title: Material properties of biomolecular condensates regulates RNA splicing and tumorigenesis

city: Charlottesville

first: Bi

last: Shi

state: Virginia

address: 1340 JPA Pinn Hall Room 6017

department: Department of Biochemistry and Molecular Genetics

institute: University of Virginia

summary: It remains largely unclear how material properties of biomolecular condensates impact physiological and pathological processes such as cancer. Here we show that AKAP95, a nuclear protein involved in gene regulation, plays an important role in tumorigenesis through directly regulating mRNA splicing. We show that AKAP95, through an intrinsic disordered region (IDR), forms liquid-like droplets in vitro and dynamic foci in nucleus. We have also identified key residues in IDR whose mutations to different residues perturb AKAP95 condensation in opposite directions. Importantly, the biological activity of AKAP95 in splice regulation is affected by either disruption of liquid condensation or enhancing the gelation of the assembly. We then show that the ability of AKAP95 in overcoming oncogene-induced senescence requires AKAP95 in an appropriate window of liquidity. These results thus link phase separation to tumorigenesis and uncover an important role of regulating the material property of protein condensates in disease including cancer.

overall_design: Gene expression and splicing of MDA-MB-MDA-MB-231 (control, AKAP95-knockdown, -rescued) cells; oncogene Myc-induced MEF (Akap95 heterozygous and knockout) rescued with or without human AKAP95 variants with different phase separation properties were determined by RNA-seq.

first: Wei

last: Li

first: Hao

last: Jiang


title: Expression data from comparison of wild type and cereblon knock out murine T-cells

status: Public on May 06 2020

city: Tampa

first: Matthew

middle: S

last: Beatty

state: FL

address: 12902 USF Magnolia Drive

department: Immunology

country: USA

institute: Moffitt Cancer Center & Research Institute

summary: Thalidomide and other immunomodulatory drugs are effective therapies for certain hematological cancers where they kill tumor cells and stimulate T-cell immunity. These compounds mediate their functions by binding to and altering substrate specificity of cereblon (CRBN), an E3-ubiquitin ligase component of the DDB1/Cul4/Rbx1 complex3-5. Here, we report the results of crbn genetic deficiency in a mouse, which revealed CRBN functions as a suppressor of T-cell receptor (TCR) activation. We used microarrays to analyze the cereblon regulated gene expression changes following activation of wild type or cereblon knock out murine T-cells.

overall_design: Splenic T-cells were isolated from C57BL6 wild type or cereblon knock out mice using negative magnetic bead selection (Pan T cell Kit II, Miltenyi) and grown in complete RPMI-10 media. Purified T-cells were then collected in their naïve, unactivated state or treated with anti-CD3 (5µg/ml plate bound) and anti-CD28 (1µg/ml soluble) for 12 hours. In total, 11 biological samples were divided into four groups based on two genotypes and two activation states: (1) wild type naïve n=3, (2) crbn-/- naïve n=3, (3) wild type activated n=2, (4) crbn-/- activated n=3.

first: Rebecca

last: Hesterberg

first: Ying

last: Han

first: Mario

middle: R

last: Fernandez

first: Afua

middle: A

last: Akuffo

first: William

middle: E

last: Goodheart

first: Chunying

last: Yang

first: Christelle

last: Colin

first: Aileen

middle: Y

last: Alontaga

first: Jessica

last: McDaniel

first: Adam

middle: W

last: Mailloux

first: Julia

last: Billington

first: Lanzhu

last: Yue

first: Shonagh

last: Russell

first: Robert

middle: J

last: Gillies

first: Sang

last: Yun

first: Muhammad

last: Ayaz

first: Nicholas

last: Lawrence

first: Harshani

first: Xue-Zhong

last: Yu

first: Jianing

last: Fu

first: Lancia

middle: N

last: Darville

first: John

middle: M

last: Koomen

first: Xiubao

last: Ren

first: Jane

last: Messina

first: Kun

first: Timothy

last: Garrett

first: Anjali

last: Rajadhyasha

middle: L

last: Cleveland

first: Pearlie

middle: K

last: Epling-Burnette


title: Developmental Alterations in the Transcriptome of Three Distinct Rodent Models of Schizophrenia

status: Public on May 05 2020

city: San Antonio

first: Daniel

last: Lodge

state: Bexar

address: 7703 Floyd Curl Drive

department: Pharmacology

institute: UNIVERSITY OF TEXAS HLTH SCI CTR SAN ANTONIO

type: Expression profiling by high throughput sequencing

summary: Schizophrenia is a debilitating disorder affecting just under 1% of the population. While the symptoms of this disorder do not appear until late adolescence, pathological alterations likely occur earlier, during development in utero. While there is an increasing literature examining transcriptome alterations in patients, it is not possible to examine the changes in gene expression that occur during development in humans that will develop schizophrenia. Here we utilize three distinct rodent developmental disruption models of schizophrenia to examine potential overlapping alterations in the transcriptome, with a specific focus on markers of interneuron development. Specifically, we administered either methylazoxymethanol acetate (MAM), Polyinosinic:polycytidylic acid (Poly I:C), or chronic protein malnutrition,  on GD 17 and examined mRNA expression in the developing hippocampus of the offspring 18 hours later. Here, we report alterations in gene expression that may contribute to the pathophysiology of schizophrenia, including significant alterations in interneuron development and ribosome function.

overall_design: Timed pregnant female Sprague-Dawley rats were obtained from Envigo on gestational day 11. Either polyinosine:cytosine (Poly I:C, 7.5 mg/kg, i.p), methylazoxymethanol acetate (MAM: 22mg/kg, i.p.) or saline were administered on gestational day 17. For maternal protein malnutrition, pregnant rats had access to a low protein diet ad libitum (Envigo: TD.90016) containing 6.1% protein, 75.6% carbohydrate and 5.5% fat (3.8Kcal/g) from GD11-GD18. Control rats were fed an isocaloric diet of 20.3% protein, 61.6% carbohydrate and 5.5% fat (3.8Kcal/g: Envigo: TD.91352) from GD11-GD18.  Experiments included three pups from multiple (two) litters for a total of 6 pups per group.

first: Jennifer

last: Donegan

first: Angela

last: Boley

first: Jeremy

middle: P

last: Glenn

first: Melanie

last: Carless


title: RNA  sequencing analysis of HHV-6A-infected T cells

city: Nanjing

first: zhisheng

last: wu

address: Immunology

country: China

institute: Nanjing medical university

summary: To determine if HHV-6A infection affects cell metabolism of host cells, we conducted a global RNA sequencing analysis in HHV-6A infected cells

overall_design: Mock-infected and HHV-6A-infected HSB-2 cells were cultured for 72 h. Total RNA was extracted using TRIzol reagent (Invitrogen, USA) following the manufacturer’s instructions. A total amount of 3 μg of RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) following the manufacturer’s recommendations. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2500 platform by CapitalBio Technology. Differentially expressed genes were identified by fold-change screening. Gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed to systematically identify differentially expressed genes and the pathways associated with HHV-6A infection.

first: Zhisheng

last: Wu

first: Lingyun

last: Li

first: Huamin

last: Tang


title: Distinct functions of tissue-resident and circulating memory Th2 cells in allergic airway disease

city: BOSTON

first: ROD

last: (MD

state: MA- MASSACHUSETTS

address: 55 FRUIT ST., BULFINCH-148

department: Medicine

institute: MASSACHUSETTS GENERAL HOSPITAL

summary: We report RNA-seq data from distinct memory CD4+ T cell subsets in a murine model of allergic asthma.

overall_design: We sensitized and challenged C57BL/6 mice with intranasal house dust mite extract to generate memory CD4+ T helper type 2 (Th2) cells. We used fluorescence-activated cell sorting to isolate memory Th2 cells, based on the expression of the canonical Th2 cell surface marker ST2, and control memory Th cells (ST2-). We sorted ST2+ and ST2- Th cells from the lung parenchyma and secondary lymphoid organs (SLO) followed by RNA isolation, cDNA synthesis, and sequencing to generate approximately 30 million of 50 bp reads per sample. We performed differential gene expression analysis based on the cuttoff of 2-fold change in expression and a false discovery rate below 0.05.

first: Rod

last: Rahimi

first: Andrew

last: Luster


title: Cas12a base editors induce efficient and specific editing with low DNA damage response

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

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: Cas12a base editors induce efficient and specific editing with low DNA damage response (DNA targeted sequencing)

summary: The advent of base editors (BEs) holds a promising potential in correcting pathogenic-related point mutations to treat relevant diseases. Unexpectedly, Cas9 nickase (nCas9) derived BEs lead to DNA double-strand breaks, which can trigger unwanted cellular responses including a p53-mediated DNA damage response (DDR). Here, we showed that catalytically-dead-Cas12a (dCas12a) conjugated BEs induced no DNA break and minimally activated DDR proteins including H2AX, ATM, ATR and p53. We further developed a BEACON (Base Editing induced by human APOBEC3A and Cas12a without DNA break) system that fuses dCas12a to the engineered APOBEC3A with enhanced deamination efficiency and editing specificity. By using BEACON, efficient C-to-T editing was achieved at levels comparable to AncBE4max and only low levels of DDR and RNA off-target (OT) effects were triggered in mammalian cells. BEACON also induced in vivo base editing in mouse embryos and targeted C-to-T conversions were detected in F0 mice.

overall_design: Examination of indels and base substitutions induced by the Cas12a base editors

first: Jia

last: Chen

first: Zhen

last: Liu

first: Bei

first: Yi-Chun

last: Xiong

first: Xiao

last: Wang


title: Neuroligin 3 Splice Isoforms Shape Mouse Hippocampal Inhibitory Synaptic Function

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

summary: Synapse formation is a dynamic process essential for neuronal circuit development and maturation. At the synaptic cleft, trans-synaptic protein-protein interactions constitute major biological determinants of proper synapse efficacy. The balance of excitatory and inhibitory synaptic transmission (E-I balance) stabilizes synaptic activity and its dysregulation has been implicated in neurodevelopmental disorders including autism spectrum disorders. However, the molecular mechanisms underlying E-I balance remains to be elucidated. Here, we investigate Neuroligin (Nlgn) genes which encode a family of postsynaptic adhesion molecules that shape excitatory and inhibitory synaptic function. We identified that NLGN3 protein differentially regulates inhibitory synaptic transmission in a splice isoform-dependent manner in hippocampal CA1 synapses. Distinct subcellular localization patterns of NLGN3 isoforms contribute to the functional differences observed among splice variants. Finally, our single-cell sequencing analysis reveals that Nlgn1 and Nlgn3 are the major Nlgn genes and that Nlgn splice isoforms are highly diverse in CA1 pyramidal neurons.

overall_design: The cytosol of single cell CA1 neuron was harvested using the whole cell patch-clamp technique

first: Motokazu

last: Uchigashima

first: Ming

last: Leung

first: Takuya

last: Watanabe

first: Amy

last: Cheung

first: Masahiko

first: Kensuke

last: Futai


title: Cas12a base editors induce efficient and specific editing with low DNA damage response (RNA sequencing)

overall_design: Examination of RNA off-targets induced by the Cas12a base editors


title: RIC-seq for global in situ profiling of RNA-RNA spatial interactions

status: Public on May 04 2020

city: Beijing

first: Yuanchao

last: Xue

address: Datun Road #15

department: Institute of Biophysics

institute: Chinese Academy of Sciences

summary: Highly structured RNA molecules usually interact with each other, and associate with various RNA-binding proteins, to regulate critical biological processes. However, RNA structures and interactions in intact cells remain largely unknown. Here, by coupling proximity ligation mediated by RNA-binding proteins with deep sequencing, we report an RNA in situ conformation sequencing (RIC-seq) technology for the global profiling of intra- and intermolecular RNA–RNA interactions. This technique not only recapitulates known RNA secondary structures and tertiary interactions, but also facilitates the generation of three-dimensional (3D) interaction maps of RNA in human cells. Using these maps, we identify noncoding RNA targets globally, and discern RNA topological domains and trans-interacting hubs. We reveal that the functional connectivity of enhancers and promoters can be assigned using their pairwise-interacting RNAs. Furthermore, we show that CCAT1-5L—a super-enhancer hub RNA—interacts with RNA-binding protein hnRNPK, as well as RNA derived from the MYC promoter and enhancer, to boost MYC transcription by modulating chromatin looping. Our study demonstrates the power and applicability of RIC-seq in discovering the 3D structures, interactions and regulatory roles of RNA.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: We first developed an RNA in situ conformation sequencing technology, named RIC-seq, for global mapping RNA-RNA interactions in HeLa cells. Two biological replicates were generated for rRNA+ and rRNA- samples. To figure out the cell-to-cell random ligation rate, we mixed HeLa cells and Drosophila cells and then created a RIC-seq library for sequencing. As we found that super-enhancer lncRNA CCAT1-5L interacted with RNA-binding protein hnRNPK to regulate MYC transcription, so we further performed CLIP-seq to map hnRNPK binding sites globally. Both monomeric and dimeric hnRNPK-associated RNAs were recovered and converted into libraries for sequencing.

first: Zhaokui

last: Cai

first: Changchang

last: Cao

first: Lei

last: Ji


title: Deep phenotyping by mass cytometry and single cell RNA-sequencing reveals LYN regulated signaling profiles underlying monocyte subset heterogeneity and lifespan

city: Vancouver

first: Ken

last: Harder

state: BC

address: 2350 Health Sciences Mall

department: Microbiology & Immunology

country: Canada

institute: University of British Columbia

summary:
Rationale: Monocytes are key effectors of the mononuclear phagocyte system (MPS), playing critical roles in regulating tissue homeostasis and coordinating inflammatory reactions, including those involved in chronic inflammatory diseases such as atherosclerosis. Monocytes have traditionally been divided into two major subsets termed conventional (cMo) and patrolling (pMo) monocytes but recent systems immunology approaches have identified marked heterogeneity within these cells, and much of what regulates monocyte population homeostasis remains unknown. We and others have previously identified LYN tyrosine kinase as a key negative regulator of myeloid cell biology, however LYN’s role in regulating specific monocyte subset homeostasis has not been investigated.
Objective: We sought to comprehensively profile monocytes in order to elucidate the underlying heterogeneity within monocytes and dissect how Lyn deficiency affects monocyte subset composition, signaling, and gene expression. We further tested the biological significance of these findings in a model of atherosclerosis.
Methods and Results: CyTOF analysis of monocyte subsets and signaling pathway activation patterns in cMos and pMos revealed distinct baseline signaling profiles and far greater heterogeneity than previously described. Lyn deficiency led to a selective expansion of pMos and alterations in specific signaling pathways within these cells, revealing a critical role for LYN in pMo physiology. LYN’s role in regulating pMos was cell-intrinsic and correlated with an increased circulating half-life of Lyn-deficient pMos. Furthermore, single cell RNA sequencing revealed marked perturbations in the gene expression profiles of Lyn-/- monocytes with upregulation of genes involved in pMo development, survival, and function. Lyn deficiency also led to a significant increase in aorta-associated pMos and protected Ldlr-/- mice from high-fat diet induced atherosclerosis.
Conclusions: Together our data identify LYN as a key regulator of pMo development and a potential therapeutic target in inflammatory diseases regulated by pMos.

overall_design: 10X Genomics based single cell RNA-sequencing of Lyn+/+ and Lyn-/- leukocytes

first: Maunish

last: Barvalia

first: Kenneth


title: Hyperuricemia Predisposes to the Onset of Diabetes

city: Qingdao

first: Jie

last: Lu

address: 16 Jiangsu Rd

institute: Qingdao University

summary: To further examine the mechanisms of urate in islet β-cell death, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish primacy of streptozotocin (STZ) vs. urate. Islets were isolated from Uox-KO and WT mice with and without multiple low-dose STZ. Differentially expressed genes (DEGs) in islets of the hyperuricemic and/or diabetic mice in comparison to their respective controls represented specific Gene Ontology (GO) pathways and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional meanings.

overall_design: Diabetic mice models were intraperitoneally injected with multiple low-dose STZ at a dose of 40 mg/kg body weight daily, for 5 consecutive days. Hyperuricemic mice and their counterparts were also included.Four groups (KO, WT, STZ-KO and STZ-WT) were designed with three replications in each.

first: Changgui

last: Li


title: circRNA expression in METTL3 and YTHDC1 KNOCK-DOWN conditions

city: Rome

first: Gaia

last: Di Timoteo

state: RM

address: piazza Aldo Moro 5

country: Italy

institute: University of Rome "La Sapienza"

type: Non-coding RNA profiling by high throughput sequencing

summary: Through an siRNA based approach, we investigated the effect of the knock-down of METTL3 and YTHDC1 on circRNAs expression in HeLa cells

overall_design: Total RNA from HeLa cells treated either with siRNA against METTL3 (two biological replicates) and control siRNA (one biological replicate), together with total RNA from HeLa cells treated with a siRNA against YTHDC1 (two biological replicates) and control siRNA (two biological replicates), was analyzed using Illumina Novaseq6000.

first: Dario

last: Dattilo

first: Marco

last: Guarnacci

first: Alessio

last: Colantoni

first: Alvaro

last: Centrón-Broco

first: Francesca

last: Rossi

first: Mariangela

last: Morlando

first: Irene

last: Bozzoni


title: Integrated single-cell and bulk gene expression and ATAC-seq reveals heterogeneity and early changes in pathways associated with resistance to cetuximab in HNSCC-sensitive cell lines

city: Baltimore

first: Elana

middle: Judith

last: Fertig

state: MD

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

summary:
Background: Identifying potential resistance mechanisms while tumour cells still respond to therapy is critical to delay acquired resistance.

Methods: We generated the first comprehensive multi-omics, bulk and single-cell data in sensitive head and neck squamous cell carcinoma (HNSCC) cells to identify immediate responses to cetuximab. Two pathways potentially associated with resistance were focus of the study: regulation of receptor tyrosine kinases by TFAP2A transcription factor, and epithelial-to-mesenchymal transition (EMT).

Results: Single-cell RNA-seq demonstrates heterogeneity, with cell-specific TFAP2A and VIM expression profiles in response to treatment and also with global changes to various signalling pathways. RNA-seq and ATAC-seq reveal global changes within 5 days of therapy, suggesting early onset of mechanisms of resistance; and corroborates cell line heterogeneity, with different TFAP2A targets or EMT markers affected by therapy. Lack of TFAP2A expression is associated with HNSCC decreased growth, with cetuximab and JQ1 increasing the inhibitory effect. Regarding the EMT process, short-term cetuximab therapy has the strongest effect on inhibiting migration. TFAP2A silencing does not affect cell migration, supporting an independent role for both mechanisms in resistance.

Conclusion: Overall, we show that immediate adaptive transcriptional and epigenetic changes induced by cetuximab are heterogeneous and cell type dependent; and independent mechanisms of resistance arise while tumour cells are still sensitive to therapy.

overall_design: Time course RNA-seq data for 3 head and neck squamous cell caricionma cell lines treated with cetuximab (100nM) and PBS controls.

first: Luciane

middle: T

last: Kagohara


title: N6-methyladenosine (m6A) profiling in 60 YRI LCLs

city: CHICAGO

first: Zijie

last: Zhang

state: IL

department: Chemistry

institute: University of Chicago

summary: N6-methyladenosine (m6A), the most abundant messenger RNA (mRNA) modification, has emerged as a critical post-transcriptional mechanism that regulates various aspect of mRNA metabolism including pre-mRNA processing, mRNA export, mRNA stability and translation efficiency. However the genetics basis of m6A is largely unexplored. In this work, we mapped m6A-QTLs in 60 LCLs and used the resulting tens of thousands of QTLs to provide insights to m6A biology and its contribution to human complex trait.

overall_design: We sequenced the m6A (using MeRIP-seq) in LCLs derived from 60 YRI individuals that have genotype as well as many other molecular traits data analyzed before. Briefly, LCLs were purchased from the Coriell Institute and cultured following the standard instruction. Cells were harvest at 0.7 – 1 million/ml density and total RNA were extracted using Trizol.  Poly-T beads were used to further purify the mRNA followed by m6A immunoprecipitation and sequencing.  Each LCL was split into two technical replicates upon receipt of the cells. The two replicates were processed independently thereafter and each sequenced at 30 million reads. The sequencing data of technical replicates were pooled at reads alignment.

first: Xin

last: He

first: Chuan


title: RNA-seq of CD4+ T cell subsets in LCMV infection

status: Public on May 03 2020

city: La Jolla

first: Jinyong

last: Choi

address: 9420 Athena Circle

department: Center for Infectious Disease and Vaccine Research

institute: La Jolla Institute for Immunology

summary: T follicular helper (TFH) cells are a distinct type of CD4 T cells that are essential for most antibody and B lymphocyte responses. TFH regulation and dysregulation is involved in a range of diseases. Bcl6 is the lineage defining transcription factor of TFH cells and its activity is essential for TFH cell differentiation and function. However, how Bcl6 controls TFH biology has largely remained unclear, at least in part due to intrinsic challenges of connecting repressors to gene upregulation in complex cell types with multiple possible differentiation fates. Multiple competing models were tested here by a series of experimental approaches to determine that Bcl6 exhibits negative autoregulation and controls pleiotropic attributes of TFH differentiation and function (migration, costimulation, inhibitory receptors, and cytokines) via multiple repressor-of-repressor gene circuits.

overall_design: 7 samples, 3 replicates each, naïve or Day 7 LCMV infection, SMARTA CD4 T cell subsets

first: Shane

last: Crotty


title: Characterization of resistance to prexasertib in ovarian cancer cell line OVCAR5

status: Public on May 02 2020

city: Bethesda

first: Jayakumar

last: Nair

address: 10 center drive

department: Women malignancies Branch

institute: National Cancer Institute

summary: We developed a CHK1 inhibitor Prexasertib resistant strain of ovarian cancer cell line OVCAR5 in lab. This was used to compare transcriptome profiles to study changes in expression profiles of genes that might be involved with resistance.  Total RNA was isolated from three replicate cultures of OVCAR5R (IC50 viability >3 micromolar Prexasertib) and 3 replicate cultures of parental OVCAR5 (IC50 viability=7.5nM) and then subjected to Hiseq4000 illumina RNA-seq analysis, with paired end sequencing. Data file contains CPM-TMM values after zoom normalization.

overall_design: Transcriptome analysis of OVCAR5 and its Prexasertib resistant variant OVCAR5R

first: Jung-Min

last: Lee


title: Effect of prexasertib on disease progression and survival in High grade serous ovarian cancer patients

summary: The goal of this study was to compare transcription profiles of high grade serous ovarian cancer (HGSOC) patients at Day 0 and Day 15 of a single course Prexasertib treatment at 105mg/m2 intravenously over 1 hour.  HGSOC patients recruited for this study were women aged 18 and older with most (79%) showing platinum resistant or refractory disease. Total RNA from patients before (Day 0, n=18) and 2 weeks after Prexasertib treatment (Day15, n=11) were prepared from frozen biopsies, and analysed using HiSeq4000 using Illumina TruSeq Stranded Total RNA Library Prep and paired-end sequencing.  Data is shown as quartile normalized CPM-TMM values. Patient survival and response was monitored till end of study.  Our study show that prexasertib has clinical benefit in HGSOC patients.

overall_design: Transcriptome analysis of HGSOC patients before and after a 2 week treatment with Prexasertib


title: Structural interaction between DISC1 and ATF4 underlying transcriptional and synaptic dysregulation in an iPSC model of mental disorders

city: Philadelphia

first: Yijing

last: Su

address: Levy 326

department: Department of Oral Medicine

institute: University of Pennsylvania

summary: Analysis of gene expression alteration in iPSC-derived cortical neurons with ATF4 overexpression

overall_design: Total RNA obtained from 4-week-old forebrain neurons derived from C3 and C3 with ATF4 over-expression.

first: Xinyuan

last: Wang

first: Hongjun

last: Song

first: Mingjie

first: Guo-li

last: Ming


title: NAD+ controls circadian reprogramming through PER2 nuclear translocation to counter aging

city: San Francisco

first: Louis

last: Ptacek

state: CA

institute: University of California San Francisco

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Disrupted sleep-wake and molecular circadian rhythms are a feature of aging associated with metabolic disease and reduced levels of NAD+, yet whether changes in nucleotide metabolism control circadian behavioral and genomic rhythms remains unknown. Here we reveal that supplementation with the NAD+ precursor nicotinamide riboside (NR) markedly reprograms metabolic and stress-response pathways that decline with aging through inhibition of the clock repressor PER2. NR enhances BMAL1 chromatin binding genome-wide through PER2K680 deacetylation, which in turn primes PER2 phosphorylation within a domain that controls nuclear transport and stability and which is mutated in human advanced sleep phase syndrome. In old mice, dampened BMAL1 chromatin binding, transcriptional oscillations, mitochondrial respiration rhythms, and late evening activity are restored by NAD+ repletion to youthful levels with NR. These results reveal effects of NAD+ on metabolism and the circadian system with aging through the spatiotemporal control of the molecular clock.

overall_design: 199 libraries were generated in this study. They include ChIP-Seq, RNA-Seq, and ATAC-seq experiments to determine the effect of NAD+ on SIRT1, BMAL1, HSF1, H3K9Ac, and H3K27Ac during aging. Replicates are indicated in the final position of the title of each library. Inputs for ChIP-Seq experiments consist of equimolar pools of replicates within each group.

first: Daniel

middle: C

last: Levine

first: Heekyung

last: Hong

first: Benjamin

last: Weidemann

first: Kathryn

last: Ramsey

first: Alison

middle: H

last: Affinati

first: Mark

last: Schmidt

first: Jonathan

last: Cedernaes

first: Chiaki

last: Omura

first: Rosemary

last: Braun

first: Choogon

first: Charles

last: Brenner

first: Clara

middle: B

last: Peek

first: Joseph

last: Bass


title: Mutations in FAM50A suggest that Armfield XLID syndrome is a spliceosomopathy (zebrafish)

city: Chicago

first: Erica

last: Davis

address: 225 E Chicago Avenue

department: Advanced Center for Translational and Genetic Medicine (ACT-GeM)

institute: Ann & Robert H Lurie Children's Hospital of Chicago

summary: Intellectual disability (ID) is a heterogeneous clinical entity and includes an excess of males who harbor variants on the X-chromosome (XLID). We report rare FAM50A missense variants in the original Armfield XLID syndrome family localized in Xq28 and four additional unrelated males with overlapping features. Our fam50a knockout (KO) zebrafish model exhibits abnormal neurogenesis and craniofacial patterning, and in vivo complementation assays indicate that the patient-derived variants are hypomorphic. RNA sequencing analysis from fam50a KO zebrafish show dysregulation of the transcriptome, with augmented spliceosome mRNAs and depletion of transcripts involved in neurodevelopment. Zebrafish RNA-seq datasets show a preponderance of 3’ alternative splicing events in fam50a KO, suggesting a role in the spliceosome C complex. These data are supported with transcriptomic signatures from cell lines derived from affected individuals and FAM50A protein-protein interaction data. In sum, Armfield XLID syndrome is a spliceosomopathy associated with aberrant mRNA processing during development.

overall_design: To investigate the impact of fam50a dysfunction in an in vivo neurodevelopmental context, we performed transcriptomics studies using RNA isolated from heads of fam50a CRISPR KO and wild type zebrafish larvae at 2 dpf (five biological replicates each)

last: Schwartz


title: RNA-seq of CD4+ T cell subsets in KLH-gp61 immunization

first: Jinyong

last: Choi

overall_design: 7 samples, 4 replicates each, naïve or Day 8 KLH-gp61 immunization, SMARTA CD4 T cell subsets

first: Shane

last: Crotty


title: CD4+ T cell subsets in LCMV infection and KLH-gp61 immunization

overall_design: Refer to individual Series


title: ATAC-seq of CD4+ T cell subsets in LCMV infection

first: Huitian

last: Diao

first: Bingfei

last: Yu


title: Genome-wide 5-hydroxymethylcytosine (5hmC) emerges at early stage of in vitro hepatocyte differentiation [Methylation]

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

type: Methylation profiling by genome tiling array

summary: How cells reach different fates despite using the same DNA template, is a basic question linked to differential patterns of gene expression. Since 5-hydroxymethylcytosine (5hmC) emerged as an intermediate metabolite in active DNA demethylation, there have been increasing efforts to elucidate its function as a stable modification of the genome. Recently we described TET1-mediated enrichment of 5hmC on the promoter region of the master regulator of hepatocyte identity, HNF4A, which precedes differentiation of liver adult progenitor cells in vitro. Here we asked whether 5hmC is involved in hepatocyte differentiation.  We found a genome-wide increase of 5hmC as well as a reduction of 5-methylcytosine at early hepatocyte differentiation, a time when the liver transcript program is already established. Furthermore, we suggest that modifying s-adenosylmethionine (SAM) levels through an adenosine derivative could decrease 5hmC enrichment, triggering an impaired acquisition of hepatic identity markers. These results suggest that 5hmC is a regulator of differentiation as well as an imprint related with cell identity. Furthermore, 5hmC modulation could be a useful biomarker in conditions associated with cell de-differentiation such as liver malignancies.

overall_design: Bisulfite and oxidative bisulfite converted DNA from 16 samples were hybridised to the Illumina Infinium EPIC Human Methylation Beadchip

first: Jesus

last: Rodriguez-Aguilera


title: Mutations in FAM50A suggest that Armfield XLID syndrome is a spliceosomopathy (human)

overall_design: To investigate the impact of FAM50A mutations on the transciptome, we performed RNAseq studies using RNA isolated from transformed lymphocyte cells derived from FAM50A patients (K9648, p.Trp206Gly and K9656, p.Glu254Gly) and a healthy control male of northern European origin (three biological replicates in each condition)


title: Failed apoptosis enhances melanoma cancer cells aggressiveness

summary: Recent evidence shows that partial mitochondrial permeabilization and non-lethal caspase activation occur under certain circumstances, though it remains unclear how failed apoptosis impacts established cancers. Using a cancer cell model to trigger non-lethal caspase activation based on either BH3-only protein expression or chemotherapy treatment, we found that melanoma cancer cells failing to undergo complete apoptosis have a particular transcriptomic signature associated with focal adhesions, transendothelial migration and modifications of actin cytoskeleton.

overall_design: To assess the effects of failed apoptosis, we used a BiFC-based (bi-molecular fluorescence complementation) caspase reporter assay  expressed via lentiviral transduction into human melanoma cell lines with different metastatic potentials. We then added a doxycycline-inducible system controlling the expression of the pro-apoptotic truncated BID (tBID) protein, capable of activating BAX and thus inducing rapid MOMP and cell death. Caspase positive (VC3AI+ve/DAPI-ve/AnnexinV-ve) and negative ( VC3AI-ve/DAPI-ve/AnnexinV-ve cells) cells were sorted for gene expression analysis.

first: Gabriel

last: Ichim


title: Genome-wide 5-hydroxymethylcytosine (5hmC) emerges at early stage of in vitro hepatocyte differentiation

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


title: Genome-wide High Resolution Mapping of Mitotic DNA Synthesis Sites and Common Fragile Sites by Direct Sequencing [WGS]

status: Public on May 01 2020

city: Hangzhou

first: Fang

last: Ji

state: Zhejiang

address: Zijingang campus of Zhejiang University, No.866 of Yuhangtang Road

institute: Zhejiang University

summary: Common fragile sites (CFSs) are genomic loci prone to the formation of breaks or gaps on metaphase chromosomes.  Here, we seek to map human CFSs with high resolution on a genome-wide scale by sequencing the sites of mitotic DNA synthesis (MiDASeq) that are specific for CFSs. We generated a nucleotide-resolution atlas of MiDAS sites (MDSs) that covered most of know CFSs, and comprehensively analyzed their sequence characteristics and genomic features.

overall_design: Whole genome sequencing  of U2OS cells subjected to Aphidicolin(0.3uM) treatment for 18 h

first: Hongwei

last: Liao

first: Sheng

last: Pan


title: Genome-wide 5-hydroxymethylcytosine (5hmC) emerges at early stage of in vitro hepatocyte differentiation [Expression]

overall_design: Total RNA obtained from HepaRG human liver cancer cell lines after 7 days of differentiation and exposure to the adenosine derivative IFC-305.

first: Szilvia

last: Ecsedi


title: Genome-wide High Resolution Mapping of Mitotic DNA Synthesis Sites and Common Fragile Sites by Direct Sequencing


title: Genome-wide High Resolution Mapping of Mitotic DNA Synthesis Sites and Common Fragile Sites by Direct Sequencing [RNA-seq]

overall_design: RNA sequencing of U2OS cells subjected to Aphidicolin(0.3uM) treatment for 18 h


title: Genome-wide High Resolution Mapping of Mitotic DNA Synthesis Sites and Common Fragile Sites by Direct Sequencing [MiDA-seq]

overall_design: Sequencing the sites of mitotic DNA synthesis (MiDASeq) that are specific for CFSs in three cell lines.


title: Characterization of the immune profile of oral tongue squamous cell carcinomas with advancing disease

city: Shatin

first: Katie

last: Meehan

state: Northern Territories

address: Rooms 84026 - 31, 6th Floor, Lui Che Woo Clinical Sciences Building

country: Hong Kong

institute: Chinese University of Hong Kong

summary: We investigated whether a unique immune response was instigated with the development of oral tongue squamous cell carcinomas (OTSCC), with/without nodal involvement, with/without recurrent metastatic disease, or within tumor involved nodes. 110 FFPE samples were collected from a retrospective cohort of 67 OTSCC patients and 10 non-cancerous tongue samples. Targets including CD4, CD8, FOXP3, PD-L1 and PD-1 were analyzed by immunohistochemistry. The Nanostring PanCancer Immune Profiling Panel was used for gene expression profiling. Data were externally validated in the TCGA head and neck (HNSCC), melanoma and lung squamous cell carcinoma (LSCC) cohorts. A 24-immune gene signature was identified that discriminated more aggressive OTSCC cases, and although not prognostic in HNSCC was associated with survival in other TCGA cohorts (improved survival for melanoma, p<0.001 and worse survival for LSCC, p=0.038). OTSCC exhibited concordant gene and IHC features characterized by a TH-2 biased, pro-inflammatory profile with upregulated B cell and neutrophil gene activity and increased CD4, FOXP3 and PD-L1 expression (p<0.001 for all by IHC). Compared to less advanced disease, nodal involvement and recurrent OTSCC did not induce a different immune response although recurrent disease was characterized by significantly higher PD-L1 expression (p=0.004 by SP263, p=0.013 by 22C3, p=0.004 for gene expression). Identification of a gene signature associated with different prognostic effects in other cancers highlights common pathways of immune dysregulation that are impacted by the tumor origin. The significant immunosuppressive signaling in OTSCC indicates primary failure of immune system to control carcinogenesis emphasizing the need for early, combination therapeutic approaches.

overall_design: This retrospective, cohort study included up to 40 OTSCC cases and 6 non-cancer controls. The OTSCC cases included cases without nodal involvement, cases with nodal involvement and cases with recurrent metastatic disease.

first: Annette

last: Lim


title: Whole genome sequencing of two Holstein cattle

city: Beltsville

first: George

middle: E.

last: Liu

state: Maryland (MD)

address: 10300 Baltimore Ave Bldg 306

institute: USDA-ARS

type: Genome variation profiling by high throughput sequencing

summary: In this study, we generated whole genome sequencing data from two Holstein cows using Lung tissue.

overall_design: The lung DNA samples of the two Holstein cows were sequenced using the Illumina NextSeq550 platform, with the Nextera library preparation and sequence generation according to the manufacturer's protocols. NGSQCToolkit v2.3.3 was used to trimmed adapter sequences and low quality reads. All the clean reads were mapped on the reference genome (ARS-UCD1.2) using BWA v0.7.12 software. We only used the reliable mapped reads for SNP calling. The SNP positions within the aligned reads compared to the reference genome were detected using the pileup function in SAMtools v.1.7 utilities. SNPs were predicted with a minimum mapping quality (-Q) of 20 and with the minimum and maximum read depths of 3 and 100, respectively.

first: Yang

last: Zhou

first: Shuli


title: GlioM&M: Web-based tool for studying circulating and infiltrating monocytes and macrophages in glioma

city: Charlestown

first: Erik

last: Abels

state: Massachusetts

address: 149 13th Street

department: Neurology

institute: Massachusetts General Hospital

summary:
Monocytes, macrophages and microglia make up a large part of the glioma environment and have an important role in maintaining and propagating glioma progression. Targeting these cells to inhibit their tumor promoting effect and reprogramming them into an anti-tumor phenotype has been one of the focal points of glioma therapy. In this study we have analyzed the transcriptomes of 8 different monocyte subgroups derived from the brain and the blood of glioma bearing mice. This includes the immune expression profile of blood-derived monocytes versus tumor infiltrating monocytes identifying increased expression of both pro- and anti-inflammatory pathways in tumor infiltrating monocytes. To identify new markers and targets for therapy in these different cell populations, we created a user-friendly web-based tool accessible at www.glioma-monocytes.com (temporary password 'MM2MM2'). In addition, this tool can be used for validation purposes and to elucidate gene expression profiles of tumor interacting-monocytes and macrophages as well as blood-derived circulating monocytes.
Analysis of the transcriptomal profile of monocyte in a glioma mouse model
Result: Infiltrating monocytes and macrophages express a high level of activation as compared to blood monocytes

overall_design: mRNA expression of monocytes isolated from tumor-bearing brain were analyzed by RNAseq, using Illumina Nextseq.

middle: R

first: Sybren

last: Maas

first: Eric

last: Tai

first: David

last: Ting

first: Xandra

middle: O

last: Breakefield

first: Marike

last: Broekman

first: Joseph

last: Khoury


title: PD-1 blockade-unresponsive human tumor-infiltrating CD8+ T cells are marked by loss of CD28 expression and rescued by IL-15

city: Seoul

first: Kyung Hwan

last: Kim

address: 50-1 Yonsei-ro

country: South Korea

institute: Yonsei University College of Medicine

summary: Blockade of programmed death-1 (PD-1) reinvigorates exhausted CD8+ T cells, resulting in tumor regression in cancer patients. Recently, reinvigoration of exhausted CD8+ T cells following PD-1 blockade was shown to be CD28-dependent in mouse models. Herein, we examined the role of CD28 in anti-PD-1-induced human T-cell reinvigoration using tumor-infiltrating CD8+ T cells (CD8+ TILs) obtained from non-small cell lung cancer patients. Single cell analysis demonstrated a distinct expression pattern of CD28 between mouse and human CD8+ TILs. Furthermore, we found that human CD28+CD8+, but not CD28–CD8+ TILs, responded to PD-1 blockade irrespective of B7/CD28 blockade, indicating that CD28 co-stimulation in human CD8+ TILs is dispensable for PD-1 blockade-induced reinvigoration, and loss of CD28 expression rather serve as a marker of anti-PD-1-unresponsive CD8+ TILs. Transcriptionally and phenotypically, PD-1 blockade-unresponsive human CD28–PD-1+CD8+ TILs exhibited characteristics of terminally exhausted CD8+ T cells with low TCF1 expression. Notably, CD28–PD-1+CD8+ TILs had preserved machinery to respond to IL-15, and IL-15 treatment enhanced proliferation of CD28–PD-1+CD8+ TILs as well as CD28+PD-1+CD8+ TILs. Taken together, we demonstrate loss of CD28 expression as a marker of PD-1 blockade-unresponsive human CD8+ TILs with TCF1– signature and provide mechanistic insights into combining IL-15 with anti-PD-1.

overall_design: CD28-PD-1+ vs CD28+PD-1+CD8+ TILs

first: Eui-Cheol

last: Shin

first: Kyung


title: Diphthamide modification of eEF2 is required for gut tumor-like hyperplasia induced by oncogenic Ras

city: Bunkyo-ku, Tokyo

first: Miura

last: Masayuki

address: 7-3-1 Hongo

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: The University of Tokyo

summary: Eukaryotic elongation factor 2 (eEF2) undergoes a unique post-translational modification called diphthamidation. Although eEF2 diphthamidation is highly conserved, its pathophysiological function is still largely unknown. To elucidate the function of diphthamidation in tumor, we examined the involvement of diphthamidation pathway enzyme Dph5 in tumor progression in Drosophila adult gut. Expression of oncogenic RasV12 in gut intestinal stem cells (ISCs) and enteroblasts (EBs) causes hypertrophy and disruption of gut epithelia, and shortened lifespan. Knockdown of dph5 ameliorated these pathogenic phenotypes. Dph5 is required for gross translation activation and high dMyc protein level in RasV12 tumor-like hyperplasia. Transcriptome analysis revealed that Dph5 is involved in the regulation of ribosome biogenesis genes. These results suggest that diphthamidation is required for translation activation partly through the regulation of ribosome biogenesis in Ras-induced tumor-like hyperplasia model in Drosophila gut.

overall_design: Total RNA was extracted from the whole gut of each mutant adult flies (15 guts/sample) .N = 4 for each group.

first: Kayoko

last: Sakurai

first: Masaki

last: Kimura

first: Masayuki

last: Miura


title: Escherichia coli exposed to biocides (antiseptics and disinfectants)

city: Davis

first: Ilias

last: Tagkopoulos

address: 451 Health Science Dr.

institute: UC Davis

summary: We compared the exposure of E. coli MG1655 to ten commonly used antiseptics and disinfectants for short (30min) and long (7-12h) term, looking for common and unique stress response elements.

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

overall_design: E. coli MG1655 was exposed to one out of ten biocides (antiseptics and disinfectants) for long (7-12h) term, in triplicate. Controls for this group (no exposure) are also in triplicate. In addition, E.coli was exposed to one out of three biocides for short term (30min). Controls for this group are also in triplicate.

first: Beatriz

last: Merchel Piovesan Pereira

first: Xiaokang

last: Wang


title: Biochemistry of spontaneous labour (the second miRNAomic study)

city: Oulu

first: Antti

last: Haapalainen

address: Aapistie 5A

department: CRC

country: Finland

institute: University of Oulu

summary: MiRNAomics of human placenta revealed miRNAs up- and down regulated at spontaneous preterm and term deliveries.

overall_design: miRNAomes were determined for placentas of spontaneous preterm, spontaneous term and elective term labours.

first: Heli

last: Tiensuu

first: Ravindra

last: Daddali


title: IL-33-PU.1 transcriptome reprogramming drives functional state transition and clearance activity of microglia in Alzheimer’s disease

city: Hong Kong

first: Nancy

last: Ip

address: Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon

summary: Impairment of microglial clearance activity contributes to beta-amyloid (Aβ) pathology in Alzheimer disease (AD). While the transcriptome profile of microglia directs microglial functions, how the microglial transcriptome can be regulated to alleviate AD pathology is largely unknown. Here, we show that injection of interleukin (IL)-33 in an AD transgenic mouse model ameliorates Aβ pathology by reprogramming microglial epigenetic and transcriptomic profiles to induce a microglial subpopulation with enhanced phagocytic activity. These IL-33–responsive microglia (IL-33RM) express distinct transcriptome signature, highlighted by major histocompatibility complex class II genes, and restored homeostatic signature genes. IL-33–induced remodeling of chromatin accessibility and PU.1 transcription factor binding at the signature genes of IL-33RM control their transcriptome reprogramming. Specifically, disrupting PU.1–DNA interaction abolishes the microglial state transition and Aβ clearance induced by IL-33. Thus, we define a PU.1-dependent transcriptional pathway that drives the IL-33–induced functional state transition of microglia, resulting in enhanced Aβ clearance.

overall_design: Single-cell transcriptomic and epigenetic profiling of microglia upon IL-33 treatment in APP/PS1 mice

first: N

first: S

middle: F

last: Lau


title: Role of Farnesoid X Receptor (FXR) in Valproic acid-induced Hepatotoxicity

city: Zürich

first: Evelin

last: Krajnc

address: Rämistrasse 100

department: Department of Clinical Pharmacology and Toxicology

country: Switzerland

institute: University Hospital Zürich

summary: Drug-induced steatosis and steatohepatitis manifest clinically as nonalcoholic fatty liver disease (NAFLD). Drugs associated with steatosis include valproic acid (VPA). VPA has been one of the most widely used antiepileptic drugs over the past 40 years. However, clinical follow-up studies have reported that more than 40% of patients who received VPA also developed fatty liver disease. Steatosis is a typical clinical effect of VPA treatment and is characterized by an abnormal accumulation of lipids in liver cells. The aim of this study is to investigate whether activation of the farnesoid X receptor (FXR) by obeticholic acid (OCA), which is an effective agent in the treatment of NAFLD, can also prevent VPA-induced steatosis. OCA is a synthetic bile acid derivative that potently activates FXR and the FXR-regulated pathways that maintain bile acid, lipid and glucose homeostasis. Female C57BL/6 mice were fed a standard chow diet or chow containing OCA (dose 250 mg/kg body weight) for four weeks. Each group was then divided into two sub-groups: one co-treated with VPA (dose 100 mg/kg body weight) and another treated with the same volume of H2O by oral gavage daily for an additional four weeks. Mice liver were isolated and RNA isolated for RNA-Seq.

overall_design: Examination of RNA samples from isolated liver treated either with VPA or VPA+OCA (six female C57BL/6 mice per treatment).


title: Distinct fibroblast functional states drive clinical outcomes in ovarian cancer and are regulated by TCF21

city: Toronto

first: Laurie

last: Ailles

state: ON

address: 101 College St.

department: Princess Margaret Cancer Centre

institute: University Health Network

summary: Recent studies indicate that cancer-associated fibroblasts (CAFs) are phenotypically and functionally heterogeneous. However, little is known about CAF subtypes and the roles they play in cancer progression. Here we identify and characterize two CAF subtypes that coexist within high grade serous ovarian cancers: Fibroblast activation protein (FAP)-high (FH) CAFs resemble the classical myofibroblast-type CAF, whereas FAP-low (FL) CAFs possesses a preadipocyte-like molecular signature.

overall_design: High-grade serous ovarian cancer single cell suspensions of 12 patients were stained for fluorescence activated cell sorting (FACS)  CD31-CD45-EpCAM-CD49e+ (CAFs) cells,  and CD31-CD45-EpCAM+CD133+ (epithelial) cells were gated for sorting based on FMO controls. Cells were sorted and  RNA was extracted immediately using the RNeasy Plus Micro kit (Qiagen).

middle: E

first: Ali

last: Hussain


title: RNA-sequencing of the infarct border zone of the mouse hearts transplanted with FOXO3-GE-MPCs

status: Public on Apr 30 2020

city: BeiJing

first: Wang

last: Kang

address: Building 104, yard 1, Beichen West Road, Chaoyang District, Beijing

institute: Beijing Institute of genome research, Chinese Academy of Sciences

overall_design: RNA-sequencing of the infarct border zone of the mouse hearts, treated with sham surgergy, coronary artery ligation or coronary artery ligation and transplanted with FOXO3-GE-MPCs

first: Guanghui

last: Liu


overall_design: Refer to individual Series


title: Analyses of transcriptomes of  mammary and lymphocyte tissues in cattle

first: George

summary: Analyses of transcriptomes of  two tissues in cattle

overall_design: We collected 2 tissues (Mammary and Lymphocyte), each tissue has two replicates.

first: Lingzhao

last: Fang


title: Analyses of methylomes of Bones in cattle

city: Beijing

first: Shengli

last: Zhang

address: 2rd, Yuanmingyuan West Road

department: Colledge of Animal Science and Techonology

institute: China Agricultural University

type: Methylation profiling by high throughput sequencing

summary: In this study, we generated whole genome bisulfite sequencing data of 2 samples for Bones in Holstein cattle. We analyzed the variations of DNA methylation among tissues compared to other tissues we generated before.

overall_design: Genomic DNA for each tissue was isolated according to the QIAamp DNA Mini Kit protocol (QIAGEN, Valencia, CA, USA). The quality of DNA samples was evaluated using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) including degradation, and potential RNA contamination, and purity (OD260/OD280), and concentration using a spectrophotometer (NanoDrop Technologies, Rockland, DE) to meet the requirements for library construction. The qualified genomic DNA from somatic tissues and sperm were used to construct a library. The library different lanes of a HiSeq X Ten (Illumina, San Diego, CA, USA) to generate 150-bp paired-end reads by Novogene (Novogene, Beijing, China).

first: Shuli


title: Rodent malaria parasite RNA does not affect mouse BeadChip results

city: Chengdu

first: Jing-wen

last: Lin

address: No. 17, Section 3, People's South Road

institute: West China Second Hospital

summary:
Rodent malaria parasite RNA hybridized on Illumina Mouse WG-6 v2.0 Expression BeadChip
To investigate whether parasite RNA interfere with mouse beadchip analaysis. Malaria parasite resides in red blood cell, therefore RNA isolated from whole infected blood contains host RNA as well as parasite RNA

sample_organism:
Plasmodium chabaudi
Mus musculus

overall_design: Parasite RNA was isolated after leukocyte depletion and RBC lysis, hyridisated to mouse beadchip array as other naïve or infected blood samples

first: Jean

last: Langhorne


title: Incorporation of In Vitro Techniques for Botanicals Dietary Supplement Safety Assessment – Towards evaluation of Developmental and Reproductive Toxicity (DART)

city: Mason

first: Yuqing

last: Shan

state: Ohio

address: 8700 mason montgomery road

institute: Procter & Gamble

summary: As complex mixtures, botanicals present unique challenges when assessing safe use, particularly when endpoint gaps exist that cannot be fully resolved by existing toxicological literature. Obtaining data for developmental and reproductive toxicity (DART) can be particularly difficult as this is a frequent data gap for botanicals. Here we explore in vitro receptor binding and enzyme activity assays as well gene expression studies as alternative tools to inform on DART relevent modes of action. Botanicals suspected to have DART effects in addition to herbs with a significant history of use were tested at biologically relevant doses to probe activity at a molecular level. Additionally, gene expression changes in a number of different cell types were analysed using the connectivity mapping approach (CMap) to identify modes of action through a functional read across approach. Together, these two data streams increase the confidence in predictions of biological mode of action and inform potential DART risk by way of potency comparisons and/or a margin of internal exposure approach.

overall_design: Five botanicals were selected to represent botanicals with a safe history of food use: Ginger, St. John’s Wort, Chaste Tree, Kava Kava, and Ashwagandha. Each of four human cell lines (A549, Ishikawa, HepG2, MCF7) was treated with 5 botanicals in 96-well plates. 3 concentrations, 3 replicates and 6h time point were used. DMSO was used as vehicle control.


title: Expression data from control and Angpt2 silenced mouse melanoma cells

city: Heidelberg

first: Ashik Ahmed

last: Abdul Pari

address: Im neuenheimer Feld 280

country: Germany

institute: German Cabcer Research Institute

summary:
The functional role of tumor cell-expressed Angpt2  still remains elusive. Here, we used mouse melanoma cells which have endgeneous Angpt2 expression and invesitgated the functional role of tumor cell-derived Angpt2.
Total RNA from control and Angpt2 silenced mouse melanoma cells (RET) was isolated and was further utilized for microarray analysis using Affymetrix  Mouse Gene 2.0 ST array.

overall_design: mRNA profiles of control (transduced with non-targeting shRNA) or Angpt2 silenced (transduced with Angpt2 shRNA) RET mouse melanoma cell line cultured for 24h in standard cell culture condition. RNA was isolated with  GenElute Mammalian Total RNA Purification Kit (Sigma). cDNA libraries were prepared and analyzed by the DKFZ Genomics core facility, according to the standard operating protocols. Three independent biological repeats were performed for all sample groups.

first: Augustin

middle: G

last: Hellmut


title: Dynamic study of the cell wall integrity signaling pathway in Aspergillus nidulans

city: Baltimore

first: Mark

middle: R.

last: Marten

address: 1000 Hilltop Circle

department: Chemical, Biochemical, and Environmental Engineering

institute: University of Maryland Baltimore County

summary: This study aims to determine the downstream impact of cell wall perturbation on the filamentous fungus, Aspergillus nidulans.Fungi were treated with micafungin during mid-exponential growth phase and RNA-sequencing was performed at 0, 5, 10, 15, 20, 25, 30, 40, 50, 60, 75, 90, and 120 minutes of exposure in 3 biological replicates.

overall_design: Here 13 timepoints (0, 5, 10, 15, 20, 25, 30, 40, 50, 60, 75, 90, and 120 minutes) after exposure to micafunign (a cell wall pertubant) from 3 biological replicates are taken.

first: Cynthia

last: Chelius

first: Samantha

last: Reese

first: Steven

last: Harris


title: C. elegans nuclear RNAi factor SET-32 is an H3K23 methyltransferase and deposits the transgenerational heritable modification of H3K23me3

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: New Jersey

address: 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University

summary: Nuclear RNAi provides a highly tractable system to study RNA-mediated chromatin changes and epigenetic inheritance. Recent studies indicate that nuclear RNAi-mediated heterochromatin is highly complex in its regulation and function. The knowledge of histone modifications that are involved in nuclear RNAi and the corresponding histone modifying enzymes remains limited. In this study, we show that the heterochromatin mark H3K23me3 is induced by nuclear RNAi at both exogenous and endogenous targets in C. elegans. In addition, RNAi-induced H3K23me3 can be inherited for at least four generations. We also demonstrate that the histone methyltransferase SET-32, methylates H3K23 in vitro. Both set-32 and the germline nuclear RNAi Argonaute, hrde-1, are required for nuclear RNAi-induced H3K23me3 in vivo. Our data poise H3K23me3 as a chromatin modification involved in the nuclear RNAi pathway and provides the field with a new target for uncovering the role of heterochromatin in transgenerational epigenetic silencing.

overall_design: In this study we tested if H3K23me1/2/3 is induced by nuclear RNAi at both the exogenous and endogenous targets. We performed oma-1 dsRNA feeding and heritable RNAi experiments. We investigated the whole genome distribution of H3K23me3 and its overlap with H3K9me3. We tested its genetic requirements in the nuclear RNAi pathway and for three histone methyltransferases in vivo: MET-2, SET-25 and SET-32 by examining oma-1 and endogenous nuclear RNAi targets as well as whole genome changes in these mutants.

first: Lianna

last: Schwartz-Orbach

first: Chenzhen

first: Simone

last: Sidoli

first: Richa

last: Amin

first: Diljeet

last: Kaur

first: Anna

last: Zhebrun

first: Julie

last: Ni


title: Redundant and additive functions of the four LEF/TCF transcription factors in lung epithelial progenitors

city: Houston

first: Kamryn

middle: Nicole

last: Gerner-Mauro

state: Texas

address: 6565 MD Anderson Blvd

department: Pulmonary Medicine

institute: MD Anderson Cancer Center

summary: Paralogs represent genetic redundancy and survive purifying selection by evolving overlapping and distinct functions. In multicellular organisms, such functional diversification can manifest as tissue and cell type specific expression, which masks possible selective pressure for genetic redundancy within a single cell type. Using in vivo genetic and genomic analyses, we show that although the 4 mammalian LEF/TCF transcription factors have evolved organ-specific functions, they function additively and redundantly, depending on gene dosage, to promote lung epithelial progenitors and do so in a linear, positive manner with beta-Catenin in the canonical Wnt signaling pathway.

overall_design: FACS-purified lung epithelial cells were processed through the Chromium Single Cell Gene Expression Solution Platform (10X Genomics)

middle: N

first: Jichao

last: Chen


title: Analyses of transcriptomes of multiple tissues in cattle

city: Beltsville

first: George

last: Liu

address: 10300 Baltimore Ave Bldg 306

summary: In this study, we generated 47 RNA-seq data for 14 tissues in Holstein cattle.  We analyzed the variations of gene expression among tissues.

overall_design: We collected 14 tissues from 4 individuals and generated 47 RNA-seq data.

first: Yang

last: Zhou

first: Lingzhao

last: Fang

first: Shuli


title: RNA-seq analysis on tissues derived from normal skin and burn eschar

city: Cincinnati

first: Latha

last: Satish

state: OH

address: 3229 Burnet Avenue

department: Research

institute: Shriners Hospitals for Children

summary: The study was designed to determine the differential gene expression occurring in burn eschar tissue in comparison to normal skin

overall_design: 9 samples


title: Dichotomous Engagement of HDAC3 Activity Governs Inflammatory Responses [GRO-Seq]

city: Philadelphia

first: Hoang

last: Nguyen

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania Perelman School of Medicine

summary: Histone deacetylase 3 (HDAC3) is unique among the HDAC superfamily of chromatin modifiers that silence transcription through enzymatic modification of histones, because interaction with nuclear receptor corepressors (NCoR1/2) is required for engagement of its catalytic activity. However, loss of HDAC3 also represses transcription. Here we report that, during lipopolysaccharide (LPS) activation of macrophages, the deacetylase activity of HDAC3 is selectively engaged at ATF3-bound enhancers that repress anti-inflammatory genes. By contrast, LPS-stimulated recruitment of HDAC3 to ATF2-bound sites without NCoR1/2 activates pro-inflammatory genes by a non-canonical mechanism whereby catalytically inactive HDAC3 stably interacts with p65. Consistent with this bimodal inflammatory modulation, deletion of HDAC3 in macrophages safeguards mice from lethal exposure to LPS, but this protection is not conferred by genetic or pharmacological abolition of HDAC3 catalytic activity. Thus, HDAC3 is a dichotomous transcriptional activator and repressor whose deacetylase-independent functions are critical in priming the innate immune system.

overall_design: Nascent RNA profiling of bone marrow-derived macrophages untreated macrophages or macrophages treated for 4 hours with either vehicle control (PBS) or LPS (5ng/ml for 4 hours)

first: Mitchell

middle: A

last: Lazar


title: Dichotomous Engagement of HDAC3 Activity Governs Inflammatory Responses [RNA-Seq]

overall_design: Transcriptomic profiling of bone-marrow derived macrophages (BMDM) harvested from control or MHD3KO mice, or peritoneal macrophages from control, MHD3KO, and NSDAD mice exposed to LPS. BMDM from MHD3KO mice were transduced with retrovirus expressing Y298F or WT HDAC3. BMDM from control and MHD3KO mice were transduced with retrovirus expressing empty vector. BMDM were then treated with vehicle control (PBS), LPS (5ng/ml for 4hour), or IL4 (10ng/ml for 24hour) before RNA were extracted for RNA-seq library preparation. For siRNA experimens, BMDM were transfected with either siControl, siAtf2, siAtf3, or siRela incubated for 48 hours before RNA extraction. Library was prepared with Illumina Truseq kit and sequenced on either Illumina Nextseq 500 or Hiseq 2000/4000 sequencer.


title: Radiation Attenuates Prostate Tumor Antiviral Responses to Vesicular Stomatitis Virus Containing Interferon-β, Resulting in Pronounced Antitumor Systemic Immune Responses

status: Public on Apr 29 2020

city: Miami

first: Wensi

last: Tao

state: Florida

address: 1550 nw 10 ave room 137

department: Radiation Oncology

institute: University of Miami

summary: Gene expression microarray analysis of LNCaP and PC3 cells grown in vitro,examine gene expression changes in response to RT potentiated VSV-hIFNβ oncolysis because of its inherent resistance to VSV-hIFNβ infection.

overall_design: LNCaP and PC3 cells were cultured in complete medium. After 24 hours, the cells were treated with VSV-hIFNβ. Twenty four hours after viral treatment, both cell lines were irradiated with 5Gy. The assay was terminated 24 h after RT.  Total RNA was extracted for microarray analysis.

first: Alan

last: Pollack


title: Dichotomous Engagement of HDAC3 Activity Governs Inflammatory Responses [ChIP-Seq]

state: PA

overall_design: Immuno-precipitation followed by high throughput sequencing of bone marrow-derived macrophages harvested from Control, MHD3KO mice,  and MHD3KO retrovirally transduced with empty or Y298F vectors, or of peritoneal macrophages from LPS-exposed WT mice in vivo


title: Dichotomous Engagement of HDAC3 Activity Governs Inflammatory Responses

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


title: Purification of pancreatic endocrine subsets from mouse islets

city: Jette

first: Willem

last: Staels

address: Laarbeeklaan 103

country: Belgium

institute: Vrije Universiteit Brussel

summary: We developed a FACS-platform for the isolation of highly purified endocrine subsets from mouse islets, based on specific differential expression of CD24 on delta-cells and CD71 on beta-cells.

overall_design: Isolation of mouse islets, dispersion of islet cells, incubation with antibodies directed against surface markers, FACS-based purification of endocrine subsets enriched in alpha-, beta-, and delta-cells

first: Claire

last: Berthault

first: Raphael

last: Scharfmann


title: KRAB domain of ZFP568 disrupts TRIM28-mediated abnormal interactions in cancer cells

first: Janani

last: Kumar

state: TX

address: 1515 Holcombe Blvd

summary: We observed changes in protein levels of EZH2, TRIM24, p53, and a substantial number of KRAB-ZF proteins in MCF7 cells upon introducing a peptide fragment containing the KRAB domain.

overall_design: mRNA profiles of MCF7 cells expressing Krab domain, knockdown of TRIM28, and Vector alone, sh scrambled control were generated using deep sequencing, in duplicate

first: Gundeep

first: Ren

last: Ren

first: Yue

last: Lu

first: Kevin

last: Lin

first: Jia

last: Li

first: Yun

last: Huang

first: Anamika

last: Patel

first: Michelle

last: Barton

first: Todd

last: Macfarlan

first: Xing

last: Zhang

first: Xiaodong

last: Cheng


title: Linking Indirect Effects of Cytomegalovirus to Modulation of Monocyte Innate Immune Function

city: Charlestown

first: Pritha

last: Sen

address: 149 13th street

institute: Massachusetts General Hospital

summary: Purpose: To use next-generation sequencing (NGS) to dissect the human monocyte-CMV host-pathogen interface.

overall_design:
Methods:  mRNA profiles of human monocytes isolated from  immunocompetent donors and subsequently infected ex vivo with CMV were generated by deep sequencing.

**Raw data for Samples GSM4728653-GSM4728660 will be submitted to dbGAP**

first: Adrian

last: Wilkie

first: Fei

last: Ji

first: Ian

middle: J

last: Taylor

first: Miguel

last: Velasquez-Palafox

first: Rosio

last: Fernandez

first: Liza

middle: M

last: Morsett

first: Erik

last: Abels

first: Rebekah

last: Lane

first: Suzanne

last: Hickman

first: Terry

middle: K

last: Means

first: Eric

middle: S

last: Rosenberg

first: Ruslan

middle: I

last: Sadreyev

first: Donald

last: Coen

first: Jay

last: Fishman

first: Joseph

last: ElKhoury

first: Yiming

last: Yang

first: Emilia

last: Vanni

first: Jean

last: Pesola

first: Bo

first: Mary

last: Piper


title: Snai2 maintains bone marrow niche cells by repressing osteopontin expression

status: Public on Apr 28 2020

city: Bronx

first: Paul

last: Frenette

state: NY

address: 1301 Morris Park Avenue , Room 101

department: Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research

institute: Albert Einstein College of Medicine

summary: Bone marrow (BM) mesenchymal stem and progenitor cells (MSPCs) are a critical constituent of the hematopoietic stem cell (HSC) niche. Previous studies have suggested that the zinc-finger epithelial-mesenchymal transition transcription factor Snai2 (also known as Slug) regulated HSCs autonomously. Here, we show that Snai2 expression in the BM is restricted to the BM stromal compartment where it regulates the HSC niche. Germline or MSPC-selective Snai2 deletion reduces the functional MSPC pool, their mesenchymal lineage output, and impairs HSC niche function during homeostasis and after stress. RNA-sequencing analysis revealed that Spp1 (osteopontin) expression is markedly upregulated in Snai2-deficient MSPCs.  Genetic deletion of Spp1 in Snai2-deficient mice, rescues MSPCs’ functions.  Thus, SNAI2 is a critical regulator of the transcriptional network maintaining MSPCs by the suppression of osteopontin expression.

overall_design: mRNA profiles were generated from FACS sorted bone marrow mesenchymal stem and progenitor cells of 8wk old control and Snai2-/- littermates in triplicates by Illumina HiSeq 2500 sequencing

first: Qiaozhi

last: Wei


title: Fungicide resistance RNA-seq on two isolates of Penicillium

status: Public on Apr 20 2020

first: Wayne

last: Jurick

state: MD

address: Building 002

department: Agricultural Research Service

institute: United States Department of Agriculture

summary: Exposure of a resistance and sensitive isolate of Penicillium to difenoconazole fungicide and acetone as a control for 24 hours.

sample_organism:
Penicillium expansum
Penicillium crustosum

overall_design: four replicates for each isolate under each condition, Resistance with difenoconazole and acetone, Sensitive with difenoconazole and acetone.

last: Jurick II

first: Franz

last: Lichtner


title: Analyses of methylomes of multiple tissues in cattle

first: George

last: Liu

institute: USDA-ARS

summary:
In this study, we generated whole genome bisulfite sequencing data of 19 samples for 13 tissues in Holstein cattle. We analyzed the variations of DNA methylation among tissues.
In this study, we generated whole genome bisulfite sequencing data of 6 samples for 5 tissues in Hereford cattle. We analyzed the variations of DNA methylation among tissues.

overall_design: Genomic DNA for each tissue was isolated according to the QIAamp DNA Mini Kit protocol (QIAGEN, Valencia, CA, USA). The quality of DNA samples was evaluated using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) including degradation, and potential RNA contamination, and purity (OD260/OD280), and concentration using a spectrophotometer (NanoDrop Technologies, Rockland, DE) to meet the requirements for library construction. The qualified genomic DNA from somatic tissues and sperm were used to construct a library. The library different lanes of a HiSeq X Ten (Illumina, San Diego, CA, USA) to generate 150-bp paired-end reads by Novogene (Novogene, Beijing, China).


title: Elucidation of DNA Methylation on N6-Adenine with Deep Learning

status: Public on Apr 22 2020

first: Tian

last: Tian

address: 3615 Civic Center Blvd

department: Center of Applied Genomics

institute: Children's Hospital of Philadelphia

summary: 6mA-DNA-IP-Seq and sequencing of Arabidopsis.  Our DeepM6A model was trained on the 6mA sites indentified by the single-molecule real-time (SMRT) sequencing. To validate the robustness of the DeepM6A model, we applied an independent DNA-6mA-IP for A. thaliana,  and predicted scores of  peaks by using the trained DeepM6A model.

first: Xiang

last: Yu


title: The DEAD-box RNA helicase CshA is required for fatty acid homeostasis in Staphylococcus aureus

status: Public on Apr 21 2020

city: Geneva

first: Julien

last: Prados

address: Rue Michel Servet 1

department: SCMU

institute: University of Geneva

summary: Staphylococcus aureus is an opportunistic pathogen that can grow in wide array of conditions: on abiotic surfaces, on the skin, in the nose, in planktonic or biofilms forms and can cause many type of infections. Consequently, S. aureus must be able to adapt rapidly to these changing growth conditions, an ability largely driven at the posttranscriptional level. RNA helicases of the DEAD-box family play an important part in this process. In particular, CshA, which is part of the degradosome, is required for the rapid turnover of certain mRNAs and its deletion results in cold-sensitivity. To understand the molecular basis of this phenotype, we conducted a large genetic screen isolating 82 independent suppressors of cold growth. Full genome sequencing revealed the fatty acid synthesis pathway affected in many suppressor strains. Consistent with that result, sublethal doses of triclosan, a FASII inhibitor, can partially restore growth of a cshA mutant in the cold. Overexpression of the genes involved in branch-chained fatty acid synthesis was also able to suppress the cold-sensitivity. Using gas chromatography analysis of fatty acids, we observed an imbalance of straight and branch-chained fatty acids in the cshA mutant, compared to the wild-type. This imbalance is compensated in the suppressor strains. Thus, we reveal for the first time that the cold sensitive growth phenotype of a DEAD-box mutant can be explained, at least partially, by an improper membrane composition. The defect correlates with an accumulation of the pyruvate dehydrogenase complex mRNA, which is inefficiently degraded in absence of CshA. We propose that the resulting accumulation of acetyl- CoA fuels straight-chained fatty acid production at the expense of the branched ones. Strikingly, addition of acetate into the medium mimics the cshA deletion phenotype, resulting in cold sensitivity suppressed by the mutations found in our genetic screen or by sublethal doses of triclosan.

overall_design: S. aureus is cold sensitive when deleting cshA gene. We produced 82 DcshA cold-suppressing strains and send them for whole genome sequencing in order to identify mutations involved in the supressing process. However, to limit library preparation cost, DNA samples were pooled into 9 groups of up to 12 DNA samples without barcoding.

first: Vanessa

last: Khemici

first: Bianca

last: Petrignani

first: Benjamin

last: Di Nolfi

first: Elodie

last: Berge

first: Caroline

last: Manzano

last: Giraud

first: Patrick

last: Linder


title: Transcriptomes of in vitro differentiated normal human urothelium

city: York

first: Simon

middle: Charles

last: Baker

address: Wentworth Way, Heslington

department: Biology Department

country: United Kingdom

institute: University of York

summary: Normal human urothelial cells from three independent donors were cultured exactly according to the method described in Cross et al. A biomimetic tissue from cultured normal human urothelial cells: analysis of physiological function. Am J Physiol Renal Physiol. 2005;289(2):F459-68. PMID: 15784840 DOI: 10.1152/ajprenal.00040.2005

overall_design: Differentiated transcriptomes of human urothelial cells from three independent donors

middle: C

first: Andrew

last: Mason

first: Jennifer

last: Southgate


title: SIX6 knockdown in Jurkat-Cas9 T-ALL cell line

status: Public on Apr 15 2020

city: Tampere

first: Laura

last: Oksa

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

institute: Tampere University

summary: T cell acute lymphoblastic leukemia (T-ALL) is a hematological malignancy strongly affected by the abnormal activity of transcription factors. Here we report a high expression of developmental transcription factor SIX6 in TAL1 subtype of T-ALL. Our data indicates that this high expression is directly regulated by binding of TAL1 and GATA3 transcription factors into an upstream enhancer element. We also looked into the potential targets of SIX6 in T-ALL and Crispr-cas9 mediated knockout of SIX6 in Jurkat cells caused significant changes in the expression of multiple genes, including genes related to mTOR signaling. In two independent patient cohorts, the high SIX6 expression shows a trend of less favourable prognosis. However, the knockout of SIX6 was not enough to have an effect on proliferation, cell cycle or viability of the Jurkat cells and overexpression of SIX6 in the T-ALL zebrafish model didn’t influence the progression of the disease. Our results show that high expression of SIX6 has a trend towards a less favourable outcome, but SIX6 doesn’t have an independent oncogenic role in T-ALL.

overall_design: mRNA expression profiler were generated from three replicates of control cells (Jurkas Cas9 empty vector) and Jurkat Cas9 SIX6 knocdown cells (knockdown made using CRISRP-Cas9 technology)

first: Saara

last: Laukkanen

first: Olli

last: Lohi


title: RNA-Seq of CD8+ T cell subsets during LCMV infection II

city: San diego

first: Ananda

last: Goldrath

address: 9500 Gilman Dr

department: Molecular Biology

institute: UCSD

summary: Tissue-resident memory CD8+ T cells (Trm) provide host protection through continuous surveillance of non-lymphoid tissues. While the relevance of Trm in diverse diseases ranging from infection to cancer is appreciated, the development and functional heterogeneity of Trm remain poorly understood. Using single-cell RNA-sequencing (scRNA-seq) and genetic reporter mice, we identified discrete lineages of intestinal antigen-specific CD8+ T cells, including a Blimp1hiId3lo tissue-resident effector cell population most prominent in the early phase of acute viral and bacterial infections, and a molecularly distinct Blimp1loId3hi tissue-resident memory population that subsequently accumulated at later infection timepoints. These distinct Trm populations where characterized by unique transcriptional programs including differential roles for transcriptional regulators Blimp1, T-bet, Id2, and Id3 in supporting and maintaining intestinal Trm heterogeneity during infection. Extending our analysis to malignant tissue, we also identified discrete populations of effector-like and memory-like CD8+ T cell populations with tissue-resident gene-expression signatures within tumors that shared features of terminally-exhausted and progenitor-exhausted T cells, respectively. Clarification of CD8+ T cell ontogeny and heterogeneity in non-lymphoid tissues holds broad implications for enhancing vaccination and immunotherapy approaches.

overall_design: 8 samples, 2 replicates each, Day 55 LCMV infection CD8+ T cell subsets

first: K

middle: D

last: Omilusik

first: J

last: Milner

first: A

middle: W


title: Circulating ceRNAs associated with hypertrophic cardiomyopathy

status: Public on Apr 14 2020

city: Guangzhou

first: Qi

last: Guo

address: Yanjiangxi Road

institute: Sun Yat-sen University

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

summary: Plasma ceRNA expression profiles were acquired by using a human ceRNA microarray.

overall_design: Whole blood was collected in venous blood collection tubes containing EDTA after fasting overnight, and plasma was separated by centrifugation.

first: Jingfeng

last: Wang


title: ZEB2-mediated EMT in CRC cell line DLD-1

status: Public on Apr 18 2020

city: Zwijnaarde

first: Jordy

last: De Coninck

address: Technologiepark 71

department: Department of Biomedical Molecular Biology

institute: University Gent

summary: We report the induction of epithelial-mesenchymal transition (EMT) in the epithelial colorectal cancer (CRC) cell line DLD-1. ZEB2 expression is sufficient to induce the downregulation of epithelial markers such as E-cadherin, claudins, keratins and occludins, while upregulating the expression of several mesenchymal markers as vimentin and fibronectin.

overall_design: 6 samples were analyzed, 1 for each condition. The different clones (WT2, WT5 and WT37) serve as three biological replicates to identify the variety.

first: Sven

last: Jonckheere

first: Joachim

last: Taminau

first: Juliette

last: Roels

first: Steven

last: Goossens

first: Geert

last: Berx


title: IL-36 signaling in keratinocytes controls early IL-23 production in Aldara®-induced skin inflammation in mice

status: Public on Apr 23 2020

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

institute: University of Geneva Medical School

summary: IL-36R signaling plays an important role in the pathogenesis of psoriasis. We ought to assess the specific function of IL-36R in keratinocytes for the pathology of Aldara®-induced psoriasis-like skin inflammation. Il36r-/- (KO) and Il36rΔK (DK) mice as well as their littermate controls, respectively Il36r+/+ (WT) and Il36rfl/fl (FL) mice, were challenged with the topical application of Aldara® on one ear during 3 or 7 days. RNASeq was performed on treated (AL) and untreated (CT) ears. Fold change analysis combined with RPKM and RT-qPCR allowed us to identify genes which were specifically regulated by IL-36R signaling in keratinocytes during the course of the treatment. We notably demonstrated that both IL-23 subunits (Il23a and Il12b) fell into this category.

overall_design: Skin mRNA profiles from WT, KO, FL and DK mice in AL and CT ears at days 3 and 7 of Aldara treatment (4-6 replicates per condition) were generated using TruSeq mRNA stranded kit on an Illumina HiSeq 4000 sequencer.

first: Jeremie

last: Goldstein

first: Assunta

last: Caruso

last: Lemeille

first: Cem

last: Gabay


title: Eye-antenna early L3 disc expression profiling in combinations of COX7a-LoF, ATF4-LoF and Notch-GoF

status: Public on Apr 10 2020

city: London

first: Sebastian

last: Sorge

address: 1 Midland Road

institute: The Francis Crick Institute

summary: Gene expression in larval, early third instar eye-antenna discs was assessed to reveal an ATF4 contribution to target gene induction following COX7a knockdown. As hypothesised, these COX7a-RNAi induced target genes require the transcription factor ATF4 for induction, irrespective of concomitant Notch pathway activation through Delta over-expression.

overall_design: Two biological replicates for eight genotypes were analysed (sixteen samples in total)

first: Jonas

last: Theelke

first: Kerem

last: Yildirim

first: Helen

last: Hertenstein

first: Ellen

last: McMullen

first: Stephan

last: Müller

first: Christian

last: Altbürger

first: Stefanie

last: Schirmeier

first: Ingrid

last: Lohmann


title: Eye-antenna early L3 disc expression profiling in COX7a-LoF and Notch-GoF

summary: Gene expression in larval, early third instar eye-antenna discs was assesed in genotypes with Notch Gain-of-Function (UAS-Delta or UAS-Notch[intra2]) over-expression or mitochondrial COX7a Loss-of-function (UAS-COX7a-RNAi) or a combination of both (UAS-Delta, UAS-COX7a-RNAi). The analysis revealed that, despite a strong genetic interaction between Notch pathway activation and knockdown of COX7a, no transcriptional cooperation or synergy was detectable in early L3 eye-antenna discs. Rather, COX7a knockdown induced a unique transcriptional signature, which further experiments revealed to be mediated by the transcription factor ATF4.

overall_design: Two biological replicates for five genotypes were analysed (ten samples in total)


title: Expression data from Canton-S and D18 adult flies

city: Dubna

first: Mikhail

last: Zarubin

address: Russia, Moscow region, Dubna, Juliot Curie, 20

country: Russia

institute: Joint Institute for Nuclear Research

summary:
Even after decades of living in the same laboratory environment two Drosophila melanogaster strains originating from North America (Canton-S) and Central Russia (D18) demonstrate a few differentially expressed genes some of which may be important for local adaptation (e.g. genes responsible for insecticide resistance). Genes with different level of expression between Canton-S and D18 strains belong to important metabolic pathways, for instance energy metabolism, carbohydrate metabolic process, locomotion, body temperature rhythm regulation and tracheal network architecture.
We used microarrays to make transcriptome profiling of two laboratory strains of different geographical origin after long-term laboratory maintenance

overall_design: 3-day-old adult flies were taken for RNA isolation from Canton-S and D18 D.melanogaster lines in 3 biologiacal repeats

first: Elena

last: Kravchenko


title: Genome-wide localization of RNA polymerase II and histone modifications in diffuse intrinsic pontine glioma cells in response to CDK9 inhibition

status: Public on Apr 12 2020

city: Aurora

first: Etienne

last: Danis

state: CO

institute: University of Colorado, Denver - Anschutz Medical Campus

summary: We report the application of chromatin immunoprecipitation for high-thoughput profiling of RNA polymerase II and histone modifications (H3K27me3 and H3K27ac) in diffuse intrinsic pontine glioma cells (DIPG) in response to CDK9 inhibition

overall_design: Examination of the localization of RNA polymerase II and two different histone modifications in DIPG cells

first: Nathan

last: Dahl

first: Rajeev

last: Vibhakar


title: Heterogeneity of tissue-resident CD8+ T cells in response to infection and malignancy

first: Ananda

last: Goldrath

state: CA

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

overall_design: Refer to individual Series


title: Next Generation Sequencing Facilitates Quantitative Analysis of Col, myb30 and MYB30-OE Transcriptomes

city: Bei Jing

first: Yan

last: Yan

address: 2 yuanmingyuan west road, haidian district,

institute: china agriculture university

summary: total mRNA profiles of 4-day-old Col (WT), MYB30 knockout mutant (myb30) and MYB30-OE were generated by deep sequencing, in triplicate, Sequencing was carried out with the Illumina HiSeq 2000 platform and the resulting reads were mapped to the reference genome of Arabidopsis thaliana (TAIR10) with TopHat (http://tophat.cbcb.umd.edu). Transcript expression was evaluated by cuffdiff (http://cufflinks.cbcb.umd.edu), and transcript abundance was estimated by fragments per kilobase of exon model per million mapped fragments (FPKM). Differentially expressed genes were selected using Student’s t-test with P<0.05.  qRT–PCR validation was performed using SYBR Green assays.

overall_design: mRNA profiles of 4-day old Col, myb30 and MYB30-OE were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.

first: Jigang

last: Li


title: Interaction of the pioneer transcription factor GATA3   with nucleosomes

status: Public on Apr 17 2020

city: Research Triangle Park

first: Paul

last: Wade

state: NC

address: 111 TW Alexander Drive

department: Laboratory of Molecular Carcinogenesis

institute: NIEHS

summary: We developed a high-resolution nucleosome mapping method to explore nucleosome positioning around GATA3 binding sites during GATA3-mediated mesenchymal-to-epithelial transition. We found specific correlations between nucleosome positioning and pioneering activities of GATA3.

overall_design: Nucleosome mapping at GATA3 binding sites

first: Motoki

last: Takaku

first: Sara

last: Grimm


title: Detection of expression differences between Col-0 and ozs3 (overly zinc sensitive 3)

status: Public on Apr 07 2020

city: Bayreuth

first: Michael

last: Weber

address: Universitätsstrasse 30

department: Plant Physiology

institute: University of Bayreuth

summary: The Zn-hypersensitive EMS mutant ozs3 (overly zinc sensitive) shows some additional pleiotropic effects compared to Col-0 wildtype. Most severe effects are a complete growth arrest at 4°C (seedling stage) and an altered root morphology even under control conditions. To detect the underlying transcriptional differences we analyzed  the root transcriptome under control and cold stress (4°C, 24h) conditions.

overall_design: Plants were cultivated for four weeks in a hydroponic system under short day conditions (8h light, 16h dark, at 23 °C). For treatment plants were transfered to 4°C for 24 h under short day conditions (8h light, 16h dark). Control plants remained at 23°C (8h light, 16h dark). After treatment roots of control- and cold-stressed-plants were harvested and total RNA was extracted using RNeasy Plant Mini Kit from Qiagen. Finally Arabidopsis Genome ATH1 Arrays (Affymetrix) were hybridized. Three biological replicates were analyzed for each condition and genotype.

first: Blen

last: Beyene

last: Clemens


title: Identification of synaptoneurosomal transcriptome engaged into translation in response to NMDA-R stimulation

city: Warszawa

first: Tomasz

middle: M.

last: Kuliński

state: Mazowieckie

address: ul. Ks. Trojdena 4

country: Poland

institute: International Institute of Molecular and Cell Biology in Warsaw

summary: Synapses are the regions of the neuron that enable the transmission and propagation of action potentials on the cost of high energy consumption and elevated demand for mitochondrial ATP production. The rapid changes in local energetic requirements at dendritic spines implies the role of mitochondria in the maintenance of their homeostasis. We have employed quantitative mass spectrometry and in vitro stimulation of isolated mouse synaptoneurosomes to create a comprehensive view of local protein synthesis in neurons. Strikingly, the second most numerus group of proteins synthetized in the synapses represented ones imported into the mitochondria. The proteomic data were further supported by sequencing of mRNAs bound with actively translating polyribosomes. Our results show that an important pool of mitochondrial proteins is locally produced at the synapse indicting that mitochondrial biogenesis take place locally in order to maintain the pool of functional mitochondria in axons and dendrites. We further show that stimulation of synaptoneurosomes induce the local synthesis of mitochondrial proteins that are transported to the mitochondria and incorporated into the protein supercomplexes of respiratory chain. This contributes to mitochondrial biogenesis in neurons and a logical consequence of this fact would be a dysregulation of mitochondrial function in the conditions that deal with dysregulated synaptic translation, such as fragile X syndrome. Indeed, we have shown mitochondrial dysfunction in synapses of Fmr1 KO mice.

overall_design: Examination of synaptoneurosomal transcriptome in comparison to polyribosomal fractions after NMDA-R stimulation, performed in  three replicates.

first: Bożena

last: Kuźniewska

first: Andrzej

last: Dziembowski

first: Magdalena

last: Dziembowska


title: Synergistic targeting of estrogen-receptor positive breast cancers by MDM2 inhibition in combination with endocrine therapy or CDK4/6 inhibition

status: Public on Apr 01 2020

city: Darlinghurst

first: Heloisa

middle: Helena

last: Milioli

state: NSW

address: 384, Victoria St

department: Cancer

country: Australia

institute: Garvan Institute of Medical Research

summary: Here we characterise the response of models of ER-positive breast cancer to treatment with the small molecule MDM2 inhibitor NVP-CGM097, a dihydroisoquinolinone derivative currently evaluated in a phase I clinical trial. We show that NVP-CGM097 reduces tumour cell viability of in vitro and in vivo models of endocrine sensitive, endocrine resistant and palbociclib (CDK4/6 inhibitor) resistant p53 wildtype (p53wt) ER-positive breast cancer. NVP-CGM097 synergises with both fulvestrant and palbociclib in models of therapy resistance. Importantly, we identify the key mechanisms of the synergistic interactions between NVP-CGM097 and endocrine therapy, which occurs through the inhibition of E2F Targets and G2M Checkpoint signalling and induction of senescence, rather than depending upon upregulation of p53 dependent apoptotic pathways. Moreover, we find these same pathways are synergistically targeted during the combination treatment of ER positive breast cancer models with NVP-CGM097 and palbociclib. This indicates the genuine potential of MDM2 inhibition as therapy in advanced ER-positive breast cancer as combination endocrine therapy and CDK4/6 inhibitor treatment becomes embedded as standard of care.

overall_design:
Experimental Design: In vitro and in vivo models were treated with NVP-CGM097 alone and in combination with fulvestrant or palbociclib. We perform cell viability, cell cycle, apoptosis and senescence assays to evaluate antitumor effects in treatment naïve and therapy resistant ER positive cell lines. We further assess the drug effects in patient-derived xenograft (PDX) models of endocrine-sensitive and -resistant breast cancer.
Results: We demonstrate that NVP-CGM097 inhibits tumour cells in multiple clinically relevant models of ER-positive breast cancer. Activation of p53 by NVP-CGM097 leads to cell cycle arrest and increased apoptosis in p53-wildtype breast cancer cell lines, and reduces tumour growth in a PDX model. NVP-CGM097 in combination with fulvestrant or palbociclib do not enhance apoptosis, but instead yields profound downregulation of cell cycle-related transcriptional programmes. Cell lines resistant to fulvestrant or palbociclib become senescent upon treatment with combination therapy, and a fulvestrant resistant PDX model reduces tumour growth with combined NVP-CGM097 and fulvestrant treatment.

middle: H

first: Neil

last: Portman


title: N6-methyladenosine and RNA secondary structure affect transcript stability and translation during systemic salt stress in Arabidopsis

city: Philadelphia

first: Marianne

last: Kramer

state: PENNSYLVANIA

address: 433 South University Ave

department: Biology

institute: University of Pennsylvania

summary: After transcription, a messenger RNA (mRNA)  is further post-transcriptionally regulated by several features including RNA secondary structure and covalent RNA modifications (specifically N6-methyladenosine, m6A). Both RNA secondary structure and m6A have been demonstrated to regulate mRNA stability and translation as well as have been independently linked to plant response to excess salt concentrations in the soil. However, the effect of m6A on regulating RNA secondary structure and the combinatorial interplay between these two RNA features during salt stress response has yet to be studied. Here, we globally identify RNA-protein interactions and RNA secondary structure during systemic salt stress. This analysis reveals that RNA secondary structure is highly dynamic during salt stress, which is independent of changes in RNA-protein interactions. Conversely, we find that m6A is anti-correlated with RNA secondary structure in a condition-specific manner, with salt-specific m6A resulting in a decrease in mRNA secondary structure during salt stress. Remarkably, we show that the combination of salt-specific m6A deposition and the associated loss of RNA secondary structure results in increases in mRNA stability and translation of transcripts encoding proteins involved in responses to abiotic stresses. In total, our comprehensive analyses reveal an important epitranscriptome, secondary structure-mediated post-transcriptional regulatory mechanism involved in plant long-term salt stress response and adaptation.

overall_design: Protein interaction profile sequencing (PIP-seq_ in the nuclei of Arabidopsis thanliana rosette leaves treated with or without long term salt stress. These are crosslinked with formaldehyde and treated with two Rnases (ssRNase and dsRNase) in two biological replicates over three lanes of sequencing

first: Brian

last: Gregory


title: CdrL ChIP-seq data for the paper "CdrS is required for cell division site placement but not elongation in hypersaline-adapted archaea"

status: Public on Apr 04 2020

city: Durham

first: Amy

last: Schmid

address: 125 Science Dr.

institute: Duke University

summary: Precise control of the cell cycle is central to the physiology of all cells. In prior work we demonstrated that archaeal cells maintain a constant cell size; however, the regulatory mechanisms underlying the cell cycle remain unexplored in this domain of life.  In this study we use genetics, functional genomics, and quantitative imaging to identify and characterize the CdrSL gene regulatory network in a model species of archaea. We demonstrate the central role of these ribbon-helix-helix family transcription factors in the regulation of cell division. In this GEO series related to this study, we use ChIP-seq analysis to demonstrate the binding of CdrL to the upstream region of the cdrS-ftsZ2 locus. We conclude that the CdrSL-Z2 transcriptional network is required to coordinate cell division with cell growth in archaea.

overall_design: Examination of CdrL binding sites in the halophilic archaeon Halobacterium salinarum in mid-logarithmic and stationary phases of growth.


title: Porcine neutrophils infected by Salmonella

status: Public on Apr 08 2020

city: Jingzhou

first: Tinghua

last: Huang

address: Jingmi Road #266

institute: Yangtze University

summary: High-density gene expression profile of 14,151+ unique genes for 6 normal porcine neutrophild and 6 porcine neutrophils samples infected by Salmonella using deep sequencing technology.

overall_design: Peripheral blood samples were collected from 20 healthy crossbreed (Duroc × Landrace × Yorkshire) piglets from a commercial swine farm in Jingzhou, China without sacrificing the animals (ten males and ten females, four weeks old). Prior to blood extraction, the feces were tested negative for Salmonella three times. Neutrophils were isolated through density gradient centrifugation using Ficoll-PaqueTM media (GE Healthcare Life Sciences, Shanghai) as per manufacturer instructions. Luria broth and M9 minimal medium were used to culture Salmonella bacteria. The neutrophils were treated with 106 colony forming units (cfu) of Salmonella enterica serovar Typhimurium (ATCC® 14028™) as previously described [7]. Samples were collected at zero- or eight-hours post infection (hpi). Six samples from each group (zero and eight hpi) were selected for transcriptome analysis.

first: Min

last: Yao