title: Loss of primary cilia drives switching from Hedgehog to Ras/MAPK pathway

status: Public on Oct 10 2018

city: Stanford

first: Francois

last: Kuonen

address: 269 Campus Drive CCSR 2145

department: Dermatology

institute: Stanford University

summary: Basal cell carcinomas (BCCs) rely on Hedgehog (HH) pathway growth signal amplification by the microtubule-based organelle, the primary cilium. Despite naïve tumors responsiveness to Smoothened inhibitors (Smoi), resistance in advanced tumors remains frequent.  While the resistant BCCs usually maintain HH pathway activation, squamous cell carcinomas with Ras/MAPK pathway activation also arise, with the molecular basis of tumor type and pathway selection still obscure. Here we identify the primary cilium as a critical determinant controlling tumor pathway switching. Strikingly, Smoi-resistant BCCs possess an increased mutational load in ciliome genes, resulting in reduced primary cilia and HH pathway activation compared to naive or Gorlin patient BCCs. Gene set enrichment analysis of resistant BCCs with a low HH pathway signature reveals increased Ras/MAPK pathway activation.  Tissue analysis confirms an inverse relationship between primary cilia presence and Ras/MAPK activation, and primary cilia removal in BCCs potentiates Ras/MAPK pathway activation. Moreover, activating Ras in HH-responsive cell lines confers resistance to both canonical (vismodegib) and non-canonical (aPKC and MRTF inhibitors) HH pathway inhibitors, while conferring sensitivity to MAPK inhibitors. Our results provide new insights into BCC treatment and identify the primary cilium as an important lineage gatekeeper, preventing HH to Ras/MAPK pathway switching.

overall_design: Methods: mRNA profiles of DMSO or CBD-treated ASZ wild-type cells and DMSO or CBD-treated RasV12-expressing ASZ cells were generated by deep sequencing, in duplicate, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks.

first: Noelle

last: Huskey

first: Gautam

last: Shankar

first: Anthony

middle: E

last: Oro


title: Extracellular vesicle based therapeutic targeting of b-catenin to modulate anti-cancer immune responses in Hepatocellular Cancer

status: Public on Oct 02 2018

city: Jacksonville

first: Tushar

last: Patel

state: FL

address: 4500 San Pablo Road

country: USA

institute: Mayo Clinic

type: Expression profiling by high throughput sequencing

summary: Combination therapy with anti PD-1 and β -catenin siRNA delivered using biological nanoparticles provide an effective strategy for the treatment of Hepatocellular carcinoma.

overall_design: A synthetic transgenic mouse of experimental HCC induced by MET/ β-catenin expression, and extracellular vesicles as a therapeutic delivery agent were used to evaluate the efficacy of directly targeting β-catenin on response to anti-PD-1.  This series includes data only for anti-PD-1.

first: Akiko

last: Matsuda

first: Kaori

last: Ishiguro

first: Irene

middle: K

last: Yan


title: Regulation of neuroregeneration by long noncoding RNAs

status: Public on Oct 01 2018

city: Rehovot

first: Igor

last: Ulitsky

address: Hertzl St.

country: Israel

institute: Weizmann Institute of Science

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: RNA transcriptome sequencing analysis of SGC-7901 cells transfected with ENST00000431060 shRNA or control shRNA

city: Shanghai

first: Ming

middle: zhe

last: Ma

state: Shanghai

address: 270 DongAn Road

department: Department of Gastric Surgery

country: China

institute: Fudan University Shanghai Cancer Center

summary: RNA transcriptome sequencing analysis was performed in SGC-7901 cells that were transfected with ENST00000431060 shRNA or control shRNA

overall_design: mRNA profiles of SGC-7901 cells transfected with ENST00000431060 shRNA or control shRNA

first: Mingzhe


title: Regulation of neuroregeneration by long noncoding RNAs [ATAC-seq]

summary: In mammals, neurons in the peripheral nervous system (PNS) have regenerative capacity following injury, a capacity which but it is generally absent in the central nervous system (CNS). This difference is attributed, at least in part, to the intrinsic ability of PNS neurons to activate a unique regenerative transcriptional program following injury. Long noncoding RNA (lncRNA) transcripts are typically expressed in a small subset of cell types and may facilitate specificity in regulatory programs. Here we profiled gene expression following sciatic nerve crush in mice, and identified lncRNAs that act in the regenerating neurons, and which are typically not expressed in other contexts. We show that two of these lncRNAs regulate the extent of neuronal outgrowth. We then focus on one of these, Silc1, and show that it regulates neuroregeneration in cultured cells and in vivo, through cis-acting activation of the transcription factor Sox11.

overall_design: ATAC-seq of sham operated or injured, WT of Silc1-/- DRG

first: Rotem

last: Ben-Tov Perry


title: Tracing the transitions from pluripotency to germ cell fate with CRISPR screening

city: Rome

first: Jamie

last: Hackett

address: via Ramarini 32

department: Epigenetics & Neurobiology

country: Italy

institute: European Molecular Biology Laboratory (EMBL)

summary: Early mammalian development entails a series of cell fate transitions that includes transit through naïve pluripotency to post-implantation epiblast. This can subsequently give rise to primordial germ cells (PGC), the founding population of the germline lineage. To investigate the gene regulatory networks that control these critical cell fate decisions, we developed a compound-reporter system to track cellular identity in a model of PGC specification (PGC-like cells; PGCLC), and coupled it with unbiased genome-wide CRISPR screening. This enabled identification of key genes both for exit from pluripotency and for acquisition of PGC fate, with further characterisation revealing a central role for the transcription regulators Nr5a2 and Zfp296 in germline ontogeny. Abrogation of these genes results in significantly impaired PGCLC development accompanied with widespread activation (Nr5a2-/-) or inhibition (Zfp296-/-) of WNT pathway components. This leads to aberrant upregulation of the somatic programme or failure to appropriately activate germline genes in PGCLC, respectively, and consequently loss of germ cell identity. Overall our study places Zfp296 and Nr5a2 as key components of an expanded PGC gene regulatory network, and outlines a transferable strategy for identifying critical regulators of complex cell fate transitions.

sample_organism:
Mus musculus
unidentified plasmid

platform_organism:
Mus musculus
unidentified plasmid

overall_design: Sample1-36: mRNA-seq of epiblast-like cells (EpiLC), and PGCLC at day (D) 2 and D6 of differentiation; 3 biological independent replicates for following genotypes in a Stella-GFP; Esg1-tdTomato background: wild-type, Nr5a2-/-, or Zfp296-/-; Sample37-42: mRNA-seq of infected? embryonic stem cells (ESC), EpiLC and D6 PGCLC; 2 biological replicates; Sample 43-52: gRNA amplicon libraries from embryonic stem cells (ESC), EpiLC or D6 PGCLC from CRISPR screen; 2 biological independent replicates

middle: A

first: Yun

last: Huang

first: Ufuk

last: Günesdogan

first: Kristjan

last: Holm-Gretarsson

first: Toshihiro

last: Kobayashi

first: Azim

last: Surani


title: mRNA-seq of primary bone marrow derived macrophages (BMDM) after Herpes simplex virus-1 infection

city: Beijing

first: Zeming

last: Zhang

address: 38 Xueyuan Rd , Haidian District,Beijing,China

institute: Institude of Systems Biomedicine

summary: Analysis of mRNA-seq of wild type bone marrow derived macrophages reveals how bone marrow derived macrophages response to HSV-1 infection

overall_design: Primary bone marrow derived macrophages generated from bone marrow of C57BL/6 mice were infected by HSV-1 for 0 or 6 hours

first: Dandan

last: Wang

first: Fuping

last: You


title: Gene expression and methylation profile of Human non-functional Pancreatic neuroendocrine tumors (PanNETs)

city: New Brunswick

first: SAURABH

middle: V

last: LADDHA

state: NEW JERSEY

address: 195 Little Albany Street

department: Center for Systems and Computational Biology

institute: Rutgers Cancer Institute of New Jersey


title: Single cell analysis of oral mucosa basal layer cells

city: San Francisco

first: Pauline

middle: Anne Catherine

last: Marangoni

state: CA

address: 513 Parnassus Avenue, HSE15

department: OFS

institute: UCSF

summary: The purpose of this study is to assess the cellular heterogeneity within the buccal mucosal basal layer.

overall_design: Murine buccal mucosa was dissociated into a single cell suspension, and basal cells were FACS sorted based on their high level of CD104 (β4-integrin). Cells were barcoded using 10X genomics Chromium Strategy and 2 technical replicates were sequenced allowing us to look for specific sub-populations within the basal layer.

first: Kyle

middle: B

last: Jones

first: Sachiko

last: Furukawa

first: Hongfang

first: Henry

last: Pinkard

first: Rebecca

last: D'Urso

first: Rapolas

last: Zilionis

first: Allon

middle: M

last: Klein

first: Ophir

middle: D


title: Single-nucleus transcriptomic survey of cell diversity and functional maturation in the postnatal mammalian hearts

city: Philadelphia

first: Hao

last: Wu

state: PA

address: 415 Curie Boulevard

department: Genetics

institute: University of Pennsylvania

summary: A fundamental challenge in understanding cardiac biology and disease is that the remarkable heterogeneity in cell-type composition and functional states have not been well characterized at single-cell resolution in maturing and diseased mammalian hearts.  Massively parallel single-nucleus RNA sequencing (snRNA-Seq) has emerged as a powerful tool to address these questions by interrogating the transcriptome of tens of thousands of nuclei isolated from fresh or frozen tissues.  snRNA-Seq overcomes the technical challenge of isolating intact single cell from complex tissues including the maturing mammalian hearts, reduces biased recovery of easily dissociated cell types and minimizes aberrant gene expression during the whole-cell dissociation.  Here we applied sNucDrop-Seq, a droplet microfluidics-based massively parallel snRNA-Seq method, to investigate the transcriptional landscape of postnatal maturing mouse hearts in both healthy or disease state.  By profiling the transcriptome of nearly 20,000 nuclei, we identified major and rare cardiac cell types and revealed significant heterogeneity of cardiomyocytes, fibroblasts and endothelial cells in the postnatal developing heart.  When applied to a mouse model of pediatric mitochondrial cardiomyopathy, we uncovered profound cell type-specific modifications of the cardiac transcriptional landscape at single-nucleus resolution, including changes of subtype composition, maturation states and functional remodeling of each cell type.  Furthermore, we employed sNucDrop-Seq to decipher the cardiac cell type-specific gene regulatory network (GRN) of GDF15, a heart-derived hormone and clinically important diagnostic biomarker of heart disease.  Together, our results present a rich resource for studying cardiac biology and provide new insights into heart disease using an approach broadly applicable to many fields of biomedicine.

overall_design: Single-nucleus RNA sequencing analysis of postnatal maturing mouse hearts in both healthy or disease state

first: Peng

last: Hu

first: Jian

last: Liu

first: Juanjuan

last: Zhao

first: Benjamin

middle: J

last: Wilkins

first: Katherine

last: Lupino

first: Liming

last: Pei


title: Kidney-resident macrophages promote a proangiogenic environment in the normal and chronically ischemic mouse kidney

city: Rochester

first: Lilach

last: Lerman

state: MN

address: 200 1st St SW

summary: Renal artery stenosis (RAS) caused by narrowing of arteries is characterized by microvascular damage. Macrophages are implicated in repair and injury, but the specific populations responsible for these divergent roles have not been identified. Here, we characterized murine kidney F4/80+CD64+ macrophages in three transcriptionally unique populations. Using fate-mapping and parabiosis studies, we demonstrate that CD11b/cint are long-lived kidney-resident (KRM) while CD11chiMf, CD11cloMf are monocyte-derived macrophages. In a murine model of RAS, KRM self-renewed, while CD11chiMf and CD11cloMf increased significantly, which was associated with loss of peritubular capillaries. Replacing the native KRM with monocyte-derived KRM using bone marrow transplantation followed by RAS, amplified loss of peritubular capillaries. To further elucidate the nature of interactions between KRM and peritubular endothelial cells, we performed RNA-sequencing on flow-sorted macrophages from Sham and RAS kidneys. KRM showed a prominent activation pattern in RAS with significant enrichment in reparative pathways, like angiogenesis and wound healing. In culture, KRM increased proliferation of renal peritubular endothelial cells implying direct pro-angiogenic properties. Human homologs of KRM identified as CD11bintCD11cintCD68+ increased in post-stenotic kidney biopsies from RAS patients compared to healthy human kidneys, and inversely correlated to kidney function. Thus, KRM may play protective roles in stenotic kidney injury through expansion and upregulation of pro-angiogenic pathways

overall_design: CD11chiMf Sham, n=3; CD11chiMf RAS, n=4; CD11cloMf Sham, n=3; CD11cloMf RAS, n=4; KRM Sham, n=4; KRM RAS, n=3;

first: Irina

last: Leaf

first: Amrutesh

middle: S

last: Puranik

middle: O


title: Methylation Heterogeneity within Human non-functional Pancreatic neuroendocrine tumors (PanNETs)

first: SAURABH

last: LADDHA

summary:
DNA CpG methylation profiling of PanNETs patients samples were performed to understand genotype to phenotype corrlelations , novel molecular subtypes and cell of origins
The most commonly mutated genes in pancreatic neuroendocrine tumors (PanNETs) are ATRX, DAXX, and MEN1. Little is known about the cells-of-origin for non-functional neuroendocrine tumors. Here, we genotyped 64 PanNETs for mutations in ATRX, DAXX, and MEN1 and found 37 tumors (58%) carry mutations in these three genes (A-D-M mutant PanNETs) and this correlates with a worse clinical outcome than tumors carrying the wild-type alleles of all three genes (A-D-M WT PanNETs). We performed RNA sequencing and DNA-methylation analysis on 33 randomly selected cases to reveal two distinct subgroups with one group consisting entirely of A-D-M mutant PanNETs. Two biomarkers differentiating A-D-M mutant from A-D-M WT PanNETs were high ARX gene expression and low PDX1 gene expression with PDX1 promoter hyper-methylation in the A-D-M mutant PanNETs. Moreover, A-D-M mutant PanNETs had a gene expression signature related to that of alpha cells (pval < 0.009) of pancreatic islets including increased expression of HNF1A and its transcriptional target genes. This gene expression profile suggests that A-D-M mutant PanNETs originate from or transdifferentiate into a distinct cell type similar to alpha cells.

overall_design: 32 PanNETs tumor specimens were obtained from MKSCC and samples were probed for DNA CpG methylation using Illumina Methylation 450K array and processed as per manufacturers instructions

first: Saurabh

last: Laddha

first: Chang

last: Chan

first: Laura

last: Tang


title: Impact of Assisted Reproduction, Infertility, Sex, and Paternal Factors on the Placental DNA Methylome

city: Toronto

first: Rosanna

last: Weksberg

state: Ontario

address: 555 University Ave.

department: Genetics and Genome Biology

country: Canada

institute: The Hospital for Sick Children

summary: Children conceived using Assisted Reproductive Technologies (ART) have a higher incidence of growth and birth defects, attributable in part to epigenetic perturbations. Both ART and germline defects associated with parental infertility could interfere with epigenetic reprogramming events in germ cells or early embryos. Mouse models indicate that the placenta is more susceptible to the induction of epigenetic abnormalities than the embryo, and thus the placental methylome may provide a sensitive indicator of ‘at risk’ conceptuses. Our goal was to use genome-wide profiling to examine the extent of epigenetic abnormalities in matched placentas from an ART/infertility group and control singleton pregnancies (n=44/group) from a human prospective longitudinal birth cohort, the 3D Study. Principal component analysis revealed a group of ART outliers. The ART outlier group was enriched for females and a subset of placentas showing loss of methylation of several imprinted genes including GNAS, SGCE, KCNQT1OT1 and BLCAP/NNAT. Within the ART group, placentas from pregnancies conceived with IVF/ICSI showed distinct epigenetic profiles as compared to those conceived with less invasive procedures (ovulation induction, intrauterine insemination). Male factor infertility and paternal age further differentiated the IVF/ICSI group, suggesting an interaction of infertility and techniques in perturbing the placental epigenome. Together, the results suggest that the human placenta is sensitive to the induction of epigenetic defects by ART and/or infertility, and we stress the importance of considering both sex and paternal factors and that some but not all ART conceptuses will be susceptible.

overall_design: Placenta from ART smaples are compared to control samples, of note that all samples were collected from one  ART center and over the same period of time. Controls and ART samples were matched for new born sex, term gestation and matcernal age. Furthermore, an analysis comparing ART subtypes (In-vio versus in-vitro) was also performed.

first: Sanaa

last: Choufani

first: Andrei

last: Turinsky

first: Jacquetta

last: Trasler


title: Cryptochrome deletion in p53 mutant mice enhances apoptotic and anti-tumorigenic responses to UV damage at the transcriptome level

city: Istanbul

first: Ayse Derya

last: Cavga

address: Rumelifeneri Yolu, Sariyer

country: Turkey

institute: Koc University

summary: Previous studies have demonstrated that deletion of Cryptochromes (CRY) protects p53-/- mutant mice from early onset of cancer and extends their median lifespan by about 1.5 fold. In vitro studies had revealed that deletion of CRY enhances apoptosis in response to UV damage through activation of p73, and inactivation of GSK3β. However, it was not known at the transcriptome-wide level how CRY deletion delays the onset of cancer in p53-/- mutant mice. In this study, an RNA-seq approach was taken to identify the differentially regulated genes and pathways in p53-/- and p53-/-Cry1-/-Cry2-/- mouse embryonic fibroblasts following UV-induced DNA damage.  Gene Set Enrichment Analysis demonstrated that immune surveillance associated genes regulated by IFN-γ showed increased responses, as well as genes involved in TNFα signaling via NF-κB. Protein network analysis helped identify key genes such as p21, Egr3, Sirt1, Jun and Casp1 among differentially regulated genes, and revealed their interaction partners.  Collectively, the present study suggests that additional genes involved in NF-κB regulation, IFN-γ response, as well as non-coding RNAs may contribute to delaying the onset of cancer in p53-/-Cry1-/-Cry2-/- mice compared to p53-/- mutant mice.

overall_design: Polyadenylated RNA profiles of mouse embryonic fibroblasts from p53-/- and p53-/-Cry1-/-Cry2-/- knockout mice either UV treated or not treated, in two biological replicates, obtained using Illumina HiSeq 2500 platform

first: Ayse

first: Mehmet

last: Tardu

first: Ozlem

last: Keskin

first: Attila

last: Gursoy

first: Nuri

last: Ozturk

first: Ibrahim

middle: H

last: Kavaklı


title: Spontaneous functional network activity in organoids resembles programmed early human brain development

city: La Jolla

first: Gene

last: Yeo

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

institute: UCSD

summary: We describe the different cell types and their differential gene expression patterns present in six-month-old cortical organoids following single cell analysis.

overall_design: Two different experimental replicates (two parallel differentiations started simultaneously) of cortical organoids of WT CVB-iPSCs.

first: Cleber

last: Trujillo

first: Richard

last: Gao

first: Priscilla

last: Negraes

first: Isaac

last: Chaim

first: Alain

last: Domissy

first: Matthieu

last: Vandenberghe

first: Anna

last: Devor

middle: W

first: Bradley

last: Voytek

first: Alysson

middle: R

last: Muotri


title: Regulation of neuroregeneration by long noncoding RNAs [RNA-seq]

first: Igor

last: Ulitsky

overall_design: RNA-seq of intact DRG, cultured DRG neurons, and adult brain

first: Rotem

last: Ben-Tov Perry


title: Peptide design by optimization on a data-parameterized protein interaction landscape

city: Cambridge

first: Amy

last: Keating

address: 77 Massachusetts Ave

department: Biology and Biological Engineering

institute: Massachusetts Institute of Technology

summary: We applied the high-throughput interaction assay SORTCERY to measure thousands of protein-peptide binding affinities and used the data to parameterize models of the peptide-binding landscape for three members of the Bcl-2 family of proteins. We applied the models to design peptides that bound with high affinity and specificity to just one of Bcl-xL, Mcl-1, or Bfl-1. We designed additional peptides that bound selectively to two out of three of these proteins. The raw data provided are the multiplexed fastq files that serve as inputs to our analysis pipeline. Additional detail is available in our corresponding publication and at the following github repository. https://github.com/KeatingLab/sortcery_design

overall_design: DNA samples from yeast-surface display peptide libraries were deep sequenced after sorting with fluorescence activated cell sorting.

first: Justin

last: Jenson

first: Vincent

last: Xue


title: An assessment of prognostic immunity markers in breast cancer

city: Chapel Hill

first: Zhiyuan

last: Hu

state: NC

address: 450 West Dr

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: We used Targeted RNA-seq to generate a gene expression data set of the 72-gene panel (TARGETSEQ) including 483 targeted RNA-seq data of 225 breast cancer FFPE samples from Shanghai and 258 breast cancer FFPE samples from UNC at Chapel Hill. The identified gene panel and risk evaluation model iRDM were developed in training data set AFFY1951 (p<0.0001, n=1951) and further  validated in two other published gene expression datasets including Illumina beads array data METABRIC (p<0.0001, n=1997) and whole transcriptomic mRNA-seq data TCGA (p=0.00019, n=996) and in our own targeted RNA-seq data TARGETSEQ (p<0.0001, n=303) (of 483 RNA-seq samples, 303 with survival data). In conclusion, immunity gene expression were an important parameter for prognosis and therefore can be incorporated into current multi-gene assays to improve assessment of risk of distant metastasis in breast cancer.

overall_design: Gene expression were detected using Targeted RNA-seq. The fastq files were mapped to know region of human genome and gene expression raw counts were obtained and further processed using edgeR and DWD software. The normalized expression data were used for breast cancer subtype classification and risk stratification.

first: Benlong

last: Yang

first: Jeff

last: Chou

first: Yaozhong

last: Tao

first: Dengbin

last: Wu

first: Xinhong

first: Xueqing

last: Li

first: Yan

first: Yiwei

last: Chu

first: Tong

last: Zhou

first: William

last: Kaufmann

first: Lisa

last: Carey

first: Jiong


title: Epigenetic enhancer marks and transcription factor binding influence Vk gene rearrangement frequencies in pre-B cells and pro-B cells

first: Salvatore

last: Loguercio

state: California

address: 10550 North Torrey Pines Rd

department: MB

institute: TSRI

summary: Deep sequencing has the potential to provide great insight into the composition of the antibody repertoire and is now widely used. To date there has not been a study directly comparing relative rearrangement frequencies obtained with unbiased amplification from genomic DNA (gDNA) and cDNA from the same set of cells to elucidate any differences. Here we use a recently developed method for unbiased amplification of gDNA and directly compare the data to the unbiased RNA IgK repertoire from the same pre-B cell pool. We find that ~20% of Vk genes have relative rearrangement frequencies > 2-fold up or down in the RNA vs DNA libraries, including many members of the Vk4, Vk3 and Vk6 families. Regression analysis indicates that Ikaros and E2A binding are associated with strong promoters. Within the pre-B repertoire, we found that the vastly unequal Vk gene rearrangement frequencies are best predicted by epigenetic marks of enhancers. In particular, the levels of newly arising H3K4me1 peaks associated with many Vk genes in pre-B cells are most predictive of rearrangement levels. Comparison of IgK rearrangements that occur in pro-B cells and pre-B cells from the same mice reveal a pro-B cell bias towards usage of Jk-distal Vk genes, particularly Vk 10-96 and surrounding genes. Regression analysis indicates that PU.1 binding is the highest predictor of high Vk gene rearrangement frequency in pro-B cells. Lastly, repertoires of iEk -/- pre-B cells reveal that the intronic enhancer actively influences Vk gene usage and displays a germline transcriptional sphere of influence extending to Vk 6-15, overlapping with the deficit in Jk proximal Vk gene usage. These represent previously unknown roles for iEk in addition to its major function in stimulating overall IgK rearrangement.

overall_design: Input and immunoprecipitated DNA was given to the Next Generation Sequencing Core (TSRI, La Jolla, CA) where it was prepared for massively parallel sequencing on Illumina HiSeq2000.

first: Eden

last: Kleiman

first: Ann

last: Feeney


title: AP-induced hyperphagia is associated with a unique hypothalamic gene expression signature that is abrogated by adjuvant drug treatment

first: Olivia

last: Osborn

address: 9500 Gilman Drive

department: Medicine

summary: Antipsychotic-induced hyperphagia is associated with a unique hypothalamic gene expression signature that is abrogated by adjuvant drug treatment.

overall_design: C57BL/6 female mice were purchased from Jackson labs at 9 weeks of age. All mice were fed normal chow until 10 weeks of age. Olanzapine was compounded into high fat diet (HFD) (45 kcal% from fat) at a concentration of 54 mg/kg of diet (OLZ-HFD, Research Diets, Inc., D09092903, New Brunswick, NJ). Control animals were fed HFD (45 kcal % from fat D09092903) . Minocycline (MINO) was administered in the drinking water at a dose of 0.6mg/ml. At 10 weeks of age mice were randomly divided into four treatment groups (control, OLZ, MINO and OLZ + MINO) and fed these diet/water combinations for the 12 week duration of the study. Mice were then sacrificed and hypothalami dissected for RNA seq analyses.

first: Michael

last: Petrasheck


title: Expression data from browning inguinal white adipose tissue in UCP1/ApoE-DKO mice

city: Kasugai

first: Hitoshi

last: Yamashita

address: 1200 Matsumoto-cho

department: Biomedical Sciences

country: Japan

institute: Chubu University

summary:
Differentiation of brown adipocytes is a crucial process for adaptive thermogenesis, which is stimulated by various factors. We found robust browning of inguinal white adipose tissue in UCP1/ApoE-DKO mice, but not  in ApoE-KO mice, under high-fat diet condition.
We used microarray to determine the genes specifically regulated  in the browning  white adipose tissue in  UCP1/ApoE-DKO mice.

overall_design: Male 9-week-old littermates of ApoE-KO and UCP1/ApoE-DKO mice were given a high-fat diet.  After 9 weeks, inguinal white adipose tissues were isolated for RNA extraction and hybridization on Affymetrix microarray. The RNA samples from three mice in each genotype were mixed for array analysis.


title: Gene array analysis of WT and TAOK3 KO T cells

city: Montreal

first: Joao Vitor

middle: Silva

last: Ormonde

state: QC

address: 1160 Pine Avenue West, Room 603

institute: McGill University

summary: RNA from cells at steady state was subjected to gene array analysis

overall_design: Assessment of gene expression of TAOK3 KO T cells at steady state

first: Zhigang

first: Camille

last: Stegen

first: Joaquin

last: Madrenas


title: Gene expression profiles of alveolar macrophages isolated from wild type (WT) and A20 conditional knockout mice after BLM exposure

first: shanshan

last: liu

address: No.1 Xian Nong Tan St. Xi Cheng District

institute: Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College

summary: Although recent progressions have provided significant mechanistic insights into the pathogenesis of pulmonary fibrosis (PF), few of anti-PF therapeutics show certain promise for this devastating disease. Chronic or repeated lung injury results in chronic inflammation, which functions as a major driven force to promote PF development. Here we report that chronic lung injury inactivates ubiquitin-modifying enzyme A20 to cause a progressive accumulation of transcription factor C/EBPb in macrophages, which produce a number of pro-fibrotic factors to promote PF development. Elevated GSK-3b expression, in response to chronic lung injury, interacts with and phosphorylates A20 to suppress C/EBPb degradation in macrophages. Enforced expression of A20 or pharmacological acceleration of C/EBPb degradation by a peptide restores the A20 activity and provides potent therapeutic efficacy against experimental PF. Our studies reveal a regulatory mechanism of the GSK-3b-A20-C/EBPb axis in alveolar macrophages, by targeting which can treat PF and fibroproliferative lung diseases.

overall_design: mRNA profiles of alveolar macrophages from WT and A20 conditional knockout mice were generated by deep sequencing, in triplicate, using Illumina Hiseq.

first: Shan-shan

last: Liu

first: Xiao-xi

last: Lv


title: RNA-seq analysis of control and NRDE2-depleted breast cancer cells

status: Public on Sep 30 2018

city: Oxford

first: Alan

last: Jiao

state: MA

address: Old Road Campus Research Building

country: United Kingdom

institute: Ludwig Institute for Cancer Research, Oxford University

summary:
Purpose: investigate transcriptomic changes following depletion of the NRDE2 gene
Methods: MDA-MB-231 breast cancer cells were transfected with 20nM control or NRDE2-targeting siRNAs, and RNA was collected after 48h for RNA-seq analysis
Results: We analyzed si-Control and si-NRDE2-treated samples in triplicate (~46-64 million reads per sample) and find that the near-complete loss of NRDE2 results in generally modest changes in gene expression, with only 84 genes deregulated >2-fold. We also identify 342 introns which are differentially retained in NRDE2-depleted cells.
Conclusions: NRDE2 is required for suppressing intron retention in a subset of genes

overall_design: mRNA profiles of control and si-NRDE2-treated MDA-MB-231 cells were generated in triplicate by RNA-seq, using the Illumina NextSeq500 platform

first: Frank

last: Slack

middle: L


title: Transcriptome of human non-functional pancreatic neuroendocrine tumors (PanNETs)

first: SAURABH

last: LADDHA

summary: The most commonly mutated genes in pancreatic neuroendocrine tumors (PanNETs) are ATRX, DAXX, and MEN1. Little is known about the cells-of-origin for non-functional neuroendocrine tumors. Here, we genotyped 64 PanNETs for mutations in ATRX, DAXX, and MEN1 and found 37 tumors (58%) carry mutations in these three genes (A-D-M mutant PanNETs) and this correlates with a worse clinical outcome than tumors carrying the wild-type alleles of all three genes (A-D-M WT PanNETs). We performed RNA sequencing and DNA-methylation analysis on 33 randomly selected cases to reveal two distinct subgroups with one group consisting entirely of A-D-M mutant PanNETs. Two biomarkers differentiating A-D-M mutant from A-D-M WT PanNETs were high ARX gene expression and low PDX1 gene expression with PDX1 promoter hyper-methylation in the A-D-M mutant PanNETs. Moreover, A-D-M mutant PanNETs had a gene expression signature related to that of alpha cells (pval < 0.009) of pancreatic islets including increased expression of HNF1A and its transcriptional target genes. This gene expression profile suggests that A-D-M mutant PanNETs originate from or transdifferentiate into a distinct cell type similar to alpha cells.

overall_design: Evaluation of Cell of origins for non-functional PanNETs and genotype to phenotype correlations in PanNETs

first: Saurabh

last: Laddha

first: Chang

last: Chan


title: Aggressive gene expression signiture of waldenstrom macroglobulinemia with deletion 6q

city: Tachikawa

first: NAOHIRO

last: SEKIGUCHI

state: Tokyo

address: 3256, Midori

department: Hematology

institute: Disaster Medical Center

summary:
Waldenstom macroglobulinemia (WM) with 6q del is still unknown. In the present study, we analyzed gene expression signiture of WM with 6q del.
B-cell receptor signaling pathway, and IL21/IL21-R pathway were up-regulated in WM with 6q del.

overall_design: retrospective study, 8 cases were utilized

first: Naohiro

last: Sekiguchi


title: Human SETMAR is a DNA sequence-specific histone-methylase with a broad effect on the transcriptome

city: Leicester

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

institute: University of Leicester

summary: Transposons impart dynamism to the genomes they inhabit and their movements frequently rewire the control of nearby genes. Occasionally, their proteins are domesticated when they evolve a new function. SETMAR is a protein methylase with a sequence-specific DNA binding domain. It began to evolve about 50 million years ago when an Hsmar1 transposon integrated downstream of a SET-domain methylase gene. Here we show that the DNA-binding domain of the transposase targets the enzyme to transposon-end remnants and that this is capable of regulating gene expression, dependent on the methylase activity. When SETMAR was modestly overexpressed in human cells, almost 1500 genes changed expression by more than 2-fold (65% up- and 35% down-regulated). These genes were enriched for the KEGG Pathways in Cancer and include several transcription factors important for development and differentiation. Expression of a similar level of a methylase-deficient SETMAR changed the expression of many fewer genes, 77% of which were down-regulated with no significant enrichment of KEGG Pathways. Our data is consistent with a model in which SETMAR is part of an anthropoid primate-specific regulatory network centered on the subset of genes containing a transposon end.

overall_design: Examination of the effect of SETMAR or SETMAR N210A expression on U2OS transcriptome and ChIP-exo of Flag-SETMAR in U2OS cells.

first: Ronald

last: Chalmers


title: Repurposing of promoters and enhancers during mammalian evolution

first: Francesco Nicola

last: Carelli

address: Henry Wellcome Building of Cancer and Developmental Biology,  Tennis Court Road

institute: University of Cambridge

summary: The spatiotemporal control of gene expression exerted by promoters and enhancers is central for organismal development, physiology and behaviour. These two types of regulatory elements have long been distinguished from each other based on their function, but recent work highlighted common architectural and functional features. It also suggested that inheritable alterations in the epigenetic and sequence context of regulatory elements might underlie evolutionary changes of their principal activity, which could result in changes in the transcriptional profile of genes under their control or even facilitate the birth of new genes. Here, based on integrated cross-mammalian analyses of DNase hypersensitivity, chromatin modification and transcriptional data, we provide support for this hypothesis by detecting 445 regulatory elements with signatures of activity turnover in sister species from the primate and rodent lineages (termed "P/E" elements). Through the comparison with outgroup species, we defined the directionality of turnover events, which revealed that most instances represent transformations of putative ancestral enhancers into promoters, leading to the emergence of species-specific transcribed loci or 5' exons. Notably, P/E elements have distinct GC sequence compositions and stabilizing 5' splicing (U1) regulatory motif patterns, which may predispose them to functional repurposing during evolution. Moreover, we trace changes in the U1 and polyadenylation signal densities and distributions that accompanied and likely drove the evolutionary activity switches. Overall, our work highlights functional repurposing as a notable mechanism that likely facilitated regulatory innovation and the origination of new genes and exons during mammalian evolution.

sample_organism:
Callithrix jacchus
Macaca mulatta
Homo sapiens
Oryctolagus cuniculus
Mus musculus
Rattus norvegicus

overall_design: 78 single-end strand-specific RNA-seq libraries were generated from polyA-selected RNA from four organs (brain, heart, kidney and liver) from human, macaque, marmoset, mouse, rat and rabbit samples.

first: Francesco

middle: N

first: Angélica

last: Liechti

first: Jean

last: Halbert

first: Maria

last: Warnefors

first: Henrik

last: Kaessmann


title: Epigenetic Enhancer Marks and Transcription Factor Binding Influence Vkappa Gene Rearrangement in Pre-B Cells and Pro-B Cells

first: Salvatore

last: Loguercio

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

overall_design: Refer to individual Series


title: Discovery of inhibitors of the HSP90-Calcineurin-NFAT pathway against glioblastoma

city: Houston

first: Yubin

last: Zhou

state: TX

address: 2121 W Holcombe Blvd

department: Institute of Biosciences and Technology

institute: Texas A&M University

summary: We report the application of mRNA sequencing technology for high-throughput profiling of genes expression changes in U87 glioblastoma cells after treatment with compound YZ129 that we identified in our screen. By analyzing the total mRNA sequencing between YZ129 treatment group and the DMSO control group, we identified that 181 genes were significantly downregulated (changed >2 folds), while 226 genes were significantly upregulated (changed >2 folds). The downregulated genes were mainly associated with hypoxia (ALDOC, TMEM45A, F3, FOS, GFBP1, etc), glycolysis (SLC2A1, ANGPTL4, ENO2, LDHA, PGM, PFKFB3, etc.), PI3K/AKT/mTOR pathway (AK4, SLC2A1, PDK1, PGM1, PLOD2, TUBA4A, etc.), EMT (epithelial-mesenchymal transition) (VEGFA, ID2, COL1A1, FOXC2, LOXL2, etc.), G2/M checkpoint (UBE2C, FBXO5 (Emi1), TOP2A, MCM5/6), etc. some of the upregualted genes may contribute to the possible chemoresistance, such as FOSB, INHBA, EDN1, IRS2, KDM6B. This study yields a global view on molecular response to YZ29 treatment in GBM cells at mRNA level.

overall_design: Examination of gene expression changes in U87 glioblastoma cells after treatment with drug YZ129 (versus DMSO control)


title: 4 NSCLC cell lines treated with GDC-0973, AZ-628 or a combination of both

city: South San Francisco

first: Christiaan

middle: Nicolaas

last: Klijn

address: 1 DNA Way

department: Bioinformatics and Computational Biology

country: Netherlands

institute: Genentech

summary: RNA was purified cancer cell lines. The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech. The ID of this project in Genentech's ExpressionPlot database is PRJ0013114

overall_design: RNA from NSCLC cell lines after treatment with either DMSO, GDC-0973, AZ-628 or the combination of AZ-628 and GDC-0973 all at 0.1 micro-molar concentration.


title: Integrated Multi-omic Analysis of Esthesioneuroblastomas Identifies Two Subgroups Linked to Cell Ontogeny

city: Illkirch

first: Gabriel

middle: G

last: Malouf

address: 1 rue Laurent Fries

department: Cancer and functional genomics

country: France

institute: IGBMC

summary: We report here the multi-omics analysis of esthesioneuroblastomas, which is a rare cancer arising from the olfactory bulb. We discovered ENB can be grouped in two subtypes, namely basal and neural ENBs. We also uncovered high rates of mutations (~35%) in basal ENB subgroup.

overall_design: We report here the multi-omics analysis of esthesioneuroblastomas using whole-exome sequencing (n=27), RNA sequencing (n=19) and DNA methylation profiling (n=26).

first: Marion

last: Classe

first: Hui

last: Yao

first: Xiaoping

last: Su


title: Transcriptomic response to etoposide treatment in immune cell lines

status: Public on Sep 29 2018

city: cambridge

first: olivier

last: papapietro

state: Select

address: addenbrooke's hospital

department: medicine

institute: University cambridge

summary: RNA-seq analysis of the effects of etoposide treatment on transcriptomes of human pre-B, mature B, T and myeloid cell lines.

overall_design: We studied 2 pre-B cell lines (NALM-6, 697), 1 mature B cell line (RAMOS), 1 T cell line (JURKAT) and 2 myeloid cell lines (THP-1, U937). Cells were left untreated or treated with 10uM of etoposide for 4 hours. All experiments were done in triplicate, except for the etoposide-treated 697 cells and untreated U937 cells that were studied in duplicate.

first: Sergey

last: Nejentsev

first: Olivier

last: Papapietro


title: Transcriptome analysis of control and TFEB/TFE3 DKO MEFs and RAW264.7 in response to DNA Damage

city: Bethesda

first: Mehdi

last: Pirooznia

state: MD

address: 12 SOUTH DR

institute: National Institutes of Health


title: Transcriptome analysis of control and TFEB/TFE3 DKO RAW264.7 in response to DNA Damage

summary: We analyze the contribution of the transcription fators TFEB and TFE3 to the DNA Damage Response (DDR)

overall_design: Control and TFEB/TFE3 DKO RAW264.7 were treated with etoposide for 8 hours and the mRNA profiles were analyzed by RNA-seq

first: Rosa

last: Puertollano


title: Transcriptome analysis of control and TFEB/TFE3 DKO MEFs in response to DNA Damage

overall_design: Control and TFEB/TFE3 DKO MEFs were treated with etoposide for 8 hours and the mRNA profiles were analyzed by RNA-seq


title: Gene expression in day 4 pregnant uterus

status: Public on Sep 28 2018

city: Xiamen

first: Wenbo

last: Deng

state: Fujian

address: Xiang'an Road

department: School of Medicine

institute: Xiamen University

summary: To detect the gene profiles in receptive uterus, two independent uteri are collected from pregnant day 4 mice and subjected to RNA-Seq. After aligned to mouse mm9 by Tophat2, RPKM value was calculated by Edger. Our results show that HMGB1 is one of the most abundant gene in the whole HMG family. The expression of HMGB1 was further confirmed by qPCR, ISH and immunofluorescence. The expression of HMGB1 was found expressed in very cells, indicating the essential role of HMGB1 for reproduction. This RNA-Seq data provides fundamental information for our further physiological study of HMGB1.

overall_design: Total RNAs in whole uterus from two independent mouse were extracted by TRIzol and purified by ploy-A before subjected to RNA-Seq by HiSeq2500. The expression of level of each gene is normalized to RPKM.

first: S

middle: K

last: Dey


title: RNA sequencing of mouse liver cancer cell lines with YAP/TAZ mutations

first: Matthew

middle: T

last: Chang

department: Bioinformatics

summary: RNA from cell lines derived from YAP-S127A, YAP-5SA and TAZ-S89A mouse liver tumors.    The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech.  The ID of this project in Genentech's ExpressionPlot database is PRJ0014900

first: Anwesha


title: KMT2B is selectively required for neuronal transdifferentiation [ChIP-seq]

city: Milano

first: Giuseppe

last: Testa

address: Via Adamello, 16

institute: European Institute of Oncology & University of Milano, Italy

summary: Transdifferentiation of fibroblasts into induced Neuronal cells (iNs) by neuronal-specific transcription factors Brn2, Myt1l and Ascl1 is a paradigmatic example of inter-lineage conversion across epigenetically distant cells. Despite tremendous progress on the transcriptional hierarchy underlying transdifferentiation, the enablers of the concomitant epigenome resetting remain to be elucidated. Here we investigated the role of KMT2A and KMT2B, two histone H3 lysine 4 methylases with cardinal roles in development, through individual and combined inactivation. We found that Kmt2b, whose human homologue’s mutations cause dystonia, is selectively required for iN conversion through the suppression of the alternative myocyte program and the induction of neuronal maturation genes.

overall_design: In order to study the role of KMT2A and KMT2B during transdifferentiation, we employed conditional mouse strains carrying: i) the exon 2 of Kmt2a and/or Kmt2b flanked by LoxP sites; ii) the knock-in of the YFP-coding gene into one Rosa26 allele, downstream of a LoxP-flanked transcription termination cassette (STOP cassette); and iii) the gene coding for the tamoxifen-inducible version of Cre recombinase knocked into the second Rosa26 allele (Glaser et al., 2006; Kranz et al., 2010; Testa et al., 2004). MEFs were derived from Kmt2a (and/or Kmt2b)fl/fl Cre+ YFP+  embryos and from Kmt2a+/+Kmt2b+/+ Cre+ YFP+ or Kmt2afl/+ Cre+ YFP+  for Kmt2a conditional KO (cKO) as controls (Figure 1A), and were subjected to transdifferentiation. The epigenome of MEFs and transdifferentiating cells after 5 and 13 days of BAM treatment was profiled by ChIP-seq for H3K4me3 and H3K27me3.

first: Giulia

last: Barbagiovanni

first: Pierre-Luc

last: Germain

first: Pietro

last: Lo Riso


title: Unique pattern of neutrophil migration and function during tumor progression

status: Public on Sep 27 2018

city: Philadelphia

first: Priyankara

last: Wickramasinghe

address: 3601 Spruce Street

institute: The Wistar Institute

summary: Although neutrophils have been linked to the formation of the pre-metastatic niche, the mechanism of their migration to distant uninvolved tissues has remained elusive. We report that bone marrow neutrophils from mice with early-stage cancers exhibited much more spontaneous migration to tissues. These cells lacked immunosuppressive activity but had elevated rates of oxidative phosphorylation and glycolysis, and much more production of ATP. Their enhanced spontaneous migration was mediated by the binding of ATP to purinergic receptors. In ectopic tumor models and the late stages of cancers, bone marrow neutrophils demonstrated potent immunosuppressive activity. However, these cells had metabolic and migratory activity indistinguishable from that of control neutrophils. A similar pattern of migration was observed in neutrophils and polymorphonuclear myeloid-derived suppressor cells from patients with cancer. These results elucidate the dynamic changes that neutrophils undergo in cancer and demonstrate the mechanism of neutrophils’ contribution to early tumor dissemination.

overall_design: RNA-seq for BM neutrophils from control, one-week and three-week LL2 tumor bearing mice

first: Dmitry

last: Gabrilovich

first: Sima

last: Patel


title: Epigenetic extinction of fetal programming promotes leukemia stem cell activity

city: Vancouver

first: Martin

last: Hirst

state: British Columbia

address: 2125 East Mall

department: Microbiology and Immunology

institute: University of British Columbia

summary: Acute leukemias are aggressive malignancies of developmentally arrested hematopoietic progenitors. We sought here to explore the possibility that changes in hematopoietic stem/progenitor cells during aging might alter the biology of leukemias arising from this tissue compartment. Using a mouse model of acute T-cell leukemia, we found that leukemias generated from fetal liver (FL) and adult bone marrow (BM) differed dramatically in their leukemia stem cell activity with FL leukemias showing markedly reduced serial transplantability as compared to BM leukemias. We present evidence that this difference is due to NOTCH1-driven autocrine IGF1 signaling which is active in FL cells, but restrained in BM cells by EZH2-dependent H3K27 trimethylation. Further, we confirmed this mechanism is operative in human disease, and show that enforced IGF1 signaling effectively limits leukemia stem cell activity. These findings demonstrate that resurrecting dormant fetal programs in adult cells may represent an alternate therapeutic approach in human cancer.

overall_design: Examination of H3K27me3 in 2 mouse cell types

first: Vincenzo

last: Giambra

first: Samuel

last: Gusscott

first: Deanne

last: Gracias

first: Raymond

last: Song

first: Sonya

last: Lam

first: Patrizio

last: Panelli

first: Kateryna

last: Tyshchenko

first: Catherine

last: Jenkins

last: Hoofd

first: Alireza

last: Lorzadeh

first: Annaick

last: Carles

first: Connie

last: Eaves

first: Andrew

middle: P

last: Weng


title: IKZF2 is required for myeloid leukemic stem cells by driving self-renewal and inhibiting the myeloid differentiation program II

city: New York

first: Hyein

middle: Sophia

last: Cho

state: NY

address: 430 E 67th St

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

summary: We report that IKZF2 is required for maintaining chromatin accessibility in leukemic stem cells in myeloid leukemia. RNA seq and ATAC-seq were performed to investigate the changes in chromatin accessibility of differentially expressed genes in leukemic stem cells when IKZF2 was absent. We found that IKZF2 maintains open accessibility in self-renewal transcription factor motifs such as HOXA9 sites whereas motifs of differentiation transcription factors including C/EBPs are kept closed.

overall_design: 3 Ikzf2 CUT&RUN, each 2 technical replicates; 2 Negative control, each 2 technical replicates

first: Michael

last: Kharas

first: Sun-Mi

last: Park

first: Antoine

last: Gruet

first: Hyunwoo

first: Christina

last: Leslie


title: Activin/Smad2 and Wnt/β-catenin upregulate HAS2 and ALDH3A2 to facilitate mesendoderm differentiation of human ESCs

city: Beijing

first: Bofeng

last: Liu

address: Haidian District

department: School of Life Science

institute: Tsinghua University

summary: Activin and Wnt signaling are necessary and sufficient for mesendoderm (ME) differentiation of human embryonic stem cells (hESCs). In this study, we report that during the Activin and Wnt induced ME differentiation, Activin/Smad2 induces decrease of the repressive histone modification H3K27me3 by promoting proteasome-dependent degradation of EZH2. As a result, recruitment of the forkhead protein FOXH1 on open chromatin regions integrates the signals of Activin/Smad2 and Wnt/β-catenin to activate the expression of the ME genes including HAS2 and ALDH3A2. Knockdown of HAS2 and ALDH3A2 greatly attenuates ME differentiation. These findings unveil a pathway from extracellular signals to epigenetic modification-mediated gene activation during ME commitment.

overall_design: H1 human embryonic stem cell cells were treated with 25ng/ml Activin A, 25ng/ml Wnt3a, or both (AW) for 6 h and then harvested for ATAC-seq.

first: Xuanhao

last: Xu

first: Wei

last: Xie

first: Yeguang

last: Chen


title: IKZF2 is required for myeloid leukemic stem cells by driving self-renewal and inhibiting the myeloid differentiation program


title: Impact of Human T-cell Leukemia Virus-1 and Epstein-Barr Virus Infections on B-cell Lymphoma and Adult T-cell Leukemia/Lymphoma Developments

city: Tokyo

first: Masumichi

last: Saito

address: Musashimurayama

department: Department of Safety Research on Blood and Biological Products

institute: National Institute of Infectious Diseases

summary:
We established HTLV-1/EBV co-infected cell lines from Adult T-cell Leukemia/Lymphoma (ATLL) patients, and found that they are derived from germinal center (GC) B-cells or transitional B-cells between GC-B-cells and memory B-cells by using gene expression profiling (GEP) analysis.
Expression of CD25 and TSLC1, which are diagnostic markers of ATLL cells, were identified in the ATLL-derived B-cell lines as discriminators of EBV-imortalized cell lines, indicating that HTLV-1 infection leads to express CD25 and TSLC1.

overall_design:
The three cell lines LMY3B, OATL9 and LHM115 represent three independent B cell lines established by isolating peripheral blood from three different HTLV-1+ patients.

Primary naïve, GC and memory B-cells were selected to identify the derivation of ATLL-derived B-cell lines, and diffuse large B-cell lymphoma cell lines and EBV-immortalized cell lines were used to characterize tumorigenicity of ATLL-derived B-cell lines.

first: Antony

middle: B

last: Holmes

first: Hidekatsu

last: Iha

first: Hiroo

last: Hasegawa


title: Dilated cardiomyopathy vs Myocarditis

city: Heidelberg

first: Sören

last: Meyer

address: Im Neuenheimer Feld 410

country: Germany

institute: University Hospital Heidelberg

summary: Sequencing data of biopsies from Myocarditis and DCM patients

overall_design: Sequencing from 11 DCM and 5 myocarditis heart biopsy samples


title: DNA methylation study of satellite cells from the rotator cuff and gastrocnemius muscles of mice

first: Christopher

last: Mendias

address: 535 E 70th St

institute: Hospital for Special Surgery

type: Methylation profiling by high throughput sequencing

summary: The samples consist of cells from two muscle types in mice – rotator cuff and gastrocnemius muscles. The aim of the project is to study the methylation differences between the two muscle types, specifically in genes involved in adipogenesis and muscle regeneration in the rotator cuff muscle with the gastrocnemius muscle being the control.

overall_design:
Specimens from rotator cuff and gastrocnemius muscles were harvested from inducible transgenic Pax7CreERT2:R26RtdTomato mice. After muscle digestion, cells were isolated. Muscle satellite cells expressing tdTomato were collected via fluorescence activated cell sorting. These sorted satellite cells from the rotator cuff and gastrocnemius samples were then used for ERRBS.
Enhanced Reduced Representation Bisulphite Sequencing (ERRBS) was performed as described in Akalin et al., 2012., with modifications to account for the lowest amount of gDNA (2.5ng) available for library “RCSC4”. The modifications are as follows: universally methylated non-indexed adapters were used for ligation, and the gel size selection was done in one fragment from 150 to 500pb. Each library was sequenced as a single lane on the HiSeq 2500.
ERRBS analysis was carried out on all these samples.

first: Karthik

last: Padmanabhan

first: Manuel

last: Schubert

first: Jonathan

last: Gumucio


title: TERT Promoter DNA methylation landscape in human cancer cell lines and tumors

city: Toronto

first: Donghyun

last: Lee

address: 686 Bay Street

department: Genetics and Genome Biology

institute: The Hospital for Sick Children

summary: We assessed methylation landscape near the human TERT promoter in various normal samples and tumor samples, to assess the unique hypermethylation phenotype that exist in human cancers

overall_design: DNA from various tissues (i.e. human cancer cell lines, normal cells, and tumor tissue) were extracted and analyzed with bisulfite targeted sequencing of the TERT promoter

first: Martin

last: Komosa

first: Uri

last: Tabori


title: Expression data from immature V2 and DP cells in the thymus of Sox4 conditional knockout mice and wild type mice

status: Public on Sep 26 2018

city: Worcester

first: Joonsoo

last: Kang

address: 368 Plantation St.

department: Pathology

institute: University of Massachusetts Medical School

summary: To determine Sox4 function during intrathymic αβ T cell development, global transcriptome analysis was performed and suggested a deficit in miR181 expression in Sox4-deficient DP thymocytes.

overall_design: Thymus immature TCRγδ V2 cells and CD4+ CD8+ double positive T cells are sorted from two weeks old mice for RNA extraction and hybridization on Affymetrix microarrays.

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Mettl14 is essential for epitranscriptomic regulation of striatal function and learning

city: Chicago

first: Jessica

last: Koranda

state: IL

address: 974 E 57th Street

institute: University of Chicago

summary: N6-methyladenosine (m6A) regulates mRNA metabolism and translation, serving as an important source of post-transcriptional regulation. To date, the functional consequences of m6A deficiency within the adult brain have not been determined. To achieve m6A deficiency, we deleted Mettl14, an essential component of the m6A methyltransferase complex, in two related yet discrete mouse neuronal populations: striatonigral and striatopallidal. Mettl14 deletion reduced striatal m6A levels without altering cell numbers or morphology. Transcriptome-wide profiling of m6A-modified mRNAs in Mettl14-deleted striatum revealed downregulation of similar striatal mRNAs encoding neuron- and synapse-specific proteins in both neuronal types, but striatonigral and striatopallidal identity genes were uniquely downregulated in each respective manipulation. Upregulated mRNA species encoded non-neuron-specific proteins. These changes increased neuronal excitability, reduced spike frequency adaptation and profoundly impaired striatal-mediated behaviors. Using viral-mediated, neuron-specific striatal Mettl14 deletion in adult mice, we further confirmed the significance of m6A in maintaining normal striatal function in the adult mouse.

overall_design: Correlation overall changes in mRNA expression and change in m6A-RNA enrichment in adult mice following either conditional genetic deletion of Mettl14 in striatonigral or striatopallidal neruons or viral-mediated pan-neuronal deletion in adult mice using deep sequencing techniques.

first: Xioaxi

last: Zhuang

first: Hailing

last: Shi

first: Chuan

last: He


title: Aberrant hyperediting of myeloma transcriptome by ADAR1 confers oncogenicity and is a marker of poor prognosis

city: Singapore

first: Wee

middle: Joo

last: Chng

address: 5 Lower Kent Ridge Road

department: Haematology-Oncology

country: Singapore

institute: National University Cancer Institute, Singapore

summary: We constructed strand-specific cDNA libraries of 23 total RNA samples (human cell lines and patient samples) and sequenced the libraries using Hiseq 4000 platform. More than 80 millions of mappable reads for each sample have been obtained.

overall_design: The clinical importance of RNA editing in myeloma disease pathogenesis was elucidated by comparing the global editing events in the primary clinical samples. RNA was extracted from the plasma cells of the healthy volunteers and myeloma patients (from different disease stages) and paired end, 100bp RNA sequencing was conducted. Only high confidence editing events (at least 20 reads count and more than 10% absolute editing frequency) were considered for downstream analyses. Functional importance of ADAR1 in RNA editing was investigated by looking at the effects of differential ADAR1 expression after knocking down and overexpressing ADAR1 in myeloma cell lines. Likewise, only high confidence editing events were included into the analyses.

first: Phaik

last: Teoh

first: Omer

last: An


title: Sequential dendritic cell activation with innate and adaptive signals

city: Paris

first: Lucia

last: Pattarini

address: 26 rue D' Ulm

institute: Institut Curie

summary: How sequential stimulation regulates immune cell function remain largely unexplored. We used human primary dendritic cells as a cellular model to asses the impact of sequential activation on cell function at the systems level. We found that innate priming modified the response to sequential activation by CD40L at the transcriptional and functional level. Moreover, we found that sequential activation modulted DC diversity.

overall_design: Human primary blood Dendritic cells were treated with innate signals for 20 hours, extensively washed and treated or not with CD40L for 6 and 12 hours before samples were collected

first: Antonio

last: Cappuccio

first: Elisabetta

last: Volpe

first: Vassili

last: Soumelis


title: Protein Syndesmos is a novel RNA binding protein that regulates primary cilia formation [Ribo-seq]

city: Napoli

first: Danilo

last: Swann Matassa

address: Via Sergio Pansini 5

department: Molecular Medicine and Medical Biotechnology

institute: University of Naples “Federico II”

summary: We show here that NUDT16L1/TIRR/Syndesmos (SDOS) interacts with another important cancer-linked protein, the chaperone TRAP1, associates with actively translating polyribosomes and represses translation. Moreover, we demonstrate that SDOS binds directly RNA in living cells. Combining individual gene expression profiling, nucleotide cross-linking and immunoprecipitation (iCLIP), and ribosome profiling, we discover several crucial pathways regulated post-transcriptionally by SDOS.

overall_design: Evaluation of differentially translated transcripts in SDOS-eGFP over eGFP expressing cells

first: Rosario

last: Avolio

last: Matassa


title: Exonuclease domain-containing 1 enhances MIWI2 piRNA biogenesis via its interaction with TDRD12

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

type: Non-coding RNA profiling by high throughput sequencing

summary: PIWI proteins and their associated small RNAs called PIWI-interacting RNAs (piRNAs) restrict transposon activity in animal gonads to ensure fertility. Distinct biogenesis pathways load piRNAs into the PIWI proteins MILI and MIWI2 in the mouse male embryonic germline. While most of MILI piRNAs derive via a slicer-independent pathway, a MILI slicer endonuclease-initiated pathway loads nuclear MIWI2 with a series of phased piRNAs. Tudor domain-containing 12 (TDRD12) and its interaction partner Exonuclease domain-containing 1 (EXD1) are required for loading MIWI2, but only Tdrd12 is essential for fertility, leaving us with no explanation for the physiological role of Exd1. Using an artificial piRNA precursor, we demonstrate that MILI-triggered piRNA biogenesis is greatly reduced in the Exd1 mutant. The situation deteriorates in the sensitized Exd1 mutant (Exd1-/-; Tdrd12+/-), where diminished MIWI2 piRNA levels de-repress LINE1 retrotransposons, causing infertility. Thus, EXD1 enhances slicing-triggered MIWI2 piRNA biogenesis via a functional interaction with TDRD12.

overall_design: Small RNA sequencing was used to identify differences in piRNA levels between various Exd1 and Tdrd12 mouse mutants. Total small RNAs were sequenced together with immunopurified MILI and MIWI2 associated piRNAs.

first: Radha

last: Pandey

first: David

last: Homolka

first: Opeyemi

last: Olotu

first: Ravi

last: Sachidanandam

first: Noora

last: Kotaja


title: Next Generation Sequencing Analyzes Transcriptome after  TMEM126A overexpression and knockdown

city: shanghai

first: Wei

last: Jin

state: Shanghai

address: 688 Hongqu road

department: breast cancer surgery

institute: Fudan University

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to identify the differential expression genes after TMEM126A overexpression or knockdown.
Methods:Total cell mRNA profiles of TMEM126A-knockdown MDA-MB-231 cells (sh-NC vs shT126A) and TMEM126A-overexpression MCF10-Ca1a cells(pCDH vs T126A) were generated by deep sequencing, using Illumina HiSeq 2500. The sequence reads that passed quality filters were analyzed at the gene-level quantification, analysis of differentially expressed
genes (DEGs), cluster analysis, GO and KEGG enrichment and qRT–PCR validation was performed using SYBR Green assays.
Conclusions: Our study represents the first detailed analysis of TMEM126A overexpression and knockdown transcriptomes, with 2 cell lines, generated by RNA-seq technology. Our results show that NGS offers a comprehensive information for the downstream molecular mechanism.

overall_design: Using Next Generation Sequencing to analyze the differential gene expression beteewn pCDH vs TMEM126A overexpression in MCF10-Ca1a and sh-NC vs TMEM126A knockdown in MDA-MB-231.

first: H

last: Sun

first: W


title: KMT2B is selectively required for neuronal transdifferentiation

first: Giuseppe

last: Testa

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

overall_design: Refer to individual Series


title: Detailed genomic and molecular characterization of Indian induced pluripotent stem cell lines

city: Bangalore

first: Odity

last: Mukherjee

state: Karnataka

address: GKVK

department: ADBS

country: India

institute: Institute of Stem Cells and Regenerative Medicine (InStem)

summary: We report the application of RNA sequencing technology for high-throughput profiling of control iPSC lines

overall_design: RNA-seq of three iPSC lines and neural stem cells derived from the same iPSC lines.

first: Shweta

last: Joshi

first: Shubhra

last: Acharya

first: Mahendra

last: Rao


title: KMT2B is selectively required for neuronal transdifferentiation [RNAseq]

address: Via Adamello, 16

institute: European Institute of Oncology & University of Milano, Italy

summary: Transdifferentiation of fibroblasts into induced Neuronal cells (iNs) by neuronal-specific transcription factors Brn2, Myt1l and Ascl1 is a paradigmatic example of inter-lineage conversion across epigenetically distant cells. Despite tremendous progress on the transcriptional hierarchy underlying transdifferentiation, the enablers of the concomitant epigenome resetting remain to be elucidated. Here we investigated the role of KMT2A and KMT2B, two histone H3 lysine 4 methylases with cardinal roles in development, through individual and combined inactivation. We found that Kmt2b, whose human homologue’s mutations cause dystonia, is selectively required for iN conversion through the suppression of the alternative myocyte program and the induction of neuronal maturation genes.

overall_design: In order to study the role of KMT2A and KMT2B during transdifferentiation, we employed conditional mouse strains carrying: i) the exon 2 of Kmt2a and/or Kmt2b flanked by LoxP sites; ii) the knock-in of the YFP-coding gene into one Rosa26 allele, downstream of a LoxP-flanked transcription termination cassette (STOP cassette); and iii) the gene coding for the tamoxifen-inducible version of Cre recombinase knocked into the second Rosa26 allele (Glaser et al., 2006; Kranz et al., 2010; Testa et al., 2004). MEFs were derived from Kmt2a (and/or Kmt2b)fl/fl Cre+ YFP+  embryos and from Kmt2a+/+Kmt2b+/+ Cre+ YFP+ or Kmt2afl/+ Cre+ YFP+  for Kmt2a conditional KO (cKO) as controls (Figure 1A), and were subjected to transdifferentiation. After 13 days of BAM treatment, cells were FACS sorted for PSA-NCAM expression, and the transcriptome of positive and negative cells were independently profiled.

first: Giulia

last: Barbagiovanni

first: Pierre-Luc

last: Germain

first: Pietro

last: Lo Riso


title: Next Generation Sequencing Facilitates Quantitative Analysis of Gene expression profile in CD8+ T cells with TOX-overexpression

status: Public on Sep 25 2018

city: Nanjing

first: qifeng

last: he

state: JIANGSU

address: zhongshan Road

department: general surgery

institute: nanjing university

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived TOX associated transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis. Methods: mRNA profiles of human CD8+ T cell overexpressed by TOX lentivirus or NC lentiviruswere generated by deep sequencing, in triplicate, using Illumina. qRT–PCR validation was performed using TaqMan and SYBR Green assays          Conclusions: Our study represents the first detailed analysis of TOX associated transcriptomes generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

first: xiaochen

last: wang

first: beicheng

last: sun


title: ChIP-seq for RNAPII before and after transcription inhibition

first: Benjamin

last: Martin

state: BC

address: 2350 Health Sciences Mall

department: Biochemistry

institute: UBC

summary: The FACT (FAcilitates Chromatin Transactions) complex is a conserved complex that maintains chromatin structure on transcriptionally active genes. Consistent with this, FACT is enriched on highly expressed genes, but how it is targeted to these regions is unknown. In vitro, FACT binds destabilized nucleosomes, supporting the hypothesis that FACT is targeted to transcribed chromatin through recognition of RNA polymerase-disrupted nucleosomes. In this study, we used high resolution analysis of FACT occupancy in S. cerevisiae to test this hypothesis. We demonstrate that FACT interacts with nucleosomes in vivo and its interaction with chromatin is dependent on transcription by any of the three RNA polymerases. Deep sequencing of micrococcal nuclease (MNase)-resistant fragments shows that FACT-bound nucleosomes exhibit differing nuclease sensitivity compared to bulk chromatin, consistent with a modified nucleosome structure being the preferred ligand for this complex. Interestingly, a subset of FACT-bound nucleosomes may be “overlapping di-nucleosomes”, in which one histone octamer invades the ~147 bp territory normally occupied by the adjacent nucleosome. While the differing nuclease sensitivity of FACT-bound nucleosomes could also be explained by the demonstrated ability of FACT to alter nucleosome structure, transcription inhibition restores nuclease resistance suggesting that it is not due to FACT interaction alone. Collectively these results are consistent with a model in which FACT is targeted to transcribed genes through preferential interaction with RNA polymerase-disrupted nucleosomes.

overall_design: Saccharomyces cerevisiae yeast cells were arrested in G1 with alpha factor and treated with 1,10-phenanthroline for 15 minutes. ChIP-seq was performed for RNAPII from sonicated lysates.

middle: J

first: LeAnn

last: Howe


title: Analysis of transcriptomes and open chromatin regions of sub-populations of human Tregs

city: Bethesda

first: Mehdi

last: Pirooznia

address: 12 SOUTH DR

institute: National Institutes of Health


title: ARID3a Gene Profiles are Strongly Associated with Human Interferon Alpha Production

city: Norman

first: Carol

last: Webb

state: Oklahoma

address: Stephenson Parkway

department: Department of Medicine

institute: OUHSC

summary: Percentages of ARID3a-expressing low density neutrophils in SLE patients correlate with lupus disease activity and Type I IFN production. ARID3a protein levels also correlate with interferon expression in plasmacytoid dendritic cells. Gene profiles mechanistically link ARID3a with inflammatory pathway regulation.

overall_design: Correlation analysis of genes associated with IFNa and/or ARID3a protein levels in neutrophils and pDCs of SLE patients.

first: Josh

last: Garton


title: The Effect of TLR2 Activation on  Transcriptome of IFN-induced Microglia

city: Shanghai

first: Jiawen

last: Qian

address: 130 Dong'an Road

department: Immunology

summary: In murine glioma models, TLR2 is selectively upregulated in glioma-associated microglia. We found that TLR2 activation led to down-regulation of MHC-II in microglia. Therefore, we examined the effect of TLR2 activation on IFN-gamma-induced microglial transcriptome by in vitro culture of murine adult microglia. In the study, we confirmed that TLR2 activation led to Ciita shutdown and inhibition of MHC-II related genes, which also revealed the role of TLR2 in inducing APC disability and tumor immune escape. In addition, this work can be used to reveal the transcriptional characteristics of murine microglia during IFN-gamma and TLR2 activation.

overall_design: Examination of transcriptional characteristics in murine adult microglia under TLR2 agonist and IFN-gamma treatments.

first: Yiwei

last: Chu


title: The Mcm2-Ctf4-Pola axis facilitates parental histone transfer to lagging strands

status: Public on Sep 24 2018

city: New York

first: zhiguo

last: zhang

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

summary: Although essential for epigenetic inheritance, the transfer of parental histone (H3-H4)2 tetramers that contain epigenetic modifications to replicating DNA strands is poorly understood. Here, we show that the Mcm2-Ctf4-Pol axis facilitates the transfer of parental (H3-H4)2 tetramers to lagging strands of DNA replication forks. Mutating the H3-H4 binding domain of Mcm2, a subunit of the CMG (Cdc45-MCM-GINS) replicative helicase that translocates along leading strands, impairs the transfer of parental (H3-H4)2 to lagging strands. Similar effects are observed in Ctf4 and Pol-primase mutants that disrupt the connection of the CMG helicase via Ctf4-Pol to lagging strands. Our results support a model whereby parental (H3-H4)2 displaced from nucleosomes through leading-strand DNA replication are transferred to lagging strands for nucleosome assembly via the CMG-Ctf4-Pol complex.

overall_design: We synchronized yeast cells (Wild type and other mutant cells) at G1 and released into early S phase in the presence of BrdU, and with or without hydroxyurea (HU). We then performed BrdU immunoprecipitation using anti-BrdU antibodies following single-strand DNA library preparation and sequencing (ssSeq). we also performed protein ChIP followed by single-strand DNA sequencing (ChIP-ssSeq) for Ctf4, H3K56ac, H3K4me3, T7-tag, and HA-tag. Also eSPAN for Ctf4, H3K56ac, H3K4me3, T7-tag, and HA-tag. The sequencing tag was mapped to both Watson (red) and Crick (blue) strands of the reference genome.

first: Haiyun

last: Gan

first: Albert

last: Cardona Serra

first: Chuanhe

last: Yu

first: Zhiguo

last: Zhang


title: DNA Methylation data from frozen placental tissue

city: Grand Forks

first: Kate

last: Claycombe-Larson

state: ND

address: 2420 2nd Avenue North

department: ARS

institute: USDA

type: Methylation profiling by genome tiling array

summary:
Maternal obesity alters placental tissue function and morphology with a corresponding increase in local inflammation.
We and others showed that placenta size, inflammation and fetal growth are regulated by maternal diet and obesity status. Maternal obesity alters placental DNA methylation which in turn could likely impact gene transcription of
of proteins critical for normal fetal development. RNA-binding motif single-stranded interacting protein 1 (RBMS1) is expressed by the placenta and likely modulates DNA replication and transcription regulation.
Serum RBMS1 protein concentration is increased with maternal obesity and RBMS1 gene expression in liver tissue is induced by a high-fat diet and inflammation. However, it is not yet known whether placental RBMS1 mRNA expression and DNA methylation are altered by maternal obesity.

overall_design: Methylation profiles of frozen placental tissue samples from overweight/obese (BMI>25) and non-overweight (BMI<25) were anaylzed

last: Claycombe

first: Archana

last: Dhasarathy

first: Amy

last: Bundy

first: Atrayee

last: Bhattacharya

first: Diane

last: Darland

first: Junguk

last: Hur

first: Danielle

last: Perley

first: LuAnn

last: Johnson

first: James

last: Roemmich


title: DNA Methylation in Breast Cancers: Differences based on Estrogen Receptor Status and Recurrence

city: Amherst

first: Kathleen

last: Arcaro

state: Massachusetts

address: 240 Thatcher Road LSL1 N529, University of Massachusetts

department: Veterinary and Animal Science

institute: University of Massachusetts- Amherst

summary: DNA methylation plays a role in the etiology of primary breast cancers. We analyzed paired primary and second breast tumors to elucidate the role of methylation in recurrence. Methylation profiles from paired primary and second breast tumors of 23 women were assessed using the HumanMethylation450 BeadChip. Twelve women had ERpos primary and second tumors, five had estrogen receptor negative (ERneg) primary and second tumors, and six had an ERpos primary tumor but an ERneg second tumor. Stratifying tumors by occurrence revealed that the greater methylation previously associated with ERpos tumors, is more pronounced in primary tumors than in second tumors. Further, ERneg second tumors are more methylated than ERpos second tumors among women who had ERpos primary tumors. Pathway analyses using gene lists generated from comparisons of methylation in ERpos primary tumors from the paired sets with ERpos tumors from 6 women without recurrences, identified differences between groups based on the ER status of the second tumor. Hypermethylated genes of significantly enriched pathways were differentially associated with survival. DNA methylation profiles of ERpos primary breast tumors support the development and use of tumor methylation profiles for stratifying women with breast cancer both for prognosis and therapy.

overall_design: Primary tumors (referred to as first tumors) were matched to a second tumor from the same woman in either the ipsilateral or contralateral breast. HumanMethylation450 Bead Chip (HM450 BC) data were obtained for 46 paired tumors and assigned group labels for ease of reading as follows: 12 tumor pairs from women with ERpos first (A1) and ERpos second tumors (A2), 5 tumor pairs from women with ERneg first tumors (B1) and ERneg second tumors (B2), and 6 tumor pairs from women with ERpos first tumors (C1) and ERneg second tumors (C2). Additionally, 6 ERpos tumors from women with no breast cancer recurrence after a 7-year follow up period were included for methylation analysis.

first: Kristin

middle: E

last: Williams

first: Rahul

middle: M

last: Jawale

first: Sallie

middle: S

last: Schneider

first: Christopher

last: Otis

first: Brian

last: Pentecost

middle: F


title: Genome-wide Profiling of H3K27ac binding in human cancer cell lines

first: Juan

last: Yan

address: 555 Zuchongzhi Road

department: Antitumor Pharmacology

institute: Shanghai Institute of Materia Medica

summary: Upregulation of enhancer of zeste 2 polycomb repressive complex 2 subunit (EZH2) and its associated histone H3 lysine 27 (H3K27) trimethylation frequently occur in human cancer, yet both preclinical and clinical evidence suggested the very limited benefit of EZH2-targeted therapies. This study investigated the underlying mechanisms from a perspective of EZH2 inhibition-caused histone modification crosstalk. A mass spectrometry approach enabled us discovering the alteration of global histone modifications responding to EZH2 inhibition. Feedback upregulation of H3K27 acetylation (H3K27ac) level is closely associated with limited drug response to EZH2 inhibition across multiple cancer types. H3K27ac alteration caused transcriptional activation of oncoproteins confers drug resistant to EZH2 inhibition. Here we used ChIP-Seq analysis to identify the alteration of genome-wide H3K27ac bingding sites with EZH2 inhibitor treatment in human cancer cell lines.

overall_design: Examination of H3K27ac modification in 3 human cancer cell lines （Pfeiffer, U2932 and SMMC-7721）.

first: Meiyu

last: Geng

first: Jian

last: Ding


title: Transcriptomes change differerntly in differernt cancer cells upon EPZ-6438 treatment

summary:
Purpose: The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) to find out the difference between EZH2 inhibitor treatment and DMSO group in each cancer cell line, and find the relationship between transcriptomes change and drug sensivitity.
Methods: mRNA profiles of cell lines were generated using  Illumina PE150, then GSEA was used for cellular pathways analysis
Results:  The result showed 53 common oncogenic signatures were enriched in RNA-seq data. For example, KRAS.300_UP.V1_UP, MEK_UP.V1_UP were statistically enriched in the RNA-seq data. In addition, some oncogenic signatures were only enriched in certain cancer cell lines. For example, 101 and 12 signatures from the RNA-seq were statistically enriched in U2932 and SMMC-7721, respectively.
Conclusions: Our study systematically examined the cellular transcriptomes affected by EPZ-6438, with biologic replicates, generated by RNA-seq technology. EZH2 inhibition results in the transcriptional activation of multiple onco-pathways in a cell-context dependent manner, which may underline the resistance to EZH2 inhibition.

overall_design: mRNA profiles of 3 cancer cell lines treated with 1 μM EPZ-6348 or DMSO for 6 days, using NEBNext® UltraTM RNA Library Prep it for Illumina® (NEB, USA).


title: Kinetics of Adult hematopoietic stem cell differentiation in vivo

first: Efthymia

last: Papalexi

address: 101 avenue of americas

institute: New York Genome Center

summary: Adult hematopoiesis has been studied in terms of progenitor differentiation potentials,  whereas its kinetics in vivo is poorly understood. We combined inducible lineage tracing  of endogenous adult hematopoietic stem cells (HSC) with flow cytometry and single-cell  RNA sequencing to characterize early steps of hematopoietic differentiation in the  steady state. Labeled cells, comprising primarily long-term HSC and some short-term  HSC, produced megakaryocytic lineage progeny within one week, in a process that  required only 2-3 cell divisions. Erythroid and myeloid progeny emerged simultaneously  by 2 weeks, and included a progenitor population with expression features of both  lineages. Myeloid progenitors at this stage showed diversification into granulocytic,  monocytic and dendritic cell types, and rare intermediate cell states could be detected.  In contrast, lymphoid differentiation was virtually absent within the first 3 weeks of  tracing. These results show that continuous differentiation of HSC rapidly produces  major hematopoietic lineages and cell types, and reveal fundamental kinetic differences  between megakaryocytic, erythroid, myeloid and lymphoid differentiation.

first: Samik

last: Upadhaya

first: Catherine

last: Sawai


title: Transcriptional landscape changes during human embryonic stem cell derivation

city: Gent

first: Laurentijn

last: Tilleman

address: Ottergemsesteenweg 460

country: Belgium

institute: Ghent University

summary: Currently, there is only minimal information elucidating the transcriptional changes occurring during the in vitro transition of the inner cell mass (ICM) towards the human embryonic stem cell (hESC) stage and the role played by the post inner cell mass intermediate (PICMI). In this study, we perform in-depth analysis of the transcriptional heterogeneity between these three stages of hESC derivation in order to correlate their downstream effects on pluripotency states and differentiation. We reveal that although PICMI is transcriptionally in close proximity to the hESC profile and distinct from ICM, it exhibits upregulation of primordial germ cell markers, dependence on LIF signaling, upregulation of naïve pluripotency-specific signaling networks and appears to be a switching point from naïve to primed pluripotency. This indicates similarities with mouse epiblast-like cells displaying a transient state of pluripotency, between naïve and primed pluripotent states. Overall, we highlight the need to gain insight into the molecular and transcriptional landscape during hESC derivation, which will further help in the derivation of human PGCs and naïve hESCs in vitro which remains inefficient.

overall_design: Biological triplicates of hESC, PICMI and ICM were sequenced

first: S

last: Warrier

first: J

last: Taelman

first: L

first: M

last: Van der Jeught

first: G

last: Duggal

last: Lierman

last: Popovic

first: A

last: Van Soom

last: Peelman

first: F

last: Van Nieuwerburgh

first: D

last: Deforce

last: Chuva de Sousa Lopes

first: P

last: De Sutter

first: B

last: Heindryckx


title: Protein Syndesmos is a novel RNA binding protein that regulates primary cilia formation [iCLIP-seq]

first: Danilo

last: Swann Matassa

summary: We show here that SDOS interacts with another important cancer-linked protein, the chaperone TRAP1, associates with actively translating polyribosomes and represses translation. Moreover, we demonstrate that SDOS binds directly RNA in living cells. Combining individual gene expression profiling, nucleotide cross-linking and immunoprecipitation (iCLIP), and ribosome profiling, we discover several crucial pathways regulated post-transcriptionally by SDOS.

overall_design: iCLIP combined with high-throughput sequencing was used to generate a transcriptome-wide binding map of SDOS.

first: Rosario

last: Avolio

first: Aino

last: Järvelin


title: Protein Syndesmos is a novel RNA binding protein that regulates primary cilia formation


title: Intrinsic immunity employs 2’,5’-oligoadenylate signaling to establish privileged translation of interferons β and l

city: Princeton

first: Alexei

last: Korennykh

state: New Jersey

address: 201 Schultz Laboratory

department: Molecular Biology

institute: Princeton University

summary: RNAseq of control vs poly-IC treated A549 cells shows IFN induction.

overall_design: Poly-A pulldown and RNAseq

first: Alisha

last: Chitrakar

first: Sneha

last: Rath


title: Dust mite potently activates Th17/Th22 pathways and models multiple inflammatory skin conditions in humans

first: James

last: Krueger

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

summary: House dust mite/HDM atopy patch test/APT elicits positive reactions in the majority of atopic dermatitis/AD and healthy individuals. Experimental systems for new-onset/chronic AD are needed to support rapid therapeutic development, particularly since animal models representing AD pathology in humans are lacking. HDM APT historically simulated AD, but its suitability to model the emerging AD skin phenotype as Th2/Th22 polarized with Th1 and Th17 components is unknown. To assess whether HDM APT tissues reproduce acute or chronic AD, positive HDM APT (n=14) were compared with nonlesional, acute (<72hrs; n=10), and chronic phase AD biopsies (n=8), allergic contact reactions (to nickel [n=10] and fragrance [n=3])  using arrays.

overall_design: 14 patients with positive dust mite reactions, were compared to 8 AD patients (acute and chronic lesions). 8 patients out of 14 patients with positive dust mite reactions did not have positive reactions to nickel or fragrance. 5 patients out of 14 patients with positive dust mite reactions had positive reactions to nickel. 1 patient out of 14 patients with positive dust mite reactions had positive reaction to fragrance. 5 other patients with positive nickel reactions and 2 other patients with fragrance reaction but not dustmite reactions were included in the study. The study considered a total of 29 patients (8 Atopic Dermatitis and  21 dust mite/nickel/fragrance positive reactions). Lesional and Non Lesional skin for AD patients were analyzed. Atopic patch skin and non lesional skin for dust mite/nickel/fragrance patients were analyzed. For patients with more than one positive patch reaction a sample from each atopy patch test reaction was obtained. We are submiting here only the samples  from dust mite atopic patch skin (14) and the non lesional skin samples related to patients with positive dust mite reaction only (8). The other samples have been submited in: series accession no. GSM815426, GSM815427, GSE36842 and GSE36842.

first: Emma

last: Guttman-Yassky


title: Molecular diversification of regulatory T cells in non-lymphoid tissues

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Foxp3+CD4+ regulatory T (Treg) cells accumulate in certain non-lymphoid tissues, where they control diverse aspects of organ homeostasis, partly via a direct impact on neighboring non-immune cells. Populations of tissue-Tregs, as they have been termed, have transcriptomes distinct from those of their counterparts in lymphoid organs and other non-lymphoid tissues. Exploiting recent advances in profiling the chromatin accessibility and gene expression of rare cell populations, we examined the diversification of Tregs in visceral-adipose tissue, skeletal muscle and the colon vis-à-vis lymphoid organs from the same individuals. The unique transcriptomes of the various tissue-Treg populations reflected layering of tissue-restricted stretches of accessibility over a “primed” landscape of sites already open in the spleen, where they were tagged by super-enhancers and “bivalent” histone marks of transcriptional activation and repression. Tissue-restricted chromatin accessibility and gene expression correlated with the binding motifs of a small number of transcription-factor (TF) families repeatedly enriched across the various non-lymphoid tissues. However, a bioinformatically and experimentally validated transcriptional network constructed using a combination of chromatin-accessibility and single-cell transcriptomic data predicted usage of different TF-family members in the different tissues. The network analysis also revealed that tissue-restricted and ubiquitously acting TFs were integrated into feed-forward loops to enforce tissue-specific gene expression in non-lymphoid-tissue Treg cells. Overall, this study provides a framework for understanding the epigenetic dynamics of T cells operating in non-lymphoid tissues, which should inform strategies for specifically targeting them.

overall_design: Tregs were isolated from visceral-adipose tissue, injured skeletal muscle, and colonic lamina propria. For each tissue, Tregs were also isolated from the spleen at the time of harvest and ATAC-seq (Assay for Transposase-Accessible Chromatin) was performed. The experiment was done in duplicates for all populations.  Each VAT, muscle, colon sample was paired with a spleen sample taken from the same animal. For example, Treg_ATAC_VAT_1 and Treg_ATAC_Spl_wVAT_1 come from the same animal. Mouse IDs are also provided so that samples can be easily matched by mouse.

first: Joanna

middle: R

last: DiSpirito

first: Christophe

last: Benoist

first: Diane

last: Mathis


title: Next Generation Sequencing Quantitative Analysis of Srf-regulated Transcriptomes in mouse cardiomyocytes during cardiomyocyte maturation [exp2]

city: boston

first: Yuxuan

last: Guo

address: 320 Longwood Ave, Enders 1250,

department: Department of Cardiology

institute: Boston childrens hospital

summary: The goal of this study is to analyze the impact of Srf overexpression on transcription during cardiomyocyte maturation in mouse

overall_design:
Wildtype mice were injected with AAV9-cTNT-SRF-2A-GFP to overexpress Srf specifically in neonatal cardiomyocytes in mouse.  AAV9-cTNT-GFP was used as control.  Three biological replicates were analyzed in each group.
In each experiment, cardiomyocytes were isolated by retrograde collagenase perfusion and purified by fluorescence activated cell sorting.
Total RNA was extracted from FACS sorted cells. RNA-seq libraries were generated using SMART-seq and Nextera kits and were sequenced on a NextSeq500 sequencer. FASTQ Data were aligned by STAR and count matrix generated by FeatureCounts.

first: William

last: Pu


title: Effects of Hnf4a deletion in the nephron lineage during kidney development

city: Cincinnati

first: Joo-Seop

last: Park

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

summary: The goal of our study is to determine if Hnf4a is required for the formation of proximal tubules during kidney development.

overall_design:
Method: Hnf4a floxed allele was deleted in the nephron lineage using Six2GFPcre. Mouse embryonic kidneys at E18.5 were collected and subjected to RNA-seq analysis
Examination of 4 groups; two controls (Hnf4a c/+ ; Six2GFPcre) and two mutants  (Hnf4a c/c ; Six2GFPcre)

first: Sierra

last: Marable

first: Eunah

last: Chung


title: Next Generation Sequencing Quantitative Analysis of Srf-regulated Transcriptomes in mouse cardiomyocytes during cardiomyocyte maturation [exp1]

summary: The goal of this study is to analyze the role of Srf in transcriptional analysis during cardiomyocyte maturation in mouse

overall_design:
Srf-F/F (mutant) and Srf-F/+ (control) mice were injected with AAV9-cTNT-Cre to deplete Srf specifically in cardiomyocytes in vivo at two different stages. Three biological replicates were analyzed in each group. Thus a total of 12 samples were analyzed.
In neonatal knockout model, AAV was injected at post natal day 1 (P1) and cardiomyocytes collected at P14. In adult knockout model, AAV was injected at P60 and cardiomyocytes collected at P90
In each experiment, cardiomyocytes were isolated by retrograde collagenase perfusion and purified by fluorescence activated cell sorting.
Total RNA was extracted from FACS sorted cells. RNA-seq libraries were generated using SMART-seq and Nextera kits and were sequenced on a NextSeq500 sequencer. FASTQ Data were aligned by STAR and count matrix generated by FeatureCounts.


title: Systematic analysis of gene expression profiles controlled by hnRNP Q and hnRNP R, two closely related human heterogeneous nuclear ribonucleoproteins.

city: Trieste

first: Maurizio

last: Romano

address: Via A. Valerio 28

department: Department of Life Sciences

institute: University of Trieste

summary: hnRNPQ and the highly related hnRNPR regulate expression of genes related with neuronal and immune functions

overall_design: SH-SY5Y cells were treated with siRNA anti-hnRNPQ (n=3), or anti-hnRNPR  (n=3), or anti-Luciferase  (n=3)

first: Emanuele

last: Buratti


title: ATAC-seq data from naïve Tregs, memory Tregs and CD161+ Tregs

first: Mehdi

last: Pirooznia

summary: We analyze open chromatin regions of three populations of human Tregs

overall_design: CD4+CD25+ cells were isolated from peripheral blood of three healthy donors and then cell sorted to CD4+CD25hiCD127loCD45RA+ (naïve), CD4+CD25hiCD127loCD45RA-CD161- (memory) and CD4+CD25hiCD127loCD45RA-CD161+ Tregs, then open chromatin regions analyzed by ATAC-seq

first: Giovanni

last: Povoleri


title: Discovering in vivo cytokine eQTL interactions from a lupus clinical trial

city: Cambridge

middle: Elisabeth

last: Davenport

state: Cambridgeshire

address: Hinxton

institute: Wellcome Sanger Institute

summary: Background: Cytokines are critical to human disease and are attractive therapeutic targets given their widespread influence on gene regulation and transcription. Defining the downstream regulatory mechanisms influenced by cytokines is central to defining drug and disease mechanisms. One promising strategy is to use interactions between expression quantitative trait loci (eQTLs) and cytokine levels to define target genes and mechanisms.   Results: In a clinical trial for anti-IL-6 in patients with systemic lupus erythematosus we measured interferon (IFN) status, anti-IL-6 drug exposure and whole blood genome-wide gene expression at three time points (379 samples from 157 individuals). First, we show that repeat transcriptomic measurements increases the number of cis eQTLs identified compared to using a single time point by 64%. Then, after identifying 4,818 cis-eQTLs, we observed a statistically significant enrichment of in vivo eQTL interactions with IFN status (p<0.001 by permutation) and anti-IL-6 drug exposure (p<0.001). We observed 210 and 72 interactions for IFN and anti-IL-6 respectively (FDR<20%). Anti-IL-6 interactions have not yet been described while 99 of the IFN interactions are novel. Finally, we found transcription factor binding motifs interrupted by eQTL interaction SNPs, pointing to key regulatory mediators of these environmental stimuli and therefore potential therapeutic targets for autoimmune diseases. In particular, genes with IFN interactions are enriched for ISRE binding site motifs, while those with anti-IL-6 interactions are enriched for IRF4 motifs.   Conclusion: This study highlights the potential to exploit clinical trial data to discover in vivo eQTL interactions with therapeutically relevant environmental variables.

overall_design: Whole blood RNA-seq of 379 samples (across 3 time points) from 157 individuals with systemic lupus erythematosus

first: Tiffany

last: Amariuta

first: Maria

last: Gutierrez-Arcelus

first: Kamil

last: Slowikowski

first: Harm-Jan

last: Westra

first: Yang

last: Luo

first: Ciyue

last: Shen

first: Deepak

middle: A

last: Rao

first: Ying

last: Zhang

first: Stephen

last: Pearson

first: David

last: von Schack

first: Jean

last: Beebe

last: Bing

first: Sally

last: John

first: Michael

last: Vincent

first: Baohong

first: Soumya

last: Raychaudhuri