinoma) and normal adjecent esophageal tissue as well as cancer metastasis tissue.  We found that ECT2 (Epithelial cell transformation sequence 2)  is highly expressed in esophageal squamous cell carcinoma compared with adjacent normal tissues by microarray analysis, and we further analyzed the expression of ECT2 in 40 patients by qRT-PCR, and found that ECT2 is indeed high in cancer tissues.  Expressed in normal tissues adjacent to cancer.  We first confirmed the overexpression of ECT2 in ESCC, further confirming the signaling pathway in the oncogenisis of ESCC.

overall_design: 3 ESCC (esophageal squamous cell carcinoma) patients' ESCC tissues, adjacent normal tissues, and cancer metastasis tissues were obtained by surgery, and the whole genome (lncRNA and mRNA) microarray analysis was performed.

first: Binyu

last: Sun

first: Qiongqiong

last: Wei

first: Xiaomei

last: Huang


title: The phosphate exporter XPR1/SLC53A1 is required for the tumorigenicity of ovarian cancer.

city: Yayoi, Bunkyo-ku

first: Tomoatsu

last: Hayashi

state: Tokyo

institute: The University of Tokyo

summary: Ovarian cancer is the fifth cause of cancer-related death in women. Ovarian clear cell carcinoma (OCCC) is a chemotherapy-resistant epithelial ovarian cancer with poor prognosis. As a basis for the development of therapeutic agents that may improve the prognosis of OCCC, we performed a screen for proteins critical for the tumorigenicity of OCCC using the CRISPR/Cas9 system. Here we show that knockdown of the phosphate exporter XPR1/SLC53A1 induces the growth arrest and apoptosis of OCCC cells in vitro. Moreover, we demonstrate that knockdown of XPR1/SLC53A1 inhibits the proliferation of OCCC cells xenografted into immunocompromised mice. These results suggest that XPR1/SLC53A1 plays a critical role in the tumorigenesis of OCCC cells. We speculate that XPR1/SLC53A1 might be a promising molecular target for the therapeutic treatment of OCCC.

overall_design: RNA profiles of ovarian cancer cells (OVISE, TOV21G, ES2, JHOC5) treated with control (Mock, siNC#1, siNC#2; n = 3) or XPR1 siRNA (siXPR1#1~#3; n = 3).

first: Yoko

last: Nagayoshi

first: Ayako

last: Kawabata

first: Aikou

last: Okamoto

first: Tetsu

last: Akiyama


title: Microarray expression data of HT-29 cells treated with spautin-1 or buformin under 2DG- or tunicamycin-stressed conditions

city: Koto-ku

first: Hitomi

last: Shirahama

address: Ariake 3-8-31

institute: Japanese Foundation for Cancer Research

summary: Spautin-1 as well as buformin showed preferential cytotoxicity under 2-deoxy-D-glucose (2DG)-stressed, but not tunicamycin-stressed conditions in HT-29 cells. By a microarray-based transcription analyses, we previously identified an unfolded protein response (UPR) expression signature, consisting of 246 probes up- or down-regulated in glucose starvation- and 2DG-stressed HT-29 and other cancer cell lines. Thus, we compared the effects of spautin-1 and buformin on the UPR transcriptional program. The two UPR inhibitors partly canceled 2DG-induced, but not TM-induced changes in UPR expression signature, indicating that spautin-1 can indeed suppress the UPR transcriptional program under 2DG-stressed conditions.

overall_design: HT-29 cell lines were treated with 10 µM spautin-1 or 300 µM buformin under 10 mM 2DG- or 1 mg/mL tunicamycin-stressed conditionds for 18 hours. Vehicle (DMSO) control samples were also preapred.

first: Kazuhiro

last: Kunimasa

first: Satomi

last: Tsukahara

first: Chika

last: Ikeda

first: Masaru

last: Koido

first: Akihiro

last: Tomida


title: Degradome sequencing of urine-derived ADO2-iPSCs

city: Shenzhen

first: Minglin

last: Ou

address: No.1017, Dongmen North Road, Luohu District

department: Clinical Medical Research Center of The Second Clinical Medical College

institute: Jinan University

type: Non-coding RNA profiling by high throughput sequencing

summary: To identify potential miRNA–mediated targets associated with osteopetrosis at the genome-wide level, two small RNA libraries and a degradome library were constructed from the ADO2-iPSCs and normal control human iPSCs (NC-iPSCs) for deep sequencing.

overall_design: Degradome sequencing (DS) was used to validate cleaved targets of the identified miRNAs between the ADO2-iPSCs and NC-iPSCs libraries.

first: Chunhong

last: Li


title: Tamoxifen Activates PI3Kinase Signaling in Uterine Cancer and Substitutes for the lack of PIK3CA Mutations

city: Boston

first: Rinath

last: Jeselsohn

state: MD

address: 450 Brookline Ave, D728

department: Medical Oncology

institute: DFCI

summary: Tamoxifen treatment in breast cancer patients increases their risk of developing uterine cancer that is more likely of poor prognosis. However, the exact mechanism leading to this increased and the worse outcomeendometrial cancer risk following tamoxifen exposure are still unknown, and effective preventive strategies are lacking. To address this question, we performed whole-exome sequencing of 21 (discovery cohort) and digital droplet PCR for 40 (validation cohort ) tamoxifen-associated uterine cancers. We identified genomic features that have been previously reported for uterine cancer, including recurrent mutations in PTEN, KRAS, TP53 and ARIDA1 and copy number alterations in the RTK and PI3K pathway. However, we also found that tamoxifen-associated uterine cancers have a substantially low frequency of PIK3CA and PIK3R1 mutations, the most prevalent mutations in non-tamoxifen-associated uterine cancers. Moreover, overall survival is significantly worse in uterine tumors without PIK3CA mutations, which could explain the observed poor prognosis in tamoxifen-associated uterine cancers . We also performed in vivo studies of normal uterine tissue and show that tamoxifen activates the PI3Kinase pathway and increases proliferation that in turn is abrogated by the PI3Kinase inhibitor, alpelisib. Together, this study uncovers the unique molecular profile of tamoxifen-associated uterine cancer and , offers mechanistic insights in the observed increase in endometrial cancer risk following tamoxifen treatment and a potential preventive approach. Moreover, we here describe for the first time a new general principle that a drug, as a side effect, can activate a pathway which would otherwise only be activated if a somatic mutation would have occurred thereby mimicking the effect of a driver mutation for cancer.

overall_design: RNA-seq of ovarectomized female mouse epithelial endometrial cells, in presence of estrogen, or estrogen deprivation alone or in addition to tamoxifen or tamoxifen plus alpelisib, using Illumina HiSeq 2000.

first: Agostina

last: Nardone

first: Francisco

last: Hermida Prado


title: RNA demethylase ALKBH5 promotes tumorigenesis in multiple myeloma

city: Hangzhou

first: Yifan

last: Hou

address: No. 79, Qingchun Rd

institute: Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University


title: RNA demethylase ALKBH5 promotes tumorigenesis in multiple myeloma [RNA-seq]

summary: We here report ALKBH5, a m6A RNA demethylase, as a crucial oncogene in multiple myeloma (MM). Using various MM models, we demonstrated a critical requirement of ALKBH5 for MM cell proliferation in vitro and in vivo. RNA-seq was applied to compare the expression profile of MM cells with or without ALKBh5 knockdown.

overall_design: RNA-seq of RPMI-8226 and CAG cells with or without shRNA-mediated ALKBH5 konckdown

first: Zhen

last: Cai


title: Extracellular vesicles derived from tumor cells as a trigger of energy default in the skeletal muscle

city: Torino

first: Giovanni

last: Birolo

state: TO

address: Via Santena 19

department: Medical Sciences

country: Italy

institute: University of Turin

summary: We analyzed the sncRNA profile of MVs found in C26 cells conditioned medium. In parallel, we isolated circulating MVs found in the plasma of C26-bearing mice and compared the expression of sncRNAs to circulating MVs of control animals, aiming to reveal new mediators of muscle wasting or molecular biomarkers that could be used for diagnostic purposes.

overall_design: (1) SncRNA profiles of C26 cells medium-derived MVs (TMVs), (2) Expression of sncRNA in plasma-derived MVs of control and C26-bearing mice.

first: Paola

last: Costelli

first: Marc

last: Beltrà


title: Single Transcriptional Factor (PU.1) Efficiently Leads Human iPS Cells to Functional Microglia

city: Tokyo

first: Iki

last: Sonn

address: Shinjyuku-ku, Shinanomachi 35

institute: Keio University

summary: We developed an efficient method of generating microglia (hiMGLs) from human induced pluripotent stem cells (iPSCs) through forcing the expression of single transcription factor, PU.1. By using this method, we were abled to harvest a great deal of microglia in about three weeks. Transcriptome profile revealed that our hiMGLs well resembled characteristics of human primary microglia. Furthermore, we confirmed that transient over-expression of PU.1 would not change gene expression of microglia in central nervous system or neurological diseases.

overall_design: Comparing if transient over expression of PU.1 would transcriptionally change microglia.

first: Fumiko

last: Ozaki

first: Sho

last: Yoshimatsu

first: Satoru

last: Morimoto

first: Hirotaka

last: Watanabe

first: Hideyuki

last: Okano


title: BMSC-derived exosomal miR-27a-3p and miR-196b-5p regulate bone remodeling in ovariectomized rats

first: Guohua

last: Lai

state: Guangdong

address: NO.1333,Xinhu Road,Baoan District

institute: Shenzhen Hospital,Southern Medical University

summary: BMSC-derived exosomes from ovariectomized rats (OVX-Exo) and sham-operated rats (Sham-Exo) were co-cultured with bone marrow-derived macrophages to study their effects on osteoclast differentiation. Next-generation sequencing was utilized to identify the differentially expressed miRNAs (DE-miRNAs) in OVX-Exo and Sham-Exo, while target genes were analyzed using bioinformatics. The regulatory effects of miR-27a-3p and miR-196b-5p on osteogenic differentiation of BMSCs and osteoclast differentiation were verified by gain-of-function and loss-of-function analyses.Osteoclast differentiation was significantly enhanced in the OVX-Exo treatment group compared to the Sham-Exo group. Twenty DE-miRNAs were identified in OVX-Exo and Sham-Exo, among which miR-27a-3p and miR-196b-5p promoted the expressions of osteogenic genes in BMSCs. In contrast, knockdown of miR-27a-3p and miR-196b-5p increased the expressions of osteoclastic genes in osteoclasts. These 20 DE-miRNAs were found to target 11435 mRNAs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed that these target genes were involved in several biological processes and osteoporosis-related signaling pathways.

overall_design: MiRNA profiles of BMSC-derived exosomes from ovariectomized rats and sham-operated rats

first: Hongxun

last: Sang


title: Transcriptomes Analysis of 4NQO induced-esophageal tumors of Wild Type and S100A14 CKO mice

city: Beijing

first: Xukun

last: Li

address: No.17 Panjiayuan Nanli, Chaoyang District

department: Department of Radiation Oncology

institute: NCC

summary:
Purpose: To fully realize the potential molecular mechanism that S100A14 deficiency enhances esophageal carcinogenesis
Methods: Total RNA of esophageal tumors in 4NQO WT and 4NQO S100A 14 CKO group mice was extracted with TRIzol Reagent. RNA libraries were constructed using an Illumina TruSeq RNA Sample Preparation kit according to the manufacturer’s protocol. A total of 150 base paired-end reads were sequenced using the Novaseq 6000 S4 platform. The read alignment was conducted using TopHat 2.0.13, and relative transcript abundances and differentially expressed genes were determined using the DESeq R package.
Results: We identified 14,157 transcripts in esophageal tumors of  4NQO WT and 4NQO S100A14 CKO group mice. Approximately 8% of the transcripts showed differential expression between the esophageal tumors of  4NQO WT and 4NQO S100A 14 CKO group mice, with a fold change ≥1.0 and p value <0.05.
Conclusions: Our study represents the first analysis of esophageal tumors derived from S100A14 CKO mice with biologic replicates, generated by RNA-seq.

overall_design: mRNA profiles of 4NQO induced-esophageal tumors of Wild Type and S100A14 CKO mice

first: Hongyan

last: Chen


title: Transcriptomics analysis of human iPSC-derived dopaminergic neurons reveals a novel model for sporadic Parkinson’s disease

city: Maastricht

first: Julian

last: Krauskopf

address: Universiteitssingel 50

country: Netherlands

institute: Maastricht University

summary: First, we differentiated human iPSCs into dopaminergic neurons. To reproduce and to study sporadic PD, the cells were subsequently exposed to increasing concentrations of the neurotoxin MPP+, which is considered the standard for experimentally inducing Parkinsonism. Resulting cells were examined using temporal transcriptomics analysis at various time-points after 24h of exposure. The transcriptomics analysis revealed a strong time- and dose-dependent response with genes overrepresented across pathways involved in PD etiology such as “Parkinson’s Disease”, “Dopaminergic signaling” and “calcium signaling”.

overall_design: First, we differentiated human iPSCs into dopaminergic neurons.  Cells were examined using temporal transcriptomics analysis at various time-points after 24h of exposure to the neurotoxin MPP+.


title: Notch activity in tumor cells shapes interferon-gamma response and immune microenvironment in glioma

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

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

overall_design: Refer to individual Series


title: mRNASeq of glioma cells

summary: In mouse models of PDGF-driven glioma where Notch is tumor-suppressive, we find that Notch activity shapes interferon-response in tumor cells and the local immune microenvironment early during tumor progression. Notch inhibition disturbs cytokine expression by tumor cells, altering recruitment and activation of immune cell populations and favoring hyper-proliferative "immune niche" independent growth. Genetic inactivation of Notch in glioma cells also attenuates their response to interferon-gamma, establishing a non-cell autonomous inhibitory feedback loop that further promotes immune evasion and aggressiveness. Hence, we propose that Notch signaling levels in tumor cells are key to orchestrate immune escape and microenvironment independency during brain tumor formation.

overall_design: Expression profiles of PDGF+Trp53-/- glioma cells from tumors with four different Notch mutant genotypes (Rbpj-/-, Notch1-/-Notch2-/-, Notch1-/-, and Notch2-/-) and tumors with intact Notch signaling (PDGF+Trp53-/- control tumors)

first: Robert

last: Ivanek

first: Elena

last: Parmigiani

first: Verdon

last: Taylor

first: Claudio

last: Giachino


title: Gene expression of KYSE410 cells  with treatment of 10 uM FAK inhibitor (defactinib) for 4 hours and 24 hours

first: lingyuan

last: zhang

address: 52 Fucheng Road, Haidian District, Beijing, China

institute: BEIJING INSTITUTE FOR CANCER RESEARCH

summary:
KYSE410 cells were treated with 10 uM defactinib for 4 hours and 24 hours,and KYSE410 cells were collected for gene expression analysis using Agilent SurePrint G3 Human Gene Expression v3 (8×60K) Microarray.
Investigation of the critical gene of KYSE410 cells treated by defactinib.

overall_design: We designed this experiment to screen for gene whose expressions are effected by defactinb treatment.

first: Lingyuan

last: Zhang

first: Jie


title: Effects of  20-week exercise on whole-blood genome-wide DNA methylation profile in children with overweight/obesity

city: Granada

first: AUGUSTO

middle: MIGUEL

last: ANGUITA-RUIZ

state: Granada

address: Cruz, 6.

institute: ISGLOBAL

summary: In this project, the effects of a 20-week exercise intervention on whole blood genome-wide DNA methylation signatures (CpG sites level) in boys and girls with overweight/obesity (OW/OB) were investigated. Twenty-three children (10.05 ± 1.39 years, 56% girls) with OW/OB, were randomized to either a 20-week exercise intervention (exercise group [EG]; n=10; 4 boys/ 6 girls), or to  usual lifestyle (control group [CG] (n=13; 6 boys/ 7 girls). Whole blood genome-wide DNA methylation and transcriptome profile (RNA-seq) analyses were performed before and after the intervention period. Changes in the DNA methylation sites of 485 and 386 CpGs were induced by the exercise intervention (compared to the control group) in boys and girls respectively  (p < 0.001). These CpG sites mapped to loci enriched in distinct gene pathways related to metabolic diseases, fatty acid metabolism, and immune function in boys or girls (p < 0.05). In boys, changes on the DNA methylation status of 87 CpG sites (from the subset of 485 significant CpGs) associated with changes in the gene expression levels of 51 gene transcripts which were regulated by exercise (p < 0.05). Among girls, changes on DNA methylation at 46 CpG sites (from the initial 386 significant CpGs) were associated with changes in the gene expression levels of 30 gene transcripts affected by exercise. Gene transcripts affected by exercise-induced DNA methylation were related to obesity, metabolic syndrome, and inflammation. Nevertheless, none of the presented analyses survived multiple testing correction (FDR > 0.05). This multi-omics approach reveals that exercise may regulate gene pathways involved in metabolism and immune functions in blood cells of boys and girls with OW/OB. These preliminary results provide an important first step to characterize the molecular response to exercise interventions in pediatric populations.

overall_design: Bisulphite converted DNA from the 23 individual in two time points (baseline and t1; 46 samples) were hybridised to the Infinium Methylation EPIC array (Illumina, San Diego, CA, USA).

first: Abel

last: Plaza-Florido

first: Augusto

last: Anguita-Ruiz

first: Signe

last: Altmäe

first: Concepción

last: Aguilera-García

first: S

last: Reitzner

first: Carl

last: Sundberg

first: F

last: Ortega


title: Single-cell RNA-sequencing of immune cells (CD45+) from the tumor microenvironment

summary: In mouse models of PDGF-driven glioma where Notch is tumor-suppressive, we find that Notch activity shapes interferon-response in tumor cells and the local immune microenvironment early during tumor progression. Notch inhibition disturbs cytokine expression by tumor cells, altering recruitment and activation of immune cell populations and favoring hyper-proliferative "immune niche" independent growth. Genetic inactivation of Notch in glioma cells also attenuates their response to interferon-gamma establishing a non-cell autonomous inhibitory feedback loop that further promotes immune evasion and aggressiveness. Hence, we propose that Notch signaling levels in tumor cells are key to orchestrate immune escape and microenvironment independency during brain tumor formation.

overall_design: CD45+ immune cells from pools of 9 healthy brains, 15 control tumors and 9 Rbpj-/- tumors were purified by FACS and analyzed by single cell RNA-seq.


title: High throughput ribosome profiling of E. coli expressing a library of heterologous proteins

city: La Jolla

first: Wun Kiat Justin

last: Tan

state: California

address: 9500 Gilman Drive #0412, PFBH 414

institute: UCSD

summary: Heterologous gene expression to expand the native genetic capability of E. coli is the backbone of protein expression and metabolic engineering. The goal of this study was to determine how the identity of the heterologous gene expressed affected the host cell transcriptome. We generated a library of E. coli expressing 46 heterologous genes through an identical rhamnose inducible expression system and perform high throughput ribosome profiling.

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

first: Justin

first: Bernhard

middle: O

last: Palsson


title: Identification of genes downregulated after Mettl3 knockdown under DNA damage conditions in E1A;HRasV12 expressing mouse embryonic fibroblasts

city: Stanford

first: Nitin

last: Raj

state: CA

address: 269 Campus Drive, CCSR-South, Rm 1240, MC5152

department: Radiation Oncology

institute: Stanford University

summary: The goal of the study was to identify those genes that are downregulated after Mettl3 knockdown under DNA-damage condition in oncogene-expressing mouse embryonic fibroblasts

overall_design: We performed RNA-seq to identify those genes that are downregulated after Mettl3 knockdown under DNA-damage. We utilized oncogene-expressing fibroblasts expressing control shRNAs or shRNAs directed against Mettl3 to acutely knockdown Mettl3, and we treated cells for 6 hours with o,2 ug/ml of doxorubicin before performing RNA-seq.

first: Laura

middle: D

last: Attardi


title: DNA methylation analysis of porcine blastocyst from oocyte exposed to the high level of NEFAs

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

summary: The DNA methylation pattern in blastocyst that developed from oocytes exposed to the high level of NEFAs was investigated.  Genome-wide DNA methylation analysis was performed by microarray using EDMA platform.

overall_design: Two condition experiment,  4 pools of 10 blastocysts, collected on Day 7 and Day 8

first: Meihong

last: Shi


title: Transcriptomic analysis of porcine blastocyst from oocyte exposed to the high level of NEFAs

summary: The transcriptome pattern in blastocyst that developed from oocytes exposed to the high level of NEFAs was investigated. Genome-wide transcriptome analysis was performed by micro array using EDMA platform.


title: A small molecule screen identified N-Acetyl-L-cysteine for promoting ex vivo growth of single circulating tumor cell

city: Los Angeles

first: Min

last: Yu

address: 1450 Biggy Street, NRT 3507

department: USC Norris Comprehensive Cancer Center, Keck School of Medicine

institute: University of Southern California

summary: CTCs contain a small subset of metastatic precursors that can form metastases in secondary organs, and provide a resource to identify mechanisms underlying metastasis-initiating properties. Despite technological advancements that allow for highly sensitive approaches of detection and isolation, CTCs are very rare and often present as single cells, posing an extreme challenge for ex vivo expansion after isolation. Here, using previously established patient-derived CTC lines, we performed a small molecule drug screening to identify compounds that can improve ex vivo culture efficiency for single CTCs. We found that N-acetylcysteine (NAC) and other antioxidants can promote ex vivo expansion of single CTCs, facilitating subsequent functional analyses.

overall_design: single CTCs from the BRx68 were treated with various compounds as listed below for either 6 or 13 days and RNA sequencing analyses were performed to investigate the effects of the compounds on cells gene expression over time.

first: Yu

last: Min

first: Teng

last: Teng

first: Mohamed

last: Kamal


title: Brain neuronal cell nuclei with exceptionally high levels of hydroxymethylcytosine

city: Athens

first: Robert

last: Schmitz

state: GA

address: B416 Davison Life Sciences

institute: University of Georgia

summary: We recently reported that a significant subpopulation of adult mouse brain cellular nuclei (NeuN-High) have highly decondensed chromatin characteristic of multipotent cells types (Yu et al., DNEU, 2015). Herein we show that NeuN-High nuclei also have significantly higher levels of 5´-hydroxymethylcytosine (5hmC), a rate limiting intermediate in the turnover of modified cytosine. TET-assisted bisulfite sequencing demonstrated that 5hmC levels in NeuN-High nuclei spiked rapidly from 20% to nearly 40% of CG dinucleotides at the start of gene regions for various classes of the most highly transcribed neuron-specific genes, but were variably distributed among different functional gene categories and in well-defined gene regions. NeuN-Low neuronal and non-nueronal neuronal nuclei had significantly lower levels of 5hmC for all classes of expressed genes. In summary, these data support the view that an elevated turnover rate for chromatin modifications may potentiate the cellular memory of the most active subclasses of neurons.

overall_design: TAB-seq data was collected from genomic DNA isolated from NeuN-High, NeuN-Low and NeuN-Neg Mus musculus brain cell nuclei.


title: Chromatin accessibility in the mouse intestinal epithelium across different regions and life stages

city: Piscataway

first: Michael

last: Verzi

state: NJ

address: 145 Bevier Road

institute: Rutgers, the State University of New Jersey

summary: We compare the epigenomes of mouse intestinal epithelial cells at different intestinal regions and life stages of the mouse. We use a sequencing assay for transposase accessible chromatin (ATAC-seq) to determine highly accessible genomic regions. We determine regions that are differentially accessible between intestinal regions (duodenal crypt, duodenal villus, and colon) and between life stages (12-to-15-day-old/juvenile, 90-day-old/adult, and 21-month-old/geriatric).

overall_design: The experiment was designed to compare chromatin accessibility between mice of different ages and within different regions of the intestinal tract. The mouse subjects were divided into three age groups: juvenile mice, which were harvested twelve to fifteen days after birth; adult mice, which were harvested three months after birth; and geriatric mice, which were harvested twenty-one months after birth. Each age group includes three biological replicates (nine mice total). The sequencing data for a proximal colon sample from one geriatric mouse replicate in the colon were discarded due to poor DNA quality. Duodenum epithelial cells and colon epithelial cells were extracted from juvenile mice. Duodenum villus epithelial cells, duodenum crypt epithelial cells, and colon epithelial cells were extracted from adult mice. Duodenum villus epithelial cells, duodenum crypt epithelial cells, and proximal colon epithelial cells were extracted from geriatric mice. Each age and tissue combination formed a condition (8 conditions total).

first: Dennis

last: Aldea

first: Lei

last: Chen

first: Sylvia

last: Christakos


title: Long noncoding RNA expression profiles in intermittent parathyroid hormone induced cementogenesis

status: Public on Jul 06 2022

city: Chengdu

first: Tiancheng

last: Li

address: No. 14, 3rd section of Renmin South Road

institute: West China Hospital of Stomatology, Sichuan University

summary: The aim of this study was to explore the involvement of long noncoding RNAs (lncRNAs) during intermittent parathyroid hormone (PTH) induced cementogenesis.

overall_design: OCCM-30 cells at 80% confluence were treated with 100 ng/ml PTH (dissolved in 0.1% acetic acid), while the control group was treated with 0.1% acetic acid. The treatment of PTH or acetic acid lasted for the first 6 hours in each cycle (one cycle represented 24 hours), then OCCM-30 cells were treated with fresh medium containing no PTH or acetic acid during the subsequent 18 hours in each cycle. After 2 cycles of PTH treatment, cells were harvested and tested. All the samples with three biological replicates were hybridized for each condition (PTH group and control group).

first: Tiangcheng

first: Yuyu


title: RNA demethylase ALKBH5 promotes tumorigenesis in multiple myeloma [m6A-seq]

first: Yifan

last: Hou

summary: We here report ALKBH5, a m6A RNA demethylase, as a crucial oncogene in multiple myeloma (MM). Using various MM models, we demonstrated a critical requirement of ALKBH5 for MM cell proliferation in vitro and in vivo. To identify the potential mRNA targets of ALKBH5, we conducted m6A-seq with mRNA samples enriched from MM cells with or without ALKBH5 knockdown.

overall_design: m6A-seq of RPMI-8226 cells with or without shRNA-mediated ALKBH5 konckdown

first: Zhen

last: Cai


title: Single-cell RNA-seq reveals sequential trophoblast transition during human embryo implantation

first: Xiangxiang

last: Jiang

state: Beijing

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

summary: We performed single-cell RNA sequencing (scRNA-seq) analysis of human post-implantation  trophoblast cells. A hierarchical model was established, which was characterized by the sequential and stepwise development of two primitive cytotrophoblast cell (pCTB) subtypes after the trophectoderm (TE), two primitive syncytiotrophoblast (pSTB) subtypes, and migrative trophoblast cells (MTB). Further analysis characterized a new subtype of fusion-competent cells, which not only prepare for fusion to form primitive syncytiotrophoblast but also possess migration ability, which could be dual-function cells during implantation.  Our work allows for reconstruction of sequential trophoblast cell transcriptional programs transition during implantation and provides a valuable resource to study pathologies in early pregnancy, such as recurrent implantation failure.

overall_design: Combining the in vitro culture of human embryos to the post-implantation stage with scRNA-seq technology, we developed a comprehensive resource characterizing the transcriptional dynamics of trophoblast specification. RNA was extracted from 12 human embryos from day 8 to day 13.

first: Yiming

last: Wang

first: Hongmei


title: eIF1-eIF4G1 inhibitors uncover alternative translation activation of stress-response genes via enhanced ribosome loading and 5’UTR translation [MARS-seq]

city: Rehovot

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

country: Israel

institute: Weizmann Institute of Science

summary: The Ribo-seq and TI-seq analysis following i14G1s (eI1-eIF4G1 inhibitors) treatments uncover opposing roles of eIF1-eIF4G1 and eIF4E-eIF4G1 in scanning-dependent and independent translation. Furthermore, i14G1s inhibition of eIF4G1-eIF1 resulted in translation activation of ER/UPR stress-response genes via enhanced ribosome loading, elevated 5’UTR translation at near cognate AUGs, and unexpected concomitant upregulation of coding-region translation.

overall_design: Ribo-seq and TI-seq analysis was performed either in HEK293T cells treated with either DMSO (vehicle control), i14G1-10  or i14G1-12.

first: Urmila

last: Sehrawat

first: Ora

last: Haimov

first: Ana

middle: T

last: Harush

first: Alexander

last: Plotnikov

first: Rivka

last: Dikstein


title: eIF1-eIF4G1 inhibitors uncover alternative translation activation of stress-response genes via enhanced ribosome loading and 5’UTR translation


title: Binding of cyclin D1  with genomic DNA  revealed by  CHIP-seq in mouse embryonic fibroblasts (MEFs)

city: Wynnewood

first: Xuanmao

last: Jiao

state: PA

address: 100 E Lancaster Ave, LIMR R234

department: Pennsylvania Cancer and Regenerative Medicine Research Center

institute: Baruch S. Blumberg Institute

summary: The CHIP-seq methods were used to determine the binding of cyclin D1 to mouse genomic DNA. The detailed description of this dataset can be found in the publication "ChIP sequencing of cyclin D1 reveals a transcriptional role in chromosomal instability in mice" in Journal of Clinical Investigation (https://www.jci.org/articles/view/60256).

overall_design: Two antibodies were used.

first: Richard

middle: G

last: Pestell

first: Mathew

last: Casimiro


title: Coordinated transcriptional and catabolic programs support iron dependent adaptation to RAS-MAPK pathway inhibition in pancreatic cancer [RNA-Seq]

city: San Francisco

first: Mirunalini

last: Ravichandran

address: 513 Parnassus Avenue, HSW 1301

department: Anatomy

institute: University of California, San Francisco

summary: In this study, human pancreatic ductal adenocarcinoma cells lines (KP4, MiaPaca2) were treated with the MEK inhibitor, Trametinib or DMSO for 48hrs prior to RNA-seq profiling to evaluate significant gene expression changes associated with MEK inhibition. To assess the role of transcription factors MYC and TFE3 in regulation of gene expression changes associated with MEK inhibition, we performed chromatin immunoprecipitation using antibodies against c-MYC and TFE3 in KP4 cells following 48hrs of Trametinib or DMSO treatment.

overall_design: Two human pancreatic cancer cell lines, KP4 and MiaPaca2 were treated with DMSO or Trametinib for 48h in triplicates and the gene expression changes were analyzed by RNA-Sequencing.

first: Charles

first: Yin

last: Shen

first: Rushika

last: Perera


title: Coordinated transcriptional and catabolic programs support iron dependent adaptation to RAS-MAPK pathway inhibition in pancreatic cancer [ChIP-Seq]

overall_design: Human pancreatic cancer cell, KP4 was treated with DMSO or 100nM Trametinib for 48h and chromatin immunoprecipitation was performed for c-MYC and TFE3.


title: Transcription factor Sp9 is a negative regulator of D1-type MSN development [RNA-Seq]

city: Shanghai

first: Zhenmeiyu

last: Li

address: 138 Yi Xue Yuan Road

institute: Fudan University

summary:
The striatum is the main input structure of the basal ganglia, receiving information from the cortex and the thalamus and consisting of D1- and D2- medium spiny neurons (MSNs). D1-MSNs and D2-MSNs are essential for motor control and cognitive behaviors and have implications in Parkinson’s Disease. In the present study, we demonstrated that Sp9 positive progenitors produced both D1-MSNs and D2-MSNs and that Sp9 expression was rapidly downregulated in postmitotic D1-MSNs. Furthermore, we found that sustained Sp9 expression in lateral ganglionic eminence (LGE) progenitor cells and their descendants led to promoting D2-MSNs identity and repressing D1-MSNs identity during striatal development. As a result, sustained Sp9 expression resulted in an imbalance between D1-MSNs and D2-MSNs in the mouse striatum. In addition, the fate-changed D2 like-MSNs survived normally in adulthood. Taken together, our finding supported that Sp9 was sufficient to promote D2-MSNs identity and repress D1-MSNs identity, and Sp9 was a negative regulator of D1-MSNs fate.
The striatum is the main input structure of the basal ganglia, receiving information from the cortex and the thalamus and consisting of D1- and D2- medium spiny neurons (MSNs). D1-MSNs and D2-MSNs are essential for motor control and cognitive behaviors and have implications in Parkinson’s Disease. In the present study, we demonstrated that Sp9 positive progenitors produced both D1-MSNs and D2-MSNs and that Sp9 expression was rapidly downregulated in postmitotic D1-MSNs. Furthermore, we found that sustained Sp9 expression in lateral ganglionic eminence (LGE) progenitor cells and their descendants led to promoting D2-MSNs identity and repressing D1-MSNs identity during striatal development. As a result, sustained Sp9 expression resulted in an imbalance between D1-MSNs and D2-MSNs in the mouse striatum. In addition, the fate-changed D2 like-MSNs survived normally in adulthood. Taken together, our finding supported that Sp9 was sufficient to promote D2-MSNs identity and repress D1-MSNs identity, and Sp9 was a negative regulator of D1-MSNs fate.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for E16.5 striatum between Dlx5/6-CIE; Rosa-Sp9-OE/+ mice and Dlx5/6-CIE mice

first: Zhengang

last: Yang


title: Gene-expression analysis after intratumoral treatment with CMV-derived peptides

city: Bethesda

first: Nicolas

last: Cuburu

address: 37 convent drive

department: CCR

institute: NIH/NCI

summary:
Analysis of whole tumor mRNA with nanostring PanCancer Immune profiling platforrm
In the study presented, we analyzed the expression of  770 genes from the total tumor RNA extracted from 24 solid murine tumors

overall_design: 24 samples, 4 replicates per treatment group, tumor samples were harvested 48hrs after the last of 3 consecutive intratumoral injections

first: John

last: Schiller


title: Alterations of cardiac protein kinases in cyclic nucleotide-dependent signaling pathways in human ischemic heart failure

city: HELSINKI

first: Chunguang

last: Wang

address: BIOMEDICUM Helsinki 2U, Tukholmankatu 8

department: Cardiovascular Research Unit

country: Finland

institute: Minerva Foundation Institute for Medical Research

summary: Impaired protein kinase signaling is a hallmark of ischemic heart disease (IHD). Limited treatment options are available due to inadequate understanding of the pathological mechanisms. Identification of the key kinases in the pathogenesis of IHD with an effort to find potential therapeutic strategies is of high importance. Cardiac kinase activity in end-stage human IHD left ventricles (LVs) and the alteration in related signaling pathways were investigated by kinomics, transcriptomics, and proteomics, and by integration of the multi-omics datasets. Protein kinase A (PKA) and protein kinase G (PKG) ranked on top in the activity shift among the cardiac kinases. In the IHD LVs, PKA activity decreased markedly compared with that of controls (62% reduction, p=0.0034) whereas PKG activity remained stable although the amount of PKG protein increased remarkably (65%, p=0.003). mRNA levels of adenylate cyclases (ADCY 1, 3, 5, 9) and cAMP-hydrolysing phosphodiesterases (PDE4A, PDE4D) decreased significantly, while no statistically significant alterations were observed in that of PKGs (PRKG1 and PRKG2) and guanylate cyclases (GUCYs). mRNA level of CNP decreased remarkably whereas those of BNP, ANP and nyprilysin increased significantly in the IHD LVs. Proteomics analysis uncovered a significant reduction in proteins of ‘Energy metabolism’ and ‘Muscle contraction’ in the patients. Multi-omics integration highlighted intracellular signaling by second messengers as the top enriched Reactome pathway. The deficiency in cAMP/PKA signaling pathways is strongly implicated in the pathogenesis of IHD. Natriuretic peptide CNP could be a potential therapeutic target for the modulation of cGMP/PKG signaling.

overall_design: In an effort to identify novel cardiac kinases potentially involved in IHD and to expand our understanding of the cardiac kinome to search for potential therapeutic targets, we compared control and end-stage IHD human hearts by using an integrated kinomics, transcriptomics, and proteomics approach which allowed evaluation of the global profile changes.

first: Juuso

middle: H

last: Taskinen

first: Heli

last: Segersvärd

first: Katariina

last: Immonen

first: Riikka

last: Kosonen

first: Johanna

last: Tolva

first: Mikko

last: Mäyränpää

first: Petri

last: Kovanen

first: Vesa

last: Olkkonen

first: Juha

last: Sinisalo

first: Mika

last: Laine

first: Ilkka

last: Tikkanen

first: Päivi

last: Lakkisto


title: Coordinated transcriptional and catabolic programs support iron dependent adaptation to RAS-MAPK pathway inhibition in pancreatic cancer

first: Mirunalini

last: Ravichandran

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

overall_design: Refer to individual Series


title: Single-cell RNA-seq analysis of a soft-tissue sarcoma model reveals the critical role of tumor expressed MIF in shaping macrophage heterogeneity. [CITE-Seq 2]

city: Houston

first: Jlenia

last: Guarnerio

state: TX

address: 6767 Bertner Ave

institute: MD Anderson Cancer Center

summary: The standard of care is unsuccessful to treat recurrent and aggressive soft-tissue sarcomas. Interventions aimed at targeting components of the tumor microenvironment have shown promise for many solid tumors, yet have been only marginally tested for sarcoma, partly because knowledge of the sarcoma microenvironment composition is limited. We employed single-cell RNA-sequencing to characterize the immune composition of an undifferentiated pleiomorphic sarcoma mouse model, showing that macrophages in the sarcoma mass exhibit distinct activation states. Sarcoma cells used the pleiotropic cytokine Macrophage Migration Inhibitory Factor (MIF) to interact with macrophages expressing the CD74 receptor to switch macrophages’ activation state and pro-tumorigenic potential. Blocking the expression of MIF in sarcoma cells favored the accumulation of macrophages with inflammatory and antigen-presenting profiles, hence reducing tumor growth. These data may pave the way for testing new therapies aimed at re-shaping the sarcoma microenvironment, in combination with the standard of care.

overall_design: We performed scRNA sequencing to profile the major cell types present in the microenvironment of a murine sarcoma model. We transplanted p53-/- Ccne1+ mouse sarcoma cells subcutaneously on polyurethane scaffolds into 6 recipient mice, and allowed to grow until reaching ~1cm3 in size. The tumors were extracted, digested to single-cell suspensions, and partially enriched for CD45+ immune cells. The samples were individually hashtagged using 6 unique sequenceable oligonucleotides, pooled together in equal proportions, and were captured on the 10X Genomics Chromium platform for single-cell 3’ RNA sequencing, using 2 reactions to target ~10,000 cells total.

first: Emily

middle: Y

last: Ko


title: Single-cell RNA-seq analysis of a soft-tissue sarcoma model reveals the critical role of tumor expressed MIF in shaping macrophage heterogeneity.


title: Single-cell RNA-seq analysis of a soft-tissue sarcoma model reveals the critical role of tumor expressed MIF in shaping macrophage heterogeneity. [bulk RNA-Seq]

overall_design: We performed bulk RNA-seq of sarcoma cells sorted from whole mouse tumors. To see how tumor Mif expression affected cell-autonomous pathways, p53-/- Ccne1+ mouse sarcoma cells were first transduced with (i) Cas9 and either a control sgRNA (sgSCR) or a guide targeting Mif (sgMif) in the case of the knockout experiment, or with (i) Cas9 and either a control shRNA (shSCR) or one targeting Mif (shMif), in the case of the knockdown experiment. The MIF-KO/KD and MIF-WT sarcoma cells were transplanted subcutaneously on polyurethane scaffolds into recipient mice, and allowed to grow until reaching ~1cm3 in size. Tumors were extracted, digested into single-cell suspensions, FACS-purified on the basis of a fluorescent marker, and submitted to RNA-seq.