title: Study on Cyanidin Metabolism in Flower colors of Pink-flowered Strawberry Based on Transcriptome Sequencing and Metabolite Analysis

status: Public on Jan 29 2019

city: Shenyang

first: Li

last: Xue

address: Dongling Road No. 120

institute: Shenyang Agricultural University

summary: Pink-flowered strawberry is a new promising ornamental flower derived from intergeneric hybridization (Fragaria × Potentilla) with bright color, prolonged flowering period and edible fruits. However, the transcriptional events underlying anthocyanins biosynthesis pathway have not been fully characterized in its petal coloration. The pigment compounds accumulated in its fruits were the same as cultivated strawberry, but different from in its flowers. To gain insights into the regulatory networks related to anthocyanin biosynthesis and identify key genes, we performed an integrated analyses of the transcriptome and metabolomes involved in red petals at three development stages (Bud stage (L), Coloration beginning stage (Z) and Big bud stage (D)) of pink-flowered strawberry. Transcript and metabolite profiles were generated through high-throughput RNA-sequencing and high-performance liquid chromatography coupled with mass spectrometry, respectively. The results showed that the main pigments of red and dark pink petals were anthocyanins, among which cyanidins were the main compounds. There were no anthocyanins detected in white-flowered hybrids. A total of 50 285 non-redundant unigenes were obtained from the transcriptome databases, among which 59 differentially expressed genes could be identified as putative homologues of flower coloration related genes. Based on a comprehensive analysis relating pigmentation compounds to gene expression profiles, the mechanism of flower color formation was examined in pink-flowered strawberry. Furthermore, a new hypothesis explaining the lack of color phenotype of the white-flowered strawberry hybrids from the level of the transcriptome. The expression patterns of FpDFR gene and FpANS gene corresponded to the accumulation patterns of cyanidin contents in pink-flowered strawberry hybrids with different shades of pink; Whereas other anthocyanin biosynthesis genes were weakly related flower color deepened. Moreover, FpANS, FpBZ1 and FpUGT75C1 genes were the key factors that lead to the inability to accumulate anthocyanins in the white petals of PFS hybrids. Meanwhile, the competitive effect of FpFLS gene and FpDFR gene may further inhibit anthocyanin synthesis. The data presented herein are important for understanding of the molecular mechanisms underlying the petal pigmentation and will be powerful for integrating into novel genes that are potential targets for breeding new valuable pink-flowered strawberry cultivars.

overall_design: Three petal development stages [Bud stage (L,CK), Coloration beginning stage (Z) and Big bud stage (D)] of pink-flowered strawberry. were used to construct nine libraries with three biological replicates, which were named as PH_L1, PH_L2, PH_L3, PH_Z1, PH_Z2, PH_Z3, PH_D1, PH_D2 and PH_D3, respectively.

first: Jiajun

last: Lei


title: CDK4/6 inhibitors target SMARCA4-determined cyclin D1 deficiency in hypercalcemic small cell carcinoma of the ovary (II)

status: Public on Feb 04 2019

city: Montreal

first: Sidong

last: Huang

state: Quebec

address: 3655 promenade Sir-William-Osler

department: Biochemistry

country: Canada

institute: McGill University

type: Expression profiling by high throughput sequencing

summary: Inactivating mutations in SMARCA4 (BRG1), a key SWI/SNF chromatin remodelling gene, underlie small cell carcinoma of the ovary, hypercalcemic type (SCCOHT). To reveal its druggable vulnerabilities, we perform kinase-focused RNAi screens and uncover that SMARCA4-deficient SCCOHT cells are highly sensitive to the inhibition of cyclin-dependent kinase 4/6 (CDK4/6). SMARCA4 loss causes profound downregulation of cyclin D1, which limits CDK4/6 kinase activity in SCCOHT cells and leads to in vitro and in vivo susceptibility to CDK4/6 inhibitors. SCCOHT patient tumors are deficient in cyclin D1 yet retain the retinoblastoma-proficient/p16INK4a-deficient profile associated with positive responses to CDK4/6 inhibitors. Thus, our findings indicate that CDK4/6 inhibitors, approved for a breast cancer subtype addicted to CDK4/6 activation, could be repurposed to treat SCCOHT. Moreover, our study suggests a novel paradigm whereby critically low oncogene levels, caused by loss of a driver tumor suppressor, may also be exploited therapeutically.

overall_design: The effect of CDK6 knockdown and palbociclib treatment on SCCOHT cells.

first: Yibo

first: Radia

middle: M

last: Johnson

first: William

middle: D

last: Foulkes


title: Defining the dynamic chromatin landscape of nephron progenitors

status: Public on May 09 2019

city: New Orleans

first: Samir

middle: S

last: El-Dahr

state: LA

address: 1430 Tulane Ave

department: Pediatrics

country: USA

institute: Tulane University School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Six2+ cap mesenchyme cells, also called nephron progenitor cells (NPC), are a multipotent stem cell population and precursors of all epithelial cell types of the nephron, the filtering unit of the kidney. In mammals, formation of new nephrons ceases perinatally associated with a surge in NPC differentiation. Current evidence indicates that perinatal “old” NPC have a greater tendency to exit the progenitor niche and differentiate into nascent nephrons than their embryonic “young” counterparts. Understanding the biological underpinnings of NPC aging may offer insights to rejuvenate old NPC and expand the progenitor pool. In the present study, we compared the chromatin landscape of young and old NPC and found common features reflecting their shared lineage but also intrinsic differences in chromatin accessibility and enhancer landscape supporting the view that old NPC and epigenetically poised for differentiation. Annotation of open chromatin regions and active enhancers uncovered the transcription factor Bach2 as a potential link between the pro-renewal MAPK/AP1 and pro-differentiation Six2/b-catenin pathways that might be of critical importance in regulation of NPC fate. Our data provide the first glimpse of the dynamic chromatin landscape of NPC and serve as a platform for future studies of the impact of genetic or environmental perturbations on the epigenome of NPC.

overall_design:
Bulk ATAC_seq on nephron progenitor cells from representative stages of the kidney

Chip-seq from E13.5 and P0 Nephron Progenitor Cells with H3K4me1, H3K27me3 and H3K27ac.
Nephron Progenitor cells (NPCs) were isolated by Magnetic Activated Cell Sorting (MACS) from  E13.5 and P0 CD1 mouse kidneys. The NPCs were cultured in nephron progenitor expansion medium (NPEM) and passaged twice before the cells were subjected to ChIP-seq for H3K4me1, H3K27me3, and H3K27ac.


title: Comparing Wilms tumor primary samples to patient-derived xenografts

status: Public on Feb 14 2019

city: Memphis

first: Tong

last: Lin

state: TN

address: 262 Danny Thomas Place

department: Biostatistics

institute: St. Jude Children's Research Hospital

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

overall_design: Refer to individual Series


title: An evolutionarily-conserved Wnt3/β-catenin/Sp5 feedback loop restricts head organizer activity in Hydra

status: Public on Jan 18 2019

city: Geneva

first: Leonardo

last: Beccari

address: 30 Quai Ernest Ansermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva


title: RNA sequencing results of L1-FGGY+/- lung squamous cell carcinoma tumor samples

status: Public on Jan 04 2019

city: New York

first: Zeguo

last: Sun

address: 1468 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

summary: In order to explore pathways which were affected by L1-FGGY in lung squamous cell carcinoma (LUSC), we performed RNA sequencing on L1-FGGY+/- LUSC tumor samples. We identified 1529 (826 up and 703 down) dysregulated genes in L1-FGGY positive tissues with an adjusted p value less than 0.05. The KEGG enrichment analysis indicated that many signaling pathways were upregulated in L1-FGGY positive tissues, including glutathione metabolism, metabolism of xenobiotics by cytochrome P450, arachidonic acid metabolism, metabolic pathways, and glycerolipid metabolism, most of which were metabolic pathways, especially in lipid-related metabolism.

overall_design: RNA sequencing profiles of L1-FGGY+/- LUSC tumor samples were generated by deep sequencing, in triplicate, using Illumina NovaSeq, followed by differential expression analysis and KEGG enrichment analysis.

first: Rui

last: Zhang


title: An evolutionarily-conserved Wnt3/β-catenin/Sp5 feedback loop restricts head organizer activity in Hydra [ChIP-Seq]

summary: Head regeneration in Hydra requires the transformation of gastric tissue into a head organizer that produces a head activator and a head inhibitor. Here we report the decipherment of a long-standing question in developmental biology, the identification of the transcription factor Sp5 as a key head inhibitory component. We show that Sp5 has an apical to basal graded expression pattern in intact Hydra, its expression is induced upon Wnt/β-catenin signaling activation and when knocked-down triggers the formation of multiple heads and axes in homeostatic and regenerative conditions. Our data indicate that Sp5 acts in a feed-forward loop to robustly regulate its own expression and that Sp5 prevents head formation by repressing the Wnt3 promoter. This Sp5 mediated Wnt antagonism is conserved and was invented early in metazoan evolution to set up axial patterning.

overall_design: ChIP seq analysis of Sp5 occupancies in human HEK293 cells transfected with expression vectors codig either for Hydra Sp5 or Zebrafish Sp5 proteins.The genomic occupancies mutant versions of these proteins lacking the Sp5 DNA binding domain were also tested. EAch experimental conditions was tested in 2 independent biological replicates.

first: M

last: Vogg

first: L


title: RNAseq of nestin-expressing murine brainstem progenitors infected with ACVR1 WT or R206H ACVR1 with and without H3.1K27M

status: Public on Jan 25 2019

first: Oren

middle: Josh

last: Becher

state: NY

address: 1468 Madison Avenue, A21-02

institute: Mount Sinai

summary: Diffuse intrinsic pontine glioma (DIPG) is an incurable pediatric brain tumor, resulting in the death of 200-300 children each year in the United States. Recently it was discovered that approximately 25% of all DIPG cases harbor activating mutations in ACVR1, a gene that encodes Activin A receptor (ALK2), a receptor in the bone morphogenetic protein (BMP) pathway, and that DIPGs with ALK2 mutations commonly harbor an H3.1K27M mutation. Herein, we used the RCAS/TVA retroviral system to study the effects of ACVR1 mutations and H3.1K27M on DIPG pathogenesis. In vitro expression of R206H ACVR1 with and without H3.1K27M in nestin-expressing brainstem progenitors resulted in upregulation of mesenchymal markers and gene set enrichment analysis (GSEA) revealed Stat3 pathway activation.  Neonatal expression of ACVR1 R206H or G328V in combination with H3.1K27M and p53 deletion in nestin-expressing brainstem progenitors induced glioma-like lesions expressing mesenchymal markers with Stat3 activation but was not sufficient for full gliomagenesis. In combination with platelet-derived growth factor A (PDGFA) signaling, ACVR1 R206H and H3.1K27M significantly decreased survival and increased tumor incidence. We demonstrate that targeting the BMP signaling pathway may be an effective therapeutic strategy to treat ACVR1 R206H mutant DIPGs. Exogenous Noggin expression at tumor initiation significantly increased tumor latency and treatment of ACVR1 R206H mutant murine DIPGs with LDN212854, an ACVR1 inhibitor, significantly prolonged their survival. We confirm relevance of our model to the human disease as human DIPG models with ACVR1 mutations were also sensitive to treatment with LDN212854 in vitro. Altogether, our studies demonstrate that ACVR1 R206H and H3.1K27M promote tumor initiation, accelerate gliomagenesis, promote a mesenchymal profile in part due to Stat3 activation, and identify LDN212854 as a promising compound to treat children with DIPG.

overall_design: We use RNAseq to study the transcriptomal effects of ACVR1 WT or R206H ACVR1 mutation alone and in combination with H3.1K27M mutation on murine nestin-expressing brainstem progenitors at P3-5 (using RCAS/TVA). Key findings were validated by Real-Time PCR.

first: Christine

last: Hoeman

first: Samantha

last: Gadd


title: Transcriptional profiling of Tregs and Teffs sorted from murine skin

status: Public on Dec 02 2018

city: San Francisco

first: Kelly

last: Remedios

state: CA

address: 513 Parnassus Ave, HSW1201B

institute: UCSF

summary: The goal of this study was to identify transcripts that were preferentially expressed in skin-resident Tregs relative to skin-resident Teffs.

overall_design: mRNA was isolated from Tregs and Teffs FACS sorted from the skin of 6 week old FOXP3-GFP reporter mice.

first: Tiffany

last: Scharschmidt

first: Michael

last: Rosenblum

middle: A


title: High-throughput, Efficient, and Unbiased Capture of Small RNAs from Low-input Samples for Sequencing

status: Public on Jan 31 2019

first: Cassandra

last: Belair

address: 35 Medical Center Way

department: Urology

type: Non-coding RNA profiling by high throughput sequencing

summary: We developed a high-throughput sequencing protocol that efficiently captures small RNAs from low input samples while minimizing inherent biases associated with library production.  The protocol was builds on previously published method that adds a barcode to samples at the earliest step in preparation such that all downstream manipulations can be performed on a pool of many samples thereby greatly reducing reagent usage and workload. We optimized adapter concentrations and showed modified adapters greatly increases the efficiency of small RNA capture. This work also demonstrates that unique molecular identifiers incorporated into the adapters can be used to bioinformatically remove PCR duplication.

overall_design: The analysis was performed with replicates as indicated in the sample titles.

first: Robert

middle: H

last: Blelloch


title: The high resolution transcriptome of Plasmodium falciparum gametocytes

status: Public on Dec 10 2018

city: Singapore

first: Zbynek

last: Bozdech

state: Select if applicable

department: Molecular Genetics&Cell Biology

country: Singapore

institute: Nanyang Technological University

summary: The gametocyte transcriptomes were generated in P.falciparum parasites of 3D7 strain after PfHP1 depletion aming to determin the transriptional profiles of sexual stages during the parasites gametocyte development.

overall_design: There are total 12 transcriptome collected at the 1st to 12th day during the parasites gametocyte development.

first: Till

last: Voss

first: Lei

last: Zhu

first: Miguel

middle: T

last: Mollà


title: Plucked hair follicles from patients with chronic discoid lupus erythematosus show a disease-specific molecular signature

status: Public on Oct 31 2018

city: Leeds

first: Adewonuola

last: Alase

state: West Yorkshire

address: Beckett St

department: LIRMM

country: United Kingdom

institute: University of Leeds

summary:
When faced with clinical symptoms of scarring alopecia – the standard diagnostic pathway involves a scalp biopsy which is an invasive and expensive procedure. Furthermore, clinical activity of scarring alopecias is often difficult to assess as symptoms of permanent damage and signs of activity can overlap or be difficult to distinguish. Here we report that gene expression analysis of only a small number of hair follicles (HF) plucked from lesional areas of the scalp is sufficient to characterise chronic discoid lupus erythematosus (CDLE). Lesional and non-lesional HFs were extracted from the scalp of patients with CDLE, psoriasis and healthy controls. The expression profile from CDLE HFs coincides with published profiles of CDLE from skin biopsy and was consistent with histopathological diagnostic features of CDLE.
We therefore propose that information obtained from this non-invasive approach are sufficient to diagnose scalp LE.

overall_design: Human hair follicles (HFs) from 4 healthy individuals (male and female aged 22-55), 7 patients with CDLE (female aged 20-75) from both lesional and non-lesional areaswere plucked out. The hair shaft was cut off and the white sheath (inner and outer root sheath) containing epidermal keratinocytes were used for this study. Plucked hair follicles were embedded longitudinally in OCT and 3-5 µm thick frozen sections were cut using a cryostat and collected in RNase free universal tubes. This was followed by the addition of lysis buffer (ReliaPrep™ RNA Cell Miniprep System, Promega, Wisconsin, USA) to the cut hair follicle sections and stored on dried ice prior to RNA extraction, which was carried out according to the manufacturer’s protocol.

first: Mohammad

last: Shalbaf

first: Miriam

last: Wittmann

first: Jelena

last: Pistolic

first: Anna

last: Berekmeri

last: Yuzaiful

first: Edward

last: Vital

first: Mark

middle: J

last: Goodfield


title: Transcriptional and functional analysis of Bifidobacterium animalis subsp. lactis exposure to tetracycline

status: Public on Sep 27 2018

city: Madison

first: Wesley

middle: w.

last: Morovic

state: WI

address: 3329 Agriculture Dr.

department: Genomics & Microbiome Science

institute: DuPont Nutrition & Health

summary: Commercial probiotic bacteria must be tested for acquired antibiotic resistance elements to avoid potential transfer to pathogens. The European Food Safety Authority recommends testing resistance using microdilution culture techniques previously used to establish inhibitory thresholds for the Bifidobacterium genus. Many Bifidobacterium animalis subsp. lactis strains exhibit increased resistance to tetracycline, historically attributed to the ribosomal protection gene tet(W). However, some strains that harbor genetically identical tet(W) genes show various inhibition levels suggesting that other genetic elements also contribute to observed differences. Here, we adapted several molecular assays to confirm the inhibition of B. animalis subsp. lactis strains Bl-04 and HN019, and employed RNA-seq to assess the transcriptional differences related to genomic polymorphisms. We detected specific stress responses to the antibiotic by correlating ATP concentration to viable genome copies from droplet digital PCR, and found that the bacteria were still metabolically active in high drug concentrations. Transcriptional analyses revealed that several polymorphic regions, particularly a novel multi-drug efflux transporter, were differentially expressed between the strains in each experimental condition, likely having phenotypic effects. We also found that the tet(W) gene was up-regulated only during sub-inhibitory tetracycline concentrations, while two novel tetracycline resistance genes were up-regulated at high concentrations. Furthermore, many genes involved in amino acid metabolism and transporter function were up-regulated while genes for complex carbohydrate utilization, protein metabolism, and CRISPR-Cas systems were down-regulated. These results provide high-throughput means for assessing antibiotic resistance and determine the genetic network that contributes to the global tetracycline response between two highly related probiotic strains.

overall_design: Two bacterial strains, B. lactis Bl-04 and B. lactis HN019. Control (ISO_0): colonies picked into MRS broth to O.D. 0.16-2.0, diluted 1:500, and grown to O.D. 0.14-0.30 (early log phase; three treatments: 1) (ISO_4) as control, but exposed to 4 µg/mL tetracycline, 2) (LOG_8) as control, but not diluted 1:500 and exposed to 8 µg/mL tetracycline, 3) (LOG_32) as control, but not diluted 1:500 and exposed to 32 µg/mL tetracycline. Two replicates of each.

first: Paige

last: Roos

first: Bryan

last: Zabel

first: Claudio

last: Hidalgo-Cantabrana

first: Anthony

last: Kiefer

first: Rodolphe

last: Barrangou


title: Transcriptomic study of Arabidopsis roots overexpressing the brassinosteroid receptor BRL3, in control conditions and under severe drought

status: Public on Sep 04 2018

city: Cerdanyola

first: Fidel

last: Lozano-Elena

state: Barcelona

address: Edifici CRAG - Campus UAB

department: Molecular Genetics

country: Spain

institute: Center for Research in Agricultural Genomics (CRAG)

summary: Abstract: Drought is the primary cause of global agricultural losses and represents a major threat to worldwide food security. Currently, plant biotechnology stands out as the most promising strategy to increase crop growth in rain-fed conditions. The main mechanisms underlying drought resistance have been uncovered by studies of plant physiology and by engineering crops with drought-resistant genes. However, plants with enhanced drought resistance usually display lower levels of growth, highlighting the need to search for novel strategies capable of uncoupling drought resistance from growth. Here, we show that the brassinosteroid family of receptors, in addition to promoting growth, guides phenotypic adaptation to a great variety of drought stress traits analyzed herein. Whilst mutations in the ubiquitously localized BRI1 receptor pathway show an enhanced drought resistance at the expense of plant growth, we found that vascular-enriched BRL3 receptors confer drought tolerance without penalizing overall growth. Systematic analyses reveal that upon drought stress the BRL3 receptor pathway triggers the synthesis and mobilization of osmoprotectant metabolites, mainly proline and sugars. This preferentially occurs in the vascular tissues of the roots and favors overall plant growth. Altogether, our results uncover a new role for the spatial control of BR signaling in drought tolerance, and offer a novel strategy to address food security issues in an increasingly water-limited climate.

overall_design: 28 days old root system were collected from soil, quickly washed in water and flash-frozen. Experiment with a bifactorial design. Factor one is the genotype, which include WT (Col-0) and 35S:BRL3. Factor two is the condition, which include control (Properly watered) and 5 days of drought (water-hold) conditions. 3 Biological replicates were collected per each genotype and condition.

first: Norma

last: Fàbregas

first: Ana

middle: I

last: Caño-Delgado


title: Multi-omic profiling of single nuclei uncovers regulatory diversity of brain cell types and diseases

status: Public on Dec 12 2019

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

type: Methylation profiling by high throughput sequencing

summary: Most existing single-cell techniques can only make one type of molecular measurements. Although computational approaches have been developed to integrate single-cell datasets, their efficacy still needs to be determined with reference to authentic single-cell multi-omic profiles. To address this challenge, we devised single-nucleus methylCytosine, Chromatin accessibility and Transcriptome sequencing (snmC2T-seq) and applied the approach to post-mortem human frontal cortex tissue. We developed a computational framework to evaluate the quality of finely defined cell types using multi-modal information and validated the efficacy of computational multi-omic integration methods. Correlation analysis in individual cells revealed gene groups showing distinct relations between methylation and expression. Integration of snmC2T-seq with other multi- and single- modal datasets enabled joint analyses of the methylome, chromatin accessibility, transcriptome, and chromatin architecture for 63 human cortical cell types. We reconstructed the regulatory lineage of these cortical cell types and found pronounced cell-type-specific enrichment of disease risks for neuropsychiatric traits, predicting causal cell types that can be targeted for treatment.

overall_design: snmC2T-seq and snATAC-seq

first: Chongyuan

last: Luo

first: Hanqing

last: Liu

first: Fangming

last: Xie

first: Wayne

last: Doyle

first: Ethan

last: Armand

first: Sheng-Yong

last: Niu

first: Jingtian

last: Zhou

first: Dong-Sung

last: Lee

first: Bang-An

last: Wang

last: Bartlett

first: Rosa

last: Castanon

first: Angeline

last: Rivkin

first: Jacinta

last: Lucero

last: Nery

first: Jesse

last: Dixon

first: Bing

last: Ren

first: M

last: Behrens

first: Eran

last: Mukamel


title: DET1-mediated degradation of a SAGA-like deubiquitination module controls H2Bub homeostasis [ChIP-seq]

status: Public on Aug 31 2018

city: Paris

first: Fredy

last: BARNECHE

address: Rue d'Ulm

department: IBENS

country: France

institute: CNRS

summary: DE-ETIOLATED 1 (DET1) is an evolutionarily conserved component of the ubiquitination machinery that mediates the destabilization of key regulators of cell differentiation and proliferation in multicellular organisms. In this study, we provide evidence from Arabidopsis that DET1 is essential for the regulation of histone H2B monoubiquitination (H2Bub) over most genes by controlling the stability of a plant deubiquitination module (DUBm). In contrast with yeast and metazoan DUB modules that are associated with the large SAGA complex, the Arabidopsis DUBm only comprises three proteins (hereafter named SGF11, ENY2 and UBP22) and appears to act independently as a major H2Bub deubiquitinase activity. Our study further unveils that DET1-DDB1-Associated-1 (DDA1) protein interacts with SGF11 in vivo, linking the DET1 complex to light-dependent ubiquitin-mediated proteolytic degradation of the DUBm. Collectively, these findings uncover a signaling path controlling DUBm availability, potentially adjusting H2Bub turnover capacity to the cell transcriptional status.

overall_design: 16 ChIP-seq libraries were sequenced.

first: Clara

last: Bourbousse

first: Ouardia

last: Ait-Mohamed

first: Martin

last: Rougée

last: Barneche


title: DET1-mediated degradation of a SAGA-like deubiquitination module controls H2Bub homeostasis


title: DET1-mediated degradation of a SAGA-like deubiquitination module controls H2Bub homeostasis [RNA-seq]

overall_design: 12 RNA-seq libraries were sequenced.


title: Molecular Signatures of Multiple Myeloma Progression through Single Cell RNA-Seq

status: Public on Nov 17 2018

city: Rochester

first: Jie

last: Sun

state: MN

address: 200 First Street SW

institute: Mayo Clinic

summary: Multiple myeloma (MM) is a malignant plasma cell disorder with well-defined clonal genetic/cytogenetic abnormalities.  However, cellular heterogeneity is a key factor in MM’s progression, therapeutic decision, and response to treatment. Single cell whole transcriptome profiling (scRNA-Seq) offers an opportunity to dissect this molecular heterogeneity during MM progression to better understand the disease and guide rational therapy.  Here, we examined 597 CD138 positive cells from 15 patients at different stages of MM progression using scRNA-Seq.  We selected 790 genes based on a Coefficient of Variation (CV) approach which organized cells into four clusters (L1-L4) based on unsupervised clustering. Plasma cells from each patient contained a mixed population of plasma cells at different state of aggressiveness based on gene expression signature reflecting the inter-cellular heterogeneous nature of MM.  Cells in the L1 group is characterized by low level expression of genes involved in the oxidative phosphorylation, Myc targets, and mTORC1 signaling pathway having most cells from MGUS patients (p < 1.2x10-14).  In contrast, low level of these genes in L1 group increased progressively and were the highest in the L4 group containing only cells from high-risk MM patients with t(4;14) translocations.   Furthermore, 44 genes consistently overexpressed by pair-wised comparisons of the four groups strongly associated with a reduced overall survival in MM patients (APEX trial, p < 0.0001; Hazard Ratio (HR), 1.83; 95% CI, 1.33 to 2.52), particularly those in the bortezomib treated group (p < 0.0001; HR, 2.00; 95% CI, 1.39 to 2.89).  No survival significance was observed for the dexamethasone treated group.   Our study at the resolution of single cells showed that there is a mixed population of cells in each patient at different stages of MM progression and these cells can be organized into four different subgroups (L1 to L4).  Consistent overexpression of the 44 genes from L1 to L4 groups is associated with patient outcome and treatment response.  Our results show that oxidative phosphorylation, Myc target, and mTORC1 signaling genes are significant pathways for MM progression and affect MM prognosis and treatment stratification.

overall_design: 597 single cell libraries passed QC and were included in the downstream analysis

first: Jin

last: Jang

first: Ying

last: Li

first: Amit

last: Mitra

first: Lintao

last: Bi

first: Alexej

last: Abyzov

first: Andre

last: van Wijnen

first: Linda

middle: B

last: Baughn

first: Brian

last: Van Ness

first: Vincent

last: Rajkumar

first: Shaji

last: Kumar

last: Jen


title: APOBEC mutation drives early-onset squamous cell carcinomas in recessive dystrophic epidermolysis bullosa

status: Public on Aug 01 2018

city: Philadelphia

first: Andrew

last: South

state: PA

address: 233 S 10th Street

department: Dermatology and Cutaneous Biology

institute: Thomas Jefferson University

summary: RNA-sequencing of RDEB SCC tumors and RDEB normal skin

overall_design: RNA was isolated from fresh frozen samples and used for RNA-sequencing

first: Kenneth

last: Tsai


title: circRNA expression in breast cancer

status: Public on Jul 07 2018

city: Shantou

first: Jianzhen

last: Xu

address: No.22 Rd Xinling

country: China

institute: Shantou University Medical College


title: Hierarchical roles of mitochondrial PAPI and Zucchini in Bombyx germline piRNA biogenesis

status: Public on Mar 01 2018

city: Tokyo

first: Yuka

middle: W.

last: Iwasaki

address: 35 Shinanomachi, Shinjuku-ku,

department: Department of Molecular Biology

country: Japan

institute: Keio University School of Medicine

summary: PIWI-interacting RNAs (piRNAs) are germline-enriched small RNAs that control transposons to maintain genome integrity1,2,3. To achieve this, piRNAs bind PIWI proteins upon being processed from piRNA precursors1,2,3. Bioinformatic studies of piRNA biogenesis in Drosophila showed that the piRNA 5′ end is formed by PIWI-Slicer or Zucchini (Zuc) endonucleolytic cleavage, while the 3′ end is formed by Zuc or Nibbler (Nbr) 3′-to-5′ exonucleolytic activity4,5,6. piRNA 3′-end formation in Bombyx was shown to be mediated by PNLDC1/Trimmer (Trim) 3′-to-5′ exonuclease7, while piRNA intermediates are bound with PIWI anchored onto mitochondrial protein PAPI8. However, the requirement for Zuc and Nbr in piRNA biogenesis in Bombyx has not been elucidated. Here, we applied biochemical approaches to understand their involvement in piRNA biogenesis and revealed that Zuc endonuclease, but not Trim and Nbr exonucleases, plays a crucial role in Bombyx piRNA 3′-end formation. Loss of Zuc had little effect on the levels of Trim and Nbr, but led to the aberrant accumulation of piRNA intermediates within the PAPI complex, which were processed to mature piRNAs by recombinant Zuc. Zuc copurified with PAPI, and PAPI exerted RNA-binding activity only when Siwi coexisted with it and PAPI was phosphorylated, suggesting that complex assembly proceeds via a hierarchical process. Bioinformatic analyses of piRNA intermediates within the PAPI complex revealed that both the 5′ and the 3′ ends showed the hallmark of PIWI-Slicer, yet no phasing pattern was observed in mature piRNAs. These findings strongly support the notion that, in Bombyx piRNA, the 5′ end is formed by PIWI-Slicer, but independently of Zuc, while the 3′ end is formed by Zuc endonuclease. The Bombyx piRNA biogenesis is simpler than that of Drosophila, which is reasonable considering that Bombyx has no transcriptional silencing machinery relying on phased piRNAs.

overall_design:
Two RIP-seq libraries: RIP libraries were prepared from RNA associated with PAPI immunoprecipitates (with size selection at 65-100nt).
Six smRNA-seq libraries: small RNA libraries were prepared from small RNA associated with Flag-Siwi and Flag-Ago3 immunoprecipitates (with size selection at 23-35nt).

first: Kazumichi

last: Nishida

first: Kazuhiro

last: Sakakibara

first: Mikiko

middle: C

last: Siomi


title: Single-cell Multi-omics Sequencing and Analyses of Human Colorectal Cancer

status: Public on Nov 29 2018

city: Beijing

first: Yu

last: Hou

state: Beijing

address: No.5 Yiheyuan Street

department: School of life sciences

institute: Peking University

summary: Although genomic instability, epigenetic abnormality, and gene expression dysregulation are hallmarks of colorectal cancer, these features have not been simultaneously analyzed at single-cell resolution. Using optimized single-cell multi-omics sequencing together with multi-regional sampling of the primary tumor, lymphatic and distant metastases, we provide insights beyond intratumoral heterogeneity. Genome-wide DNA methylation levels were relatively consistent within a single genetic sub-lineage. The genome-wide DNA demethylation patterns of cancer cells were consistent in all 10 sequenced patients. Our work demonstrates the feasibility of reconstructing genetic lineages, and tracing their epigenomic and transcriptomic dynamics with single-cell multi-omics sequencing.

overall_design:
Single cell RNA-seq and Bisulfite-seq on whole cells or by TrioSeq2.

[scTrioSeq2Rna and scTrioSeq2Met Samples]
Sample Title structure: Library_PatientID_SamplingPositions_CellID
SamplingPositions abbreviations:
PT:  Primary Tumor
LN:  Lymph Node metastasis
ML:  Liver Metastasis
MP:  Post-treatment Liver Metastasis

first: Shuhui

last: Bian

first: Fuchou

last: Tang


title: Epigenetic profiling for the molecular classification of metastatic brain tumors

status: Public on Aug 28 2018

city: Santa Monica

first: Dave

last: Hoon

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

summary: Genome-wide DNA methylation profiling of brain metastases from lung cancer, breast cancer, and melanoma samples. The Illumina Infinium 450K Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 methylation sites in formalin-fixed paraffin-embedded (FFPE) samples from brain metastases. Samples included 30 breast cancer brain metastases, 18 lung cancer brain metastases, 37 melanoma brain metastases, and 4 samples with brain metastases from patients with uncertain primary.

overall_design: Bisulfite converted DNA samples from 89 specimens were analyzed by using the Illumina Infinium 450K Human Methylation BeadChip.

first: Matthew

middle: P

last: Salomon

first: Diego

last: Marzese

first: Javier

last: Orozco


title: Dynamic Patterns of Threat-associated Gene Expression in the Amygdala and Blood

status: Public on Jul 06 2018

city: Atlanta

first: Adriana

last: Lori

state: GA

address: 101 Woodruff Circle

department: PsychDepartment of Psychiatry and Behavioral Sciences

institute: Emory University

summary:
Purpose: Identification the biological response to fear and stress in both brain and blood is vital for investigators performing peripheral studies of psychiatric traits.   The goal of this study was to determine genes responsive to fear conditioning (FC), a well-characterized rodent model of threat-exposure, in the presence or absence of prior stress history, providing insight into the physiological processes underlying traumatic memory formation and trauma-related disorders such as PTSD.
Methods: RNA sequencing was performed in blood and amygdala from mice that underwent fear conditioning (FC) with and without prior immobilization stress history (Immo+FC), or untreated animals (home cage HC). Libraries were prepared using the Illumina TruSeq™ RNA kit as per manufacturer’s instructions.  Libraries were normalized and 8 samples were multiplexed in each lane of the flowcell. PhiX was used as an internal control on each lane to monitor the error statistics. Cluster generation was performed on the V3 flowcell on the Illumina cBot. The clustered flowcell was then sequenced on the Illumina HiSeq1000 system employing a single-end 101 cycles run. Alignment to the mm10 UCSC Mouse Assembly was performed using STAR version 2.3 (Dobin et al, 2013); parameters were set using the annotation as a splice junction reference.  Sample reads were assembled into transcript models using cufflinks (v2.1.1) which were then merged and processed with cuffdiff v2.1.1, (Trapnell et al, 2012) to produce per sample FPKM expression levels and estimate differential expression between the sample groups.
Results: In the amygdala, 607 genes associated with FC vs. HC (FDR<.05). In the same tissue, 516 genes showed different expression in response of immobilization (Immo+FC) compared to the FC group (FDR<.05). In the blood of the same animals, 468 genes had distinct changes in expression (Immo+FC vs FC; FDR<.05) and were enriched for biological processes such as inflammation and cytokine signaling.
Conclusions: This study identified genes and pathways that respond to threat in the amygdala and blood of animals with and without a prior stress history. Future studies will be needed to examine the necessity, function and relevance of these regulated genes in human clinical stress and trauma-related disorders including.

overall_design: Each group (FC; IMMO+FC; HC) consisted of 12 mice (C57BL/6J) pooled into 6 samples for sequencing  with Illumina TruSeq™ RNA. The final dataset contained the following number of samples: for blood 5 Immo+FC, 5 FC, and 4HC; for amygdala 4 Immo+FC, 6 FC, and 6 HC.

first: Stephanie

last: Maddox

first: Sumeet

last: Sharma

first: Raül

last: Andero

first: Kerry

last: Ressler

first: Alicia

middle: K

last: Smith

first: Nirav

last: Patel

first: Gregory

last: Tharp


title: Single-nucleus and single-cell transcriptomes compared in matched cortical cell types

status: Public on Dec 06 2018

city: Seattle

first: Allen

last: Institute

state: WA

address: 615 Westlake Ave N

institute: The Allen Institute for Brain Science

summary: Transcriptomic profiling of complex tissues by single-nucleus RNA-sequencing (snRNA-seq) affords some advantages over single-cell RNA-sequencing (scRNA-seq). snRNA-seq provides less biased cellular coverage, does not appear to suffer cell isolation-based transcriptional artifacts, and can be applied to archived frozen specimens. We used well-matched snRNA-seq and scRNA-seq datasets from mouse visual cortex to compare cell type detection. Although more transcripts are detected in individual whole cells (~11,000 genes) than nuclei (~7,000 genes), we demonstrate that closely related neuronal cell types can be similarly discriminated with both methods if intronic sequences are included in snRNA-seq analysis. We estimate that the nuclear proportion of total cellular mRNA varies from 20% to over 50% for large and small pyramidal neurons, respectively. Together, these results illustrate the high information content of nuclear RNA for characterization of cellular diversity in brain tissues.

overall_design: scRNA-seq of 463 single nuclei and 463 matched single cells from mouse primary visual cortex (VISp) and 30 control samples. Note that single cell data respresents a small subset of VISp cells from GEO series GSE115746.

first: Trygve

middle: E

last: Bakken

first: Rebecca

last: Hodge

first: Jeremy

last: Miller

first: Zizhen

last: Yao

first: Thuc

middle: N

last: Nguyen

first: Brian

last: Aevermann

first: Eliza

last: Barkan

first: Darren

last: Bertagnolli

first: Tamara

last: Casper

first: Nick

last: Dee

first: Emma

last: Garren

first: Jeff

last: Goldy

first: Lucas

last: Graybuck

last: Kroll

first: Roger

last: Lasken

first: Kanan

last: Lathia

first: Sheana

last: Parry

first: Christine

last: Rimorin

first: Richard

last: Scheuermann

first: Nicholas

last: Schork

first: Soraya

last: Shehata

first: Michael

last: Tieu

first: John

middle: W

last: Phillips

first: Amy

last: Bernard

first: Kimberly

first: Hongkui

last: Zeng

first: Ed

last: Lein

first: Bosiljka

last: Tasic


title: Gene expression dynamics during regeneration of Eisenia fetida

status: Public on Jul 03 2018

city: Delhi

first: Beena

last: Pillai

address: Mathura Road

country: India

institute: IGIB

summary: Earthworms show a wide spectrum of regenerative potential with certain species like Eisenia fetida, a terrestrial redworm, capable of regenerating more than two-thirds of their body while other closely related species, such as Paranais litoralis seem to have lost this ability. Earthworms belong to the phylum annelida, in which the genomes of the marine oligochaete Capitella telata, and the freshwater leech Helobdella robusta have been sequenced and studied. Herein, we report the de novo assembled transcriptome of Eisenia fetida (Indian isolate), along with an analysis of the transcriptomic changes during regeneration. We also used de novo assembled RNAseq data to identify genes that are differentially expressed during regeneration, both in the newly regenerating cells and in the adjacent tissue.

overall_design: Gene Expression profiles of E.fetida, before and 15,20 or 30 days after cutting were generated by deep sequencing, in triplicate, using Illumina.

first: Surendra

middle: S

last: Patel

first: Aksheev

last: Bhambri


title: Prospective Molecular Profiling of Circulating Tumor Cells from Patients with Melanoma Receiving Combinatorial Immunotherapy

status: Public on Jun 26 2018

first: Dave

last: Hoon

summary: Transcriptomic profiling of circulating tumor cells obtained from the blood of three melanoma patients on immunotherapy.

overall_design: RNA-Seq analysis were generated by using Illumina HiSeq 2500.

first: Matthew

last: Salomon

first: Sandy

last: Hsu

first: Nellie

last: Nelson


title: Presence of meniscus tear alters gene expression profile of anterior cruciate ligament tears

status: Public on Jan 23 2018

city: St. Louis

first: Muhammad Farooq

last: Rai

state: MO

address: 660 S. Euclid Ave.

department: Orthopaedic Surgery

institute: Washington University School of Medicine

summary: Anterior cruciate ligament (ACL) tears occur in isolation or in combination with other intra-articular injuries such as meniscus tears. The impact of injury pattern on the molecular biology of the injured ACL is unknown. Here, we tested the hypothesis that the biological response of the ACL to injury varies based on the presence or absence of concomitant meniscus tear. RNA-seq analysis was performed on 28 ACL tears remnants (12 isolated, 16 combined). 16,654 transcripts were differentially-expressed between isolated and combined injury groups at false-discovery-rate of 0.05. Due to the large number of differentially expressed transcripts, we undertook an Ensembl approach to discover features that acted as hub-genes that did not necessarily have large fold-changes or high statistical significance, but instead had high biological significance. Our data revealed a negatively-correlated turquoise-module containing 5960 transcripts (down-regulated in combined injury) and a positively-correlated blue-module containing 2260 transcripts (up-regulated in combined injury). TNS1, MEF2D, NOTCH3, SOGA1, and MLXIP were highly-connected hub-genes in the turquoise-module and SCN2A, CSMD3, LRC44, USH2A, and LRP1B were critical hub-genes in the blue-module. Transcripts in the turquoise-module were associated with biological-adhesion, actin-filament organization, cell-junction assembly, and cell-matrix adhesion. The blue-module transcripts were enriched for neuron-migration and exocytosis-regulation. These findings indicate a loss of healing and gain of neurogenic signaling in combined ACL and meniscus tears, suggesting they have diminished potential for repair. The biological response of the ACL to injury could have implications for the healing potential of the ligament and the long-term health of the knee.

overall_design: RNA isolated from ACL remnants was subjected to RNA-seq to study gene transcripts differentially expressed between isolated (ACL injury only) and combined (ACL + meniscus injury) groups.

first: Muhammad

middle: F

first: Eric

middle: D

last: Tycksen

first: Marcus

last: Rothermich

first: Lei

last: Cai

first: Robert

last: Brophy


title: RNA-Sequencing Analysis of AVF-CKD Murine Model

status: Public on Jun 27 2018

first: Daniel

middle: Rothschild

last: OBrien

address: 200 First St. SW

institute: The Mayo Clinic

summary: We studied a murine AVF in mice with chronic kidney disease (CKD).

overall_design: Venous mRNA of 7 day sham and AVF-CKD mice were sequenced using an Illumina HiSeq 2000.

first: Karl

last: Nath


title: MiR-200a Regulates CDK4/6 Inhibitor Effect by Targeting CDK6 in Metastatic Melanoma

status: Public on Jun 20 2018

summary: Three metastatic melanoma cell lines (BD-0548-ME, DP-0574-ME and WP-0614-ME) were transfected with miR precursors: hsa-miR negative control (NC) or hsa-miR-200a-3p precursors (miR-200a). The objective of this experiment was to determine miR-200a targets in metastatic melanoma cell lines. We selected low -miR-200a expression cell lines and then we overexpressed miR-200a or NC. Finally, we compared the metastatic melanoma cell lines with miR-200a overexpression (miR-200a) to the same cell line transfected with the negative control miR (NC).

overall_design: Total RNA was extracted from three melanoma cell lines and RNA-Seq by using Illumina HiSeq 2500.

first: Matias

middle: A

last: Bustos

first: Shigheshi

last: Ono

first: Diego

middle: M

last: Marzese


title: DNA methylation at enhancers identifies distinct breast cancer lineages

status: Public on Nov 15 2017

city: Oslo

first: Thomas

last: Fleischer

address: Ullernchausséen 70

department: Department of Cancer Genetics, Institute for Cancer Research

country: Norway

institute: Oslo University Hospital

type: Methylation profiling by genome tiling array

summary: Breast cancers exhibit genome-wide aberrant DNA methylation patterns. To investigate how these affect the transcriptome and which changes are linked to transformation or progression, we apply genome-wide expression-methylation quantitative trait loci (emQTL) analysis between DNA methylation and gene expression. On a whole genome scale, in cis and in trans, DNA methylation and gene expression have remarkably and reproducibly conserved patterns of association in three breast cancer cohorts (n=104, n=253 and n=277). The emQTL associations form two main clusters, one relates to tumor infiltrating immune cell signatures and the other to estrogen receptor signaling. In the estrogen related cluster, using ChromHMM segmentation and transcription factor ChIP-seq data, we identify transcriptional networks regulated in a cell lineage-specific manner by DNA methylation at enhancers. These networks are strongly dominated by ERα, FOXA1 or GATA3 and their targets were functionally validated using knock-down by siRNA or GRO-seq analysis after transcriptional stimulation with estrogen.

overall_design: Bisulphite converted DNA from the 285 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip

first: Xavier

last: Tekpli

first: Anthony

last: Mathelier

first: Shxiong

last: Wang

last: Nebdal

first: Hari

last: Dhakal

first: Kristine

last: Kleivi Sahlberg

first: Ellen

last: Schlichting

first: Anne-Lise

last: Børresen-Dale

first: Elin

last: Borgen

first: Bjørn

last: Naume

first: Ragnhild

last: Eskeland

first: Arnoldo

last: Frigessi

first: Jörg

last: Tost

first: Antoni

last: Hurtado

first: Vessela

last: Kristensen


title: Menin-MLL inhibitors block oncogenic transformation by MLL fusion proteins in a fusion partner independent manner

status: Public on Jun 09 2018

city: Gaithersburg

first: Jingya

state: Maryland

address: 1 Medimmune Way

summary: Chromosomal rearrangements of the Mixed Lineage Leukemia (MLL) gene result in fusion proteins which retain the N-terminal portion of MLL fused with one of more than 70 different fusion partners. The high diversity of MLL fusion partners raises a question whether it is possible to develop a general therapeutic strategy to block the oncogenic activity of MLL fusion proteins in a fusion partner independent manner. We have demonstrated that blocking the menin-MLL interaction using small molecule inhibitor inhibits oncogenic activity of different MLL fusion proteins according to a mechanism that is independent on the fusion partner.

overall_design: MLL-AF9, MLL-AF6 and MLL-AF1P transformed cells were treated with the menin-MLL inhibitor MI-2-2

first: Jolanta

last: Grembecka

first: Tomek

last: Cierpicki

first: Trupta

last: Purohit


title: Blood-Derived DNA Methylation Signatures of Crohn’s Disease and Severity of Intestinal Inflammation

status: Public on Apr 03 2018

first: Alicia

last: Smith

summary: Crohn’s disease is a relapsing inflammatory disorder with a variable clinical course. While most patients present with purely an inflammatory phenotype (B1) at diagnosis, a subgroup (~20%) rapidly progresses to complicated disease manifestations that include stricturing (B2) within 5 years. DNA methylation is a key epigenetic mechanism that can regulate gene expression and thereby influence the development and progression of complex diseases. Site-specific DNA methylation differences have been reported in peripheral blood of patients with Crohn’s disease, but investigation of the temporal relationship between methylation and disease is required to establish whether the methylome plays a causal role and can be leveraged for therapeutic benefits. To this end, we conducted an epigenome-wide study of methylation (~850K sites) in peripheral blood at diagnosis and during follow-up from the RISK pediatric Crohn’s disease inception cohort. While some methylation changes associated with Crohn’s disease might be causal, in peripheral blood the vast majority are found to be a transient consequence of inflammation and thus a symptom of disease.

overall_design: DNA methylation was assessed in peripheral blood from pediatric non-IBD controls and patients with Crohn's disease at two time points - at diagnosis and follow-up. Peripheral blood DNA was extracted, bisulfite converted and genome-wide DNA methylation was interrogated using the HumanMethylationEPIC BeadChip (Illumina).

last: Somineni

first: Suresh

last: Venkateswaran

first: Varun

last: Kilaru

first: Urko

last: Marigorta

first: Angela

last: Mo

first: David

middle: T

last: Okou

first: Richard

last: Kellermayer

first: Kajari

last: Mondal

first: Dawayland

last: Cobb

first: Thomas

last: Walters

first: Anne

last: Griffiths

first: Joshua

last: Noe

first: Wallace

middle: V

last: Crandall

first: Joel

last: Rosh

last: Mack

first: Melvin

last: Heyman

first: Susan

last: Baker

first: Michael

last: Stephens

first: Robert

last: Baldassano

first: James

last: Markowitz

first: Marla

last: Dubinsky

first: Judy

last: Cho

first: Jeffrey

last: Hyams

first: Lee

last: Denson

first: Greg

last: Gibson

middle: J

last: Cutler

first: Karen

last: Conneely

first: Subra

last: Kugathasan


title: Profiling of differential RNAs in SORBS2-depleted ovarian cancer cells and control cells

status: Public on Feb 20 2018

city: Chengdu

first: Shengtao

last: Zhou

address: #17, Renmin South Road

department: Department of Obstetrics and Gynecology

institute: West China Second Hospital, Sichuan University

summary: In this study, we examined the differential RNA profile of SORBS2-depleted ovarian cancer cells compared with control cells

overall_design: We used RNA sequencing to compare the differential RNAs of SORBS2-depleted ovarian cancer cells compared with control cells


title: Next Generation Sequencing Facilitates Quantitative Analysis of yeast cells lacking either M-2 dsRNA or both L-A-lus and M-2 dsRNA viruses

status: Public on Jul 26 2017

city: Vilnius

first: Elena

last: Serviene

address: Akademijos 2

country: Lithuania

institute: Nature Research Centre

summary: Here we determine the impact upon the loss of M-2 dsRNA alone and both L-A-lus along with M-2 on the host S. cerevisiae transcriptional changes. By performing profiling of the whole transcriptomes, we determined 486 genes differentially expressed after curing of yeast cells from M-2 dsRNA and 715 genes affected by the elimination of both M-2 and L-A-lus dsRNAs.

overall_design: Examination of host gene expression in response to the loss of viral infection.

first: Juliana

last: Luksa


title: Atrazine Induced Epigenetic Transgenerational Inheritance of Disease, Lean Phenotype and Sperm Epimutation Pathology Biomarkers

status: Public on Aug 08 2017

city: Pullman

last: Skinner

address: Abelson 507

department: SBS

institute: WSU

summary: This study examined the potential transgenerational actions of the herbicide atrazine.  The F1 generation offspring (directly exposed as a fetus) derived from the F0 generation exposed gestating female rats did not develop disease, but weighed less compared to controls. The F2 generation (grand-offspring) was found to have increased frequency of testis disease, increased frequency of tumor development in males and females (predominately mammary tumors), early onset puberty in males, and decreased body weight in females compared to controls. The transgenerational F3 generation rats were found to have increased frequency of testis disease, early onset puberty in females, behavioral alterations and a lean phenotype in males and females involving a reduced adipocyte size, decreased body mass index (BMI) and reduced adiposity. The frequency of multiple diseases was significantly higher in the transgenerational F3 generation atrazine lineage males and females. The sperm differential DNA methylation regions (DMRs), termed epimutations, induced by atrazine were identified. A comparison of control versus atrazine lineage sperm identified 519 DMRs (p<10-6) for the F1 generation, 431 DMR (p<10-5) for the F2 generation, and 958 DMR (p<10-9) for the transgenerational F3 generation sperm.

overall_design: Outbred gestating female rats were transiently exposed to a vehicle control or atrazine. The F1 generation offspring were bred to generate the F2 generation and then the F2 generation bred to generate the F3 generation. The F1, F2 and F3 generation control and atrazine lineage rats were aged and various pathologies investigated. The male sperm were collected to investigate DNA methylation differences between the control and atrazine lineage sperm. MeDIP-seq was used to measure methylation in each sample.

first: Margaux

last: McBirney

first: Setphanie

last: King

first: Michelle

last: Pappalardo

first: Elizabeth

last: Houser

first: Margaret

last: Unkefer

first: Eric

last: Nilsson

first: Ingrid

last: Sadler-Riggleman

first: Daniel

last: Beck

first: Paul

last: Winchester


title: Effects of Acute Aerobic Exercise on Whole Genome Nucleosome Maps in Skeletal Muscle of Lean vs Overweight/Obese Men

status: Public on Dec 30 2017

city: Shreveport

first: Tara

last: Henagan

address: 1501 Kings Hwy

department: Medical School

institute: Louisiana State University Health Sciences Center - Shreveport

summary: Acute aerobic exercise has been shown to improve skeletal muscle mitochondrial function and completeness of fatty acid β-oxidation which contribute to improved insulin sensitivity. The effectiveness of acute exercise on improving mitochondrial adaptations, leading to improved insulin sensitivity, in overweight/obese (Ov/Ob) individuals is controversial. This study aimed to determine the effects of acute exercise on epigenetic regulation, specifically nucleosome positioning, of genes involved in skeletal muscle mitochondrial adaptations in lean vs Ov/Ob men.

overall_design: 30 men, aged 19-30 years, were recruited and divided into two groups: lean (BMI<25, 18.5- 24.1 kg/m2, n=15) and Ov/Ob (BMI≥25, 25.5- 36.9 kg/m2, n=15). Vastus lateralis muscle biopsy samples were collected at rest, following an overnight fast (Pre; n=14 in lean Pre and n=15 in Ov/Ob Pre). Subjects then ingested a standardized high-carbohydrate breakfast (7 kcal/kg; 60% carbohydrate, 25% fat, 15% protein). Four hours later, they performed an acute bout of cycling exercise (50% VO2max, expending ~650 kcal) and vastus lateralis muscle biopsy samples were collected immediately after the exercise bout (Post; n=15 in lean Post and in Ov/Ob Post). Mononucleosomal DNA was extracted from vastus lateralis muscle samples (n=5 per group) and MNase-seq was performed using the Illumina platform and analyzed via HOMER and custom scripts, as previously described (Henagan, TM et al 2015).

first: Prasad

last: Devarshi

first: Aarin

last: Jones

first: Wayne

last: Campbell

first: Erin

last: Taylor

first: Jessica

last: Ellis


title: Analysis of the DNA accessibility upon multiple histone H1 variants by ATAC-seq (6 samples)

status: Public on Aug 14 2017

city: Barcelona

first: Albert

last: Jordan

address: Baldiri Reixac 4

department: Molecular Genomics

institute: IBMB-CSIC

summary:
Combined depletion of H1.2 and H1.4 has a strong deleterious effect in the cancer cells examined, and induces a strong interferon (IFN) response with up-regulation of many IFN-stimulated genes (ISGs), which is not seen in individual H1 knock-downs.
Although H1 participates to repress ISG promoters, its activation upon H1 KD is mainly generated by the activation of the IFN response through cytosolic nucleic acids receptors, IFN synthesis and JAK-STAT pathway activation.
The IFN response may be triggered by the expression of noncoding dsRNAs generated from heterochromatic repeats or endogenous retroviruses upon H1 KD.
H1 KD promotes the appearance of accessibility sites genome wide and, particularly, at satellites and other repeats.

overall_design: 6 samples

last: Vallés

first: Andrea

last: Izquierdo-Bouldstridge


title: Gene expression by high-throughput sequencing of T47D-MTVL human breast cancer cells upon H1.4 knock-down and multiple H1 variants

summary: Gene expression of T47D-MTVL human breast cancer cells expressing Dox-inducible shRNAs against histone H1.4 (120sh) or multiple H1 variants (225sh)

overall_design: Stable breast cancer-derived cell lines expressing an shRNA against one of each of the histone H1 isoforms in response to doxycycline (Dox) were grown for six days in the presence or absence of Doxicycline, RNA extracted and high-thorughput sequenced. Cell lines used: inducible shRNA against H1.4 or multiple H1 variants and random shRNA-expression vector.


title: Integrative Analysis of the Pekin Duck (Anas anas) MicroRNAome during Feather Follicle Development

status: Public on Aug 11 2017

city: hefei

first: xing

middle: yong

last: chen

state: anhui

address: 130 West Changjiang Road

department: School Of Animal Science And Technology

institute: Anhui Agricultural University

summary: The quality and yield of duck feathers are very important economic traits that might be controlled by miRNA regulation. The aim of the present study was to investigate the mechanism underlying the crosstalk between individual miRNAs and the activity of signaling pathways that control the growth of duck feathers during different periods.

overall_design: We conducted a comprehensive investigation using Solexa sequencing technology on the Pekin duck microRNAome over six stages of feather development at days 11, 15, and 20 of embryonic development (during the hatching period), and at 1 day and 4 and 10 weeks posthatch.

first: Xingyong

last: Chen

first: Zhaoyu

last: Geng


title: Epigenetic Regulation of KPC1 Ubiquitin Ligase Affects the NF-κB Pathway in Melanoma

status: Public on Sep 01 2017

first: Dave

last: Hoon

summary: Melanoma is a highly aggressive cancer with increasing incidence rates and a poor survival, particularly in patients with AJCC stage IV and advanced stage III. Deregulation of NF-kB is linked to different pathological states, including melanoma. To identify the involvement of NF-kB pathway regulation in melanoma progression, we manipulated NF-kB pathway activation and profiled gene expression using RNA-sequencing.

overall_design: mRNA profiles of WC00060 and SR-0788 with KPC1 knockdown (siKPC1) or control (siCntl) generated by deep sequencing using Illumina HiSeq 2500.

first: Yuuki

last: Iida

first: Sandy

last: Hsu

first: Nellie

last: Nelson

first: Matthew

last: Salomon


status: Public on Apr 27 2017

overall_design: Total RNA was extracted and RNA-Seq analysis for IM-0223 melanoma cell lines with RNF123 overexpression (KPC1) or control empty vector (V0) using Illumina HiSeq 2500.


title: Effects of Acute Aerobic Exercise on Skeletal Muscle Transcriptomics in Lean vs Overweight/Obese Men

last: Henagan

summary: Acute aerobic exercise has been shown to improve skeletal muscle mitochondrial function and completeness of fatty acid β-oxidation which contribute to improved insulin sensitivity. The effectiveness of acute exercise on improving mitochondrial adaptations, leading to improved insulin sensitivity, in overweight/obese (Ov/Ob) individuals is controversial. This study aimed to determine the effects of acute exercise on epigenetic regulation of genes involved in skeletal muscle mitochondrial adaptations in lean vs Ov/Ob men.

overall_design: 30 men, aged 19-30 years, were recruited and divided into two groups: lean (BMI<25, 18.5- 24.1 kg/m2, n=15) and Ov/Ob (BMI≥25, 25.5- 36.9 kg/m2, n=15). Vastus lateralis muscle biopsy samples were collected at rest, following an overnight fast (Pre; n=14 in lean Pre and n=15 in Ov/Ob Pre). Subjects then ingested a standardized high-carbohydrate breakfast (7 kcal/kg; 60% carbohydrate, 25% fat, 15% protein). Four hours later, they performed an acute bout of cycling exercise (50% VO2max, expending ~650 kcal) and vastus lateralis muscle biopsy samples were collected immediately after the exercise bout (Post; n=15 in lean Post and in Ov/Ob Post). RNA-seq via the Illumina platform was performed. Sequences were aligned using TopHat and differential gene expression determined using Cuffdiff.


title: VDR ChIP-seq in human monocytic THP-1 cells

status: Public on Jul 18 2017

city: Kuopio

first: Carsten

last: Carlberg

address: Yliopistonranta 1D

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

summary: ChIP-seq for VDR in THP-1 cells after stimulation with the the natural VDR ligand 1,25-dihydroxyvitamin D3 (1,25(OH)2D3)

overall_design: THP-1 cells were treated for 2 or 24 h with 100 nM 1,25(OH)2D3 or vehicle before ChIP assay

first: Sabine

last: Seuter

first: Antonio

last: Neme


title: Cell specific deletion of PGC-1α from medium spiny neurons causes transcriptional alterations and age related motor impairment

status: Public on Jun 27 2017

city: Birmingham

first: Rita

last: Cowell

state: AL

address: 2000 9th Avenue South

department: Neuroscience

institute: Southern Research

summary: Microarray data of RNA collected from wild type and PGC-1α null medium spiny neurons prior to apperance of vacuoles to understand affects on transcriptome.

overall_design: RNA was isolated from striatum collected from age matched (P30) wild type and PGC-1α null mice

first: Laura

last: McMeekin

first: Ye

last: Li

first: David

last: Crossman

first: Peter

last: Detloff

first: Jeremy

last: Day

first: Yuqing


title: PGC-1a Provides a Transcriptional Framework for Synchronous Neurotransmitter Release from ParvalbuminPositive Interneurons

status: Public on Jun 23 2017

summary: PGC-1a is a master regulator for cell mitochondrial and metabolism function. In this experiment neurons were infected with a PGC-1a/GFP adenovirus to examine what genes were upregulated by over expression. Known targets related to mitochondrial health were confirmed while new neuron specific targets were discovered.

overall_design: SHSY5Y cells were infected with an adenovirus containing either GFP or GFP and PGC-1a and then had their transcriptome hybridized to a microarray to observe what genes were affected.

first: Elizabeth

last: Lucas

first: Sarah

last: Dougherty

first: Courtney

last: Reid

first: Lynn

last: Dobrunz

first: Andrew

middle: B

last: West

first: John

last: Hablitz


title: Genome-wide RNA-sequencing (RNA-seq) of benign and malignant prostate cell lines without and with androgen (R1881) stimulation.

status: Public on Feb 09 2017

city: HangZhou

first: Biaoyang

last: Lin

address: 866 Yu Hang Tang Road Zi Jin Gang Campus Zhejiang University.

department: ZCNI

institute: ZheJiang University

summary: RNA-seq data were obtained from hTERT immortalized human prostate transit amplifying EP156T cells (+/- 10 nM R1881 for 48 hrs), progeny tumorigenic EPT3-M1 cells recovered from mouse metastatic tumor  (+/- 10 nM R1881 for 48 hrs) and the prostate cancer cell lines LNCaP  (+/- 10 nM R1881 for 48 hrs), VCaP (+/- 1 nM R1881 for 24 hrs) and 22Rv1 (+/- 1 nM R1881 for 24 hrs) (obtained from the American Type Culture Collection). All cells were either stimulated or not stimulated with the synthetic androgen R1881 (1 or 10 nM for 24 or 48 hrs) prior to lysis (Qiagen miRNeasy minikit lysis buffer) and total RNA purification and DNase treatment.

overall_design: Quantification of RNA expression in benign and malignant prostate cells in vitro without and with androgen stimulation

first: Karl-Henning

last: Kalland

first: Jan-Roger

last: Olsen


title: HOX13 activity reprograms cis-regulatory modules during digit development

status: Public on Dec 14 2016

city: montreal

first: Rushikesh

last: Sheth

address: 110 avenue des pins ouest

department: Genetics and Development

institute: IRCM

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

overall_design: Refer to individual Series


status: Public on Apr 29 2017

city: Santa Monica

first: Dave

last: Hoon

address: 2200 Santa Monica Boulevard

institute: Saint John's Cancer Institute


title: Epigenomic and genome structural diversity in a worldwide collection of Arabidopsis thaliana

status: Public on Jul 14 2016

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: Epigenetic variation can impact gene transcription and may play roles in phenotypic diversity and adaptation. Here we report 1,107 high quality single-base resolution methylomes, and 1,210 transcriptomes from the 1001 Arabidopsis Genomes population. Analyses reveal strong effects of geographic origin on average DNA methylation levels, alterations of gene expression by epialleles and a highly complex genetic basis for DNA methylation. Physical genome maps for nine of the most diverse accessions revealed how transposable elements and other structural variations shaped the epigenome to allow rapid adaptation to environmental changes, with strong emphasis on disease resistance. Analysis of the cistromes and epicistromes in these accessions revealed a significant association between both methylation and nucleotide variation and the conservation of transcription factor binding sites. The Arabidopsis thaliana 1001 Epigenomes Project now provides a comprehensive resource to help further understand how epigenetic variation contributes to both molecular and phenotypes in natural populations of the most widely studied reference plant.

overall_design:
RNA-seq profiling of 728 Arabidopsis thaliana accessions
Please note that the sample 'Cod-0 (9836)' is missing from the data columns in the normalized expression matrix  ('ath1001_tx_norm_2016-04-21-UQ_gNorm_normCounts_k4.tsv') since the read count distribution from this sample was incompatible with the upper-quartile normalization method applied to all the samples, therefore excluded  from the expression matrix.

first: Shao-shan

middle: C

last: Huang

first: Taiji

last: Kawakatsu

first: Florian

last: Jupe

first: Robert

last: Schmitz

first: Mark

last: Urich

first: Rosa

last: Castanon

last: Nery

first: Huaming

last: Chen


title: Transcriptome alterations induced by steroid receptors agonists in primary neurons and astrocytes

status: Public on May 01 2016

city: Krakow

first: Marcin

last: Piechota

address: Smetna 12

department: Molecular Neuropharmacology

country: Poland

institute: Institute of Pharmacology PAS

summary:
We utilized whole-genome microarrays (Illumina Mouse WG-6) to measure changes in mRNA abundance levels induced by steroid hormones in primary neurons and astrocytes. To stimulate gene expression we treated neuronal and astroglial cultures with glucocorticoid receptor agonist (dexamethasone), mineralocorticoid (aldosterone), progesterone (progesterone), androgen (5α-dihydrotestosterone) and estrogen 2 (β-estradiol).
Keywords: Hormonal response

overall_design: Microarray experiment was designed to determine the effects of steroid receptor agonists. The ex vivo experiments were conducted using mouse striatal neurons and astrocytes from primary cultures. To stimulate gene expression we treated neuronal and astroglial cells with dexamethasone (100 nM), aldosterone (200 nM), progesterone (200 nM), 5α-dihydrotestosterone (200 nM) and β-Estradiol (200 nM) for 4 h. Control cells were treated with vehicle. Four independent biological replicates of the microarray were prepared for each experimental group.

first: M

last: Korostynski


title: Family case report: C14orf132 gene is possibly related to IUGR and extremely low birth weight

status: Public on Aug 01 2016

city: Perth

first: Sulev

last: Koks

state: Western Australia

address: 90 South Street

department: Centre for Molecular Medicine and Innovative Therapeutics

country: Australia

institute: Murdoch University

summary: Background: Despite of extensive research the genetic component of extremely low birth weight in newborns has remained obscure.    Results: The aim of the case study was to identify candidate gene(s) causing extremely low birth weight (ELBW) in newborns and hypotrophy in infants. A four-member family was studied: mother, father and two ELBW-phenotype children. The studies were carried out due to the medical conditions of the second child at birth and post-partum: peculiar phenotype, micro-anomalies, recurrent infections, suspicion of autoimmune hepatitis, multifactorial encephalopathy, and suspicion of metabolic and chromosomal abnormalities. Whole genome single nucleotide polymorphism (SNP) genotyping array was used to investigate genomic rearrangements in both affected children using peripheral blood DNA samples. Whole blood transcriptome was assessed by using RNA sequencing (RNA-seq) in all four family members. RNA-seq identified a single gene – C14orf132 differentially expressed, with the level of the transcript significantly lower in blood samples of children. Copy number variant (CNV) analysis did not reveal any pathogenic CNVs in the region of C14orf132 gene of both affected children.   Conclusion: We showed the importance of combining whole genome CNV and transcriptome analysis in identification of the candidate gene(s) in case studies. We propose the C14orf132 (chromosome 14 open reading frame 132) gene expression to be associated with the ELBW-phenotype. C14orf132 gene is a novel long non-coding RNA (lincRNA) with unknown function, which might be associated with the developmental delay through the altered gene expression  Background: Despite of extensive research the genetic component of extremely low birth weight in newborns has remained obscure.    Results: The aim of the case study was to identify candidate gene(s) causing extremely low birth weight (ELBW) in newborns and hypotrophy in infants. A four-member family was studied: mother, father and two ELBW-phenotype children. The studies were carried out due to the medical conditions of the second child at birth and post-partum: peculiar phenotype, micro-anomalies, recurrent infections, suspicion of autoimmune hepatitis, multifactorial encephalopathy, and suspicion of metabolic and chromosomal abnormalities. Whole genome single nucleotide polymorphism (SNP) genotyping array was used to investigate genomic rearrangements in both affected children using peripheral blood DNA samples. Whole blood transcriptome was assessed by using RNA sequencing (RNA-seq) in all four family members. RNA-seq identified a single gene – C14orf132 differentially expressed, with the level of the transcript significantly lower in blood samples of children. Copy number variant (CNV) analysis did not reveal any pathogenic CNVs in the region of C14orf132 gene of both affected children.   Conclusion: We showed the importance of combining whole genome CNV and transcriptome analysis in identification of the candidate gene(s) in case studies. We propose the C14orf132 (chromosome 14 open reading frame 132) gene expression to be associated with the ELBW-phenotype. C14orf132 gene is a novel long non-coding RNA (lincRNA) with unknown function, which might be associated with the developmental delay through the altered gene expression  Background: Despite of extensive research the genetic component of extremely low birth weight in newborns has remained obscure.    Results: The aim of the case study was to identify candidate gene(s) causing extremely low birth weight (ELBW) in newborns and hypotrophy in infants. A four-member family was studied: mother, father and two ELBW-phenotype children. The studies were carried out due to the medical conditions of the second child at birth and post-partum: peculiar phenotype, micro-anomalies, recurrent infections, suspicion of autoimmune hepatitis, multifactorial encephalopathy, and suspicion of metabolic and chromosomal abnormalities. Whole genome single nucleotide polymorphism (SNP) genotyping array was used to investigate genomic rearrangements in both affected children using peripheral blood DNA samples. Whole blood transcriptome was assessed by using RNA sequencing (RNA-seq) in all four family members. RNA-seq identified a single gene – C14orf132 differentially expressed, with the level of the transcript significantly lower in blood samples of children. Copy number variant (CNV) analysis did not reveal any pathogenic CNVs in the region of C14orf132 gene of both affected children.   Conclusion: We showed the importance of combining whole genome CNV and transcriptome analysis in identification of the candidate gene(s) in case studies. We propose the C14orf132 (chromosome 14 open reading frame 132) gene expression to be associated with the ELBW-phenotype. C14orf132 gene is a novel long non-coding RNA (lincRNA) with unknown function, which might be associated with the developmental delay through the altered gene expression.  Background: Despite of extensive research the genetic component of extremely low birth weight in newborns has remained obscure.    Results: The aim of the case study was to identify candidate gene(s) causing extremely low birth weight (ELBW) in newborns and hypotrophy in infants. A four-member family was studied: mother, father and two ELBW-phenotype children. The studies were carried out due to the medical conditions of the second child at birth and post-partum: peculiar phenotype, micro-anomalies, recurrent infections, suspicion of autoimmune hepatitis, multifactorial encephalopathy, and suspicion of metabolic and chromosomal abnormalities. Whole genome single nucleotide polymorphism (SNP) genotyping array was used to investigate genomic rearrangements in both affected children using peripheral blood DNA samples. Whole blood transcriptome was assessed by using RNA sequencing (RNA-seq) in all four family members. RNA-seq identified a single gene – C14orf132 differentially expressed, with the level of the transcript significantly lower in blood samples of children. Copy number variant (CNV) analysis did not reveal any pathogenic CNVs in the region of C14orf132 gene of both affected children.   Conclusion: We showed the importance of combining whole genome CNV and transcriptome analysis in identification of the candidate gene(s) in case studies. We propose the C14orf132 (chromosome 14 open reading frame 132) gene expression to be associated with the ELBW-phenotype. C14orf132 gene is a novel long non-coding RNA (lincRNA) with unknown function, which might be associated with the developmental delay through the altered gene expression.

overall_design: 4 samples, 2 controls and 2 cases

first: Airi

last: Tiirats

first: Triin

last: Viltrop

first: Ene

last: Reimann

last: Kõks

first: Andres

last: Salumets


title: Methylome and transcriptome of EAC (methylation)

city: Brisbane

first: Katia

last: Nones

state: QLD

address: 300 Herston Road

institute: QIMR Berghofer MEdical Research Institute

summary: genome-wide methylation profile of 250 samples including 125 EAC, 19 Barrett’s, 64 normal adjacent squamous and 21 normal stomach. Transcriptome data was performed for 70 samples with methylation profile (48 EAC, 4 Barrett’s and 18 normal adjacent squamous). This is the first study to use methylome, transcriptome and ENCODE data to characterize the regulatory role of methylation in EAC.

first: Lutz

last: Krause

first: Kelly

last: Loffler

first: Derek

last: Nancarrow

first: Yue

middle: H

last: Tang

first: Harald

last: Oey

first: Nicci

last: Wayte

first: Ann

last: Patch

first: Sandra

last: Brosda

first: Suzanne

last: Manning

first: Guy

last: Lampe

first: Andrew

last: Clouston

first: Janine

last: Thomas

first: Jens

last: Stoye

first: Damian

last: Hussey

first: David

middle: I

last: Watson

first: Reginald

last: Lord

first: Wayne

last: Phillips

last: Gotley

first: B

last: Smithers

last: Whiteman

first: Nicholas

middle: K

last: Hayward

first: Sean

last: Grimmond

first: Nicola

last: Waddell

middle: P

last: Barbour


title: Methylome and transcriptome of EAC

first: Katia

last: Nones

type:
Expression profiling by array
Methylation profiling by array


title: Targeting Chromatin Regulators Inhibits Leukemogenic Gene Expression in NPM1 Mutant Leukemia

status: Public on Aug 22 2016

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

summary: Homeobox (HOX) proteins and the receptor tyrosine kinase FLT3 are frequently highly expressed and mutated in acute myeloid leukemia (AML). Aberrant HOX expression is found in nearly all AMLs that harbor a mutation in the Nucleophosmin (NPM1) gene, and FLT3 is concomitantly mutated in approximately 60% of these cases. Little is known how mutant NPM1 (NPM1mut) cells maintain aberrant gene expression. Here, we demonstrate that the histone modifiers MLL1 and DOT1L control HOX and FLT3 expression and differentiation in NPM1mut AML. Using a CRISPR-Cas9 genome editing domain screen, we show NPM1mut AML to be exceptionally dependent on the menin binding site in MLL1. Pharmacological small-molecule inhibition of the menin-MLL protein interaction had profound anti-leukemic activity in human and murine models of NPM1mut AML in vitro and in vivo. Combined pharmacological inhibition of menin-MLL and DOT1L resulted in dramatic suppression of HOX and FLT3 expression, induction of differentiation, and superior activity against NPM1mut leukemia. Together, MLL1 and DOT1L are chromatin regulators that control HOX, MEIS1 and FLT3 expression and are therapeutic targets in NPM1mut AML. Combinatorial small-molecule inhibition has synergistic on target activity and constitutes a novel therapeutic concept for this common AML subtype.

overall_design: RNA sequencing data of the human AML cell lines OCI-AML2 and OCI-AML3 comparing EPZ004777 [10µM] drug treatment versus DMSO vehicle control; experiments performed in biological triplicates.

first: Michael

middle: W

last: Kühn

first: Amit

last: Sinha

first: Scott

last: Armstrong


title: Next generation sequencing analysis of DN1 transcriptomes from Wild type, gl/gl and transgenic CD2-Ostm1 gl/gl mice

status: Public on Sep 01 2016

city: Montreal

first: Jean

last: Vacher

state: QC

address: 110 pine avenue west

department: Development and cellular interactions

summary:
The goal of this study is to compare the transcriptome stability of DN1wt versus DN1gl/gl and DN1CD2-Ostm1gl/glTR
Methods: DN1 thymocytes mRNA profiles of 19-day-old wild-type (WT), osteopetrotic grey-lethal (gl/gl) and transgenic CD2-Ostm1 gl/gl mice were generated by deep sequencing,DN1 cells from 2-3 mice per genotype were pooled, no technical replicates, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: TopHat and Cufflinks. qRT–PCR validation was performed using SYBR Green assays
Results: DN1 gl/gl showed a distinctive transcriptome signature in comparison to DN1 wt and DN1 gl/glTR with respectivelly 146 and 205 differentially expressed genes and 205. Migration genes were significantly affected in DN1 gl/gl samples and RAC1 and S1PR1 gene expressions were confirmed using RT-qPCR.
Conclusions: RNA seq allowed us to identify the enhanced expression of migration genes (RAC1 and S1PR1) in DN1gl/gl, that were both normalized in the DN1 cells from transgenic gl/glTR mice, which suggests defective T cell migration associated to the osteopetrotic thymus phenotype.

overall_design: DN1 thymocytes mRNA profiles of 19-day-old wild-type (WT), osteopetrotic grey-lethal (gl/gl) and transgenic CD2-Ostm1 gl/gl mice were compared by deep sequencing,DN1 cells from 2-3 mice per genotype were pooled, no technical replicates, using Illumina HiSeq 2000.

first: Marie

last: Mutabaruka


title: Global transcriptome analysis reveals aging-related genes in Atp8b1 mutant lungs

status: Public on Apr 27 2016

city: Bar Harbor

first: Timothy

middle: Michael

last: Stearns

state: ME

address: 600 Main Street

department: Computational Sciences

institute: The Jackson Laboratory

summary: Aging is associated with progressive decline in lung function and responses to environmental stress culminating in increased incidence of lung diseases. Initial analysis of Atp8b1 (ATPase, Aminophospholipid Transporter, Class I, Type 8B, Member 1) mutant mice (on C57BL/6J background) revealed deficiency in transporter function and was associated with decreased lung function. Therefore, to further study the aging-related genes in the lungs at the molecular level, the transcriptome analysis of Atp8b1 mutant and C57BL/6J lungs were carried out at 14 M and 7_9 wks of age. Global transcriptome analysis revealed 532 differentially expressed genes in Atp8b1 mutant lungs, 157 differentially expressed genes in C57BL/6J mice and 37 overlapping genes. Interestingly, the majority of age-related (350) genes were unique to Atp8b1 mutant lungs in contrast to the 85 genes that were unique to C57BL/6J lungs. Further, Ingenuity Pathway Analysis (IPA) of aged genes in Atp8b1 mutant lungs showed enrichment of canonical signaling pathways such as xenobiotic metabolism signaling and Nrf2-mediated signaling pathway. We validated Adamts2 and Mmp13 in Atp8b1 mutant lungs by quantitative real-time PCR (qRT-PCR). In addition, Col1a1 and CxCr6 were also validated in both Atp8b1 mutant and C57BL/6J lungs, respectively. To summarize, our study provide insights into altered age-related genes in Atp8b1 lungs that are associated with mutation and environmental trigger when compared to C57BL/6J lungs.

overall_design: This experimental design had three factors: sex, strain (Atp8b1 mutant and C57BL/6J), and time (14 M and 7_9 wk). Female, C57BL/6J mice at 7_9 wks were not represented due to sexing error. The replicate size was three for all sample groups, except for male, C57BL/6J mice at 7_9 wks, which was represented by 5 replicates. A total of 23 Affymetrix Mouse 430v2 Arrays were used in gene expression analysis.

first: Ramani

last: Soundarararajan

first: Jutaro

last: Fukumoto

first: Christina

last: Turns

first: Alexander

last: Czachor

first: Emma

last: Westermann

middle: F

last: Lockey

first: Benjamin

middle: L

last: King

first: Narasaiah

last: Kolliputi


title: Whole blood gene expression profiles distinguish clinical phenotypes of venous thromboembolism [Set1]

status: Public on Nov 23 2015

city: Durham

first: Deborah

middle: A

last: Lewis

state: NC

address: 201 Trent Dr

institute: Duke University Medical Center

summary: Recurrent venous thromboembolism (VTE) occurs infrequently following a provoked event but occurs in up to 30% of individuals following an initial unprovoked event. We studied 134 patients with VTE separated into 3 groups:  (1) ‘low-risk’ patients had ≥1 provoked VTE; (2) ‘moderate-risk’ patients had no more than 1 unprovoked VTE; (3) ‘high-risk’ patients had ≥2 unprovoked VTE.  44 individuals with no history of VTE were enrolled as healthy controls.  Consented individuals were enrolled at 4 medical centers in the US.  Total RNA from whole blood was isolated and hybridized to Illumina HT-12 V4 Beadchips to assay whole genome expression.  Using class prediction analysis, we distinguished high-risk patients from healthy controls with good receiver operating curve characteristics (AUC=0.88). We also distinguished high-risk from low-risk individuals, moderate-risk individuals from healthy controls, and low-risk individuals from healthy controls with AUC’s of 0.72, 0.77 and 0.72, respectively. Using differential expression analysis, we identified genes relevant to coagulation, immune response and vascular biology, such as SELP and CD46, which were differentially expressed in at least two comparisons.  Neither approach distinguished the moderate-risk patients from the high-risk or low-risk groups.  Gene expression profiles may provide insights into biological mechanisms associated with patients at risk for recurrent VTE. Prospective studies are needed to validate these findings.

overall_design: This study includes a total of 218 samples/individuals (in 5 groups; APS, high-risk VTE, moderate-risk VTE, low-risk VTE and healthy-controls).  Samples in which the percent of probes present was 15% or less (n=51) were excluded leaving 167 samples.  The data for these 167 samples were normalized together.  However, this record represents the 132 individual samples in the following groups; high-risk (n=40); moderate-risk (n=33); low-risk (n=34); and healthy controls (n=25). The 35 samples in APS group are represented in GSE48001.

first: Sunil

last: Suchindran

first: Michele

middle: G

last: Beckman

first: W

last: Hooper

first: Althea

last: Grant

first: John

last: Heit

first: Marilyn

last: Manco-Johnson

first: Stephan

last: Moll

first: Claire

middle: S

last: Philipp

first: Kristy

last: Kenney

first: Christine

last: deStaercke

first: Meredith

middle: E

last: Pyle

first: Joseph

last: Lucas

first: Jen-Tsan

last: Chi

first: Thomas

last: Ortel


title: CTCF ChIP-seq in human monocytic THP-1 cells with replicates (4)

status: Public on Jan 02 2016

first: Carsten

last: Carlberg

summary: ChIP-seq for the insulator protein CTCF in THP-1 cells after stimulation with the the natural VDR ligand 1,25-dihydroxyvitamin D3 (1,25(OH)2D3)

overall_design: THP-1 cells were treated for 24 h with 100 nM 1,25(OH)2D3 before ChIP assay

first: Sabine

last: Seuter

first: Antonio

last: Neme


title: EHMT1 and EHMT2 inhibition induce fetal hemoglobin expression [RNA-seq]

status: Public on Nov 02 2015

city: Cambridge

last: Krill-Burger

address: 415 Main Street

department: Cancer Program

institute: Broad Institute

summary: Using UNC0638 and genetic assays to inhibit EHMT1/2 and derepress fetal hemoglobin in adult hematopoietic cells.

overall_design: RNA-Seq in primary adult human erythroid cells treated with UNC0638 or the vehicle control (DMSO) in biological triplicates.

first: Aline

last: Renneville

first: Peter

last: Van Galen

first: Matthew

last: Canver

first: Marie

last: McConkey

first: David

middle: M

last: Dorfman

first: Edward

last: Holson

first: Bradley

last: Bernstein

first: Stuart

last: Orkin

first: Daniel

last: Bauer

first: Benjamin

last: Ebert


title: NeuroD1 reprograms chromatin and transcription factor landscapes to induce the neuronal program

city: Mainz

first: Abhijeet

last: Pataskar

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

summary: Cell fate specification relies on the action of critical transcription factors that become available at distinct stages of embryonic development. One such factor is NeuroD1, which is essential for eliciting the neuronal development program and possesses the ability to reprogram other cell types into neurons. Given this capacity, it is important to understand its targets and the mechanism underlying neuronal specification. Here, we show that NeuroD1 directly binds regulatory elements of neuronal genes that are developmentally silenced by epigenetic mechanisms. This targeting is sufficient to initiate events that confer transcriptional competence, including reprogramming of transcription factor landscape, conversion of heterochromatin to euchromatin and increased chromatin accessibility, indicating potential pioneer factor ability of NeuroD1. The transcriptional induction of neuronal fate genes is maintained via epigenetic memory despite a transient NeuroD1 induction during neurogenesis. Our study not only reveals the NeuroD1-dependent gene regulatory program driving neurogenesis but also increases our understanding of how cell-fate specification during development involves a concerted action of transcription factors and epigenetic mechanisms.

overall_design:
1. Ectopic NeuroD1 was induced for 48 hours (+Dox) in ES cells for checking initiation of neuronal transcriptional program in comparison to uninduced condition (-Dox)
2. ChIP-seq was performed after 24 hours of NeuroD1 induction in ES cells.

first: Johannes

last: Jung

first: Pawel

last: Smialowski

first: Florian

last: Noack

first: Federico

last: Calegari

first: Tobias

last: Straub

first: Vijay

last: Tiwari


title: NCI-H1299 lung cancer cell line transfected with miR-34a and ghR-34a

status: Public on Jul 29 2015

city: Shinjuku-ku

first: Shin-ichiro

last: Ohno

state: Tokyo

address: 6-1-1 Shinjuku

department: Molecular Pathology

institute: Tokyo Medical University

summary:
Analysis NCI-H1299 lung cancer cells transfected with synthetic oligo mimics for microRNAs (miRNAs) miR-34a and ghR-34a.
We developed a 30-nucleotide single-strand RNA (ssRNA), termed “guide hairpin RNA (ghR),” that has a physiological function similar to that of miRNA and siRNA. The ghR caused no innate cytokine response either in vitro or in vivo. In addition, its structure does not contain a passenger strand seed sequence, reducing the potential for off-target effects relative to existing short RNA reagents. Systemic injection of ghR-form miR-34a (ghR-34a) suppressed tumor growth in a mouse model of RAS-induced lung cancer. Furthermore, ghR-34a functioned in a Dicer- and Ago2-independent manner. This novel RNAi technology may provide a novel, safe, and effective nucleic acid drug platform that will increase the clinical usefulness of nucleic acid therapy.

overall_design: MiR-34a–targeted mRNAs regulated by mRNA degradation rather than translational inhibition were identified using microarray data from miR-34 and ghR-34a transfectants.

last: OHNO

first: Masahiko

last: KURODA


title: C1 analysis using mixtures of human (HEK) and mouse (3T3) cells

status: Public on Jun 24 2015

city: Boston

first: Evan

last: Macosko

state: MA

address: 77 Avenue Louis Pasteur, NRB 260

department: Genetics

institute: Harvard Medical School

summary: A cell supsension containing an equal mix of HEK and 3T3 cells was used in the Fluidigm C1

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Suspensions of 3T3 and HEK cells were diluted down to a concentration of 250,000 per mL and mixed 1:1, then loaded onto two medium C1 cell capture chips.

middle: Z


title: Drop-Seq analysis of ERCC spike in capture

status: Public on May 20 2015

summary: A bead supsension and a solution of ERCC spike-ins at a concentration of ~100,000 molecules per droplet was used in Drop-Seq, a novel technology for high-throughput single cell mRNAseq

overall_design: An estimated 84 beads were selected for amplification.


title: Drop-Seq analysis of mixtures of human (HEK) and mouse (3T3) cells (1000/100 STAMPs) at 12.5 cells per microliter

summary: A cell supsension containing an equal mix of HEK and 3T3 cells was used in Drop-Seq, a novel technology for high-throughput single cell mRNAseq.  Cells were mixed at a final concentration of 12.5 cells per microliter in droplets.

overall_design: An estimated 570 STAMPs were selected for amplification.


title: Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets

sample_organism:
Homo sapiens
Mus musculus
synthetic construct


title: Genetic and drug perturbation of components in the NFkB signaling pathway in 11-18 cells

status: Public on Feb 03 2015

city: San Francisco

first: Saurabh

last: Asthana

state: CA

address: 1450 Third Street, Room HD276

department: Helen Diller Family Comprehensive Cancer Center

institute: UCSF

summary: Through the study of EGFR-mutant lung adenocarcinoma we show that NFkB signaling is rapidly engaged by EGFR oncogene inhibition to promote tumor cell persistence and therapy resistance. Unexpectedly, we found that EGFR oncogene inhibition induced an EGFR-TRAF2-RIP1-IKK complex that stimulated an NFkB-mediated transcriptional survival program. We identified a direct pharmacologic NFkB inhibitor, PBS-1086, that suppressed this adaptive survival program and increased both the magnitude and duration of initial EGFR TKI response in cellular and in vivo tumor models, including a novel patient-derived NSCLC xenograft. These findings unveil NFkB as a critical adaptive survival mechanism engaged in response to EGFR oncogene inhibition and identify PBS-1086 as a promising NFkB inhibitor to eliminate disease persistence and potentially prevent the emergence of resistance in patients.

overall_design: RNAseq analysis of 11-18 (EGFR-mutant lung adenocarcinoma) cells in the context of drug treatment with erlotinib and/or genetic or pharmacological inactivation of NFkB


title: Drop-Seq analysis of P14 mouse retina single-cell suspension

summary: A cell suspension was prepared from wild-type P14 mouse retinas, and single-cell mRNAseq libraries were generated with Drop-Seq.

overall_design: Drop-Seq was performed on four separate days using the same age (P14) and strain (C57BL/6).  On day 1, replicate 1 was obtained.  On day 2, replicates 2 and 3 were obtained.  On day 3, replicates 4-6 were obtained.  On day 4, replicate 7 was obtained.


title: Single Cell Methylome Signatures Reveal Distinct Neuronal Populations and Regulatory Elements in the Mammalian Cortex

status: Public on Aug 10 2017

first: Joseph

last: Ecker

summary: The mammalian brain contains diverse neuron cell types with distinct physiological, morphological and molecular characteristics. However, a comprehensive assessment of the epigenetically distinct neuronal classes is currently missing. Cytosine DNA methylation is a stable epigenetic mark that distinguishes neuron types and marks gene regulatory elements. We developed an efficient single-nucleus methylome sequencing approach that allows robust high-throughput neuron-type classification. We generated >6,000 single-nucleus methylomes and identified 16 mouse and 21 human neuronal subpopulations in the frontal cortex. Both CG and non-CG methylation exhibited cell type-specific distributions that recapitulate and extend findings from single neuron transcriptome profiling. Moreover, we found approximately 500,000 neuron-type-specific regulatory elements showing strong differential methylation in mouse and human cortex. Distinct methylation signatures identified an unique human Parvalbumin-expressing inhibitory sub-type and a layer 6 specific excitatory sub-type in mouse. Comparative epigenomic analysis showed stronger conservation of gene regulatory elements in inhibitory compared with excitatory neurons. These findings demonstrate the utility of single nucleus methylome profiling for both expanding the atlas of brain cell types and identifying regulatory elements that potentially drive these differences.

overall_design: Single Cell Methylome analysis of mouse and human frontal cortex

first: Chongyuan

last: Luo

first: Christopher

last: Keown

first: Laurie

last: Kurihara

first: Jingtian

last: Zhou

first: Yupeng

last: He

first: Junhao

last: Li

first: Rosa

last: Castanon

first: Jacinta

last: Lucero

last: Nery

first: Brian

last: Bui

first: Timothy

last: Harkins

first: Eran

last: Mukamel

first: M

last: Behrens


title: Drop-Seq analysis of mixtures of human (HEK) and mouse (3T3) cells (1000/100 STAMPs) at 50 cells per microliter

summary: A cell supsension containing an equal mix of HEK and 3T3 cells was used in Drop-Seq, a novel technology for high-throughput single cell mRNAseq.  The cells were mixed at a final concentration of 50 cells per microliter.

overall_design: An estimated 1000 STAMPs and 100 STAMPs were separately selected for sequencing to obtain both high coverage and broad coverage data