title: In vitro gene exoression comparison between the ST217 serotype 1 strain A42174 and the serotype 2 strain D39.

status: Public on Nov 12 2020

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

summary: Streptococcus pneumoniae is a frequent coloniser of the human nasopharynx and a major cause of life-threating invasive infections such as pneumonia, meningitis and sepsis. Over 1 million people die every year due to invasive pneumococcal disease (IPD), mainly in developing countries. Serotype 1 is a common cause of IPD; however, unlike other serotypes, it is rarely found in the carrier state in the nasopharynx, which is often considered a prerequisite for disease. The aim of this study was to understand this dichotomy.    We used murine models of carriage and IPD to characterise the pathogenesis of African serotype 1 (Sequence Type 217) pneumococcal strains obtained from the Queen Elizabeth Central Hospital in Blantyre, Malawi. We found that ST217 pneumococcal strains were highly virulent in a mouse model of invasive pneumonia, but in contrast to the generally accepted assumption, can also successfully establish nasopharyngeal carriage. Interestingly, we found that co-colonising serotypes may proliferate in the presence of serotype 1, suggesting that acquisition of serotype 1 carriage could increase the risk of developing IPD by other serotypes. RNAseq analysis confirmed that key virulence genes associated with inflammation and tissue invasiveness were upregulated in serotype 1. These data reveal important new insights into serotype 1 pathogenesis, with implications for carriage potential and risk of invasive disease through interactions with other co-colonising serotypes; an often overlooked factor in transmission and disease progression.

overall_design: A total of 6 samples were analysed. These samples were from 3 different growth phases and two different bacterial strains (ST217 serotype 1 strain A42174 and serotype 2 strain D39). No replicates were used.

first: Laura

last: Bricio-Moreno

first: Chrispin

last: Chaguza

first: Reham

last: Yahya

first: Rebecca

last: Shears

first: Jennifer

middle: E

last: Cornick

first: Marie

last: Yang

first: Daniel

last: Neill

first: Neil

last: French

first: Jay

middle: D

last: Hinton

first: Dean

middle: B

last: Everett

first: Aras

last: Kadioglu


title: PRMT5 promotes cancer cell migration and invasion through the E2F pathway

status: Public on Jul 28 2020

city: St. Petersburg

first: Alexander

last: Kanapin

address: 7/9 University Emb.

department: Institute for Translational Biomedicine

country: Russia

institute: St Petersburg Universoty

type: Expression profiling by high throughput sequencing

summary: We identified distinct sets of genes under the control of PRMT5 and E2F1. Some of the most highly regulated genes, such as cortactin/CTTN, influenced cell migration, invasion and adherence. We characterised the functional role of the cortactin/CTTN gene, which enabled PRMT5 through E2F1 to promote cellular migration and invasion, whilst decreasing cellular adherence. Most significantly, there was a striking coincidence between the expression of PRMT5 and E2F1 in certain human tumours, and elevated levels of PRMT5, E2F1 and cortactin/CTTN correlated with poor prognosis disease. Our results suggest a causal relationship between PRMT5, E2F1 and the migration and invasion of cancer cells, thereby highlighting an important pathway that contributes to the cancer biology of tumour cells.

overall_design: Examination of expresion profile of colorectal cancer wild type and E2F1 knockdown HCT116 cells treated with PRMT5 inhibitor

first: Wojciech

last: Barczak

first: Li

last: Jin

first: Simon

middle: M

last: Carr

first: Shonagh

last: Munro

first: Anastasia

last: Samsonova

first: Nicholas

last: La Thangue


title: Transcriptional changes in kidney allografts with histology of antibody-mediated rejection

status: Public on Nov 10 2020

city: Leuven

first: Jasper

last: Callemeyn

address: Herestraat 49

department: Microbiology, Immunology and Transplantation

country: Belgium

institute: KU Leuven University

summary:
Circulating anti-HLA donor-specific antibodies (HLA-DSA) are often absent in serum of kidney allograft recipients with biopsies demonstrating histology of antibody-mediated rejection (ABMRh).
In this multicenter study, we aimed to elucidate whether the transcriptional profile of biopsies with HLA-DSA negative ABMRh can indicate an undetected humoral etiology, or whether HLA-DSA negative ABMRh should be considered as a distinct histomolecular entity.

overall_design: We performed microarray analysis of 224 kidney allograft biopsies, collected from unique recipients in 4 European centers. The transcriptional profile of biopsies without ABMRh (n=168), DSA negative ABMRh (n=26) and DSA positive ABMRh (n=30) was compared.

first: Maarten

last: Naesens


title: Profiling expression of genes at a critical developmental timepoint in diaphragm development.

status: Public on Aug 07 2020

city: Salt Lake City

first: Gabrielle

last: Kardon

state: UT

department: Human Genetics

country: USA

institute: University of Utah

summary:
Purpose: The goal of this study is to determine what genes are expressed, and at what level, in the developing diaphragm at a timepoint shown to be critical in the initiation of congenital diaphragmatic hernias in mice. Methods: PPFs were dissected from staged mouse embryos
Methods: summary Purpose: The goal of this study is to determine what genes are expressed, and at what level, in the developing diaphragm at a timepoint shown to be critical in the initiation of congenital diaphragmatic hernias in mice. Methods: PPFs were dissected from staged mouse embryos

overall_design: Epression profile of  2 biological pooled E12.5 pleuroperitineal fold pairs (2 dissected pairs per biological replicate) to prioritize candidate genes implicated from human congenital diaphragmatic studies.

first: Eric

middle: L

last: Bogenschutz

first: Zachary

last: Fox


title: A novel patient stratification strategy to enhance the therapeutic efficacy of dasatinib in glioblastoma [Agilent]

status: Public on Oct 20 2020

city: Heidelberg

first: Obada

middle: Taleb

last: Alhalabi

address: Im Neuenheimer Feld 580 - TP3

department: Brain Tumor Translational Targets

country: Germany

institute: German Cancer Research Center DKFZ

summary: Abstract. Background: Glioblastoma is the most common primary malignancy of the central nervous system with dismal prognosis. Differential gene expression classifies IDH-wildtype glioblastoma into three subtypes: proneural, mesenchymal and classical. Dasatinib, an inhibitor of the proto-oncogene tyrosine-protein kinase SRC, is one of many therapeutics that, despite promising preclinical results, has failed to improve overall survival in glioblastoma patients in clinical trials. We examined whether glioblastoma subtypes differ in their response to dasatinib therapy and could hence be used for patient enrichment strategies in clinical trials. Methods: We carried out in silico analyses of the TCGA glioblastoma gene expression data and single-cell RNA-Seq data, in combination with in vitro experiments using glioblastoma stem-like cells (GSCs) derived from primary patient tumors with complimentary gene expression profiling and immunohistochemistry analyses of tumor samples. Results: Patients suffering from the mesenchymal subtype of glioblastoma showed higher SRC pathway activation based on gene expression profiling, and accordingly, mesenchymal cells were more sensitive to SRC inhibition by dasatinib compared to proneural and classical cells. Furthermore, SERPINH1, a heat-shock protein relevant in many cancer entities, was shown to highly correlate with dasatinib response and with the mesenchymal subtype. Notably, SRC phosphorylation status was not able to reliably predict response to dasatinib treatment. Conclusion: This work highlights the need for rational methods of patient selection for clinical trials, and retrospectively sheds light on a possible gene expression subtype-led patient stratification strategy that could have improved the outcome of SRC inhibition in patients and could have implications for future trials.

overall_design: NCH711d and NCH705 cells were inhibited in three independent experiments with DMSO and 1µM of Dasatinib. After 4 days, RNA was extracted and checked using the same method outlined earlier.

last: . Alhalabi

first: Violaine

last: Goidts


title: Molecular detection of maturation stages in the developing kidney

status: Public on Nov 19 2020

city: Kuamomoto

first: Shunsuke

last: Tanigawa

state: Kumamoto

address: 2-2-1 Chuou-ku honjyo

department: Institute of Molecular Embryology and Genetics

country: Japan

institute: Kumamoto University

summary: To identify maturation-dependent genes, we here performed single cell RNA sequencing (scRNA-seq) analysis using developing kidneys at different stages in the mouse, followed by highly sensitive in situ hybridization. We identified multiple genes expressed abundantly in newborn kidneys, but minimally at embryonic day 15.5. We then applied these maturation markers to the transplanted embryonic kidneys and found that the maturation process did not occur equally throughout nephron segments upon transplantation: glomeruli and proximal renal tubules became more mature than the other nephron segments. Thus, our scRNA-seq data at multiple stages of kidney development and identified maturation-dependent genes will serve as useful bases for assessing maturation of the developing kidney, and eventually of kidney organoids.

overall_design:
Kidney mRNA profiles of embryonic day 15.5, 17.5 and postnatal day 0 mice were generated by deep sequencing, using Illumina 10x
E12.5 embryonic kidneys were transplanted into the epididymis fat of NOD immuno deficient mice for 12 days

first: Hidekazu

last: Nagamuma

first: Koichiro

last: Miike

first: Akio

last: Kobayashi

first: Ryuichi

last: Nishinakamura


title: A genome-wide approach to delineate novel MLL4 targets involved in skeletal muscle metabolism

status: Public on Oct 01 2020

city: Nanjing

first: Zhenji

last: Gan

address: 12 Xuefu Road

department: Model Animal Research Center of Nanjing University

country: China

institute: Nanjing University

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
This experiment was conducted to identify novel MLL4 targets in skeletal muscle
Enhancers play central role in controlling gene expression in time and space. Primed enhancers are marked by histone H3 lysine 4 (H3K4) mono/di-methylation (H3K4me1/2). Mixed-lineage leukemia 4 (MLL4/KMT2D) is an evolutionarily conserved H3K4me1/2 methyltransferase that is required for enhancer activation. Here, we identified the genome-wide MLL4 occupancy in mouse skeletal muscle by ChIP-seq coupled with RNA-seq analysis. Gene ontology analysis revealed that MLL4 controls muscle fiber-type switching. We thus have revealed novel MLL4 targets involved in muscle metabolism.

overall_design: Using genome-wide approach, ChIPseq,  to delineate novel MLL4 targets involved in skeletal muscle metabolism

first: Lin

last: Liu


title: Copa mutation activates STING and perturbs thymocyte development by increasing type I interferons in the thymus.

status: Public on Jul 07 2020

city: San Francisco

first: Anthony

last: Shum

state: CA

address: 555 Mission Bay Blvd South

department: Pulmonary

institute: University of California San Francisco

summary: Pathogenic COPA variants cause a Mendelian syndrome of immune dysregulation with elevated type I interferon signaling. Given the importance of COPA in Golgi-ER transport, we speculated that type I interferon signaling in COPA syndrome involves missorting of STING. Here we show that a defect in COPI transport due to mutant COPA causes ligand-independent activation of STING. Activated STING stimulates type I interferon driven inflammation in CopaE241K/+ mice. Our results demonstrate that activated STING contributes to immune dysregulation in COPA syndrome and may be a new molecular target in treating the disease.

overall_design: Differential gene expression analysis in medullary thymic epithelial cells of CopaE241K/+ mice

middle: K

first: Walter

last: Eckalbar

first: Zimu

last: Deng

first: Christopher

middle: S

last: Law


title: Transcriptome of Tribolium castaneum selection lines (control-, drought-, heat-, heat/drought-adapted) under different climatic conditions

status: Public on Aug 15 2020

city: Zurich

first: Frederic

middle: Francois

last: Guillaume

address: Winterthurerstrasse 190

department: Evolutionary Biology and Environmental Studies

country: Switzerland

institute: University of Zurich

summary: We studied plastic and evolutionary responses in gene expression of Tribolium castaneum after beetles’ exposure to new environments that differed from ancestral control conditions in temperature, humidity or both. Using experimental evolution with ten replicated lines per condition, we were able to demonstrate adaptation (higher offspring number compared to control lines) after 20 generations. We measured whole-transcriptome gene expression with RNA-seq to infer evolutionary and plastic changes. We found more evidence for changes in mean expression (shift in the intercept of reaction norms) in adapted lines than for changes in plasticity (shifts in slopes). Plasticity was mainly preserved in selected lines and was responsible for a large part of the phenotypic divergence in expression between ancestral and new conditions. However, we found that genes with the largest evolutionary changes in expression also evolved reduced plasticity and often showed expression levels closer to the ancestral stage. Results obtained in the three different conditions were similar, suggesting that restoration of ancestral expression levels during adaptation is a general evolutionary pattern. With a larger sample in the most stressful condition, we were able to detect a positive correlation between proportion of genes with reversion of the ancestral plastic response and mean fitness per selection line.

overall_design: We used the Tribolium castaneum Cro1 strain collected from a wild population in 2010 and adapted to lab standard conditions (33°C, 70% relative humidity) for more than 20 generations. Beetles were kept in 24h darkness on organic wheat flour mixed with 10% organic baker's yeast. We sterilized flour and yeast by heating them for 12h at 80°C before use. To test for adaptation to new environmental conditions we used replicate lines and exposed them to three treatments and Control conditions. The conditions in the treatments were: Dry : 33°C and 30% relative humidity; Hot : 37°C and 70% r. h.; Hot-Dry: 37°C and 30% r. h. To generate replicate lines, we used 120 individuals (60 females and 60 males in the pupal stage from our Cro1 stock population) and placed them into a vial containing 80g medium. After seven to ten days, in which the pupae became adults, mated and laid eggs, adult beetles were removed by sieving the medium. We waited until the next generation (eggs/larvae in the medium) had reached the pupal stage and again collected 120 pupae per line to establish the next generation. Selection lines could adapt to treatment conditions for 20 generations. Before testing for adaptation, all lines stayed for one generation in control condition. Sequenced individuals were transferred to the respective condition in the egg stage and developed completely in treatment conditions. We sequenced adult reproducing females from different replicate lines under different conditions (seven Control-lines, four Dry-lines, five Hot-lines, seven Hot-Dry lines). For each selection line we used individuals from control conditions as well as individuals from treatment conditions to infer evolutionary changes (difference between Control- and Dry/Hot/Hot-Dry lines within the same condition) and plastic changes (difference between individuals from the same selection line under control and treatment conditions).

first: Eva

last: Koch

first: Frédéric


title: A role of DAO1 in oxidation of IAA amino acid conjugates revealed through metabolite, high throughput transcript and protein level analysis

status: Public on Oct 30 2020

city: Praha 6

first: Karel

last: Muller

address: Rozvojová 263

department: Lab. of hormonal regulations in plants

country: Czech Republic

institute: Institute of Experimenal Botany of the Czech Academy of Sciences

summary: After analysing auxin metabolism in auxin dependent tobacco BY-2 cell line grown in presence or absence of synthetic auxin 2,4-D we found that both conditions were similarly characterized by very low levels of endogenous indole-3-acetic acid (IAA) and its metabolites. However, metabolic profiling after exogenous application of IAA uncovered that the concentration of N-(2-oxindole-3-acetyl)-L-aspartic acid (oxIAA-Asp), the most abundantly formed auxin metabolite in the control culture, dramatically decreased in auxin-starved conditions. To describe the molecular mechanism behind this regulation, we analysed transcriptome and proteome changes caused by auxin starvation. While no changes in the expression of auxin biosynthetic machinery were observed, many genes related to auxin conjugation and degradation showed differential expression. Selected putative auxin glycosylating enzymes as well as members of the Gretchen Hagen 3 gene family involved in auxin amino acid conjugation showed both up- and down-regulation. Contrarily to that, all tobacco homologs of Arabidopsis thaliana DIOXYGENASE FOR AUXIN OXIDATION 1 (DAO1), known to be responsible for the formation of oxIAA from IAA, showed significant downregulation at both transcript and protein levels.

overall_design: Seven biological replicates of Nicotiana tabacum L. cv. Bright Yellow (BY-2)  cell culture samples cultured at auxin supplemented conditions (ctrl) and three replicates of BY-2 cell culture samples cultured at auxin-starved (AF) conditions. Samples collected 48 hours after culture inoculation.

last: Müller

first: Jan

last: Petrášek


title: Effect of antiretroviral prophylaxis on gene expression in the cervicovaginal tract and the blood

city: Seattle

first: Sean

last: Hughes

state: WA

address: 850 Republican St

institute: University of Washington

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

overall_design: Refer to individual Series


title: Effect of antiretroviral prophylaxis on gene expression in PBMCs

summary:
It is important to understand how, if at all, antiretroviral prophylaxis with tenofovir disoproxil fumarate (TDF) alone or TDF in conjunction with emtricitabine (FTC) affects gene expression.  To ask this question, we used peripheral blood mononuclear cells from women enrolled in the Genital Mucosal Substudy (GMS) [1] of the Partners PrEP Study (NCT02621242) [2]. Partners PrEP was a randomized Phase III trial of oral TDF or TDF/FTC compared to placebo, which showed that either active drug was effective at protecting against HIV-1 infection. Samples were taken after 24-36 months of oral treatment with placebo, TDF, or TDF/FTC or two months after discontinuation. Treatment adherence was based on plasma TDF concentrations.
Covariates included Nugent scores (for bacterial vaginosis), HSV-2 serology, age, and birth control method. Levels of natural and synthetic hormones (medroxyprogesterone acetate [MPA], estradiol [E2], ethinyl estradiol [EE2], levonorgestrel [LNG], etonogestrel [ENG], progesterone [P4], and norethisterone enanthate [NET-EN]) were measured in the serum.
1. Lund, J. M. et al. HIV-1-Neutralizing IgA Detected in Genital Secretions of Highly HIV-1-Exposed Seronegative Women on Oral Preexposure Prophylaxis. J. Virol. 90, 9855–9861 (2016).
2. Baeten, J. M. et al. Antiretroviral prophylaxis for HIV prevention in heterosexual men and women. N. Engl. J. Med. 367, 399–410 (2012).

overall_design: Gene expression was measured by Illumina HumanHT-12 v4 Expression BeadChips. Samples were taken after 24-36 months of oral treatment with placebo, TDF, or TDF/FTC or two months after discontinuation.

first: Florian

last: Hladik

first: Claire

middle: N

last: Levy


title: Effect of antiretroviral prophylaxis on gene expression in the endocervix

summary:
It is important to understand how, if at all, antiretroviral prophylaxis with tenofovir disoproxil fumarate (TDF) alone or TDF in conjunction with emtricitabine (FTC) affects gene expression.  To ask this question, we used cervicovaginal biopsies from women enrolled in the Genital Mucosal Substudy (GMS) [1] of the Partners PrEP Study (NCT02621242) [2]. Partners PrEP was a randomized Phase III trial of oral TDF or TDF/FTC compared to placebo, which showed that either active drug was effective at protecting against HIV-1 infection. Samples were taken after 24-36 months of oral treatment with placebo, TDF, or TDF/FTC or two months after discontinuation. Treatment adherence was based on plasma TDF concentrations. The samples in this series are thought to be endocervical biopsies on the basis of their gene expression.
Covariates included Nugent scores (for bacterial vaginosis), HSV-2 serology, age, and birth control method. Levels of natural and synthetic hormones (medroxyprogesterone acetate [MPA], estradiol [E2], ethinyl estradiol [EE2], levonorgestrel [LNG], etonogestrel [ENG], progesterone [P4], and norethisterone enanthate [NET-EN]) were measured in the serum.
1. Lund, J. M. et al. HIV-1-Neutralizing IgA Detected in Genital Secretions of Highly HIV-1-Exposed Seronegative Women on Oral Preexposure Prophylaxis. J. Virol. 90, 9855–9861 (2016).
2. Baeten, J. M. et al. Antiretroviral prophylaxis for HIV prevention in heterosexual men and women. N. Engl. J. Med. 367, 399–410 (2012).


title: Effect of antiretroviral prophylaxis on gene expression in the vagina

summary:
It is important to understand how, if at all, antiretroviral prophylaxis with tenofovir disoproxil fumarate (TDF) alone or TDF in conjunction with emtricitabine (FTC) affects gene expression.  To ask this question, we used vaginal biopsies from women enrolled in the Genital Mucosal Substudy (GMS) [1] of the Partners PrEP Study (NCT02621242) [2]. Partners PrEP was a randomized Phase III trial of oral TDF or TDF/FTC compared to placebo, which showed that either active drug was effective at protecting against HIV-1 infection. Samples were taken after 24-36 months of oral treatment with placebo, TDF, or TDF/FTC or two months after discontinuation. Treatment adherence was based on plasma TDF concentrations.
Covariates included Nugent scores (for bacterial vaginosis), HSV-2 serology, age, and birth control method. Levels of natural and synthetic hormones (medroxyprogesterone acetate [MPA], estradiol [E2], ethinyl estradiol [EE2], levonorgestrel [LNG], etonogestrel [ENG], progesterone [P4], and norethisterone enanthate [NET-EN]) were measured in the serum.
1. Lund, J. M. et al. HIV-1-Neutralizing IgA Detected in Genital Secretions of Highly HIV-1-Exposed Seronegative Women on Oral Preexposure Prophylaxis. J. Virol. 90, 9855–9861 (2016).
2. Baeten, J. M. et al. Antiretroviral prophylaxis for HIV prevention in heterosexual men and women. N. Engl. J. Med. 367, 399–410 (2012).


title: Hepatocytic c-Jun N-terminal kinases (JNK)-1/2 function determines cell fate during carcinogenesis

status: Public on Jun 08 2020

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Aberrant biliary hyperproliferation resulting from lack of differentiating signals favoring the maintenance of an immature and proliferative phenotype by biliary epithelial cells are ultimately responsible for ducto/cystogenesis and intrahepatic cholangiocarcinoma (CCA) formation. Mitogen-activated protein kinase (MAPK) signaling is pivotal for CCA-related tumorigenesis. In particular, targeted inhibition of JNK signaling has shown therapeutic potential. However, the cell-type specific role and mechanisms triggered by JNK in liver parenchymal cells during CCA remains largely unknown. Here, we aimed to investigate the relevance of JNK function in hepatocytes in experimental carcinogenesis. JNK signaling in hepatocytes was inhibited by crossing AlbCre-JNK1LoxP/LoxP mice with JNK2-deficient mice to generate Jnk1LoxP/LoxP/Jnk2−/− (JNKΔhepa) mice. JNKΔhepa mice were further interbred with hepatocyte-specific Nemo-knockout mice (NEMOΔhepa), a model of chronic liver inflammation and spontaneous hepatocarcinogenesis, to generate NEMO/JNKΔhepa mice. The impact of JNK deletion on liver damage, cell death, compensatory proliferation, fibrogenesis, and tumor development in NEMOΔhepa mice was determined. Moreover, regulation of essential genes was assessed by RT-PCR, immunoblottings and immunostains. Additionally, JNK2 inhibition, specifically in hepatocytes of NEMOΔhepa/JNK1Δhepa mice, was performed using siRNA (siJnk2) nanodelivery. Finally, active signaling pathways were blocked using specific inhibitors. Compound deletion of JNK1 and JNK2 in hepatocytes diminished hepatocarcinogenesis in both the DEN model of hepatocarcinogenesis and in NEMOΔhepa mice, but, in contrast, caused massive proliferation of the biliary ducts. Indeed, JNK deficiency in hepatocytes of NEMOΔhepa (NEMOΔhepa/JNKΔhepa) animals caused elevated fibrosis, increased apoptosis, increased compensatory proliferation, and elevated inflammatory cytokines expression, but reduced hepatocarcinogenesis. Furthermore, siJnk2 treatment in NEMOΔhepa/JNK1Δhepa mice recapitulated the phenotype of NEMOΔhepa/JNKΔhepa mice. Next, we sought to investigate the impact of molecular pathways in response to compound JNK deficiency in NEMOΔhepa mice. We found that NEMOΔhepa/JNKΔhepa livers exhibited overexpression of the IL-6/Stat3 pathway in addition to EGFR-Raf-MEK-ERK cascade. The functional relevance was tested by administering lapatinib - a dual tyrosine kinase inhibitor (TKI) of ErbB2 and EGFR signaling - to NEMOΔhepa/JNKΔhepa mice. Lapatinib effectively inhibited cystogenesis, improved transaminases and effectively blocked EGFR-Raf-MEK-ERK signaling. Our study defines a novel function of JNK in cell fate as well as hepatocarcinogenesis and opens new therapeutic avenues devised to inhibit pathways of cholangiocarcinogenesis.

overall_design: Livers were isolated from control, NEMO (NEMOΔhepa) single-knockout, NEMO/JNK1Δhepa (NEMOΔhepa/JNK1Δhepa) double-knockout, JNKΔhepa (Jnk1Δhepa/Jnk2Δhepa) double-knockout, and NEMO/JNKΔhepa (NEMOΔhepa/Jnk1Δhepa/Jnk2Δhepa) triple-knockout mice, after some of which were bile duct ligated or treated with DEN, and subjected to gene expression profiling.

first: F

middle: J

last: Cubero

first: M

middle: R

last: Mohamed

middle: V

last: Boekschoten

first: C

last: Trautwein


title: Adult nucleus accumbens single-nucleus RNA-seq dataset for "A dopamine-induced coordinated gene expression program regulates neuronal function and cocaine response"

status: Public on Jun 24 2020

city: Birmingham

first: Jeremy

middle: Jason

last: Day

state: AL

address: 1825 University Blvd

department: Neurobiology

institute: UAB

summary: This dataset contains single-nucleus RNA sequencing results from adult rat brain (nucleus accumbens) and serves as the basis for characterization of transcriptional response to cocaine (20mg/kg, intraperitoneal injection). The goal of this experiment was to define the transcriptional response to cocaine across distinct cell types in the nucleus accumbens. Single-cell sequencing was carried out on FACS-sorted nuclei isolated from these experiments using the 10X Genomics Chromium single cell sequencing platform.

overall_design: This experiment contains 4 biological samples. Samples were adult rat nucelus accumbens brain tissue isolated from rats 1hr after treatment with either saline or cocaine. Tissue was lysed to allow for nuclei collection via centrifugation. FACS-sorted nuclei were subject to 10X Genomics GEM generation and barcoding, GEM-RT cleanup and cDNA amplication, and library construction using a Chromium Single Cell 3ʹ Reagent Kit (v3 chemistry). Libraries underwent directional, paired-end PolyA+ RNA-seq on an Illumina Next-seq 500. Each sample has multiple raw fastq files, corresponding to different sequencing lanes (e.g., L001, L002, etc) and different reads (e.g., R1, R2). Additional index files are also provided for each sample and each lane (I1).

first: Robert

middle: A

last: Phillps

first: Corey

middle: G

last: Duke

first: Jennifer

last: Tuscher

first: Morgan

last: Zipperly

first: Lara

last: Ianov


title: LncRNA and mRNA expression data from TMZ-resistant cell line

status: Public on Jul 03 2020

first: Yali

last: Zhou

address: 22 Hankou Road

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

summary:
Glioblastoma multiforme (GBM) is the most common and lethal malignant primary brain tumor. Temozolomide (TMZ) is a promising chemo-therapeutic agent to treat GBM. However, resistance to TMZ develops quickly with a high frequency. The mechanisms underlying GBM cells’ resistance to TMZ are not fully understood.
Long non-coding RNAs (lncRNAs) are aberrantly expressed in many cancers and are highly involved in their pathogenesis including drug-resistence. In order to systematically study the role of lncRNAs in GBM cells' resistence to TMZ , we built gene expression profiles of TMZ-resistant cell line and TMZ-sensitive cell line using lncRNA and mRNA gene expression microarrays.

overall_design: TMZ-resistant cell line and TMZ-sensitive cell line were used for RNA extraction and hybridization on microarrays. We sought to study the expression profiles of lncRNA and mRNA in GBM cell lines and to find potential core genes in the drug-resistance of this high malignant lethal disease.

first: Hao

last: Pan


title: miR-181a initiates and perpetuates oncogenic transformation through the regulation of innate immune signaling

status: Public on Jun 07 2020

city: Ann Arbor

first: Analisa

last: DiFeo

state: Michigan

address: 1600 Huron Parkway

institute: UNIVERSITY OF MICHIGAN-ANN ARBOR

summary: Genomic instability predisposes cells to malignant transformation, however the molecular mechanisms that allow for the propagation of cells with a high-degree of genomic instability remains unclear. Here we report that miR-181a is able to transform fallopian tube secretory epithelial cells- the precursor cell type for the majority of high-grade serous ovarian cancers- through the inhibition of RB1 and simultaneously drives a cell protective inhibition of the stimulator-of-interferon-genes (STING) in order to maintain a microenvironment conducive to the propagation of cells with a high-degree of genomic instability. We found that miR-181a inhibition of RB1 leads to profound nuclear defects, genomic instability, and nuclear rupture resulting in a persistence of genomic material in the cytoplasm. While normally, this persistence of genomic material in the cytoplasm induces interferon response through STING to drive cell death, miR-181a directly downregulates STING and prevents apoptosis. The most common mechanism by which oncogenic miRNAs promote tumorigenesis is through the direct inhibition of tumor suppressor genes, however our studies highlight a new mechanism of oncomiR transformation through the combination of tumor suppressor gene inhibition and abrogation of immune surveillance that initiates and propagates tumor cell survival. Importantly, we found that miR-181a induction in ovarian patient tumors is tightly associated with decreased IFNg response and downregulation of lymphocyte infiltration amd leukocyte fraction. To date, DNA oncoviruses are the only known inhibitors of STING that allow for cellular transformation thus, our findings are the first to identify a genetic factor, miR-181a, that can downregulate STING expression, suppress activation of the immunosurveillance machinery, and impair signaling in cancer cells creating a survival advantage. Our studies support the notion that the induction of STING-mediated signaling in cancer cells could lead directly to cancer cell death however these effects are abrogated by miR-181a. Given the recent interest in the development of STING agonists as a strategy to harness the immune system to treat cancer, this study introduces novel patient selective biomarker as well as potent therapeutic target for development of the most effective combination treatments.

overall_design: Total RNA was extracted from cell lysates of FT237-001, p181a, and p181a inhibitor in triplicate and submitted for Microarray using Affymetrix Human Clariom S array and the WT Plus chemistry.


title: RNA-sequencing Reveals Altered Gene Expression in the Ventromedial Hypothalamus Following Predator Odor Exposure

status: Public on Jun 06 2020

city: Kent

first: Colleen

last: Novak

state: Ohio

address: 222 Cunningham Hall, Biological Sciences, Kent State University

department: Biological Sciences

institute: Kent State University

summary: It is unknown how the VMH regulates skeletal muscle metabolism and predator threat responses, or potential interactions between these. Because skeletal muscle has a great capacity for increasing energy expenditure and is rapidly activated by PO, understanding how the VMH regulates this process could uncover novel targets for obesity treatments. Due to lack of investigation, we sought to provide a foundation for mechanistic exploration. We report transcriptome-wide alterations of the VMH following PO exposure. Our results uncovered novel functional relationships among genes that can now be probed to better understand the dual processing role of the VMH in skeletal muscle metabolism and predator-threat responses.

overall_design: We compared two conditions run in triplicate. Specifically, we compared the RNA-seq results of 3 Sprague Dawley rats exposed to predator odor to 3 Sprague Dawley rats exposed to control odor.

first: Ashley

last: Shemery

first: Megan

last: Gibson

first: Daniel

last: Diamond


title: Arginine-rich small proteins with a domain of unknown function DUF1127 play a role in phosphate and carbon metabolism of Agrobacterium tumefaciens

status: Public on May 21 2020

city: Bochum

first: Franz

last: Narberhaus

state: NRW

address: Universitätsstraße 150

department: Microbial Biology

institute: Ruhr University Bochum

summary: The genome of Agrobacterium tumefaciens C58 harbors three genes encoding small proteins (<50 aa) with a domain of unknown function DUF1127 (ATU_RS08170, ATU_RS08175, ATU_RS21905). To investigate their function we created a triple-deletion mutant lacking those genes. Total RNA was isolated from A. tumefaciens wild type and from the triple mutant (∆∆∆) at optical densities (OD) of 0.5 and 1.5, and after 24 h of growth (30 °C in YEB medium at 180 rpm) and sequenced on an Illumina platform.  For data analysis, 672 small regulatory RNA (sRNA) genes annotated by Wilms et al. (1), Lee et al. (2) and Möller et al. (3) were added to the genome. At OD 0.5 a total of 76 genes showed significantly altered expression in ΔΔΔ. The number increased to 896 and 2,575 genes at OD 1.5 and after 24 h, respectively. 15 genes were upregulated in all three growth phases in ΔΔΔ. At ODs 0.5 and 1.5 numerous genes associated with glycine/serine synthesis were upregulated in the mutant. Additionally, phosphorus starvation and denitrification genes were highly induced at OD 1.5, whereas almost all sugar ABC-transporter genes were downregulated. Overall, the results demonstrate a great impact of DUF1127 proteins on the transcriptome of A. tumefaciens.      1.  Wilms I, Overlöper A, Nowrousian M, Sharma CM, Narberhaus F. 2012. Deep sequencing uncovers numerous small RNAs on all four replicons of the plant pathogen Agrobacterium tumefaciens. RNA Biol 9:446–57.  2.  Lee K, Huang X, Yang C, Lee D, Ho V, Nobuta K, Fan JB, Wang K. 2013. A genome-wide survey of highly expressed non-coding RNAs and biological validation of selected candidates in Agrobacterium tumefaciens. PLoS One 8:e70720.  3.  Möller P, Overlöper A, Förstner KU, Wen TN, Sharma CM, Lai EM, Narberhaus F. 2014. Profound impact of Hfq on nutrient acquisition, metabolism and motility in the plant pathogen Agrobacterium tumefaciens. PLoS One 9:e110427.

overall_design: Illumina RNA sequencing of the transcriptomes of Agrobacterium fabrum C58 wild type and a triple deletion mutant ∆L4 (∆ATU_RS21905) ∆atu1667 (∆ATU_RS08170) ∆atu8161 (∆ATU_RS08175) lacking all three short DUF1127 proteins.

first: Alexander

last: Kraus

first: Mareen

last: Weskamp

last: Zierles

first: Miriam

last: Balzer

first: Ramona

last: Busch

first: Jessica

last: Eisfeld

first: Jan

last: Lambertz

first: Marc

last: Nowaczyk


title: Combined TP53 and RB1 Loss Promotes Prostate Cancer Resistance to a Broad Spectrum of Cancer Therapeutics and Confers Vulnerability to Replication Stress

status: Public on Jun 01 2020

first: Ilsa

last: Coleman

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: Prostate cancers (PC) with loss of the potent tumor suppressors TP53 and RB1 exhibit poor outcomes that include resistance to androgen receptor (AR) pathway antagonists. TP53 and RB1 also influence cell plasticity and are frequently lost in PCs with neuroendocrine (NE) differentiation. Therapeutic strategies that address these aggressive variant PCs are urgently needed. Using deep genomic profiling of 410 metastatic biopsies, we determined the relationships between combined TP53 and RB1 loss and PC phenotypes. Notably, 40% of TP53/RB1 deficient tumors were classified as AR-active adenocarcinomas indicating that NE differentiation is not an obligate consequence of TP53/RB1 inactivation. A gene expression signature reflecting TP53/RB1 loss was associated with diminished responses to AR antagonists and reduced survival. These tumors exhibit high proliferation rates and evidence of elevated DNA repair processes. While tumor cells lacking TP53/RB1 were highly resistant to all single agent therapeutics, the combination of pharmacological PARP and ATR inhibition produced significant responses, reflecting a clinically-exploitable vulnerability resulting from replication stress.

overall_design: RNA sequencing of human prostate tumor cell lines and metastatic castration-resistant prostate cancer (mCRPC) tumors using Illumina TruSeq Stranded mRNA Library prep and sequenced on Illumina HiSeq 2500.

first: Michael

last: Nyquist

first: Alexandra

last: Corella

first: Navonil

last: De Sarkar

first: Arja

last: Kaipainen

first: Gavin

last: Ha

first: Roman

last: Gulati

first: Lisa

last: Ang

first: Payel

last: Chatterjee

first: Jared

last: Lucas

first: Colin

last: Pritchard

first: Gail

last: Risbridger

first: John

last: Isaacs

first: Bruce

last: Montgomery

first: Colm

last: Morrissey

first: Eva

last: Corey

first: Peter

last: Nelson


title: Cisplatin induces inefficiently translated short transcripts in long genes

status: Public on Apr 30 2020

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

summary: We explored the regulation of intronic polyadenylation (IPA) by cisplatin, and its impact on the translatome.

overall_design: To identify regulations of IPA isoform expression relative to the last exon of genes in the processes of cisplatin response and resistance, we performed 3'-seq analyses and compared cisplatin-treated versus mock cells, and  cisplatin-resistant versus sensitive cells (all conditions in triplicates).

first: Martin

last: DUTERTRE

first: Iris

last: TANAKA

first: Mandy

last: CADIX

first: Sophie

last: MICHALLET

first: Ludovic

last: TESSIER

first: Hussein

last: MORTADA

first: Pierre

last: GESTRAUD

first: Virginie

last: RAYNAL

first: Sylvain

last: BAULANDE

first: Didier

last: AUBOEUF

last: SERVANT

first: Stéphan

last: VAGNER

first: Béatrice

last: EYMIN


title: Neuroinflammation and EIF2 signaling persist despite antiretroviral treatment in an HiPSC tri-culture model of HIV infection

status: Public on Apr 27 2020

city: Philadelphia

first: James

last: Garifallou

state: Pennsylvania

address: 3615 Civic Center Boulevard, ARC1014

department: Neonatology

institute: Children's Hospital of Philadelphia


title: Effect of antiretroviral prophylaxis on gene expression in the ectocervix

first: Sean

last: Hughes

summary:
It is important to understand how, if at all, antiretroviral prophylaxis with tenofovir disoproxil fumarate (TDF) alone or TDF in conjunction with emtricitabine (FTC) affects gene expression.  To ask this question, we used ectocervical biopsies from women enrolled in the Genital Mucosal Substudy (GMS) [1] of the Partners PrEP Study (NCT02621242) [2]. Partners PrEP was a randomized Phase III trial of oral TDF or TDF/FTC compared to placebo, which showed that either active drug was effective at protecting against HIV-1 infection. Samples were taken after 24-36 months of oral treatment with placebo, TDF, or TDF/FTC or two months after discontinuation. Treatment adherence was based on plasma TDF concentrations.
Covariates included Nugent scores (for bacterial vaginosis), HSV-2 serology, age, and birth control method. Levels of natural and synthetic hormones (medroxyprogesterone acetate [MPA], estradiol [E2], ethinyl estradiol [EE2], levonorgestrel [LNG], etonogestrel [ENG], progesterone [P4], and norethisterone enanthate [NET-EN]) were measured in the serum.
1. Lund, J. M. et al. HIV-1-Neutralizing IgA Detected in Genital Secretions of Highly HIV-1-Exposed Seronegative Women on Oral Preexposure Prophylaxis. J. Virol. 90, 9855–9861 (2016).
2. Baeten, J. M. et al. Antiretroviral prophylaxis for HIV prevention in heterosexual men and women. N. Engl. J. Med. 367, 399–410 (2012).

first: Florian

last: Hladik

first: Claire

last: Levy


title: Neuroinflammation and EIF2 signaling persist despite antiretroviral treatment in an HiPSC tri-culture model of HIV infection [bulk RNA-seq]

summary: HIV-Associated Neurocognitive Disorders (HAND) affect over half of HIV-infected  individuals, despite antiretroviral therapy (ART). Therapeutically targetable  mechanisms underlying HAND remain elusive, partly due to a lack of a proper model.  We developed a human-induced pluripotent stem cell (HiPSC) based model,  independently differentiating HiPSCs into neurons, astrocytes, and microglia, and  systematically combining to generate a tri-culture with or without HIV-infection and  ART. Single cell RNAseq analysis on tri-cultures with HIV-infected microglia revealed  inflammatory signatures in the microglia and EIF2 signaling in all three cell types.  Treatment with the antiretroviral compound EFZ mostly resolved these signatures.  However, EFZ increased RhoGDI and CD40 signaling in the HIV-infected microglia.  This activation was associated with a persistent increase in TNFa production by  microglia. This work establishes a tri-culture that recapitulates key features of HIV  infection in the CNS and provides a new model to examine the effects of infection, its  treatment, and other co-morbid conditions.

overall_design: 16 Bulk RNAseq samples were analyzed across 5 treatment groups for differential expression analysis where "WT" samples made up the untrt group, "WT_HIV" samples made up the trt1 group, "MDM" samples made up the trt2 group, "HA" samples made up the trt3 group, and "SC/iAST" samples made up the trt4 group.

last: Ryan

first: Michael

last: Gonzalez

middle: P

first: Frederick

middle: C

last: Bennett

first: Kimberly

last: Williams

first: Hakon

last: Hakonarson

first: Stewart

last: Anderson

first: Kelly

last: Jordan-Sciutto


title: A Tudor-domain containing protein, SIMR-1, mediates silencing of piRNA target mRNAs by the Mutator Complex

city: Arlington

first: Alicia

middle: Kathryn

last: Rogers

state: Texas

address: 1225 W Mitchell Street

department: Department of Biology

institute: University of Texas at Arlington

type: Non-coding RNA profiling by high throughput sequencing

summary: piRNAs play a critical role in the regulation of transposons and other germline genes. In Caenorhabditis elegans, silencing of piRNA target genes is mediated by the Mutator complex, which synthesizes high levels of siRNAs through the activity of an RNA-dependent RNA polymerase. However, how mRNAs recognized by the piRNA pathway are handed off to the Mutator pathway is unclear. Here, we identify the Tudor domain-containing protein, SIMR-1, as a key mediator of this handoff. Interestingly, SIMR-1 also localizes to distinct subcellular foci adjacent to P granules and Mutator foci, two phase-separated condensates that are the sites of piRNA-dependent mRNA recognition and Mutator complex-dependent siRNA amplification, respectively. Thus, our data suggests a role for multiple perinuclear condensates in organizing the piRNA pathway and promoting silencing by the Mutator complex.

overall_design: 10 small-RNA seq libraries in duplicate, 14 single replicate small-RNA seq libraries, and 10 mRNA-seq libraries in triplicate were generated and analyzed.

first: Carolyn

last: Phillips

first: Kevin

last: Manage

first: Celja

last: Uebel

first: Katerina

last: Arca


title: Analysis of the expression profiles of back skin and excisional wound-derived fibroblasts FACS-sorted from mice overexpressing activin A.

status: Public on Apr 14 2020

city: Chicago

first: Mateusz

last: Wietecha

state: IL

address: 801 S Paulina St

department: Oral Biology

institute: University of Illinois Chicago

summary: Overexpression of activin A by keratinocytes accelerates excisional wound healing in mice. Activin-promoted wound healing is mediated via the stroma, specifically by the wound immune cells and fibroblasts. To determine if activin A alters the gene expression profile of wound fibroblasts, we performed RNA-sequencing of fibroblasts FACS-sorted from excisional skin wounds of activin overexpressing mice. We found that activin induces a pro-fibrotic gene expression profile of these fibroblasts, leading to the upregulation of genes involved in collagen biosynthesis and remodeling.

overall_design: CD45-negative/CD140a-positive live cells (fibroblasts) were FACS-sorted from back skin (BS) and excisional skin wounds (5-days post-injury, 5dw) of activin overexpressing mice (K14-Act) and their wild-type (WT) littermates. The experiment was performed in triplicates; for each replicate, material from 3 mice of corresponding genotype and tissue was pooled. The expression profiles of the sorted fibroblasts were analyzed by RNA-sequencing.

first: Sabine

last: Werner


title: The HDAC Inhibitor Sodium Butyrate Prevents Allergic Rhinitis and Alters lncRNA and mRNA Expression Profiles in the Nasal Mucosa of Mice

status: Public on Mar 23 2020

city: Xi’an

first: jie

middle: wang

last: wang

state: shanxi

address: 17 Changle Western Road

department: Department of Otolaryngology-Head and Neck Surgery

institute: Xijing Hospita,Air Force Military Medical University

summary: Our previous research confirmed that histone deacetylase inhibitor sodium butyrate (NaB), delivered intranasally, has exhibits therapeutic effects on a mouse model of allergic rhinitis (AR). However, whether it is effective on AR when administered orally and prophylactically, as well as its potential effects on gene expression, remained unknown. Methods: In this study, we investigated the preventive effect of NaB on AR when added to the diet of newly weaned mice and evaluated changes in lncRNA and mRNA expression profiles in the nasal mucosa. Mice were randomly divided into three groups as follows: C group (control group, no treatment), AR group (treated with ovalbumin [OVA]), and NaB+AR group (treated with both OVA and NaB). The NaB+AR group was given NaB in their feed (30 g/kg), whereas the other two groups were fed normal feed from 3 weeks to 6 weeks of age. At 7 weeks of age, OVA administration was initiated to induce AR in the AR and NaB+AR  groups. Then, behavioral assessments, western blotting, and gene analysis were performed.

overall_design: Mice were randomly divided into three groups(n = 30 per group)  as follows: C group (control group, no treatment), AR group (treated with ovalbumin [OVA]), and NaB+AR group (treated with both OVA and NaB). The NaB+AR group was given NaB in their feed (30 g/kg), whereas the other two groups were fed normal feed from 3 weeks to 6 weeks of age. mice were sacrificed under anesthesia, and the nasal mucosa was preserved in liquid nitrogen for further analysis.

first: Jie

last: Wang


title: Single cell RNA sequencing of adult regenerating mouse digit tips

status: Public on Feb 24 2020

city: Boston

first: Jessica

last: Lehoczky

state: MA

address: 60 Fenwood Rd.

department: Orthopedic Surgery

institute: Brigham and Women's Hospital

summary: Innate regeneration following digit tip amputation is one of the few examples of epimorphic regeneration in mammals. Digit tip regeneration is mediated by the blastema, the same structure invoked during limb regeneration in some lower vertebrates. By genetic lineage analyses in mice, the digit tip blastema has been defined as a population of heterogeneous, lineage restructed progenitor cells. These previous studies, however, do not comprehensively evaluate blastema heterogeneity or address lineage restruction of closely related cell types. Here we report single cell RNA sequencing of over 38,000 cells from mouse digit tip blastemas and unamputated control digit tips and generate an atlas of the cell types participating in digit tip regeneration.

overall_design: Adult wildtype FVB/NJ mice used to generate 5 distinct datasets throughout digit tip regeneration. The five stages are: unamputated (control), 11 days post-amputation, 12 days post-amputation, 14 days post-amputation, and 17 days post-amputation.


title: Maize and Cercospora zeina transcriptome analysis during gray leaf spot foliar disease

status: Public on Feb 14 2020

city: Hatfield

first: Dave

middle: Kenneth

last: Berger

state: Gauteng

address: Plant Sciences Complex, Entrance 11 - Corner Lunnon Road & Herold Street

department: Dept. Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI)

country: South Africa

institute: University of Pretoria

summary: Gray leaf spot (GLS) disease of maize is caused by the fungus Cercospora zeina in African countries, such as South Africa. The plant material was from maize inbred line B73-QTL, which was introgressed with a QTL region for resistance to GLS from the maize inbred line CML444 (Berger et al (2014) BMC Genetics 15 60  www.biomedcentral.com/1471-2156/15/60 ). This QTL was named 10G2_GLS and 10H_GLS from two field trials in KwaZulu-Natal province, South Africa in that study.  B73-QTL plants were planted in the field, and subjected to natural infection with C. zeina. This was the same field trial as B73 plants that were sampled for RNAseq and the data reported in Swart et al (2017) Mol Plant Microbe Interact 30 710-724 (2017)(GSE94442). Samples were collected from lower leaves with moderate GLS lesions and younger upper leaves of the same B73-QTL plants with very few immature GLS lesions. The first aim of the experiment was to compare the maize transcriptomes during C.zeina challenge between B73 (from GSE94442 data) and B73-QTL plants (this study). The second aim was to identify novel transcripts expressed from the QTL region, which may underlie the quantitative disease resistance to GLS.  The third aim was to identify C. zeina genes expressed in planta during infection.

overall_design: To collect material that reflected a difference between C. zeina infected B73-QTL leaves and control B73-QTL leaf material, samples were collected from two lower GLS infected leaves (second and third leaf internode below ear), and two upper leaves with minimal GLS symptoms (second and third internode above ear), respectively. The two lower leaves from each plant were pooled prior to RNA extraction, and the two upper leaves from each plant were pooled prior to RNA extraction. Upper and lower leaf samples from three maize B73-QTL plants were subjected to RNA sequencing individually. The three maize plants were selected randomly as one plant per row from three rows of ten B73-QTL plants each.

first: Tanya

last: Welgemoed


title: Domain model explain propagation dynamics and stability of K27 and K36 methylation landscapes

status: Public on Apr 08 2020

city: Copenhagen

first: Anja

last: Groth

address: Blegdamsvej 3B

country: Denmark

institute: Novo Nordisk Foundation Center for Protein Research

summary: Chromatin states must be stably maintained during cell proliferation to uphold cellular identity and genome integrity. Inheritance of histone modifications across cell division is thought to be central in this process. However, the histone modification landscape is challenged by the incorporation new unmodified histones during each cell cycle and the principles that govern heritability remain poorly defined. Here, we take a quantitative approach and develop a reusable computational model that describes propagation of K27 and K36 methylation states. We measure combinatorial K27 and K36 methylation patterns by quantitative mass spectrometry on subsequent generations of histones in the presence and absence of enzymatic inhibition. Our modelling rejects active global demethylation and invoke the existence of 8 domains defined by distinct methylation endpoints. We find that K27me3 on pre-existing histones stimulates the rate of de novo K27me3 establishment, supporting a read-write mechanism in timely chromatin restoration. Finally, we provide a detailed, quantitative picture of the mutual antagonism between K27 and K37 methylation, and propose that this antagonism enhance the stability of epigenetic states across cell division.

overall_design: Quantitative ChIP-seq analysis of H3K36me2 and H3K27me3 distribution and abundance upon 7 days treatment with DMSO or EZH2 inhibitor (EPZ-6438) in E14 mESCs cells. All experiments were done in duplicates. Chromatin of Drosophila melanogater S2 cells were used as spike-in for normalization purpose. Standard ChIPseq was performed on the same cells for H3K36me3, H3K27me1, H3K27me2 and H3K27me3 to determine regions of enrichment for each of the marks.

first: Constance

last: Alabert

first: Simona

last: Graziano

first: Nazaret

last: Reverón-Gómez


title: RNA-seq in 73 B-lineage ALL patients

status: Public on Jan 23 2020

city: Memphis

first: Robert

middle: Joseph

last: Autry

state: TN

address: 262 Danny Thomas Pl, MS 313

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

summary: RNA-seq from RNA isolated from bone marrow or peripheral blood of newly diagnosed acute lymphoblastic leukemia patients on TotalXVI protocol

overall_design: LC50 determination performed with concordant RNA-seq expression analysis

first: Wenjian

last: Yang

first: William

middle: E

last: Evans


title: RNA-seq in 247 B-lineage ALL

summary: RNA-seq from RNA isolated from bone marrow or peripheral blood of newly diagnosed acute lymphoblastic leukemia patients

overall_design: RNA-seq expression analysis in primary leukemia cells


title: Gene expression profiling of multiple sclerosis brain samples

status: Public on Dec 17 2019

city: Roma

first: Eleonora

last: Arico'

state: RM

address: viale Regina Elena 299

country: Italy

institute: ISS

summary: Recent studies of cortical pathology in secondary progressive multiple sclerosis have shown that a more severe clinical course and the presence of extended subpial grey matter lesions with significant neuronal/glial loss and microglial activation are associated with meningeal inflammation, including the presence of lymphoid-like structures in the subarachnoid space in a proportion of cases.   To investigate the molecular consequences of pro-inflammatory and cytotoxic molecules diffusing from the meninges into the underlying grey matter, we carried out gene expression profiling analysis of the motor cortex from 20 post-mortem multiple sclerosis brains with and without substantial meningeal inflammation and 10 non-neurological controls.    Gene expression profiling of grey matter lesions and normal appearing grey matter not only confirmed the substantial pathological cell changes, which were greatest in multiple sclerosis cases with increased meningeal inflammation, but also demonstrated the upregulation of multiple genes/pathways associated with the inflammatory response. In particular, genes involved in tumour necrosis factor (TNF) signalling were significantly deregulated in MS cases compared to controls.

overall_design: Gene expression profiling analysis of the motor cortex from 20 post-mortem multiple sclerosis brains with and without substantial meningeal inflammation and 10 non-neurological controls

first: Roberta

last: Magliozzi

first: Pascal

last: Durrenberger

last: Aricò

first: Richard

last: Reynolds


title: Endometrial transcriptome and PGR cistrome in cycling fertile women [ChIP-seq]

status: Public on Nov 27 2019

city: RTP

first: Franco

last: Demayo

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

summary: We report the transcriptomic profile and PGR cistromic profile for endometrial biopsies obtained from fertile women during the proliferative and mid-secretory phase of the menstrual cycle

overall_design: RNA-seq analyses were conducted on whole-endometrium and epithelium during the proliferative and mid-secretory phases. In parallel, PGR ChIP-seq was conducted on whole endometrium during rhe proliferative and mid-secretory phases.

first: Ru-pin

last: Chi

first: Tianyuan

first: Nyssa

last: Adams

first: San-pin

last: Wu

first: Steven

middle: L

last: Young

first: Thomas

last: Spencer

first: Francesco


title: Cellular milieu of the neural retina informs complement immune regulation

status: Public on Jan 24 2020

first: Dwight

middle: Edward

last: Stambolian

state: PA

address: 422 Curie Blvd.

department: Opthalmalogy

institute: University of Pennsylvania

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Endometrial transcriptome and PGR cistrome in cycling fertile women [RNA-seq]

last: Wang


title: Defining the Secrebiome: the expressed secretome of the gut microbiome and its role in obese Mexican children

status: Public on Mar 16 2020

city: Cuernavaca

first: Fernanda

last: Cornejo

address: Av Universidad 2001

country: Mexico

institute: Instituto de Biotecnología UNAM

summary: high throughput sequencing of the metagenome of mexican children

overall_design: RNA seq from fecal samples of Mexican children

first: Luigui

last: Gallardo-Becerra

last: Cornejo-Granados

first: Rodrigo

last: García-López

first: Alejandra

last: Valdez-Lara

first: Shirley

last: Bikel

first: Samuel

last: Canizales-Quinteros

first: Blanca

last: López-Contreras

first: Alfredo

last: Mendoza-Vargas

first: Henrik

last: Nielsen

first: Adrián

last: Ochoa-Leyva


title: Aging induces aberrant state transition kinetics in murine muscle stem cells

status: Public on Feb 18 2020

city: San Francisco

first: Jacob

middle: Cameron

last: Kimmel

department: Biochemistry and Biophysics

institute: UCSF

summary: Label retaining and non-retaining muscle stem cells from young and aged H2B-GFP+/-;rtTA+/- were profiled by single cell RNA-seq at two timepoints

overall_design: 2 young (3 mo) and 2 aged (20 mo) H2B-GFP+/-;rtTA were labeled to track proliferative history by pulsing DOX in development (E10.5-E16.5). Label retaining and non-retaining cells were isolated from these animals by FACS. A set of cells from each animal was profiled immediately, while another set of cells was activated for 18 hours in vitro (10% HS, DMEM, culture plastic + sarcoma derived ECM) prior to profiling. Single cell RNA-seq was performed following the 10X Chromium Single Cell v2 kit.

first: Wallace

middle: F

last: Marshall

first: Andrew

middle: S

last: Brack


title: DNA Methylation Potential Energy Landscape Analysis of MLL-rearranged Acute Myeloid Leukemia (AML) and Normal hematopoietic precursors [WGBS]

status: Public on Mar 02 2020

city: Baltimore

first: Michael

last: Koldobskiy

state: MD

address: 855 N. Wolfe St.

department: Center for Epigenetics

institute: Johns Hopkins University

type: Methylation profiling by high throughput sequencing

summary: Acute myeloid leukemia (AML) carrying MLL rearrangements. We applied WGBS and the informME analysis pipeline to investigate the role of DNA methylation stochasticity in MLL-rearranged AML.

overall_design: WGBS was carried out on primary acute myeloid leukemia samples harboring KMT2A (MLL) rearrangements and on normal human myeloid progenitor cells.

last: Feinberg


title: Cdk9 and H2Bub1 signal to Clr6-CII/Rpd3S to suppress aberrant antisense transcription

city: Bronx

first: PABITRA

middle: K

last: PARUA

state: NY

address: 1300 Morris Park Avenue, Forchheimer 236, Molecular Pharmacology

department: Molecular Pharmacology

institute: Albert Einstein College of Medicine

summary: Histone H2B mono-ubiquitylation (H2Bub1) and phosphorylation of elongation factor Spt5 by cyclin-dependent kinase 9 (Cdk9) occur during transcription by RNA polymerase II (RNAPII), and are mutually dependent in fission yeast. How Cdk9 activity and H2Bub1 cooperate to regulate the expression of individual genes remains unclear. Here we show Cdk9 inhibition or H2Bub1 loss induces intragenic antisense transcription of distinct gene subsets; ablation of both pathways derepresses antisense transcription of over half the genome. H2Bub1 and phospho-Spt5 have similar genome-wide distributions; both are enriched in coding regions, and H2Bub1 levels are directly proportional to those of phospho-Spt5. Cdk9-dependence of antisense suppression correlates with high H2Bub1 occupancy, and with promoter-proximal RNAPII pausing. Combined reduction of Cdk9 activity and loss of H2Bub1 prevent recruitment of the histone deacetylase Clr6-CII to transcribed genes, and lead to decreased histone occupancy and increased histone acetylation within gene coding regions. These results uncover new pathways linking regulators of RNAPII transcription elongation to suppression of aberrant antisense transcription, and demonstrate novel interactions between co-transcriptional histone modification pathways.

overall_design:
ChIP-seq: Data represent eighteen different ChIP-seq experiments in S. pombe, performed in biological replicates. There are raw sequencing files for all biological replicates and processed files after combining the replicates.

Please note that the *Combined.bigwig processed data was generated from both rep1 and rep2 data combined and is available as Series supplementary files.

first: Pabitra

last: Parua

first: Miriam

last: Sansó

first: Jason

last: Tanny


title: Interferon-β corrects massive gene dysregulation in multiple sclerosis:  Short-term and long-term effects on immune regulation and neuroprotection

status: Public on Sep 27 2019

first: Riyue

last: Bao

address: 900 E 57 Street

department: Center for Research Informatics

institute: University of Chicago

summary: Background: In multiple sclerosis (MS), immune up-regulation is coupled to subnormal immune response to interferon-β (IFN-β) and low serum IFN-β levels. The relationship between the defect in IFN signalling and acute and long-term effects of IFN-β on gene expression in MS is inadequately understood. Methods: We profiled IFN-β-induced transcriptome shifts, using high-resolution microarrays on 227 mononuclear cell samples from IFN-β-treated MS Complete Responders (CR) stable for five years, and stable and active Partial Responders (PR), stable and active untreated MS, and healthy controls.  Findings: IFN-β injection induced short-term changes in 1,200 genes compared to baseline expression after 4-day IFN washout. Pre-injection after washout, and in response to IFN-β injections, PR more frequently had abnormal gene expression than CR. Surprisingly, short-term IFN-β induced little shift in Th1/Th17/Th2 gene expression, but up-regulated immune-inhibitory genes (ILT, IDO1, PD-L1). Expression of 8,800 genes was dysregulated n therapy-naïve compared to IFN-β-treated patients. These long-term changes in protein-coding and long non-coding RNAs affect immunity, synaptic transmission, and CNS cell survival, and correct the disordered therapy-naïve transcriptome to near-normal. In keeping with its impact on clinical course and brain repair in MS, long-term IFN-β treatment reversed the overexpression of proinflammatory and MMP genes, while enhancing genes involved in the oligodendroglia-protective integrated stress response, neuroprotection, and immunoregulation. In the rectified long-term signature, 277 transcripts differed between stable PR and CR patients.

overall_design: 227 samples,from 54 subjects.  27 relapsing/remitting MS (RRMS) on IFN-β therapy for 8·14 ± 0·86 years. 12 were Complete Responders to IFN-β therapy, exacerbation-free >6 months before sampling. 15 Partial R patients were stable for >6 months, and were also followed for 5 years. PR were also sampled during an exacerbation. Therapy-naïve included 10 with stable RRMS and 9 RRMS during exacerbations.  Ther were age- and sex-macthed with 8 healthy controls.

first: Xuan

last: Feng

first: Lei

last: Li

first: Florian

last: Deisenhammer

first: Barry

middle: W

last: Arnason

first: Anthony

middle: T

last: Reder


title: Acquisition of a unique mesenchymal precursor-like blastema state underlies successful adult mammalian digit tip regeneration

status: Public on Nov 15 2019

city: Toronto

first: Freda

middle: D

last: Miller

state: Ontario

address: 686 Bay Street

department: Neurosciences and Mental Health

country: Canada

institute: The Hospital For Sick Children

summary: Here, we investigate the origin and nature of blastema cells that regenerate the adult murine digit tip. We show that Pdgfra-expressing mesenchymal cells in uninjured digits establish the regenerative blastema and are essential for regeneration. Single cell profiling shows that the mesenchymal blastema cells are distinct from both uninjured digit and embryonic limb/digit Pdgfra-positive cells. This unique blastema state is environmentally determined; dermal fibroblasts transplanted into the regenerative, but not non-regenerative, digit express blastema markers and contribute to bone regeneration. Moreover, lineage tracing with single cell profiling indicates that endogenous osteoblasts/osteocytes acquire a blastema mesenchymal transcriptional state and contribute to both dermis and bone regeneration. Thus, mammalian digit tip regeneration occurs via a distinct adult mechanism where the regenerative environment promotes acquisition of a unique blastema state that allows cells from tissues like bone to contribute to regeneration of other mesenchymal tissues such as the dermis.

overall_design: High-throughput single cell transcriptomic profiles of uninjured (dataset1 and duplicate dataset), regenerating (7, 10, 14, duplicate 14 dataset, 28, 56 days post amputation) and non-regenerative (10, duplicate 10 dataset, 14 days post amputation) digit tips of C57BL/6 and transgenic Dmp1CreERT2;TdTomato (Uninjured and 14 day post amputation) adult mice, together with embryonic limbs (E11)/digit tips (E14) or neonatal (P3) digit tips of C57BL/6 mice were generated by single cell RNA sequencing, using the 10X Genomics platform. Processed data for 16 datasets are included as indicated.

first: Mekayla

middle: A

last: Storer

first: Neemat

last: Mahmud

first: Konstantina

last: Karamboulas

middle: J

last: Borrett

first: Scott

last: Yuzwa

first: Alaura

last: Androschuk

middle: V

last: Sefton

first: David

middle: R

last: Kaplan


title: Expression data of EBV-positive and EBV-negative subclones of gastric adenocarcinoma cell line AGS

status: Public on Oct 14 2019

city: Seoul

first: Suk Kyeong

last: Lee

address: 222, Banpo-daero

country: South Korea

institute: Catholic University of korea

summary: Gastric cancer is one of the most common cancers worldwide. Epstein-Barr virus-associated gastric cancer accounts for approximately 10% of all gastric cancers. EBV expresses its own proteins and miRNAs (BART miRNAs) and regulates host gene expression. In this study, we examined the effect of EBV infection on host mRNA expression. Differential gene expression was analyzed between EBV-negative human gastric cancer cell line AGS and EBV-positive human gastric cancer cell line AGS-EBV.

overall_design: Total RNA was prepared using RNAzol B reagent from five each independent cultures of AGS and AGS-EBV cells.

first: Suk


title: Tumor cell biodiversity drives microenvironmental reprogramming in liver cancer

status: Public on Oct 06 2019

city: Bethesda

first: Xin

middle: Wei

last: Wang

state: MARYLAND

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

summary: Single-cell transcriptome profiling of liver cancer biospecimens from nine hepatocellular carcinoma and ten intrahepatic cholangiocarcinoma patients.

overall_design: A total of 19 tumors were profiled. Set 1 contains scRNA-seq data of twelve samples, i.e., S16_P10_LCP18, S02_P01_LCP21, S10_P05_LCP23, S09_P04_LCP25, S08_P03_LCP26, S07_P02_LCP28, S11_P06_LCP29, S12_P07_LCP30, S20_P12_LCP35, S21_P13_LCP37, S15_P09_LCP38, and S19_P11_LCP39. Set 2 includes scRNA-seq data of seven samples, i.e., S351_P10_LCP34, S355_P13_LCP42, S358_P16_LCP46, S305_P06_LCP56, S300_P02_LCP60, 364_P21_LCP65, and S365_P22_LCP66. Detailed information can be found in samples.txt file of each Set. The last two digits of the sample ID here correspond to the sample ID in the paper (PMID: 31588021), e.g., S16_P10_LCP18 matches with H18 and S02_P01_LCP21 matches with H21.


title: Identification of a unique subtype of lung squamous cell carcinoma defined by SOX2 and a neural differentiation factor BRN2 [ChIP-seq]

status: Public on Sep 17 2019

city: New York

first: Hideo

last: Watanabe

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai

summary: Lineage-specific transcriptional regulators control differentiation states not only during normal development but also during cancer evolution. By investigating super-enhancer landscape of lung squamous cell carcinoma (LUSC), we identified a unique ‘neural’ subtype defined by Sox2 and a neural lineage factor Brn2. Robust protein-protein interaction and genomic co-occupancy of these factors indicated their transcriptional cooperation in this ‘neural’ LUSC in contrast to the cooperation of Sox2 and p63 in the classical LUSC. Introduction of p63 expression in the “neural’ LUSC invoked the classical LUSC lineage accompanied by Brn2 downregulation and increased activities of ErbB/Akt and MAPK-ERK pathways. Collectively, our data demonstrate a unique LUSC lineage featured by Sox2 cooperation with Brn2 instead of p63, for which distinct therapeutic approaches may be warranted.

overall_design:
Genome-wide profiles of histone H3K27 acetylation, Sox2 binding, p63 binding and Brn2 binding in LUSC cell lines

***************************************************************
Raw files for human/patient samples are available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) phs004458.v1.p1 for controlled access to the personally identifiable sequence data.
***************************************************************

first: Takashi

last: Sato


title: Identification of a unique subtype of lung squamous cell carcinoma defined by SOX2 and a neural differentiation factor BRN2


title: Hepatic PPARα function and lipid metabolic pathways are dysregulated in polymicrobial sepsis

status: Public on Nov 23 2019

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

institute: VIB-UGent

summary: Despite intensive research and constant medical progress, sepsis remains one of the most urgent unmet medical needs of today. Most studies have been focused on the inflammatory component of the disease, however, recent advances support the notion that sepsis is accompanied by extensive metabolic perturbations. During times of limited caloric intake and high energy needs, the liver acts as the central metabolic hub in which PPARa is crucial to coordinate the breakdown of fatty acids. The role of hepatic PPARa in liver dysfunction during sepsis has hardly been explored. We demonstrate that sepsis leads to a starvation response that is hindered by the rapid decline of hepatic PPARa levels, causing excess free fatty acids, leading to lipotoxicity, and glycerol. In addition, treatment of mice with the PPARa agonist pemafibrate protects against bacterial sepsis by improving hepatic PPARa function, reducing lipotoxicity and tissue damage. Since lipolysis is also increased in sepsis patients and pemafibrate protects after the onset of sepsis, these findings may point towards new therapeutic leads in sepsis.

overall_design: Liver RNA from mice subjected to CLP or SHAM operation followed by administration of GW7647 or DMSO (control).

first: Lise

last: Van Wynege

first: Tineke

last: Vanderhaeghen

first: Jolien

last: Vandewalle

first: Kelly

last: Van Looveren

last: Souffriau

first: Charlotte

last: Wallaeys

first: Melanie

last: Eggermont

first: Sam

last: Ernst

first: Evelien

last: Van Hamme

first: Amanda

last: Gonçalves

first: Guy

last: Eelen

last: Scott

first: Caroline

last: Rombouts

first: Lynn

last: Vanhaecke

first: Liesbet

last: De Bus

first: Johan

last: Decruyenaere

first: Peter

last: Carmeliet

first: Claude

last: Libert


title: RNA-Seq analysis of ileocecal valve and peripheral blood from Holstein cattle infected with Mycobacterium avium subsp. paratuberculosis

status: Public on Sep 14 2019

city: Derio

first: MARTA

last: ALONSO-HEARN

state: Bizkaia

address: Berreaga 1

department: Animal Health

country: Spain

institute: NEIKER

summary:
Purpose: Since the peripheral blood (PB) is the most available physiological fluid for the detection of biomarkers, in the current we examine whether it recapitulates, at least in part, the transcriptome of the ileocecal valve (ICV), the primary site of MAP colonization. For this purpose, RNA-Seq was used to identify host genes differentially expressed (DE) in ICV and PB samples collected from PTB-infected animals with focal or diffuse lesions in gut tissues versus control animals.
Methods: RNA-Seq libraries were single-end sequenced in a 1x75 format using an Illumina NextSeq 500 sequencer. The raw reads were filtered by their length (minimum size 60 bp long) and percentage of ambiguous base N less than 5 % using Prinseq-lite. Trimmed reads were subsequently mapped to the Bos Taurus reference genome (Bos_taurus.UMD3.1. version 87) with TopHat mapper. The resulting alignment files were provided to Cufflinks to generate a transcriptome assembly for each condition. These assemblies were then merged together using Cuffmerge, which is included in the Cufflinks package. This merged assembly provided a uniform basis for calculating gene and transcript expression levels in each condition. The reads and merged assembly were fed to Cuffdiff which calculates expression levels and tested the statistical significance of each observed change in expression. The fold change (in log2 scale), P-values and false discovery rates (FDR) for each gene were obtained. The genes with a FDR-adjusted threshold ˂ 0.05 were considered differentially expressed (DE) when compared to the control group.
Results: Our results demonstrated both shared, and PB and ICV-specific gene expression in response to a natural Map infection. As expected, the number of differentially expressed (DE) genes was larger in the ICV than in the PB samples. Among the DE genes in the PB and ICV samples, there were some common genes irrespective of the type of lesion including the C-X-C motif chemokine ligand 8 (CXCL8/IL8), apolipoprotein L (APOLD1), and the interferon inducible protein 27 (IFI27). The biological processes (BP) enriched in the ICV gene expression profiles from the cows with focal lesions included the killing of cells of other organism, defense response, immune response and the regulation of neutrophil chemotaxis. Two of these BP, the defense and immune response, were also enriched in the ICV and PB from the cows with diffuse lesions. Metabolic analysis of the DE genes revealed that the N-glycan biosynthesis, bile secretion, one-carbon pool by folate and purine metabolism were significantly enriched in the ICV from the cows with focal lesions. In the ICV from cows with diffuse lesions; the valine, leucine and isoleucine degradation route, purine metabolism, vitamin digestion and absorption and the cholesterol routes were enriched
Conclusions: This study is the first to simultaneously describe transcriptomic changes in PB and ICV samples of cattle naturally infected with MAP. Several important observations were made. First, by comparing the transcriptomic profiles of two MAP-targeted tissues we described both unique and overlapping changes in the transcriptome of the infected cows versus the control group. Second, our study highlighted the ability of the RNA-Seq technology to reveal roles for genes that have not been previously implicated in the host response to MAP infection. Third, our transcriptomic analysis provided potential biomarkers for the development of future diagnostic tools, vaccines and therapeutics.

overall_design: RNA-Seq libraries were prepared from the PB and ICV of 14 animals within the three categories; with focal (N=6) or diffuse (N= 5) histopathological lesions in gut tissues and control (N=3).

first: Marta

last: Alonso-Hearn

first: Maria

last: Canive


title: Endometrial transcriptome and PGR cistrome in cycling fertile women

first: Franco

last: Demayo


title: Reprogramming of Tumor-infiltrating Immune Cells in Early Stage of NSCLC

status: Public on Apr 30 2019

city: Winston-Salem

first: Qianqian

last: Song

address: 1 Medical Center Boulevard

department: Cancer Genomics and Precision Oncology

institute: Wake Forest Baptist Comprehensive Cancer Center

summary: Comparing the relative proportions of immune cells in tumor and adjacent normal tissue from NSCLC patients demonstrates the early changes of tumor immunity and provides insights to guide immunotherapy design. We mapped the immune ecosystem using computational deconvolution of bulk transcriptome data from the Cancer Genome Atlas (TCGA) and single cell RNA sequencing (scRNA-seq) data of dissociated tumors from early-stage non-small cell lung cancer (NSCLC) to investigate early immune landscape changes occurring during tumorigenesis. Computational deconvolution of immune infiltrates in 44 NSCLC and matching adjacent normal samples from TCGA showed heterogeneous patterns of alterations in immune cells. The scRNA-seq analyses of 11,485 cells from 4 treatment-naïve NSCLC patients comparing tumor to adjacent normal tissues showed diverse changes of immune cell compositions. Notably, CD8+ T cells and NK cells are present at low levels in adjacent normal tissues, and are further decreased within tumors. Myeloid cells exhibited marked dynamic reprogramming activities, which were delineated with differentiation paths through trajectory analysis. A common differentiation path from CD14+ monocytes to M2 macrophages was identified among the 4 cases, accompanied by up-regulated genes (e.g. ALCAM/CD166, CD59, IL13RA1, IL7R) with enriched functions (adipogenesis, lysosome), and down-regulated genes (e.g. CXCL2, IL1B, IL6R) with enriched functions (TNFa signaling via NF-kB, inflammatory response). Computational deconvolution and single cell sequencing analyses have revealed a highly dynamic immune reprogramming that occurs in early stage NSCLC development, suggesting that normalizing both immune compartments may represent a viable strategy for treatment of early stage cancer and prevention of progression.

overall_design: Map the immune ecosystem using computational deconvolution of bulk transcriptome data from the Cancer Genome Atlas (TCGA) and single cell RNA sequencing (scRNA-seq) data of dissociated tumors from from early-stage non-small cell lung cancer (NSCLC) to investigate early immune landscape changes occurring during tumorigenesis

first: Wei

last: Zhang

first: Elizabeth

last: Forbes

first: Guangxu

last: Jin


title: Hypoxia induces the dormant state in oocytes through expression of Foxo3

status: Public on May 28 2019

city: Fukuoka

first: So

last: Shimamoto

state: Fukuoka

address: Maidashi 3-1-1, Higashi-ku

department: Department of Developmental Stem Cell Biology

institute: Kyushu-university

summary: In mammals, most immature oocytes remain dormant in the primordial follicles in order to ensure the longevity of female reproductive life. A precise understanding of mechanisms underlying the dormancy is important for reproductive biology and medicine. In this study, by comparing mouse oogenesis in vivo and in vitro, the latter of which bypasses the primordial follicle stage, we defined the gene　expression profile representing the dormant state of oocytes. Overexpression of constitutively active FOXO3 partially reproduced the dormant state in vitro. Based on further gene expression analysis, we found that a hypoxic condition efficiently induced the dormant state in vitro. The effect of hypoxia was severely diminished by disruption of the Foxo3 gene and inhibition of hypoxia-inducible factors. Our findings provide insights into the importance of environmental conditions and their effectors for establishing the dormant state.

overall_design: Transcriptomes of oocytes isolated from in vivo ovaries at various stages or in vitro-reconstituted ovaries at various days of culture were determined by RNA-seq analysis. Transcriptomes of in vitro D21 oocytes derived from WT ESCs and Foxo3dNES Tg ESCs under a normoxic or hypoxic condition were also determined. Biologically triplicated (rep1-3) or duplicated (rep1-2) samples were analyzed.

first: Yohei

last: Nishimura

first: Go

last: Nagamatsu

first: Norio

last: Hamada

first: Haruka

last: Kita

first: Orie

last: Hikabe

first: Nobuhiko

last: Hamazaki

first: Katsuhiko

last: Hayashi


title: Impact of a pre-operative exercise intervention on breast cancer proliferation and gene expression

status: Public on Apr 10 2019

city: Boston

first: Rinath

last: Jeselsohn

address: 450 Brookline Ave, D728

department: Medical Oncology

institute: DFCI

summary: RNAseq analysis of primary breast cancer samples

overall_design: Inactive women with newly diagnosed breast cancer were randomized to an exercise intervention or mind-body control group, and participated in the study between enrollment and surgery (mean 29.3 days). Tumor were collected at baseline and surgery.

first: Jennifer

last: Ligibel


title: Global transcriptomic changes following carbon limitation and elevated carbon dioxide in Nannochloropsis oceanica IMET1: Illumina sequencing

status: Public on Jul 16 2019

city: Qingdao

first: Jian

last: Xu

state: Shandong province

address: No.189 Songling Rd, LaoShan District

department: BEGC

institute: QIBEBT-CAS

summary: Limited systems-level understanding of CO2 concentrating mechanism (CCM) and metabolic adaption in response to different CO2-level in wild oleaginous algae has hindered the development of microalgal feedstock and the knowledge of its role in global warming and oceanic acidification. Nannochloropsis are a group of small unicellular microalgae widely distributed in oceans and fresh water, which implies that it plays a crucial role in biogeochemical cycles impinged on global climate change. In addition, Nannochloropsis has been used for flue gas fixation in many large-scale and pilot-scale outdoor cultivation facilities for photosynthetic production of fuels and chemicals. To untangle the intricate genome-wide networks underlying CCM and metabolic adjustment under different CO2 concentrations in Nannochloropsis, we applied high-throughput mRNA-sequencing and reconstructed the structure and dynamics of the genome-wide functional network underlying robust microalgal CCM and  in Nannochloropsis oceanica, by tracking the genome-wide, single-base-resolution transcript change for the complete time-courses of different CO2 concentrations.

overall_design: Nannochloropsis oceanica IMET1 cells were grown in liquid cultures under continuous light (approximately 80±5 µmol photons m-2 s-1) at 25℃ and aerated by bubbling with a mixture of 5% CO2 in air. Mid-logarithmic phase algal cells were collected and washed three times with axenic seawater. Equal numbers of cells were re-inoculated in fresh medium and cultured under 5% CO2 for preadaption for one hour, and then two samples (from biological replicates) were collected as 0h samples. After the preadaption for one hour, half of them were sequentially grown under 5% in air (High carbon or HC) and other half of them were grown under 0.01% CO2   (Very low carbon or VLC) with 80±5 µmol m-2 s-1 light intensity, respectively. Cell aliquots were collected for RNA isolation after being transferred to the designated conditions for 3h, 6h, 12h and 24h. Three biological replicates of algal cultures were established under each of the above “VLC” and “HC” conditions, respectively. Two biological replicates were randomly selected to prepare mRNA-Seq library. In total, 18 samples collected at 5 time points (0h, 3h, 6h, 12h, and 24h) were used for mRNA-Seq library preparation and then submitted to Illumina HiSeq 2000 for sequencing.

first: Li

last: Wei


title: Disruption in A-to-I editing levels affects C. elegans development more than a complete lack of editing

status: Public on Apr 22 2019

city: Haifa

first: Ayelet

last: Lamm

address: Technion st

department: Biology

country: Israel

institute: Technion

summary: A-to-I RNA editing is widespread in eukaryotic transcriptomes and plays an essential role in the creation of proteomic and phenotypic diversity. Loss of ADARs, the proteins responsible for A-to-I editing, results in lethality in mammals. In C. elegans, knocking out both ADARs, ADR-1 and ADR-2, results in aberrant behavior and abnormal development. Studies have shown that ADR-2 can actively deaminate dsRNA while ADR-1 cannot. However, as most studies of C. elegans ADARs were performed on worms mutated in both ADAR genes, the effects observed cannot be attributed to a single ADAR or to the interactions between ADAR genes. Therefore, we set to study the effects of each C. elegans ADAR on RNA editing, gene expression, protein levels and the contribution of each of ADAR to the phenotypes observed in worms mutated in both genes, in order to elucidate their distinct functions. We found significant differences in the phenotypes observed in worms mutated in a single ADAR gene. Worms harboring adr-1 mutations have a significant reduction in their lifespan, while worms harboring adr-2 mutations have extended lifespan. We also observed severe abnormalities in vulva formation mainly in adr-1 mutants, and we suggest that these phenotypes are a result of an RNA editing independent function of ADR-1. Mutations in each ADAR resulted in expressional changes in hundreds of genes, and a significant downregulation of edited genes. However, very few changes in the protein levels were observed. In addition, we found that ADR-1 binds many edited genes. Our results suggest that ADR-1 has a significant function in the RNA editing process and by altering editing levels it causes the severe phenotypes that we observed. In contrast, a complete lack of RNA editing is less harmful to the worms. Furthermore, our results indicate that the effect of RNA editing on the protein content in the cell is minor and probably the main purpose of these modifications is to antagonize or enhance other gene regulatory mechanisms that act on RNA.

overall_design: RNA was extracted from wildtype C. elegans synchronized to embryo or L4 larval stage. For each stage, 3 independent biological replica RNA samples were used for construction of mRNA libraries.


title: Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single Cell RNA Sequencing

status: Public on Mar 25 2019

city: Tuebingen

first: Marja

last: Timmermans

address: Morgenstelle 32

institute: University of Tuebingen

summary:
A single cell RNA sequencing atlas of the Arabidopsis root distinguishes cells both by developmental fate and time, revealing defining expression features that depict a complex cascade of developmental progressions from stem cell through differentiation supported by mirroring waves of transcription factor expression.
Methods: mRNA profiles of 6-day-old wild-type (WT) and shortroot-knockout Arabidopsis thaliana roots were generated by deep sequencing of single cell (all) and bulk RNA libraries (wild type only), in duplicate (bulk & wild-type single cell) and singlicate (shr-3), using Illumina NextSeq. The sequence reads that passed quality filters were analyzed at the transcript level. Single Cell libraries were processed and analysed using Cell Ranger, STAR, Seurat. Bulk libraries were processed using Trimmomatic, STAR, HTSeq and DEseq2.
Results: For Single Cell - Using an optimized data analysis workflow, we mapped ~87k sequence reads per wild-type cell to the Arabidopsis genome (TAIR10) and identified a median of 4,276 genes and 14,758 transcripts per cell. In total, transcripts for 16,975 genes were detected (RPM ≥1) from wild-type cells. After correction for read depth, this represents ~90% of genes detected by bulk RNA-seq of protoplasted root tissue. Bulk RNA-seq data identified genes induced by protplasting of the Arabidopsis root which could be discounted from single cell analysis. The global gene expression profiles of pooled scRNA-seq and bulk RNA-seq are highly correlated (r = 0.9) indicating that plant scRNA-seq is highly sensitive.
Conclusions: Our high-resolution single cell RNA sequencing atlas of the Arabidopsis root captures precise temporal information for all major cell types, revealing new regulators and defining features foreach. Developmental trajectories derived from pseudotime analysis depict a finely resolved cascade of developmental progressions between stem cell and final differentiation supported by mirroring waves of transcription factor expression.

overall_design: Single cell RNA sequencing for 5,767 cells (total) from Arabidopsis (2x wild-type root replicate, 1x shr-3 mutant root replicate). Bulk RNA sequencing for Arabidopsis 2x replicates unprotoplasted roots and 2x replicates protoplasted roots.

first: Tom

last: Denyer

first: Xiaoli

last: Ma

first: Simon

last: Klesen

middle: C


title: CD56dim NK cell gene signature in melanoma patients with better and worse clinical outcomes

status: Public on Jan 03 2019

city: Pittsburgh

first: Lazar

last: Vujanovic

address: L1.33 Hillman Cancer Center, 5117 Centre Ave

department: Medicine

institute: University of Pittsburgh

summary:
Natural killer (NK) cells are innate cytotoxic and immunoregulatory lymphocytes that have a central role in anti-tumor immunity and play a critical role in mediating cellular immunity in advanced cancer immunotherapies, such as dendritic cell (DC) vaccines. Our group recently tested a novel recombinant adenovirus-transduced autologous DC-based vaccine that simultaneously induces T cell responses against three melanoma-associated antigens for advanced melanoma patients. We examined the impact of this vaccine on the NK cell profile in melanoma patients.
Relative immune cell population abundance was evaluated as previously described (Danaher et al. JITC, 2017). The abundance of the CD56dim NK cell gene signature was compared between pattients with better and worse outcome.

overall_design:
41 lesions from 19 patients were excised at three different time-points during this trial and total RNA was extracted.
Samples were profiled on the nCounter® MAX platform with the PanCancer Immune Profiling Panel

first: Afshin

last: Mashadi-Hossein

first: Sarah

last: Warren

first: Andy

last: White

first: Alan

last: Huang

first: John

middle: M

last: Kirkwood

first: Lisa

middle: H

last: Butterfield


title: Profiling of EMT-associated mitochondrial RNAs in hepatocellular carcinoma cells

status: Public on Aug 27 2019

city: Palo Alto

first: Jifan

last: Hu

state: CA

address: 3801 Miranda Ave, Bldg 100, Room E4-200

department: Palo Alto Veterans Institute for Research

institute: Stanford University Medical School

summary: Mitochondria, the powerhouse of the cell, has been recognized as the key players in cancer cell biology, including cancer metabolism, metastasis, and drug resistance. Recent studies have demonstrated a functional interplay between mitochondria and epithelial-mesenchymal transition (EMT) in cancer. To delineate the role of mitochondrial components in this interplay, we induced the EMT in hepatoma HepG2 cells. Mitochondria was isolated from EMT-HepG2 cells, untreated HepG2 cells, and normal hepatic HL7702 cells. Mitochondrial RNAs were isolated for Illumina sequencing. Identification of mitochondrial RNAs that regulate EMT or mitochondria function may serve as potential therapeutic targets for developing new strategies to treat cancers.

overall_design: HepG2 cells were seeded into 6‑well plates, and EMT was induced by 10 ng/ml TGF‑β1 in the medium was used to replace the common medium for 24‑72 h. Cells were characterized by examining the EMT markers using Epithelial-Mesenchymal Transition (EMT) Antibody Sampler Kit (#9782, Cell Signaling Technology). After confirming the EMT, cells were collected and mitochondria was isolated using Qproteome Mitochondria Isolation Kit (Cat.37612, Qiagen). Mitochondrial RNAs were extracted using the miRNeasy Mini Kit (Cat# 217004, Qiagen). Qualified RNAs were further purified by RNAClean XP Kit (Cat.A63987, Beckman Coulter, CA) and were treated with RNase-Free DNase Set (Cat.79254, QIAGEN, CA). Ribosomal RNA was removed by TruSeq Stranded Total RNA LT-(Ribo-Zero Gold rRNA Removal Kit)-Set A/B (#RS-122-2301/2302, Illumina, CA). RNA transcriptome sequencing (RNA-Seq) was performed to identify mitochondrial RNAs that are associated with EMT.

first: Jiuwei

last: Cui

first: Yijing

last: Zhao


title: Transcriptome of Tribolium castaneum in different climatic conditions

status: Public on Jul 02 2019

city: Zurich

first: Eva

last: Koch

address: Winterthurerstrasse 190

department: IEU

institute: University of Zurich

summary: We combined fitness and whole-transcriptome data of Tribolium castaneum to investigate gene expression and fitness responses to drought, heat and their combination. Fitness was reduced by both stressors and their combined effects were nearly additive. Accordingly, expression data showed that both stressors were acting mostly independently and did not interfere physiologically.  Response to heat stress resulted in a much higher number of differentially expressed genes compared to drought stress. Responses to heat and heat-drought combination were similar.

overall_design: We used the Tribolium castaneum Cro1 strain collected from a wild population in 2010 and adapted to lab standard conditions (33°C, 70% relative humidity) for more than 20 generations. The conditions in the treatments were: Hot: 37°C and 70% r. h., Dry: 33°C and 30% r. h., Hot-Dry: 37°C and 30% r. h.  RNA was extracted from the whole body of reproducing females at the age of eight weeks. mRNA was used for library preparation (using LEXOGEN kit) and single end sequencing was performed on Illumina NextSeq (75 cycles).

middle: L

first: Frédéric

last: Guillaume


title: NYGC ALS Consortium data

status: Public on Sep 20 2019

first: Hemali

last: Phatnani

address: 101 Avenue of the Americas

institute: New York Genome Center

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

Consortium contacts:
Maria Pedersen: mpedersen@nygenome.org
Hemali Phatnani: hphatnani@nygenome.org
NYGC ALS Consortium: cgndhelp@nygenome.org

overall_design:
Refer to individual Series:
GSE116622
GSE124439
GSE153960


title: Genome-wide analysis of placental gene expression in severe preterm preeclampsia

status: Public on Dec 30 2018

city: Detroit

first: Adi

last: Tarca

state: MI

address: 3990 John R. St, 4 Brush South

institute: Wayne State University

summary: Analysis of genome-wide gene expression in placentas from women with preterm severe preeclampsia, with or without HELLP syndrome, compared to gestational age-matched controls. The hypothesis tested in the present study was that placental transcriptomic changes in preeclampsia are considerably different from controls. The results provide important information on placental transcriptomic changes in preeclampsia.

overall_design: Total RNA was obtained from placentas taken from patients in the following groups: 1) preterm preeclampsia  (n=6); 2) preterm preeclampsia with HELLP syndrome (n=6); and 3) preterm controls (n=5).

first: Gaurav

last: Bhatti

first: Katalin

last: Eder

first: Andras

last: Falus

first: Roberto

last: Romero

first: Nandor

middle: G

last: Than

first: Tibor

last: Varkonyi


title: Genome-wide analysis of gene expression in BeWo cells treated with ZNF554 siRNA

summary: Analysis of the effect of ZNF554 knock-down on genome-wide gene expression in BeWo trophoblast-like cells. The hypothesis tested in the present study was that ZNF554 regulates the expression of genes involved in key functions of trophoblastic cells. The results provide important information on the functions of ZNF554 in BeWo trophoblast-like cells.

overall_design: Total RNA was obtained from BeWo cells subjected to either ZNF554 (n=3) or scrambled (n=3) siRNA treatment.

first: Susan

last: Land

first: Yi

last: Xu