title: Naïve human pluripotency stem cells respond to Wnt, Nodal and LIF signalling to produce expandable naïve extra-embryonic endoderm

status: Public on Nov 30 2019

city: Copenhagen

first: Josh

middle: M

last: Brickman

address: 3B Blegdamsvej

department: DanStem

country: Denmark

institute: Copenhagen University

type: Expression profiling by high throughput sequencing

summary: Embryonic stem cells (ESCs) can exist in at least two states that transcriptionally resemble different stages of embryonic development. Naïve ESCs resemble peri-implantation stages and primed ESCs the pre-gastrulation epiblast. In mouse, primed ESCs give rise to definitive endoderm in response to pathways downstream of Nodal and Wnt signalling. However, when these cytokines are applied to naïve ESCs, they differentiate to a cell type that approximates early primitive endoderm (PrE), the blastocyst stage progenitor layer that gives rise to the extra-embryonic endoderm. Here, we apply this context dependency to human ESCs, showing that these cytokines drive the differentiation of naïve pluripotent cells to generate extra-embryonic PrE, or hypoblast, and, as in mouse, expanded as an in vitro model for naïve extra-embryonic endoderm (nEnd) in defined conditions. Consistent with observations made in mouse, human PrE differentiation is dependent on FGF signalling in vitro, and we show, that by inhibiting FGF receptor signalling, we could simplify naïve pluripotent culture such that inhibitor requirements closer resembled those used in mouse. These nEnd cultures represent stable extra-embryonic endoderm, or human hypoblast, cell lines.

overall_design: Embryonic stem cell and endoderm types were cultured in their respective standard culture systems for 5 days, after which total RNA was isolated. After this, labelled RNA was purified by standard chemistry, libraries prepared and sequenced.

first: Joshua

first: Madeleine

last: Linneberg-Agerholm


title: EMP2 functions as a novel target for breast cancer stem cells

city: LA

first: Madhuri

last: Wadehra

state: CA

address: 675 Charles Young Dr. South/ 4726 MRL

department: Pathology and Lab Medicine

country: USA

institute: UCLA

summary: Little is know about the role of epithelial membrane protein-2 in breast cancer development or progression.  In this study, we tested the hypothesis that EMP2 may regulate the formation or self-renewal of breast cancer stem cells (BCSC) in the tumor microenvironment.

overall_design: Stable SUM149 cells were created that express a vector control or shRNA lentiviral construct.  Differential expression analysis was performed on these cell lines.

first: Christen

last: Dillard

first: Meagan

last: Kiyohara

first: Gary

last: Lazar

first: Max

last: Wicha


title: DNA methylation alternations in the offspring liver from high fat diet dams

status: Public on Nov 28 2019

city: Beijing

first: Qian

last: Zhang

address: No. 1 Shuaifuyuan, Dongcheng District

country: China

institute: Peking Union Medical College Hospital

type: Methylation profiling by genome tiling array

summary: Maternal high fat diet may disturb susceptibility in offspring. liver from maternal high fat diet has  CpG  sites that exhibit differential DNA methylationregulated compared to control.

overall_design: We performed DNA methylation array analyses of offspring liver from high fat diet dams and control diet dams (n=3 per group).

first: Xinhua

last: Xiao

first: Jia

last: Zheng

first: Ming

last: Li

first: Miao

last: Yu

first: Fan

last: Ping

first: Tong

last: Wang

first: Xiaojing


title: Large B-Cell Lymphomas in Pediatric and Young Adults Display Clinically Relevant Molecular Features Distinguishable from Adult Counterparts [cytoscan]

city: Barcelona

first: Joan

middle: Enric

last: Ramiz-Zaldivar

address: Rosselló, 153

department: Molecular Pathology Laboratory

country: Spain

institute: IDIBAPS

type: Genome variation profiling by genome tiling array

summary: Pediatric aggressive large B-cell lymphomas (LBCL) share morphological and phenotypic features with adult types but seem to have better prognosis. Additionally, a specific subtype carrying IRF4 translocations (LBCL-IRF4) has been recently identified in this age group.

overall_design: The aim of this study was to perform a complete genetic characterization of 60 Large B-cell lymphomas (LBCL) in pediatric and young adult population including LBCL with IRF4 rearrangement (LBCL-IRF4). Twenty-one LBCL-IRF4 cases, 10 High grade B-cell lymphoma, not otherwise specified, 29 diffuse large B-cell lymphoma and 6 relapsed cases with consensus diagnosis were analyzed by fluorescence in situ hybridization, copy number array, gene expression and targeted sequencing analyses of genes associated with B-cell lymphoma pathology.

first: Blanca

last: Gonzalez-Farre

middle: E

last: Ramis-Zaldivar

first: Julia

last: Salmerón-Villalobos

first: Elias

last: Campo

first: Itziar

last: Salaverria


title: Therapeutic opportunities for diffuse midline glioma identified from high-throughput combination drug screening

status: Public on Nov 29 2019

city: Stanford

first: Michelle

last: Monje

address: 265 Campus Drive G3035

department: Neurology

institute: Stanford University

summary: Diffuse midline gliomas (DMG) are a group of molecularly related malignancies occurring in midline structures of the childhood central nervous system, including thalamus, pons, and spinal cord. These cancers are characterized by high prevalence of the histone-3K27M mutation and are universally lethal, with median survival of only 9-11 months for pontine DMG (a.k.a. DIPG). In search of novel therapeutic options, we examined multiple cell models in sequential, quantitative high-throughput screens of approved and investigational drugs. This effort generated a total of 17,456 single-agent dose responses that inspired a subsequent series of HTS-enabled drug combination assessments encompassing a total of 8883 drug-drug examinations. Top combinations were validated across a panel of patient-derived cell lines representing the major DMG genotypes. In vivo testing in patient-derived xenograft models validated the combination of the multi-HDAC inhibitor panobinostat and the proteasome inhibitor marizomib as a promising therapeutic approach. Transcriptional and metabolomic surveys revealed substantial alterations to the cellular unfolded protein response and key metabolic processes following treatment with panobinostat and marizomib. Rescue of drug induced cytotoxicity and basal mitochondrial respiration with exogenous application of nicotinamide mononucleotide (NMN) or exacerbation of these phenotypes when blocking NAD+ production via NAMPT inhibition demonstrated that metabolic catastrophe drives the combination-induced cytotoxicity. This study represents the most comprehensive single-agent and combinatorial drug screen for DIPG reported to date and identifies concomitant HDAC and proteasome inhibition as a promising therapeutic strategy that underscores under-recognized metabolic vulnerabilities in DIPG. The combined screening outcomes represent a public resource for the DMG community.

overall_design: RNA-seq in patient-derived DIPG cell cultures in two replicates. Libraries were sequenced on Illumina NextSeq 500, 1x75.

first: Grant

middle: L

last: Lin


title: Large B-Cell Lymphomas in Pediatric and Young Adults Display Clinically Relevant Molecular Features Distinguishable from Adult Counterparts [Nanostring]


title: Derivation of a CDX2+/p63+ human cytotrophoblast stem cell from pluripotent stem cells in defined conditions

city: La Jolla

first: Mana

last: Parast

state: California

address: 9500 Gilman drive #0695

department: Pathology

institute: University of California San Diego

summary: We show that WA09 human embryonic stem cells (hESC) cultured in minimal media and treated with BMP4 for 4 days differentiate towards a cytotrophoblast (CTB)-like state.

overall_design: We have compared gene expression profiling of WA09 hESC cultured in minimal media and treated with BMP4 for 4 days to a panel of placental tissues (Amnion, and Stroma), primary cells (first and third trimester CTB) and placenta-derived cell lines (choriocarcinoma-derived BEWO and JEG3, and immoratalised extravillous trophoblast (EVT) cell line HTR8).

first: Yingchun

first: Francesca

last: Soncin

first: Matteo

last: Moretto-Zita

first: Anna

last: Wakeland

first: Mariko

last: Horii

first: Karen

last: Sabatini

first: Louise

middle: C

last: Laurent


title: Tumor-induced cholesterol efflux from macrophages drives IL-4 mediated reprogramming and tumor progression

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

country: France

institute: CIML

summary: Tumor-associated macrophages (TAM) have been shown to have important roles in the malignant progression of various cancers. However, macrophages also posses intrinsic tumoricidal activity and can promote the activity of cytotoxic lymphocytes, but they rapidly adopt an alternative phenotype within tumors, associated with immune-suppression and trophic functions that support tumor growth. The mechanisms that promote TAM polarization in the tumor-microenvironment remain poorly understood, these mechanisms may represent important therapeutic targets to block the tumor-promoting functions of TAM and restore their anti-tumor potential. Here we have characterized TAM in a mouse model of metastatic ovarian cancer. We show that ovarian cancer cells promote membrane-cholesterol efflux and the depletion of lipid rafts from macrophages. Increased cholesterol efflux promoted IL-4 mediated reprogramming while inhibiting IFNg-induced gene expression. These studies reveal an unexpected role for tumor-induced membrane-cholesterol efflux in driving the IL-4 signaling and the tumor-promoting functions of TAM, while rendering them refractory to pro-inflammatory stimuli. Thus, preventing cholesterol efflux in TAM could represent a novel therapeutic strategy to block pro-tumor functions and restore anti-tumor immunity.

overall_design: Gene expression profiling of CD64+CCR2+, Tim4+ and Tim4- peritoneal macrophages (PM) from naïve mice and from mice after 4, 6 or 8 weeks upon intra-peritoneal injection of ID8 cells (spontaneously transformed mouse ovarian surface epithelial cells), using Affymetrix Mouse Gene 1.0 ST Array.

first: Pieter

last: Goossens

first: Toby

last: Lawrence


title: Large B-Cell Lymphomas in Pediatric and Young Adults Display Clinically Relevant Molecular Features Distinguishable from Adult Counterparts

first: Joan

last: Ramiz-Zaldivar

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

overall_design: Refer to individual Series


title: EBF1 and PAX5 control pro-B cell expansion via inverse regulation of the c-Myc gene.

city: Lund

first: Mikael

last: Sigvardsson

address: Sölvegatan 19

country: Sweden

institute: Lund University

summary: EBF1 and PAX5 are two transcription factors targeted in human B-ALL. Their importance for normal B-cell differentiation has led to the suggestion that impaired function of these proteins contributes to the developmental block observed in B-lineage leukemia. However, increased understanding of the function of these proteins has suggested more complex roles in malignant transformation. We here report that the loss of EBF1 function in B-cell progenitors results in reduced expression of c-MYC. Ectopic expression of c-MYC rescues B-cell expansion in the absence of EBF1 both in vivo and in vitro and ChIP-seq analysis identifies multiple binding sites for EBF1 in putative regulatory elements of the mouse c-Myc gene. On the contrary, expression of PAX5 in EBF1 deficient cells resulted in down regulation of c-Myc and inhibition of cell expansion. Since both EBF1 and PAX5 bind multiple regulatory elements in the c-Myc gene, these data suggest that EBF1 and PAX5 have opposing functions with regard to regulation of c-Myc expression. This suggests the existence of a lineage restricted regulatory loop controlling the expansion of B-lineage progenitors. The binding of EBF1 and PAX5 to multiple regulatory elements in the human c-MYC gene indicate that this regulatory loop may be of relevance for our understanding of leukemia formation.

overall_design: Ebf1-/- B-cell progenitor cells extracted from murine bone marrow were transduced with constructs encoding either Ebf1 or Ebf1-ER. Transduced cells were maintained in the precense of 4-OHT (Tamoxifen) and RNA-seq was perfomed after depletion of 4-OHT from cultures.

first: Rajesh

last: Somasundaram

first: Kazuki

last: Okuyama

first: James

last: Hagman

first: Xun

last: Wang

first: Jonas

last: Ungerbäck

first: Tobias

last: Strid


title: Effect of metformin on mRNA expression, histone modifications, and chromatin accessibility in lung cancer cells

status: Public on Nov 27 2019

city: Suwon

first: Dongho

last: Kim

address: #300 Chunchun-dong, Jangan-Ku, Suwon, Kyungggi-do

department: Samsung Biomedical Research Institute

country: South Korea

institute: Sungkyunkwan University School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing


title: Inhibition of PARP 1 Protects Against Hyperglycemic-induced Neointimal Hyperplasia by Upregulating TFPI-2 Activity

city: Jinan

first: Mingxiang

last: Zhang

state: China

address: 107, jinan culture road

department: Department of Cardiology

institute: Qilu Hospital of Shandong University

summary:
To investigate the function and potential mechanism of PARP-1 poly(ADP-ribose) polymerase 1 (PARP1) in diabetic neointimal hyperplasia. Type 1 diabetes mellitus was induced using streptozotocin (STZ) in wild-type mice and PARP1-/- mice, and ligation of the left carotid artery was performed to induce neointimal hyperplasia. Ligated carotid arteries from diabetic mice developed more extensive neointimal hyperplasia and showed greater proliferation and migration than arteries from nondiabetic mice. The augmented remodeling response was absent in diabetic mice deficient in PARP1. PARP1 deficiency reduces diabetic neointimal hyperplasia by upregulating tissue factor pathway inhibitor (TFPI)-2, which acted as a suppressor of vascular smooth muscle cell (VSMCs) proliferation and migration.
The underlying mechanisms involve PARP1 that acts as a negative transcription factor by enhancing TFPI-2 promoter DNA methylation. Our studies demonstrated for the first time that Inhibition of PARP1 alleviates neointimal hyperplasia in diabetes by up-regulating TFPI-2 expression and blocking VSMC proliferation and migration. The development of PARP1 inhibitors might serve to limit mainly proliferative and migratory processes in restenosis-prone diabetic patients

overall_design: HASMCs were treated with PARP-1 inhibitor PJ34 or PBS, and total RNA was purified with the RNeasy Mini Kit (Qiagen, Hilden, Germany). The concentration and purity were checked using a NanoDrop-1000 spectrophotometer (Thermo Fisher Scientific) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Biotin-labeled cRNA was synthesized using a Genechip 3 IVT PLUS Reagent Kit (Thermo Fisher Scientific). After fragmentation, each sample was hybridized onto a GeneChip™ Human Transcriptome 2.0 Array (Thermo Fisher Scientific). The procedure was conducted following the manufacturer s protocol. Statistical analysis was performed with the statistical software program R (ver. 2.7.2, 3.1.2). The CEL files were normalized using the DFW method (R ver. 2.7.2), and PCA was performed using R ver. 3.1.2. Using the Rank Products method (R ver. 3.1.2), probe sets that met the criterion of FDR < 0.05 were extracted as DEGs. Canonical pathway analysis of the DEGs was performed with Qiagen s Ingenuity Pathway Analysis (IPA, www.qiagen.com/ingenuity) (Qiagen). Pathways with p-value < 0.05 and |Z-score| 2 were extracted as being significantly regulated.

first: B

last: Liu

first: Y

first: Z

first: F

last: Xie

first: W

last: Qiao

first: C

last: Li

first: M

first: X

last: Ji

last: Guo


title: Effect of metformin on mRNA expression in lung cancer cells

summary: The genes whose transcription was significantly altered by metformin were investigated in H1299 cells by RNA-seq. Significantly up- or down-regulated genes were identified by cutoff value of |FC| >= 1.5. Metformin significantly downregulated mRNA levels of 499 genes while upregulating 615. KEGG (Kyoto Encyclopedia of Genes and Genomes) gene enrichment analysis revealed that the highly ranked clusters were cell cycle, apoptosis, cellular senescence and p53 signaling pathways. Multiple cell cycle checkpoint genes such as CCNA, CCNB, CCNE, CDK1, E2F2, E2F6, and E2F8 were downregulated, while certain cell cycle inhibitors such as CDKN2B (p15), CDKN1A (p21), DDIT4, and GADD45 were upregulated.

overall_design: Examination of the transcriptome in H1299 cells treated with or without 5mM metformin.

first: Duk

middle: H


title: Effect of metformin on histone modifications in lung cancer cells

summary: The DNA regions that were associated with the metformin altered expressions of H3K4me3 and/or H3K27me3 were investigated by ChIP-seq, and the regions significantly up- or down-regulated by metformin were identified in H1299 cells. Over 80% of H3K4me3 were discovered within promoter regions, but less than 10% of H3K27me3 were observed in this area. Metformin significantly downregulated H3K4me3 level at the promoter regions of 1113 genes, but upregulated levels in the promoter regions of 1492 genes. Gene enrichment analysis revealed that abundant cell cycle related genes such as PIK3C3, CCNB2, CDK1, CDK6, and E2F8 were upregulated, while certain cell cycle suppressor genes such as CDKN1A (p21) and DDIT4 were downregulated. No specific biological functional cluster was detected in the H3K27me3 up- or downregulated genes.

overall_design: Examination of H3K4me3 and H3K27me3 in H1299 cells treated with or without 5mM metformin.


title: Epigenetic analysis of BlaER1 transdifferentiation

city: Badalona

first: Manel

last: Esteller

state: Barcelona

address: Ctra. de Can Ruti, Cami de les Escoles s/n

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

institute: Josep Carreras Leukaemia Research Institute (IJC)

summary: Study of BLaER1 cell line epigenetic changes induced throughout transdifferentiation. The Illumina Infinium MethylationEPIC Beadchip was used to obtain genomewide methylation profiles of BLaER1 cells at 7 different times throughout transdifferentiation treatment (0h, 3h, 12h, 24h, 48h, 72h and 168h). As a reference, the parental RCH-ACV cell line at 168h of treatment and anonymous donor blood derived macrophages were also profiled.

overall_design: Bisulphite converted DNA from BLaER1 at seven time points of transdifferentiation treatment (0h, 3h, 12h, 24h, 48h, 72h and 168h), RCH-ACV and macrophages, were hybridised to the Illumina Infinium MethylationEPIC Beadchip.

first: David

last: Piñeyro


title: Reverse Phase Protein Array (RPPA) profiling of cell signaling events in MDA-MB-468 cells and PC-3 cells treated with Akt PROTAC degrader-MS21

city: New York

first: Ramon

last: Parsons

state: New York

address: 1425 Madison Ave, L1-15C

department: Oncological Sciences

institute: Icahn school of medicine at Mount Sinai

summary: To compare the cell signaling events between PC-3 cells and MDA-MB-468 cells, we performed a Reverse Phase of Protein Array (RPPA) profiling on 468 and PC-3 Cells that treated with DMSO, AZD5363, MS21 at 1µM for 24hr respectively.

overall_design: To investigate the cell signaling alterations in the PC-3 cells and MDA-MB-468 cells induced by Akt inhibitor-AZD5363 or Akt PROTAC degrader-MS21 treatment, we treated PC-3 cells and MDA-MB-468 cells with DMSO, AZD5363 (AZD), MS21 (021) at 1 µM for 24 hr respectively. Cell lysates were extracted and subjected to RPPA analysis.

first: Jia

last: Xu


title: New, easy, quick and efficient DNA replication timing analysis by high-throughput approaches

city: Paris

first: Jean-Charles

last: Cadoret

address: 15 rue hélène Brion

institute: CNRS/ Université de Paris

summary: DNA replication must be faithful and follow a well-defined spatio-temporal program closely linked to genomic organization, transcription, epigenomic marks, intra-nuclear structures, mutation rate and cell fate determination. Replication timing (RT) analyses require complex, precise and time-consuming experimental procedures, and the study of large-size computer files. We improved the RT protocol to speed up and increase its quality and reproducibility. We partly automated the RT protocol via the IP-star robot (Diagenode) and developed a user-friendly software: the START-R suite (Simple Tool for the Analysis of the Replication Timing based on R). START-R suite is an open source software using an R script and an HTML interface to analyse DNA replication timing in a given cell line from microarray or deep-sequencing results. This new approach can be used by every biologist without specific knowledge in bioinformatics and reduces the time required for generating and analyzing data from several samples simultaneously. START-R suite detects constant timing regions (CTR) but also, and it is a novelty, it identifies temporal transition regions (TTR) and significant differences between two experimental conditions. The informatic global analysis requires less than 10 minutes.

overall_design: Nascent-DNA from early S-phase versus nascent-DNA from late S-phase.

first: Djihad

last: Hadjadj

first: Thomas

last: Denecker

first: Eva

last: Guérin

first: Su

middle: J

first: Fabien

last: Fauchereau

first: Giuseppe

last: Baldacci

first: Chrystelle

last: Maric

first: Jean


title: Transgenic expression of human C19MC miRNAs impacts placental morphogenesis

city: Pittsburgh

first: Jean-Francois

last: Mouillet

state: PA

address: 204 Craft Ave

department: MWRI - OBGYN and Reproductive Sciences

institute: University of Pittsburgh

summary: Transgenic mice carrying the human C19MC locus expressing a family of primate-specific microRNAs (miRNAs) were generated. Similar to humans, the expression of C19MC miRNAs was mainly detected in mouse placentas. We use mouse gene expression microarrays to analyze the impact of the transgenic miRNAs on mouse placenta gene expression profiles. The transgenic mice in this study were bred to homozygocy and are referred to as dTG.

overall_design: Total RNA were isolated from two placentas collected from a wild type pregnant mouse and six placentas collected from two transgenic females. Some embryos from dTG mice were substantially smaller in size although it did not reach statistical significance

first: Julie

last: Goff

first: Elena

last: Sadovsky

first: Huijie

last: Sun

first: W

middle: T

last: Parks

first: Tianjiao

last: Chu

first: Yoel


title: TTF-1/NKX2-1 and ASCL1 binding regions in NCI-H209 and NKX2-1 binding regions in NCI-H441, replicate 2

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

country: Japan

institute: University of Tokyo

summary: Although Thyroid transcription factor-1 (TTF-1, encoded by NKX2-1 gene) is highly expressed in small cell lung carcinoma (SCLC) and lung adenocarcinoma (LADC), difference in the functional roles of TTF-1 between SCLC and LADC remains to be elucidated. The aim of this study was to clarify the differences in the TTF-1 binding regions and functional roles in SCLC and LADC. Employing chromatin immunoprecipitation-sequencing (ChIP-seq) , here we compared the genome-wide TTF-1-binding profiles and the TTF-1-mediated transcriptional programs in a SCLC and a LADC cell lines. We also investigated ASCL1 binding regions in SCLC cells.

overall_design: TTF-1 and ASCL1 ChIP-seq analysis was performed in the small cell lung carcinoma cell line NCI-H209 and lung adenocarcinoma cell line NCI-H441 as independent replicates to GSE129312 and GSE51509, respectively.

first: Satoshi

last: Hokari

first: Yusuke

last: Tamura

first: Masato

last: Morikawa

first: Kohei

last: Miyazono


title: Knockdown IGF-1R triggers viral RNA sensors MDA5- and RIG-1-mediated the mitochondrial apoptosis in colonic cancer cells

first: shuqing

last: wang

address: No.10, You An Men Wai, Fengtai.

institute: Capital Medical University

summary: The important role of IGF-1R in cancers has been well established. Classical model involves IGF-1/2 binding to IGF-1R, following activation of the PI3K/Akt pathway, thereby promoting cell proliferation, apoptosis inhibition and treatment resistance. While IGF-1R has become a promising target for cancer therapy, clinical disclosures subsequently have been less encouraging. The question is whether targeting IGF/IGF-1R still holds therapeutic potential. Here we show a novel mechanism that knockdown IGF-1R surprisingly triggers cytoplasmic viral RNA sensors MDA5 and RIG-1, leading to mitochondrial apoptosis in cancer. We analyzed MDA5 and RIG-1 in the intestinal epithelium of IGF-1R knockdown mice. Igf1r+/- mice demonstrated higher MDA5 and RIG-1 than WT mice. IGF-1R knockdown-triggered MDA5 and RIG-1 was further analyzed in human cancer and normal cells. Increased MDA5 and RIG-1 were clearly seen in the cytoplasm identified by immunofluoresce in the cells silenced IGF-1R. Block off IGF-1R downstream PI3K/Akt did not impact on MDA5 and RIG-1 expression. IGF-1R knockdown-triggered MDA5 and RIG-1 and their signaling pathways were similar to those of viral RNA mimetic poly(I:C) had. IGF-1R knockdown-triggered MDA5 and RIG-1 led to cancer apoptosis through activation of the mitochondrial pathway. In vivo assay, Igf1r+/- mice strongly resisted AOM-induced colonic tumorigenesis through triggering MDA¬5- and RIG-1-mediated apoptosis. Notably, RIG-I and MDA5-mediated proapoptotic signaling pathway is preferential active in cancer cells. These data suggest that targeting IGF-1R-triggered MDA5 and RIG-1 might have therapeutic potential for cancer treatment.

overall_design: Examination of 2 different histone modifications in 2 cell types.

first: Shu

middle: Q

last: Wang

first: Xiang

middle: Y

last: Yang


title: Chronic mucocutaneous candidiasis and connective tissue disorder in humans with impaired JNK1-dependent responses to IL-17A/F and TGF-β [RNA-Seq]

city: Doha

first: Tanwir

last: Habib

address: Al Luqta Street

country: Qatar

institute: Weill Cornell Medicine Qatar

summary: Genetic etiologies of chronic mucocutaneous candidiasis (CMC) disrupt human IL-17A/F-dependent immunity at mucosal surfaces, whereas those of connective tissue disorders (CTD) often impair the TGF-β-dependent homeostasis of connective tissues. The signaling pathways involved are incompletely understood. We report a three-generation family with an autosomal dominant (AD) combination of CMC and a novel CTD that clinically overlaps with Ehlers-Danlos syndrome (EDS). The patients are heterozygous for a private splice-site variant of MAPK8, the gene encoding c-Jun N-terminal kinase 1 (JNK1), a component of the MAPK signaling pathway. This variant is loss-of-expression and loss-of-function in the patients’ fibroblasts, which display AD JNK1 deficiency by haploinsufficiency. These cells have impaired, but not abolished, responses to IL-17A and IL-17F. Moreover, the development of the patients’ TH17 cells was impaired ex vivo and in vitro, probably due to the involvement of JNK1 in the TGF-β-responsive pathway and further accounting for the patients’ CMC. Consistently, the patients’ fibroblasts displayed impaired JNK1- and c-Jun/ATF2-dependent induction of key extracellular matrix (ECM) components and regulators, but not of EDS-causing gene products, in response to TGF-β. Furthermore, they displayed a transcriptional pattern in response to TGF-β different from that of fibroblasts from patients with Loeys-Dietz syndrome and mutations of TGFBR2 or SMAD3, further accounting for the patients’ complex and unusual CTD phenotype. This experiment of Nature indicates that the integrity of the human JNK1-dependent MAPK signaling pathway is essential for IL-17A- and IL-17F-dependent mucocutaneous immunity to Candida, and for the TGF-β-dependent homeostasis of connective tissues.

overall_design: Examination of gene expression in skin fibroblasts treated with IL-17A and TGF-β1

first: Juan

last: Li

first: Marco

last: Ritelli

first: Cindy

middle: S

last: Ma

first: Geetha

last: Rao

first: Emilie

last: Corvilain

first: Salim

last: Bougarn

first: Sophie

last: Cypowyj

first: Lucie

last: Grodecká

first: Romain

last: Lévy

first: Vivien

last: Béziat

first: Lei

last: Shang

first: Kathryn

last: Payne

first: Danielle

last: Avery

first: Mélanie

last: Migaud

first: Soraya

last: Boucherit

first: Sabri

last: Boughorbel

first: Andrea

last: Guennoun

first: Maya

last: Chrabieh

first: Franck

last: Rapaport

first: Benedetta

last: Bigio

first: Yuval

last: Itan

first: Bertrand

last: Boisson

first: Valérie

last: Cormier-Daire

first: Delfien

last: Syx

first: Fransiska

last: Malfait

first: Nicoletta

last: Zoppi

first: Laurent

last: Abel

first: Tomáš

last: Freiberger

first: Harry

last: Dietz

first: Nico

last: Marr

first: Stuart

middle: G

last: Tangye

first: Marina

last: Colombi

first: Jean-Laurent

last: Casanova

first: Anne

last: Puel


title: Effect of metformin on chromatin accessibility in lung cancer cells

first: Dongho

last: Kim

summary: The DNA regions whose chromatin accessibility was significantly altered by metformin were investigated in lung cancer cells by ATAC-seq. Metformin decreased chromatin accessibility in 159 regions but increased it in 124 sites. Most regions were outside of gene promoters defined as TSS ± 3kb. The most suppressed region was 4,667bp downstream of CHAC1, and the most enhanced site was 15,111bp downstream of ERRFI1.

overall_design: Examination of the chromatin accessibility in H1299 cells treated with or without 5mM metformin.

first: Duk


title: Large B-Cell Lymphomas in Pediatric and Young Adults Display Clinically Relevant Molecular Features Distinguishable from Adult Counterparts [oncoscan]

first: Joan

last: Ramiz-Zaldivar

summary: Pediatric aggressive large B-cell lymphomas (LBCL) share morphological and phenotypic features with adult types but seem to have better prognosis. Additionally, a specific subtype carrying IRF4 translocations (LBCL-IRF4) has been recently identified in this age group.

overall_design: The aim of this study was to perform a complete genetic characterization of 60 Large B-cell lymphomas (LBCL) in pediatric and young adult population including LBCL with IRF4 rearrangement (LBCL-IRF4). Twenty-one LBCL-IRF4 cases, 10 High grade B-cell lymphoma, not otherwise specified, 29 diffuse large B-cell lymphoma and 6 relapsed cases with consensus diagnosis were analyzed by fluorescence in situ hybridization, copy number array, gene expression and targeted sequencing analyses of genes associated with B-cell lymphoma pathology.

first: Blanca

last: Gonzalez-Farre

last: Ramis-Zaldivar

first: Julia

last: Salmerón-Villalobos

first: Elias

last: Campo

first: Itziar

last: Salaverria


title: Study of the RINF-knockdown in 3 hematopoietic cell lines

first: Franck

last: Letourneur

address: 22 rue mechain

institute: INSERM

summary:
Expression data in K562, MV4-11, and UT7-5.3
We used microarrays to investigate the impact of RINF (alias CXXC5) gene silencing on whole gene mRNA expression profile

overall_design: Cells were transduced with a lentiviral vector expressing a shRNA directed against CXXC5 mRNA sequence or a control sequence

first: F

last: Pendino

first: A

last: Astori


title: Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome [ODM-nanopore-seq]

city: Göttingen

first: Elisa

last: Oberbeckmann

address: Justus-von-Liebig Weg 11

department: Molecular Biology

country: Germany

institute: University Medical Center Göttingen

summary: Mapping of nucleosomes, the basic DNA packaging unit in eukaryotes, is fundamental for understanding genome regulation as nucleosomes modulate DNA access by their positioning along the genome. A cell population nucleosome map requires two observables: nucleosome positions along the DNA (“Where?”) and nucleosome occupancies across the population (“In how many cells?”). All available genome-wide nucleosome mapping techniques are yield methods as they score either nucleosomal (e.g., MNase-seq, chemical cleavage-seq) or non-nucleosomal (e.g., ATAC-seq) DNA but lose track of the total DNA population for each genomic region. Therefore, they only provide nucleosome positions and maybe compare relative occupancies between positions but cannot measure absolute nucleosome occupancy, which is the fraction of all DNA molecules occupied at a given position and time by a nucleosome. Here, we established two orthogonal and thereby crossvalidating approaches to measure absolute nucleosome occupancy across the Saccharomyces cerevisiae genome via restriction enzymes and DNA methyltransferases. The resulting high-resolution (9 bp) map shows uniform absolute occupancies. Most nucleosome positions are occupied in most cells: 97% of all nucleosomes called by chemical cleavage-seq have a mean absolute occupancy of 90 ± 6% (± SD). Depending on nucleosome position calling procedures, there are 57-60,000 nucleosomes per yeast cell. The few low absolute occupancy nucleosomes do not correlate with highly transcribed gene bodies, but with increased presence of the nucleosome-evicting RSC chromatin remodeling complex there and are enriched upstream of highly transcribed or regulated genes. Our work provides a quantitative method and reference frame in absolute terms for future chromatin studies.

overall_design: Chromatin occupancy measurements by ODM-seq (Occupancy via DNA methylation) and ORE-seq (Occupancy via Restriction Enzymes) of several S. cerevisiae chromatin replicates

first: Michael

last: Wolff

first: Nils

last: Krietenstein

first: Mark

last: Heron

first: Jessica

last: Ellins

first: Andrea

last: Schmid

first: Stefan

last: Krebs

first: Helmut

last: Blum

first: Ulrich

last: Gerland

first: Philipp

last: Korber


title: Large B-Cell Lymphomas in Pediatric and Young Adults Display Clinically Relevant Molecular Features Distinguishable from Adult Counterparts [SNP]

first: Joan

last: Ramiz-Zaldivar

first: Blanca

last: Gonzalez-Farre

last: Ramis-Zaldivar


title: Differential Roles of the Maternal and Zygotic FGF in Neural Induction in the Zebrafish Embryo

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

institute: CABD/CSIC

summary: Comparison of ATAC-seq and RNA-seq datasets in wild type and SU5402 treated zebrafish embryos

overall_design: ATAC-seq and RNA-seq in WT and SU5402 treated zebrafish embryos

first: Hussein

middle: A

last: Saud

first: Carlos

last: Cruz

first: Sandra

last: Jiménez-Gancedo

first: Qiqiug

last: Qiu

first: Stephen

middle: W

last: Wilson

first: Jose

last: Gomez-Skarmeta

first: Tetsuhiro

last: Kudoh


title: Transcriptional profiling of mouse proximal tubular epithelial cells during injury and repair

city: St. Louis

first: Monica

last: Chang-Panesso

state: MO

address: 600 S. Euclid Ave CB 8126

department: Medicine / Nephrology

institute: Washington University in St. Louis

summary: Proximal tubule has a remarkable capacity for repair after acute kidney injury. Whether dedifferentiation or a fixed progenitor population is responsible for this repair remains the subject of ongoing controversy. We have generated a novel genetic mouse model to address this question. We generated a Kim-1-GFPCreERt2 knockin mouse line (Kim1GCE) by homologous recombination. Kim-1 is expressed exclusively in dedifferentiated proximal tubule cells. We crossed this mouse line to the EGFP-L10a mouse line to perform Translating Ribosome Affinity Purification coupled with next generation sequencing (TRAP-seq) to identify the transcriptional signature of tubular epithelial cells during the course of injury and repair. TRAP-seq was performed in kidney samples at day 2, 7, and 14 after bilateral ischemia reperfusion injury and sham.

overall_design: Bigenic Kim1-GCE; EGFPL10a heterozygous male mice (8-10 weeks old) received taxomifen 6 hours before and 24 hours after bilateral ischemia reperfusion injury. Kidneys were harvested at the designated time points for a total of four cohorts with 3 biological replicates in each group: sham, day 2, day 7, and day 14.

first: M

first: F

middle: F

last: Kadyrov

first: H

last: Wu

first: B

middle: D

last: Humphreys


title: Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome [ODM-seq]

first: Elisa

last: Oberbeckmann

first: Michael

last: Wolff

first: Nils

last: Krietenstein

first: Mark

last: Heron

first: Jessica

last: Ellins

first: Andrea

last: Schmid

first: Stefan

last: Krebs

first: Helmut

last: Blum

first: Ulrich

last: Gerland


title: Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome [ORE-seq]

first: Philipp

last: Korber


title: Evaluation of single cell classifiers for single cell RNA-seq datasets

city: Nanjing

first: Xinlei

last: Zhao

address: Sipailou 2

institute: Southeast University

summary: Three human cell lines, K562, HEK293T and A431, and one murine cell line, L929, are mixed with equal proportion in two experiments. One mixture, named Mix3, consists of K562, HEK293T and L929. The other, named Mix4, consists of K562, HEK293T, A431 and L929. These cell lines were processed with the Singleron GEXSCOPETM protocol using GEXSCOPETM Single Cell RNA Library Kit (Singleron) and sequenced on an Illumina Xten. FASTQ data were preprocessed using fastp and STAR.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Three human cell lines, K562, HEK293T and A431, and one murine cell line, L929, were cultured separately in DMEM (Thermo Fisher Gibco) with 10% fetal bovine serum (FBS) (Thermo Fisher Gibco), and 1% penicillin-streptomycin (Beyotime Biotechnology  ) in an incubator with 5% carbon dioxide at 37°C. Single cell suspension with 1×105 cells/mL in concentration in PBS (HyClone) were prepared. Two experiments were conducted. One is named as Mix3 , where K562, 293T and L929 cell suspensions were mixed in 1:1:1 ratio. The other is named as Mix4 , where cell suspensions of all four cell lines were mixed in 1:1:1:1 ratio. Mixed single cell suspensions were then loaded onto microfluidic devices and scRNA-seq libraries were constructed following Singleron GEXSCOPETM protocol using GEXSCOPETM Single Cell RNA Library Kit (Singleron). Sequencing was performed on Illumina Xten with 150 bp paired end reads to obtain a sequencing depth of approximately 6.5K reads/cell.

first: Shuang


title: Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome [MNase-seq]

overall_design: Chromatin occupancy measurements by MNase-seq, ODM-seq (Occupancy via DNA methylation) and ORE-seq (Occupancy via Restriction Enzymes) of several S. cerevisiae chromatin replicates


title: Gene regulation in gastrocnemius muscle of denervated mouse with HDAC4 inducible knockout or class IIa HDAC inhibitior NVS-HD1 treatment

city: Cambridge

first: Jun

last: Shi

state: MA

address: 181 Massachusetts Avenue

institute: Novartis Institutes for Biomedical Research

summary: Our class IIa HDAC inhibitor, NVS-HD1, inhibited HDAC4 with less than 1 nM potency while exhibiting >200 fold selectivity on class IIa HDACs compared to class I (HDAC1, 3, 8) and class IIb (HDAC6) HDACs, making it the most potent and selective class IIa HDAC inhibitor reported so far. We tested the efficacy of NVS-HD1 in the mouse denervation model, either alone or on the genetic background of HDAC4 whole-body inducible knockout (HDAC4 iRKO). Global gene expression changes in gastrocnemius muscles were profiled by RNAseq. In the innervated control legs, HDAC4 knockout or NVS-HD1 caused little changes in gene expression compared to WT mice. HDAC4 knockout or NVS-HD1 mainly reversed denervation induced changes and the genes regulated by them largely overlap, suggesting that NVS-HD1 is quite specific against class IIa HDACs.

overall_design: Transcriptional profiling was performed in gastrocnemius muscles of female WT and HDAC4 iRKO mice treated with vehicle (VEH) or NVS-HD1. Six-month old mice were subjected to denervation surgery on the left leg. On the same day of surgery, animals were dosed of VEH or 10 mg/kg NVS-HD1 twice daily for two weeks. GAS muscles from innervated control legs (CON) and denervated legs (DEN) were harvested and processed for RNA-seq analysis.

first: Jiang

last: Zhu

first: Liqing

last: Luo

first: Sherry

last: Martin

first: Samuel

last: Cadena

first: Anne-Ulrike

last: Trendelenburg

first: David

last: Glass


title: Transcriptomic profiling of ZMPSTE24 knockout endothelial cells: implication of endothelial dysfunction in HGPS

city: Rochester

first: Suowen

last: Xu

state: NY

address: 603 Elmwood Avenue

department: Medicine

institute: University of Rochester

summary: Hutchinson-Gilford progeria syndrome (HGPS) is an ultrarare and fatal disease with features of premature aging and cardiovascular diseases (atherosclerosis, myocardial infarction, and stroke). The molecular basis underlying premature aging driven cardiovascular diseases remains incompletely understood. Since endothelial dysfunction is involved in the initiation and progression of cardiovascular diseases. We hypothesized that HGPS-causing progerin (a mutant form of lamin A) and farnesylated prelamin A drives endothelial dysfunction and cardiovascular disease. In our study, we performed transcriptomic profiling of ZMPSTE24-/- mouse endothelial cells, hoping to find the missing link between progeria and atherosclerosis. We observed that ZMPSTE24-/- endothelial cells have increased farnesylated prelamin A accumulation, and show nuclear structure abnormality. Analysis of RNA-seq data revealed that multiple endothelial homeostasis-related genes and pathways are altered by ZMPSTE24 deletion. Further studies are needed to characterize the biological functions of ZMPSTE24 in the pathogenesis of progeria-associated atherosclerosis.

overall_design: Mouse lung endothelial cells (MLECs, primary culture, no passage) were isolated from ZMPSTE24 wild type (wt) and knockout (ko) mice (gifted by Prof. Loren Fong, UCLA) using CD31+ and ICAM2+-dynabeads double sorting. Cells were phenotypically validated by CD31, VE-cadherin, and vWF immunostaining and efficient DiI-oxLDL uptake. Cell purity was >99% endothelial cells. MLECs were seeded in 0.2% gelatin-coated dishes till confluence. Total RNA was isolated using the RNA-Easy Mini Plus kit (QIAGEN). High quality RNA samples (pre-assessed by Nanodrop measurements) were further processed in the Genome Research Center of the University of Rochester Medical Center. The TruSeq RNA Sample Preparation Kit V2 (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols. Briefly, mRNA was purified from 100ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis. End repair and 3’ adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate amplicons of approximately 200-500bp in size. The amplified libraries were hybridized to the Illumina single end flow cell and amplified using the cBot (Illumina, San Diego, CA) at a concentration of 8pM per lane. Single end reads of 100nt are generated for each sample and aligned to the organism specific reference genome. Sequenced reads were cleaned using Trimmomatic-0.32 before mapping some of to the mouse reference genome (GRCm38.p6) with STAR-2.4.2a. Raw read counts were obtained using HTSeq and gencode M17 mouse gene annotations. DESeq2-1.10.1 was used to perform data normalization and differential expression analysis with an adjusted p-value threshold of 0.05. Then, Cufflinks-2.0.2 Software was used with the gencode 23 human gene annotations to perform differential expression analysis with an FDR cutoff of 0.05.

first: Zheng-Gen

last: Jin

first: Cameron

last: Baker

first: John

middle: M

last: Ashton

first: Jason

middle: R

last: Myers


title: Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome

first: Elisa

last: Oberbeckmann

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

overall_design: Refer to individual Series


title: Vaccine protection against multidrug-resistant Klebsiella pneumoniae in a non-human primate model of severe lower respiratory tract infection

status: Public on Nov 26 2019

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: Klebsiella pneumoniae is a human gut communal organism and notorious opportunistic pathogen.  The relative high burden of asymptomatic colonization by K. pneumoniae is often compounded by multidrug resistance-a potential problem for individuals with significant comorbidities or other risk factors for infection.  A carbapenem-resistant K. pneumoniae strain classified as multilocus sequence type 258 (ST258) is widespread in the United States and can be resistant to many classes of clinically useful antibiotics. Thus, treatment of ST258 infections is often difficult.  Inasmuch as new preventive and/or therapeutic measures are needed for treatment of such infections, we developed an ST258 pneumonia model in cynomolgus macaques and tested the ability of an ST258 capsule polysaccharide type 2 (CPS2) vaccine to moderate disease severity.  Compared with sham-vaccinated animals, those vaccinated with ST258 CPS2 had significantly less disease as assessed by radiograph 24 h after intrabronchial installation of 108 CFUs of ST258.  All macaques vaccinated with CPS2 ultimately developed ST258-specific antibodies that significantly enhanced serum bactericidal activity and killing of ST258 by macaque neutrophils ex vivo.  Consistent with a protective immune response to CPS2, transcripts encoding inflammatory mediators were increased in infected lung tissues obtained from CPS-vaccinated animals compared with control, sham-vaccinated macaques.  Taken together, our data provide support to the idea that vaccination with ST258 CPS can be used to prevent or moderate infections caused by ST258. As with studies performed decades earlier, we propose that this approach can be extended to include multiple capsule types

overall_design: time series

first: Natalia

last: Malachowa

first: Scott

last: Kobayashi

first: Adeline

last: Porter

first: Brett

last: Freedman

first: Patrick

last: Hanley

first: Jamie

last: Lovaglio

first: Greg

last: Saturday

first: Donald

last: Gardner

first: Dana

middle: P

last: Scott

first: Amanda

last: Griffin

first: Kathleen

last: Cordova

last: Long

first: Rebecca

last: Rosenke

first: Daniel

middle: E

last: Bruno

first: Craig

last: Martens

first: Barry

middle: N

last: Kreiswirth

first: Frank

last: DeLeo


title: An atheroprotective transcriptome induced by JQ1 (a BRD4 inhibitor) in human endothelial cells

first: Suowen

last: Xu

summary: The bromodomain and extra terminal domain (BET) family of proteins, including BRD2, BRD3, and BRD4, play a key role in many cellular processes, including inflammatory gene expression, mitosis, and viral/host interaction by controlling the assembly of histone acetylation-dependent chromatin complexes. Previous studies have shown that multiple BET inhibitors (BETi), including JQ1, have therapeutic effects in cancer and cardiovascular diseases. Some BETi have entered different phases of clinical trials. Pharmacologically, JQ1 functions by displacing BET proteins from chromatin by competitively binding to the acetyl-lysine recognition pocket of BET bromodomains. JQ1 has been used as a chemical probe to investigate the role of BET bromodomains in the transcriptional regulation of cardiovascular diseases. For example, JQ1 has been shown to attenuates inflammation and experimental atherosclerosis (Mol Cell. 2014 Oct 23; 56(2): 219–231.). JQ1 has also recently been shown to reduce EndoMT and cardiac fibrosis (J Mol Cell Cardiol. 2019 Feb;127:83-96.). However, the molecular targets of JQ1 dependent or independent of BRD4 remains unknown. To depict the transcriptomic signature of JQ1 in human endothelial cells, we observed a vasoprotective and atheroprotective transcriptome by JQ1 treatment using genome-wide RNA-seq based transcriptomic profiling. JQ1 is a magic bullet in cardiovascular disease prevention. Further elucidation of new molecular targets of JQ1 will lead to the identification of potentially new therapeutic targets to treat cardiovascular diseases.

overall_design: Human umbilical vein endothelial cells (HUVECs, passage 3, 2 different donors) were seeded in 0.2% gelatin-coated dishes the day before experiment. The next day, cells were treated with BRD4 inhibitor (+)-JQ1 (10 uM, purchased from Cayman Chemicals, #11187) for 48 hours. After treatment, total RNA was isolated using the RNA-Easy Mini Plus kit (QIAGEN). High quality RNA samples (pre-assessed by Nanodrop measurements) were further processed in the Genome Research Center of the University of Rochester Medical Center. The TruSeq RNA Sample Preparation Kit V2 (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols. Briefly, mRNA was purified from 100ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis. End repair and 3’ adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate amplicons of approximately 200-500bp in size. The amplified libraries were hybridized to the Illumina single end flow cell and amplified using the cBot (Illumina, San Diego, CA) at a concentration of 8pM per lane. Single end reads of 100nt are generated for each sample and aligned to the organism specific reference genome. Sequenced reads were cleaned using Trimmomatic-0.32 before mapping some of to the human reference genome (GRCh38.p2) with STAR-2.4.2a. Raw read counts were obtained using HTSeq and gencode 23 human gene annotations. DESeq2-1.10.1 was used to perform data normalization and differential expression analysis with an adjusted p-value threshold of 0.05. Then, Cufflinks-2.0.2 Software was used with the gencode 23 human gene annotations to perform differential expression analysis with an FDR cutoff of 0.05.

first: Zheng-Gen

last: Jin

first: Cameron

last: Baker

first: John

last: Ashton

first: Jason

last: Myers


title: Transcriptomic profiling of nasopharyngeal carcinoma (NPC) and normal control samples

first: Bin

last: Zhang

address: 1470 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: To understand the genes and pathways that may potentially drive nasopharyngeal carcinoma (NPC) pathogenesis, we sought out to analyze the transcriptomic data from the disease and control samples. We used RNA-sequencing based gene expression data to identify genes differentially expressed between NPC and normal controls and then characterize the gene ontology and pathways down- or up-regulated in the disease samples.

overall_design: 7 NPC biopsy specimens and 4 normal nasopharyngeal mucosal specimens were sampled. Total RNA were extracted from these samples, and analyzed by RNA-sequencing.

first: Cheng

last: Lin

first: Jingfeng

last: Zong

first: Wansong

first: Minghui

last: Wang

first: Yuanji

first: Rui

last: Zhou

first: Shaojun

first: Qiaojuan

last: Guo

first: Honglin

last: Chen

first: Yunbin

last: Ye

first: Jianji

last: Pan


title: Expression data from Ovarian cancer wild type cells (W1) and cells resisted to Cisplatin (W1CR)

city: Poznań

first: Radosław

last: Januchowski

address: Święcickiego 6

department: Histology and Embryology

country: Poland

institute: University of Medical Sciences

summary:
Tumor cell binding to the microenvironment is regarded as onset of therapeutic resistance, referred to as cell adhesion mediated drug resistance (CAM-DR). Here we elucidate whether CAM-DR occurs in ovarian cancer cells, and contributes to still existing cisplatin resistance.
We used microarrays to detail the global programme of gene expression in ovarian cancer cell lines under different conditions: W1 whithout collagen surface, W1 with collagen surface, WiCR whithout collagen surface and W1CR cultivated on collagen surface.

overall_design: W1 and W1CR cells where cultivated on surface with or whithout collagen coat.

first: Piotr

last: Zawierucha

first: Gerd

last: Bendas

first: Kathleen

last: Wantoch von Rekowski


title: In vivo epigenetic CRISPR screen identifies Asf1a as an immunotherapeutic target in Kras-mutant lung adenocarcinoma

city: New York City

first: Alireza

last: Khodadadi-Jamayran

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

summary: Despite substantial progress in lung cancer immunotherapy, the overall response rate in KRAS-mutant lung adenocarcinoma (ADC) patients remains low. Combining standard immunotherapy with adjuvant approaches that enhance adaptive immune responsesâ€”such as epigenetic modulation of anti-tumor immunityâ€”is therefore an attractive strategy. To identify epigenetic regulators of tumor immunity, we constructed an epigenetic-focused sgRNA library, and performed an in vivo CRISPR screen in KrasG12D/P53-/- (KP) lung ADC model. Our data showed that loss of the histone chaperone Asf1a in tumor cells sensitizes tumors to anti-PD-1 treatment. Mechanistic studies revealed that tumor cell intrinsic Asf1a deficiency induced immunogenic macrophage differentiation in the tumor microenvironment by upregulating GM-CSF expression and potentiated T cell activation in combination with anti-PD-1. Our results provide a rationale for a novel combination therapy consisting of Asf1a inhibition and anti-PD-1 immunotherapy.

overall_design: ATAC seq to compare DNA accisibility in KP cell line with or without Asf1a knockout; ChIP seq to check DNA binding sites of ASF1A in H2009 cell line

first: Fei

last: Li


title: Single-cell transcriptomic profiling of mouse KrasG12DP53-/- (KP) lung tumors in response to tumor cell intrinsic Asf1a knockout (KO), anti-PD-1 or combination treatment (Asf1a KO + anti-PD-1).

summary: We performed single-cell RNA sequencing (scRNAseq) analysis on the mouse lung tissues from KP tumor-bearing mice treated with tumor cell intrinsic Asf1a KO, anti-PD-1 or combination treatment

overall_design: Single-cell RNA-sequencing libraries of mouse tissues using 10x Genomics technology.

first: Kwok-Kin

last: Wong


title: miRNA-Seq profiling of nasopharyngeal carcinoma (NPC) and normal control samples

first: Bin

type: Non-coding RNA profiling by high throughput sequencing

summary: Epstein-Barr virus (EBV) is a ubiquitous human herpesvirus associated with nasopharyngeal carcinoma (NPC). EBV encodes two groups of microRNAs (miRNAs) which are divided into BamHI fragment H rightward open reading frame 1 (BHRF1) and BamHI-A rightward transcripts (BART) microRNAs. EBV miR-BARTs have been found to be involved in the development and progression of NPC. However, the role of EBV-miR-BARTs in NPC progression remains illusive. This study aimed to investigate the role of EBV-miR-BARTs in NPC and explore the underlying mechanisms.

overall_design: 7 NPC biopsy specimens and 4 normal nasopharyngeal mucosal specimens were sampled. Micro-RNA were extracted from these samples, and analyzed by high throughput  sequencing.

first: Cheng

first: Jingfeng

last: Xu


title: Surfactant plus budesonide decreases lung and systemic responses to injurious ventilation in preterm sheep

city: Miami

first: Augusto

last: Schmidt

state: FL

address: 1611 NW 12th ave

institute: University of Miami Miller School of Medicine

summary:
Background: Intratracheal budesonide mixed with surfactant has been investigated as an alternative to decrease lung injury and prevent bronchopulmonary dysplasia in preterm infants. However, possible systemic effects are not known. Our goal was identify systemic effects of intra-tracheal instilled budesonide by transcriptome analysis of the brain and lung in a preterm lamb model of mechanical ventilation.
Methods: We performed RNA-sequencing of the fetal periventricular white matter and liver from preterm sheep after treatment with intratracheal budesonide mixed with surfactant or surfactant alone followed by mechanical ventilation. Unventilated animals were used as controls. mRNA profiles were generated from polyA selected RNA using Illumina platform. Read sequences were aligned to the sheep genome (Oar 4.0) using Bowtie2 followed read counts using featureCounts. We performed differential expression analysis  using EdgeR.
Results: We identified large and significant gene expression genes both in the liver and in the priventricular white matter in animals treated with budesonide+surfactant compared to surfactant alone and unventilated animals. There were complexes synergies and antagonism of effect of ventilation and budesonide on gene expression. Ventilation induced inflammatory signaling in the periventricular white matter and liver which was partially antagonized by budesonide. Budesonide also suppressed developmental pathways in the periventricular white matter.
Conclusions: Intratracheal budesonide had systemic effects including suppression of developmental pathways in the brain. These effects could have clinical implication in affecting the neurodevelopmental outcomes of preterm newborns.

overall_design: mRNA profiles from periventricular white matter and liver from preterm lambs treated with surfactant + budesonide vs surfactant alone vs unventilated lambs was generated by RNA-sequencing using Illumina platform.

first: Noah

last: Hillman

first: Brett

last: Kothe

first: Matthew

last: Kemp

first: Emily

last: Royse

first: Fabrizio

last: Salomone

first: Michael

last: Clarke

first: Gabrielle

last: Musk

first: Alan

middle: H

last: Jobe


title: Transcriptome analysis upon Sin3A or Sam-S knockdown or both in Drosophila cultured S2 cells

city: Detroit

first: Lori

middle: Ann

last: Pile

state: Michigan

address: 5047 Gullen Mall

department: Biological Sciences

institute: Wayne State University

summary: The SIN3 histone modifying complex regulates the expression of multiple methionine catabolic genes including SAM synthetase (Sam-S) as well as the level of S-adenosyl-methionine (SAM). To further investigate the relationship between methionine catabolism and epigenetic regulation by SIN3, we identified genes controlled by SIN3 and SAM-S. As a global transcriptional regulator, SIN3 impacted a wide range of genes. Independently, SAM-S affected a narrow range of genes. Additional genes, however, were influenced in dual knockdown cells. At some genes, SIN3 and SAM-S act independently, for others, redundantly and for a third set, in opposition. Together, the results obtained in the study of SIN3, a cofactor associated with histone modification, and SAM-S, a metabolic enzyme, uncover a complex relationship on regulating transcription.

overall_design: Drosophila S2 cells were treated with dsRNA targetting Sin3A, Sam-S and both, GFP as the control. mRNA profiling of these samples were performed by deep sequencing using Illumina Hiseq2500. Three biological replicates were performed.

first: Mengying

last: Liu

first: Nirmalya

last: Saha

first: Ambikai

last: Gajan


title: RNA-seq to compare gene expression profiles between Asf1a WT and Asf1a KO cells

first: Alireza

last: Khodadadi-Jamayran

summary: KrasG12D/P53-/-(KP)-Cas9 single clone was transfected with ctrl vector, ctrl sgRNA-1, ctrl-sgRNA-2 or ctrl-sgRNA-3 and then selected by using 5ug/ml Blasticidin, to get the 4 ctrl lines; KP-Cas9 single clone was transfected with Asf1a sgRNA-1, sgRNA-2, sgRNA-3 and new sgRNA-1 and then selected by using 5ug/ml Blasticidin, and then picked up single clones with Asf1a KO. For each Asf1a sgRNA, we selected one clone for RNA seq, so totally we have 4 Asf1a KO clones for RNA seq.

overall_design: Examination of differential gene expression profiles between Asf1a WT and Asf1a KO cells.

first: Fei

first: Kwok

middle: K


title: Induction of Sertoli-like cells from human fibroblasts by NR5A1 and GATA4

city: Beijing

first: Jianlin

last: Liang

address: Tsinghua park

department: Medical School

institute: Tsinghua University

summary: Sertoli cells are essential nurse cells in the testis that regulate the process of spermatogenesis and establish the immune-privileged environment of the blood-testis-barrier (BTB). The induction of human Sertoli cells from fibroblasts could provide cellular sources for fertility and transplantation treatments. Here, we report the in vitro reprogramming of human fibroblasts to Sertoli cells and characterize these human induced Sertoli-like cells (hiSCs). Initially, five transcriptional factors (NR5A1, GATA4, WT1, SOX9 and DMRT1) and a gene reporter carrying the AMH promoter were utilized to obtain the hiSCs. We further reduce the number of reprogramming factors to two, i.e., NR5A1 and GATA4, and show that these hiSCs have transcriptome profiles that are similar to those of primary human Sertoli cells. Consistent with the known cellular properties of Sertoli cells, hiSCs attract endothelial cells and exhibit high number of lipid droplets in the cytoplasm. More importantly, hiSCs can sustain the viability of spermatogonia cells harvested from mouse seminiferous tubules. In addition, hiSCs suppress the production of IL-2 and proliferation of human T lymphocytes. When hiSCs were cotransplanted with human embryonic kidney cells, these xenotransplanted human cells survived longer in mice with normal immune systems. hiSCs also allow us to determine a gene associated with Sertoli-only syndrome (SCO), CX43, is indeed important in regulating the maturation of Sertoli cells.

overall_design: Examination of whole transcriptome in 7 cell types.

last: Wang

first: Jing

last: He

first: Jian

last: Du

first: Kehkooi

last: Kee


title: Transcriptomic profiling of mRNA and miRNA from nasopharyngeal carcinoma (NPC) and normal control samples

city: New York

first: Bin

last: Zhang


title: HL-60 cells following treatment with different compounds

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI


title: CENP-A associated lncRNAs influence chromosome segregation in human cells

city: Bethesda

first: David

last: Sturgill

state: MARYLAND

address: Building 41, Rm B622

department: NCI

summary: Transcription occurs ubiquitously throughout non-coding parts of the genome, including at repetitive alpha-satellite DNA elements which comprise the majority of human centromeres. The function of temporally regulated centromeric transcription, and transcripts, is consequently a topic of intense investigation. In this study, we use high throughput approaches to identify and describe lncRNAs associated with the centromere specific histone variant CENP-A that arise from the transcription of specific centromeres at early G1, which we then show are physically associated with centromeres, and which are functionally necessary for accurate chromosome segregation. Targeted depletion of one such centromeric RNA, which originates from a single centromere, is sufficient to increase the frequency of chromosome segregation defects. These data support the emerging paradigm of the necessity of centromere-specific lncRNAs in the integrity of faithful chromosome segregation.

overall_design: RNA-immunoprecipitation followed by Illumina sequencing (RIP-Seq) on chromatin associated or nucleoplasmic RNA.

first: Delphine

last: Quénet

first: Minh

last: Bui

first: Marin

last: Olson

first: Yamini

last: Dalal


title: Single-Cell Transcriptomes of Cerebral Cortex in Embryonic 18 Days

city: Shanghai

first: Peng

last: Jian

address: 320 Yue Yang Road

department: Institute of Neuroscience

institute: University of Chinese Academy of Sciences

summary: Cajal-Retzius cells have important role in cerebral cortex development, such as secreted Reln protein, maintain normal lays of  cerebral cortex. To explore novel secretory protein of Cajal-Retzius cells and to survey the roles of Cajal-Retzius cells in cerebral cortex development, we analyzed transcriptome profiles of 6753 single cells of the embryonic 18 days.

overall_design: Examination mouse cerebral cortex of embryonic 18 days

last: Tang

first: Zhen-Ge

last: Luo


title: H3K9 acetylation and di-methylation changes in HL-60 cells following treatment with different compounds

summary: We investigate the effects of GCN5 and LSD1 inhibition in acute myeloid leukemia. Therefore, we characterized acetylation and di-methylation changes by ChIP-seq in AML cells (AML M2 cell line HL-60) following treatment with ATRA, MB3, GSK-LSD1 and their combinations.

overall_design: 15 samples in 3 groups: H3K9ac, H3K9me2 and Input DNA are provided for treatments with ATRA, ATRA+MB3, ATRA+GSK-LSD1, ATRA+GSK-LSD1 and ATRA+GSK-LSD1+MB3

first: Melanie

last: Kahl

first: Martin

last: Bens

first: Tino

last: Schenk


title: Comparative transcriptome analysis of Asparagus officinalis and A. kiusianus in response to Phomopsis asparagi

city: Tottori

first: Mostafa

last: Abdelrahman

address: Hamasaka

department: Arid Land Research Center

institute: Tottori University

summary: We report the application of high-throughput transcriptome profiling of susceptible A. officinalis and resistant wild A. kiusianus 24 and 48 hour post-inoculated (24 hpi anf 48 hpi) with P. asparagi infection.

sample_organism:
Asparagus officinalis
Asparagus kiusianus

overall_design: Examination of 2 Asparagus species, 3 conditions (control, 24 hpi and 48 hpi) and 3 biological replicates for each.

first: Akira

last: Kanno


title: RNA-seq of HL-60 cells following treatment with different compounds

summary: We investigate the effects of GCN5 and LSD1 inhibition in acute myeloid leukemia. Therefore, we characterized gene expression changes by RNA-seq in AML cells (AML M2 cell line HL-60) following treatment with ATRA, MB3, GSK-LSD1 and their combinations.

overall_design: 21 samples in 7 groups: Untreated (3 samples), ATRA (3 samples), ATRA+MB3 (3 samples), ATRA+GSK-LSD1 (3 samples), ATRA+GSK-LSD1+MB3 (3 samples), MB3 (3 samples) and GSK-LSD1 (3 samples)


title: Prmt6 is an essential regulator of pluripotency and reprogramming

city: san francisco

first: Yen-Sin

last: Ang

state: CALIFORNIA

address: 1650 Owens Street

institute: Gladstone Institute, UCSF

summary: Illumina Beadchip array analyses of mouse embryonic stem cell gene expression profiles upon knockdown of Prmt6 vs GFP control.

overall_design: Total of 6 samples; Prmt6_shRNA1, Prmt6_shRNA2, GFP_shRNA ; all performed in duplicates

first: Ye

last: Yuan

first: Chi-Yeh

last: Chung

first: Su-Yi

last: Tsai

first: Betty

last: Chang

first: Avinash

last: Waghray

first: Michael

last: Rendl

first: Ihor

last: Lemischka


title: Unravelling the diagnostic dilemma of pancreatic head lesions: A circulating microRNA panel to diagnose distal cholangiocarcinoma

city: Amsterdam

first: Elisa

last: Giovannetti

address: De Boelelaan 1117

department: Medical Oncology

country: Netherlands

institute: VUmc

summary: Introduction: Accurate diagnosis of distal cholangiocarcinoma (CCA) and pancreatic ductal adenocarcinoma (PDAC) is a challenge with clinical consequences. Both are lethal malignancies with distinct therapeutic options. This study aimed to identify a circulating microRNA (miRNA) signature to diagnose and discriminate distal CCA from PDAC.  Methods: In the discovery phase, microarray profiling of 752 miRNAs was performed on plasma samples of seven patients with distal CCA and seven age- and sex-matched healthy controls. Significant candidate miRNAs were selected for validation based on predefined selection criteria. In the validation phase, these miRNAs were analyzed by RT-qPCR in an independent cohort of healthy controls (n=32), benign periampullary disease (n=20), distal CCA (n=24), and age- sex- and stage-matched PDAC (n=24). Data were normalized to a combination of two reference genes. The optimal diagnostic combination of miRNAs was determined by logistic regression. Sensitivity and specificity were evaluated by ROC curves and AUC values.   Results: In the discovery phase, 19 miRNAs were significantly deregulated in patients with distal CCA compared to healthy controls. In the validation phase, 12 candidate miRNAs were selected for validation by RT-qPCR based on pre-defined selection criteria. A two-miRNA panel of downregulated miR-16 and upregulated miR-877 was able accurately distinguish distal CCA from benign disease as well as from PDAC.   Conclusion: This is the first study to identify a combined panel of plasma miRNAs which shows promising diagnostic capability to serve as distal CCA signature with the potential to discriminate distal CCA from PDAC.

overall_design: For the discovery cohort of this study, a microarray was performed on 7 healthy individuals and 7 patients with distal CCA.Plasma samples were collected at diagnosis and RNA was isolated using the small RNA isolation kit (Exiqon). Technical duplicated were included in the subsequent analysis. The plasma miRNA expression levels of healthy individuals were compared to distal CCA.

first: Laura

middle: L

last: Meijer

first: Jisce

last: Puik

first: Tessa

last: Le Large

first: Michal

last: Heger

first: Frederike

last: Dijk

first: Niccola

last: Funel

first: Thomas

last: Wurdinger

first: Ingrid

last: Garajova

first: Nicole

middle: C

last: van Grieken

first: Mark

last: vd Wiel

first: Geert

last: Kazemier


title: Establishment and disease modeling of non-small cell lung cancer organoids

city: Toronto

first: Ming-Sound

last: Tsao

state: Ontario

address: 101 College St

department: Princess Margaret Cancer Research

country: Canada

institute: University Health Network

summary:
Purpose: The goal of this study is to establish and molecularly characterize non-small cell lung cancer (NSCLC) organoids. Generation of NSCLC organoids would provide additional preclinical models for drug screening and biomarker discovery.
Methods: Patient lung tumors and previously established patient-derived xenografts (PDX) were processed to generate organoids. Total RNA was extracted and subjected to RNA-seq to examine the gene expression similarity between patient/PDX/organoid of the same model using t-SNE clustering.
Results: Through RNA-sequencing, we generated TPM values of patient, PDX and organoid samples of 5 models. t-SNE analysis showed that the patient/PDX/organoid of the same models clustered together. The lung adenocarcinoma samples formed a separate cluster from the squamous cell carcinoma samples based on gene expression.
Conclusions: Our study introduces the establishment of NSCLC organoids and demonstrates the gene expession similarity of the organoid model to its corresponding PDX and patient sample.

overall_design: mRNA profiles of human non-small cell lung cancer patient tissue, patient-derived xenograft and organoids were generated by RNA sequencing

first: Ruoshi

last: Shi

first: Quan

last: Li


title: Paternal nicotine enhances fear memory, reduces nicotine administration and alters hippocampal genetic and neural function in offspring

status: Public on Nov 25 2019

city: University Park

first: Lisa

last: Goldberg

state: Pennsylvania

address: 130 Biobehavioral Health Bldg, Penn State University

department: Biobehavioral Health

institute: Penn State University

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


city: Paris

first: Javier

last: Gilabert-Juan

address: 11, Marcelin Berthelot

department: CIRB

institute: College de France

summary: to gain insight into how Mcph1 inactivation affected cell cycle progression and survival of neocortical progenitors at the molecular level, we took advantage of primary cultures of mouse neuroprogenitor cells (mNPCs) that we derived from cortices dissected on E12.5 wild type (WTNPCs) and Mcph1 full knock-out (KONPCs) embryos, and that we amplified as neurospheres. We then conducted comparative transcriptomic analyses between WTNPCs and KONPCs, which revealed differential expression of genes controlling the cell cycle. For instance Chk1 was significantly down-regulated KONECs compared to WTNPCs. Moreover, genes related to metabolic pathways, in particular 93 nuclear genes encoding mitochondrial proteins, also stood out among differentially expressed genes and brought out oxidative phosphorylation as one of the most affected pathway.

first: Jeannette

last: Nardelli


title: Paternal nicotine enhances fear memory, reduces nicotine administration and alters hippocampal genetic and neural function in offspring [Bisulfite-seq]

summary: We tested the effects of chronic paternal nicotine exposure in C57BL6/J mice on hippocampal DNA methylation in F1 offspring.

overall_design: Examination of differential DNA methylation in the hippocampus of offspring from males treated chronically with nicotine or males treated chronically with saline.

middle: J

last: Gould


title: UM171 induces a homeostatic inflammatory-detoxification response supporting human HSC self-renewal

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

institute: Institute for Research in Immunology and Cancer

summary: Elucidation of the molecular cues required to balance adult stem cell self-renewal and differentiation is critical for advancing cellular therapies. Herein, we report that the hematopoietic stem cell (HSC) self-renewal agonist UM171 triggers a balanced pro- and anti-inflammatory/detoxification network that relies on NFKB activation and protein C receptor-dependent ROS detoxification, respectively. We demonstrate that within this network, EPCR serves as a critical protective component as its deletion hypersensitizes primitive hematopoietic cells to pro-inflammatory signals and ROS accumulation resulting in compromised stem cell function. Conversely, abrogation of the pro-inflammatory activity of UM171 through treatment with dexamethasone, cAMP elevating agents or NFKB inhibitors abolishes EPCR upregulation and HSC expansion. Together, these results show that UM171 stimulates ex vivo HSC expansion by establishing a critical balance between key pro- and anti-inflammatory mediators of self-renewal.

overall_design:
Human HSC self-renewal
Single cell sequencing of CD34+ cord blood cells exposed to UM171 for 2 days

first: Jalila

last: Chagraoui

first: Bernhard

last: Lehnertz


title: AML5_DMSO vs UM171

summary: UM171 effect on AML5 cell lines (kinetic)

overall_design: OCI-AML5 cell line and OCI-AML5 cells engineered to express sgRNA against EPCR (EPCR null cell) were exposed to DMSO or UM171. RNA were extracted from sorted subsets and sequences were obtained with an illumina HiSeq 2000 sequencer.


title: The G9a histone methyltransferase inhibitor BIX-01294 modulates gene expression during gametocyte development and transmission

first: Manuel

last: Llinas

address: Millennium Science Complex, Pollock Rd

department: Biochemistry and Molecular Biology

summary: Transmission of the malaria parasite Plasmodium falciparum from the human to the mosquito is initiated by sexual precursor cells, the gametocytes. Gametocytes are formed in response to stress signals and following up-take by a blood-feeding Anopheles mosquito initiate sexual reproduction. Gametocytes need to fine tune their gene expression in order to develop inside the mosquito to continue life-cycle progression. Previously we showed that post-translational histone acetylation controls gene expression during gametocyte development and transmission. However, the role of histone methylation remains poorly understood. We here use the histone G9a methyltransferase inhibitor BIX-01294 to investigate the role of histone methylation in regulating gene expression in gametocytes. Growth assays demonstrated that BIX-01294 inhibits intraerythrocytic replication with an IC50 of 13.0 nM. Furthermore, BIX-01294 significantly impairs gametocyte maturation and reduces the formation of gametes and zygotes. Comparative transcriptomics between BIX-01294-treated and untreated immature, mature and activated gametocytes demonstrated greater than 1.5-fold deregulation of over 359 genes. The majority of these genes are transcriptionally down-regulated in the activated gametocytes and could be assigned to transcription, translation, and signaling indicating a contribution of histone methylations in mediating gametogenesis. Our combined data shows that inhibitors of histone methylation may serve as a multi-stage antimalarials.

overall_design: Plasmodium falciparum Percoll enriched immature (stages II-IV) gametocytes (imGC), mature (stage V) gametocytes (mGC), and gametocytes at 1 h post-activation with 100 µM Xanthurenic acid at RT (aGC) were obtained. Each enriched gametocyte sample was treated with BIX-01294 at IC90 concentrations (0.12 µM) or with 0.5% vol. DMSO (untreated control) for 1 h and 6 h, respectively and total RNA was isolated using the Trizol reagent (Invitrogen) according to the manufacturer’s protocol. The extracted RNA was then processed for microarray analysis.

first: Che

last: Ngwa

first: Meike

last: Kiesow

first: Lindsey

last: Orchard

first: Afia

last: Farrukh

last: Llinás

first: Gabriele

last: Pradel


title: Transcriptomic Analysis Reveals Flavonoid Biosynthesis of Syringa oblata Lindl. in Response to Different Light Intensity

city: Harbin

first: Yanhua

address: College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang, Harbin, Heilongjiang 150030, P.R. China

institute: Northeast Agricultural University

summary: Background: Hazy weather significantly increase air pollution and affect light intensity which may also affect medicinal plants growth. Syringa oblata Lindl. (S. oblata), an effective anti-biofilm medicinal plants, is also vulnerable to changes in plant photoperiods and other abiotic stress responses. Rutin, one of the flavonoids, is the main bioactive ingredient in S. oblata that inhibits Streptococcus suis biofilm formation. Thus, the present study aims to explore the biosynthesis and molecular basis of flavonoids in S. oblata in response to different light intensity.  Results: In this study, it was shown that compared with natural (Z0) and 25% ~ 35% (Z2) light intensities, the rutin content of S. oblata under 50% ~ 60% (Z1) light intensity increased significantly. In addition, an integrated analysis of metabolome and transcriptome was performed using light intensity stress from two kinds of light intensities which S. oblata was subjected to: Z0 and Z1. The results revealed that differential metabolites and genes were mainly related to the flavonoid biosynthetic pathway. We found out that 13 putative structural genes and a transcription factor bHLH were significantly up-regulated in Z1. Among them, integration analysis showed that 3 putative structural genes including 4CL1, CYP73A and CYP75B1 significantly up-regulated the rutin biosynthesis, suggesting that these putative genes may be involved in regulating the flavonoid biosynthetic pathway, thereby making them key target genes in the whole metabolic process.  Conclusions: The present study provided helpful information to search for the novel putative genes that are potential targets for S. oblata in response to light intensity.

overall_design: Examination of 2 different Light Intensity of S. oblata

first: Yan-Hua


title: Expression profiling of cervical cancer cells with IGF2R knock down

city: Tokyo

first: Masayuki

last: Komatsu

address: 5-1-1, Tsukiji, Chuo-ku

institute: National Cancer Center Research Institute

summary:
From comprehensive expression analysis of RNAseq data, IGF2R was found to correlate with poor prognosis in cervical cancer. Gene knockdown of IGF2R lead to cell death in cervical cancer. To reveal its biological function, we performed microarray analysis using IGF2R knockdown cervical cancer cells.
We used microarrays to detail the gene expression alteration by IGF2R gene knockdown by siRNA transfection.

overall_design: BOKU and SKG-I, cervical cancer cell lines were selected as samples. We prepared two set of each condition, transfection of control and IGF2R siRNA. These samples were collected at 72 hours after siRNA transfection

first: Takashi

last: Takeda

first: Rie

last: Komatsuzaki

first: Hiroki

last: Sasaki


title: Expression of Heterologous OsDHAR Gene Improves Glutathione (GSH)-Dependent Antioxidant System and Maintenance of Cellular Redox Status in Synechococcus elongatus PCC 7942

city: Deagu

first: Young-Saeng

last: Kim

address: 80, Daehak-ro

institute: Kyungpook National University

summary: An excess of reactive oxygen species (ROS) can cause severe oxidative damage to cellular components in photosynthetic cells. Antioxidant systems, such as the ascorbate-glutathione cycle, regulate redox status in cells to guard against such damage. Dehydroascorbate reductase (DHAR, EC 1.8.5.1) catalyzes the glutathione-dependent reduction of oxidized ascorbate (dehydroascorbate) and contains a redox active site and glutathione binding-site. The DHAR gene is important in biological and abiotic stress responses involving reduction of the oxidative damage caused by ROS. In this study, a transgenic microalgae (TA) strain was constructed by cloning the Oryza sativa L. japonica DHAR (OsDHAR) gene controlled by an isopropyl β-D-1-thiogalactopyranoside (IPTG)-inducible promoter (Ptrc) into the Synechococcus elongatus PCC 7942 strain of cyanobacteria to study the functional activities of OsDHAR under oxidative stress caused by hydrogen peroxide exposure. OsDHAR expression increased the growth of S. elongatus PCC 7942 under oxidative stress by reducing the levels of hydroperoxides and malondialdehyde (MDA) and mitigating the loss of chlorophyll. DHAR and glutathione S-transferase activity were higher than in the wild-type (WT) strain. Additionally, overexpression of OsDHAR in S. elongatus PCC 7942 greatly increased the glutathione (GSH)/glutathione disulfide (GSSG) ratio compared to ascorbic acid (AsA)/dehydroascorbate (DHA) ratio in the presence or absence of hydrogen peroxide. These results strongly suggest that DHAR attenuates deleterious oxidative effects via the glutathione (GSH)-dependent antioxidant system in cyanobacterial cells. The expression of heterologous OsDHAR in S. elongatus PCC 7942 protected cells from oxidative damage through a GSH-dependent antioxidant system via GSH-dependent reactions at the redox active site and GSH binding site residues during oxidative stress.

sample_organism: Synechococcus elongatus PCC 7942 = FACHB-805

overall_design: Cyanobacterial mRNA profiles of normal and stressed samples that WT and TA were performed as paired-end sequencing, in triplicate, using HiSeq 2000 (Illumina).

first: Seong-Im

last: Park

first: Jin-Ju

first: Joseph

middle: S

last: Boyd

first: Joris

last: Beld

first: Arnaud

last: Taton

first: Kyoung-In

last: Lee

first: Il-Sup

first: James

last: Golden

first: Ho-Sung

last: Yoon


title: circ-GSK3beta Promotes metastasis in esophageal squamous cell carcinoma by targeting GSK3beta to augment beta-catenin Signaling

city: Guangzhou

first: hu

middle: xue

last: ting

address: NO.107 Yanjiangxi Road  Guangzhou

institute: Huxueting

summary: Circular RNAs, a novel class of noncoding RNAs, have recently drawn lots of attention in the pathogenesis of human cancers. However, the role of circRNAs in esophageal squamous cell carcinoma remains unclear. In this study, we aimed to identify novel circRNAs that regulate ESCC progression and explored their regulatory mechanisms and clinical significance in ESCC. We found that CircGSK3beta exerts critical roles in promoting ESCC metastasis and may serve as an exploitable therapeutic target for patients with ESCC. The plasma level of circGSK3beta have promising potential to serve as a novel diagnostic and prognostic biomarker for ESCC detection.

overall_design: We investigated the differential expression profiles of circRNA in three pairs of  esophageal squamous cancer tissues and the corresponding adjacent non-cancerous tissues. The data of each group are collected from independent experiments in triplicate. Transcriptomic analysis was carried out using a microarray.

first: Xueting

last: Hu

first: Huayue

last: Lin


title: Global co-transcriptional splicing in Arabidopsis and the correlation with splicing regulation in mature RNAs

first: shaofang

last: Li

state: Beijing

address: No 50, ZhanghuaLu, HAIDIAN

department: Beijing Vegetable Research Center

institute: Beijing Academy of Agriculture and Forestry Science

summary: RNA splicing and spliceosome assembly in eukaryotes occur mainly during transcription. However, co-transcriptional splicing has not yet been explored in plants. Here, we showed that in Arabidopsis thaliana, nearly all introns undergo co-transcriptional splicing and this occurs with higher efficiency for introns in protein-coding genes than for noncoding RNAs. Co-transcriptional splicing efficiency correlates with density of 19 epigenetic modifications. Total intron number and intron position are two predominant sequence features that correlate with co-transcriptional splicing efficiency, and introns with alternative 5′ or 3′ splice sites are less efficiently spliced. Furthermore, we found that trans-acting protein mutations lead to more introns with increased splicing defects in nascent RNAs than in mature RNAs, and that introns with increased splicing defects in mature RNAs are inefficiently spliced at the co-transcriptional level. Our results not only uncovered widespread co-transcriptional splicing in Arabidopsis, but also uncovered features that may affect or be affected by co-transcriptional splicing efficiency.

overall_design: To study the co-transcriptional splicing in Arabidopsis and possible roles at splicing factors, RNA-seq libraryies were contrusted using total tissue and chromatin fraction in wild type and mutants defective in splicing including mac3a mac3b and prl1 prl2.

first: Shaofang


title: Transcriptional changes after spinal cord injury: recruitment of afferents distal to the site of injury

city: Farmington

first: Richard

last: Mains

state: CT

address: 263 Farmington Ave

department: Neuroscience

institute: UConn Health

summary: Nociceptors are thought to play an important role in chronic pain, but the heterogeneity of this population has made it challenging to understand the underlying mechanisms that attribute pain modalities to specific cell types. We screened for transcript changes within a population of dorsal root ganglion (DRG) cells that are known to be responsible for pain transduction 4 days following spinal cord injury (SCI) to identify genes not previously known to play a role in the transition from chronic to acute pain. We identified genes that had not previously been recognized as major contributors in the development of chronic pain, as well as confirmed previously identified transcription factors already known to play a role in chronic pain.

overall_design: Examination of mRNA profiles in subpopulation of dorsal root ganglion cells after spinal cord injury, followed by quantitative PCR analysis.

first: Jessica

last: Yasko


title: Conjunctival melanoma copy number alterations and correlation with mutation status, tumor features and clinical outcome

city: Liverpool

first: Sarah

last: Coupland

address: West Derby Street

department: Molecular and Clinical Cancer Medicine

country: United Kingdom

institute: University of Liverpool

summary: Relatively little is known about the genetic aberrations of conjunctival melanomas (CoM) and their correlation with clinical and histomorphological features as well as prognosis. The aim of this large collaborative multicentre study was to determine potential key biomarkers for metastatic risk and any druggable targets for high-risk metastatic CoM. Using Affymetrix Single Nucleotide Polymorphism genotyping arrays on 59 CoM, we detected frequent amplifications on chromosome (chr) 6p and deletions on 7q, and characterised mutation-specific copy number alterations. Deletions on chr 10q11.21-26.2, a region harbouring the tumor suppressor genes, PDCD4, SUFU, NEURL1, PTEN, RASSF4, DMBT1 and C10orf90 & 99 significantly correlated with metastases (Fisher’s Exact, p≤0.04), lymphatic invasion (Fisher’s Exact, p≤0.02), increasing tumor thickness (Mann-Whitney, p≤0.02) and BRAF mutation (Fisher’s Exact, p≤0.05). This enhanced insight into CoM biology is a step towards identifying patients at risk of metastasis and potential therapeutic targets for systemic disease.

overall_design: 59 samples in total: 52 primary and 7 locally recurrent conjuncitval melanoma (CoM)

first: Nihal

last: Kenawy

first: Helen

last: Kalirai

last: Sacco

last: Lake

first: Steffen

last: Heegaard

first: Ann-Cathrine

last: Larsen

first: Paul

middle: T

last: Finger

first: Tatyana

last: Milman

first: Kimberly

last: Chin

first: Carlo

last: Mosci

first: Francesco

last: Lanza

first: Alexande

last: Moulin

first: Caroline

middle: A

last: Schmitt

first: Jean

last: Caujolle

first: Célia

last: Maschi

first: Marina

last: Marincovic

first: Azzam

last: Taktak

first: Heinrich

last: Heimann

first: Bertil

last: Damato


title: The Glucocorticoid Receptor Interferes with Progesterone Receptor-Dependent Genomic Regulation in Breast Cancer Cells

city: Autonomous CIty of Buenos Aires

first: Santiago

middle: Andres

last: Rodriguez Segui

address: Intendente Guiraldes s/n

country: Argentina

institute: IFIBYNE-UBA-CONICET

summary: The glucocorticoid and progesterone receptors (GR and PR) are closely related members of the steroid receptor family. Despite sharing similar structural and functional characteristics; the cognate hormones display very distinct physiological responses. In mammary epithelial cells, PR activation is associated with the incidence and progression of breast cancer, whereas the GR is related to growth suppression and differentiation. Despite their pharmacological relevance, only a few studies have compared GR and PR activities in the same system. Using a PR+/GR+ breast cancer cell line, here we report that either glucocorticoid-free or dexamethasone-activated GR inhibits progestin-dependent gene expression associated to epithelial-mesenchymal-transition and cell proliferation. When both receptors are activated with their cognate hormones, PR and GR can form part of the same complex according to co-immunoprecipitation, quantitative microscopy, and sequential ChIP experiments. Moreover, genome-wide studies in cells treated with either dexamethasone or R5020, revealed the presence of several regions co-bound by both receptors.  Surprisingly, GR also binds novel genomic sites in cells treated with R5020 alone. This progestin-induced GR binding was enriched in REL DNA motifs and located close to genes coding for chromatin remodelers. Understanding GR behavior in the context of progestin-dependent breast cancer could provide new targets for tumor therapy.

overall_design: Examination of GR and PR genomewide binding sites in a mammary epithelial cell line expressing both receptors.

first: Maria

middle: F

last: Ogara

last: Rodríguez-Seguí

first: Melisa

last: Marini

first: A

last: Nacht

first: Martin

last: Stortz

first: Valeria

last: Levi

first: Diego

last: Presman

first: Guillermo

last: Vicent

first: Adali

last: Pecci


title: ALDH1A2 Is a Candidate Tumor Suppressor Gene in Ovarian Cancer”

city: Seoul

first: Jae-Hoon

last: Kim

address: 211, Eonju-ro, Gangnam-gu

department: Department of Obstetrics and Gynecology

institute: Gangnam Severance Hospital

summary: nalysis of mechano-regulation of tenocyte metabolism at gene expression level. The hypothesis tested in the present study was that cyclic tensile strain influence the balance of anabolism/catabolism of tenocytes. Results provide important information of the response of tenocyte to cyclic tensile strain, such as specific mechano-responsive genes, up- or down-regulated specific anabolic/catabolic cellular functions.

overall_design: Total RNA obtained from isolated tendon fascicles subjected to 1 or 24 hours in vitro cyclic tensile strain compared to unstrained control fascicles.


title: Transcriptome of MTB H37Rv in glucose L-lactate and pyruvate

city: London

first: Luiz

middle: Pedro

last: de Carvalho

address: 1 Midland Road

department: Laboratory of Mycobacterial Metabolism and Antibiotic Research

institute: The Francis Crick

summary: Mycobacterium tuberculosis has specialised its metabolism to reside extra- and intra-cellularly in the human host. Nutrient availability and their concentrations can vary dramatically in these niches. Lactate is abundant during infection and it is an important signalling molecule regulating the immune response. In addition, lactate is abundant in blood, epithelial mucosa and a number of  other relevant compartments in the host. Interestingly, previous studies have demonstrated that lactate and one of its possible first degradation products, pyruvate, allow superior growth compared to glucose and fatty acids in vitro for M. tuberculosis. Based on this information, we performed a "multi-omics" investigation to study the metabolism of pyruvate and lactate in M. tuberculosis. We employed TraDIS, transcriptomics, proteomics and stable isotopic labelling coupled with mass spectrometry-based metabolomics. Our studies reveal the structure of M. tuberculosis metabolic network associated with catabolism of pyruvate and lactate. Together these findings lead us to reconsider some well-accepted "truths" on carbon metabolism in M. tuberculosis.

overall_design: Comparison of transcriptional profiles induced at 6h and 24h after shift to one carbon source selected between glucose, pyruvate and lactate in H37Rv

first: Agnese

last: Serafini

first: Stuart

last: Horswell


title: Pleiotropic effects of the rne∆MTS allele on RNA degradation

city: Toulouse

first: Laurence

last: Girbal

address: 135 avenue de rangueil

institute: TBI

summary: Localization of RNase E to the inner membrane in Escherichia coli is well documented, but the functional consequences of this localization are largely unknown. Here we characterize the rne∆MTS strain, which expresses cytoplasmic RNase E (cRNase E). CsrB and CsrC regulatory RNAs are stabilized in the rne∆MTS strain resulting in leaky glycogen expression. There is a small but significant global slowdown in mRNA degradation with no bias considering function or localization of encoded proteins. RNase E is a stable protein, but cRNase E is unstable with a half-life equal to the doubling time of exponentially growing cells. cRNase E instability is compensated by increased synthesis. Co-purification experiments show that cRNase E associates with RhlB, enolase and PNPase to form a cytoplasmic RNA degradosome. Measurements in multiple turnover assays show that there is no difference in Km or kcat between cRNase E and RNase E. In contrast to the global slowdown of mRNA degradation, the inactivation of a ribosome-free lacZ transcript is faster in the rne∆MTS strain. We discuss how the association of RNase E with the inner cytoplasmic membrane is important for carbon storage regulation, degradation of polyribosomal mRNA, protection of ribosome-free transcripts from inactivation and stability of RNase E.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: A microarray study was performed to estimate genome-wide mRNA half-lives in two E. coli K12 MG1655 strains, rne+ and rne(ΔMTS), cultured in M9+glucose (3g/l). In mid-exponential phase, sampling was before the addition of rifampicin (500 µg/l) for transcription arrest and over the time after rifampicin addition. Total RNA was then extracted from each sample. Each array measures the expression level of 4,254 genes from Escherichia coli MG1655 with eight 60-mer probes per gene in duplicates. Three independent kinetics were performed for each strain.

first: Lydia

last: Hadjeras

first: Leonora

last: Poljak

first: Marie

last: Bouvier

first: Quentin

last: Morin-Ogier

first: Isabelle

last: Canal

first: Muriel

last: Cocaign-Bousquet

first: Agamemnon

last: Carpousis


title: Transcriptome profiles of porcine oocytes with different developmental competence

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

summary: the objectives of this study was to identify and analyze the transcriptome profiles of porcine oocytes aspirated from follicles of different sizes which showed differences in developmental competence and chromatin configurations using RNA high throughput sequencing technology

overall_design: Cumulus-oocyte complexes (COCs) were aspirated from large (LO; 3-6 mm) or small (SO; 1.5-1.9 mm) ovarian follicles and tested for developmental competence and chromatin configurations. RNA libraries were constructed from both oocyte groups and then sequenced on an Illumina HiSeq4000

first: Lucie

last: Nemcova

first: Matej

last: Murin

first: Jiri

last: Kanka

first: Jozef

last: Laurincik

first: Radek

last: Prochazka