title: Notch2 complements Notch1 to mediate inductive signaling that initiates early T cell development

city: Isehara

first: Hiroyuki

last: Hosokawa

state: Kanagawa

address: 143 Shimokasuya

department: Department of Immunology

institute: Tokai University School of Medicine

summary: Notch signaling is the dominant intercellular signaling input during the earliest stages of T cell development in the thymus. Although Notch1 is known to be indispensable, we show that it does not mediate all Notch signaling in pre-commitment stages: Notch2 initially works in parallel to promote early murine T cell development and antagonize other fates. Notch-regulated target genes before and after T-lineage commitment change dynamically, and we show that this partially reflects shifts in genome-wide DNA binding by RBPJ, the transcription factor activated by complex formation with the Notch intracellular domain. Although Notch signaling and transcription factor PU.1 can activate some common targets in pre-commitment T progenitors, Notch signaling and PU.1 activity have functionally antagonistic effects on multiple targets, delineating separation of pro-T cells from alternative PU.1-dependent fates. These results define a distinct mechanism of Notch signal response that distinguishes the initial stages of murine T-cell development.

overall_design:
ChIP-seq; Five to ten million of Phase1 or Phase2 cells were fixed with 1 mg/ml DSG (Thermo Scientific) in PBS for 30 min at RT followed by additional 10 min with addition of formaldehyde up to 1%.  The reaction was quenched by addition of 1/10 volume of 0.125M glycine and the cells were washed with HBSS (Gibco).  Pelleted nucleus were dissolved in lysis buffer (0.5% SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris-HCl (pH 8) and PIC) and sonicated on a Bioruptor (Diagenode) for 18 cycles of 30sec sonication followed by 30sec rest, with max power.  Five microg of anti-Rbpj mAbs (a mixture of 2.5 microg of 5313 (CST) and 2.5 microg of ab180588 (Abcam)) were pre-bound to Dynabeads anti-Rabbit Ig (Invitrogen) and then added to the diluted chromatin complexes in parallel aliquots. The samples were incubated overnight at 4 Â°C, then washed and eluted for 6 h at 65 Â°C in ChIP elution buffer (20 mM Tris-HCl, pH 7.5, 5 mM EDTA 50 mM NaCl, 1% SDS, and 50 microg/ml proteinase K). Precipitated chromatin fragments were cleaned up using Zymo ChIP DNA Clean & Concentrator. ChIP-seq libraries were constructed using NEBNext ChIP-Seq Library Preparation Kit (E6240, NEB) and sequenced on Illumina HiSeq2500 in single read mode with the read length of 50 nt.
RNA-seq; Total RNA was isolated from 200,000 cells using an RNAeasy MicroKit (Qiagen).  Libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (E7530, NEB) from ~1 microg of total RNA following manufacturer's instructions.  Libraries were sequenced on Illumina HiSeq2500 in single read mode with the read length of 50 nt.

first: Maile

last: Romero-Wolf

first: Boyoung

last: Shin

first: Wen

last: Zhou

last: Koizumi

first: Ellen

last: Rothenberg


title: Chemotherapy negatively impacts the tumor immune microenvironment in NSCLC: An analysis of pre- and post-treatment biopsies in the multi-center SAKK19/09 study

status: Public on Jul 14 2020

city: Bern

first: Adian

middle: F

last: Ochaenbein

address: Murtenstrasse 35

department: Department of Biomedical Research

country: Switzerland

institute: University and University Hopsital of Bern

summary:
Background: Over the past few years, immune checkpoint inhibitors have changed the therapeutic landscape of non-small-cell lung cancer (NSCLC). Response to immune checkpoint inhibitors correlates with a pre-existing anti-tumoral immune response. Checkpoint inhibitors have been introduced as second line therapy and are only very recently used as monotherapy or in combination with chemotherapy as first line treatment of NSCLC. However, the effect of conventional first line platinum-based chemotherapy on the immune infiltrate in the tumor is largely unknown.
Methods: We measured the gene expression of a custom set of 201 cancer- and immune-related genes in 100 NSCLC tumor biopsies collected before chemotherapy and 33 re-biopsies after platinum-based chemotherapy at the time point of progression. For 29 patients matched pre- and post-chemotherapy samples could be evaluated.
Results: We identified a cluster of 47 co-expressed immune genes, including PDCD1 (PD1) and CD274 (PD-L1), along with three other co-expression clusters. Chemotherapy decreased the average gene expression of the immune cluster while no effect was observed on the other three cluster. Within this immune cluster, CTLA4, LAG3, TNFRSF18, CD80 and FOXP3 were found to be significantly decreased in patient-matched samples after chemotherapy.
Conclusion: Our results suggest that conventional platinum-based chemotherapy negatively impacts the immune microenvironment at the time point of secondary progression.

overall_design: In the study presented here, gene expression was measured in NSCLC biopsies before chemotherapy and at progression after chemotherapy

first: Michael

middle: A

last: Amrein

first: Adrian

last: Ochsenbein


title: Transcriptomic profilling of dental pericytes, an RNAseq approach

status: Public on Jul 13 2020

city: London

first: Val

last: Yianni

address: Guy's Hospital, Great Maze Pond

department: Centre for Craniofacial & Regenerative Biology

country: United Kingdom

institute: King's College London

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Transcriptomic profilling of dental pericytes, an RNAseq approach [scRNA-Seq]

summary: Profilling of pericytes derived from molar and incisors of XLacZ4 mice

overall_design: 32 molar single cells and 32 incisor single cells

first: Paul

last: Sharpe


title: Epigenetic field cancerization in breast cancer using subject-matched tumor, ipsilateral-normal, and contralateral-normal tissues

status: Public on Jul 10 2020

city: Lebanon

first: Meghan

middle: E.

last: Muse

state: NH

address: One Medical Center Drive, DHMC

department: Epidemiology

country: USA

institute: Geisel School of Medicine at Dartmouth

type: Methylation profiling by genome tiling array

summary: Emerging work has demonstrated that histologically normal (non-tumor) tissue adjacent to breast tumor tissue shows evidence of molecular alterations related to tumorigenesis, referred to as field cancerization effects. Although changes in DNA methylation are known to occur early in breast carcinogenesis and the landscape of breast tumor DNA methylation is profoundly altered compared with normal tissue, there have been limited efforts to identify DNA methylation field cancerization effects in histologically normal breast tissue adjacent to tumor. Matched tumor, histologically normal tissue of the ipsilateral breast (ipsilateral-normal), and histologically normal tissue of the contralateral breast (contralateral-normal) were obtained from nine women undergoing bilateral mastectomy. Laser capture microdissection was used to select breast epithelial cells from normal tissues, and neoplastic cells from tumor specimens for genome-scale measures of DNA methylation with the Illumina HumanMethylationEPIC array. We identified substantially more CpG loci that were differentially methylated between contralateral-normal breast and tumor tissue (63,271 CpG loci q < 0.01), than between ipsilateral-normal tissue and tumor (38,346 CpG loci q < 0.01). In addition, we identified differential methylation in ipsilateral-normal relative to contralateral-normal tissue (9,562 CpG loci p < 0.01). Hypomethylated loci in ipsilateral normal relative to contralateral were significantly enriched for breast cancer-relevant transcription factor binding sites including those for ESR1, FoxA1, and GATA3. Hypermethylated loci in ipsilateral-normal relative to contralateral-normal tissue were significantly enriched for CpG island shore regions.

overall_design: Bisulphite converted DNA from subject-matched, laser capture microdissected contralateral normal breast tissue, ipsilateral normal breast tissue, and breast tumor tissue were hybridized to the Illumina HumanMethylationEPIC beadchip.

middle: E

first: Alexander

middle: J

last: Titus

first: Lucas

last: Salas

first: Owen

middle: M

last: Wilkins

first: Chelsey

last: Mullen

first: Kelly

last: Gregory

first: Sallie

middle: S

last: Schneider

first: Giovanna

last: Crisi

first: Rahul

last: Jarwale

first: Christopher

middle: N

last: Otis

first: Brock

middle: C

last: Christensen

first: Kathleen

last: Arcaro


title: RNA sequencing of fibroblasts from patients with pathogenic KAT5 variants

status: Public on Jul 11 2020

city: Montréal

first: Sophie

last: Ehresmann

state: Quebec

address: 110 Avenue des pins

country: Canada

institute: IRCM

summary: KAT5 encodes an essential lysine acetyltransferase previously called TIP60 involved in gene expression, DNA repair, chromatin remodeling, apoptosis and cell proliferation; but it remains unclear whether variants in this gene causes a genetic disease. Here, we study three individuals with heterozygous de novo missense variants in KAT5 that affect normally invariant residues, with one at the chromodomain (p.Arg53His) and two at or near the acetyl-CoA binding site (p.Cys369Ser and p.Ser413Ala). All three individuals have cerebral malformations, seizures, global developmental delay or intellectual disability, and severe sleep disturbance. Progressive cerebellar atrophy was also noted. Histone acetylation assays with purified mutant KAT5 demonstrated that the variants decrease or abolish the ability of the resulting NuA4/TIP60 multi-subunit complexes to acetylate the histone H4 tail in chromatin. Transcriptomic analysis in patient-derived fibroblasts showed deregulation of multiple genes controlling development. Moreover, there was also upregulated expression of PER1 (a key gene involved in circadian control), in agreement with sleep anomalies in all the patients. In conclusion, dominant missense KAT5 variants cause histone acetylation deficiency with transcriptional dysregulation of multiples genes, thereby leading to a neurodevelopmental syndrome with sleep disturbance, cerebellar atrophy and facial dysmorphisms suggesting a recognizable syndrome.

overall_design: RNA from fibroblasts derived from affected patients and healthy controls was sequenced using RNAseq. RNA from one affected individual (NM_003638.3_c.1237C>G) and two healthy controls was sequenced in duplicates, while RNA from a second affected individual (NM_003638.3_c.1105T>A) and four more controls was sequenced with one replicate each. Differential analyses were conducted using all healthy samples versus all affected samples.

first: Philippe

last: Campeau


title: Comparison of gene expression profiles in hearts exposed to pressure overload (PO) with or without sildenafil treatment in PERK wild type (flx) or PERK cardiac-specific knockout 8cko) mice.

city: Bunkyo-ku

first: Takashi

last: Shimizu

country: Japan

institute: University of Tokyo

summary: Recently, it is reported that sildenafil suppresses maturation of PO-induced miRNAs. However, the mechanism of how sildenafil coupled NO-cGMP-PKG signaling affects this maturation was not unraveled. Here, we show that PERK-mediated suppression of miRNAs by sildenafil is vital to keep mitochondrial homeostasis, using cardiac-specific PERK knockout (cko) mice.

overall_design: Total 12 samples were derived from hearts exposed to PO with or without sildenafil treatment in PERK wild type (flx) or PERK cko mice.

first: Ryo

last: Nakaki


title: ChIP-Seq for FOXA2 in PC3 cell line with GSK treatment and VEH control

city: Boston

first: Changmeng

last: Cai

state: Massachusetts

address: 100 William T. Morrissey Blvd.

institute: University of Massachusetts Boston

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We show in prostate cancer cells that LSD1 co-localizes with FOXA1 and active enhancer markers, and that LSD1 inhibition globally disrupts FOXA1 chromatin binding.

overall_design: ChIP-Seq of FOXA2 was performed in PC3 cells treated with vehicle or  GSK2879552

first: Shuai

last: Gao

first: Dong

last: Han

first: Sujun

last: Chen

first: Housheng

middle: H

last: He


title: Mitochondrial fusion drives oxidative metabolism to immortalize neural stem cells during tumorigenesis

city: Berlin

first: Ana

last: Veloso

state: Berlin

address: Hannoversche Strasse 28

country: Germany

institute: Berlin Institute for Medical Systems Biology (BIMSB-MDC)

summary: Metabolic reprogramming is a key feature of many cancers, but how and when it contributes to tumorigenesis remains unclear. Here, we demonstrate that metabolic reprogramming induced by mitochondrial fusion can be rate-limiting for immortalization of tumor initiating cells (TICs) and trigger their irreversible dedication to tumorigenesis. Using single-cell transcriptomics, we find that Drosophila brain tumors contain a rapidly dividing stem cell population defined by upregulation of oxidative phosphorylation (OxPhos). We combine targeted metabolomics and in-vivo genetic screening to demonstrate that OxPhos is required for tumor cell immortalization but is dispensable in the neural stem cells (NSCs) giving rise to the tumors. Employing an in-vivo NADH/NAD+ sensor, we show that NSCs increase OxPhos precisely during immortalization. Blocking OxPhos or mitochondrial fusion stalls the TICs in quiescence and prevents tumorigenesis through impaired NAD+ regeneration. Our work establishes a unique connection between cellular metabolism and the immortalization of tumor initiating cells.

overall_design: SMART-Seq2 single-cell RNA-seq of control neuroblasts and bratRNAi tumor neuroblasts in Drosophila melanogaster third instar larvae

first: François

last: Bonnay

first: Victoria

last: Steinmann

first: Robert

middle: P

last: Zinzen

first: Juergen

last: Knoblich


title: RNA-Seq dataset from FACS-isolated L2 and T1 neurons (Drosophila melanogaster).

city: Los Angeles

first: Maureen

last: Sampson

state: CA

address: 695 Charles Young Drive

department: Molecular Toxicology

institute: UCLA

summary: We report transcripts from isolated L2 and T1 neurons.

overall_design: L2 or T1 neurons were specifcied by L2-split-GAL4 or T1-LexA driving GFP. GFP+ cells were isolated by FACS for RNA extraction and sequencing. RNA-Seq was performed using SMART-Seq protocol.

first: Fuying

first: Shivan

last: Bonanno

first: Kathy

last: Myers Gschweng


title: Transcriptomic profilling of dental pericytes, an RNAseq approach [bulk RNA-Seq]

first: Val

last: Yianni

overall_design: Molar vs Incisor

first: Paul

last: Sharpe


title: ChIP-Seq for HOXB13 in LNCaP cell line with GSK treatment and VEH control

overall_design: ChIP-Seq of HOXB13 was performed in LNCaP cells treated with vehicle or  GSK2879552


title: Role of Rnf40-dependent histone monoubiquitination in peripheral nervous system myelination [RNA-Seq]

city: Erlangen

first: Michael

last: Wegner

state: Bavaria

address: Fahrstr. 17

department: Institut of Biochemistry

summary: To address the role of monoubiquitination of histone H2B at lysine 120 (H2Bub1), we inactivated the responsible E3 ligase by deleting Rnf40 in developing Schwann cells. Rnf40 becomes important for proper Schwann cell development shortly before and during differentiation. Its absence in Schwann cells leads to a peripheral neuropathy. RNA-Seq studies were performed on sciatic nerves from control mice and mice with a Schwann cell-specific deletion of Rnf40 to analyze changes in gene expression. These revealed substantial changes in the expression of genes associated with myelination, lipid metabolism and cell adhesion.

overall_design: We generated mRNA profiles of sciatic nerves from 14-day old control mice (ctrl; carrying floxed Rnf40 alleles) and mice with a Schwann cell-specific Rnf40 deletion (cko; carrying Rnf40 alleles in combination with a Dhh::Cre transgene) using the Illumina HiSeq 2500 platform.

first: Franziska

last: Fröb

first: Elisabeth

last: Sock


title: The chromatin-binding protein PHF6 functions as an E3 ubiquitin ligase of H2BK120 via H2BK12Ac recognition for activation of trophectodermal genes

city: Seoul

first: Sungryong

last: Oh

address: 599 Gwanak-ro, Gwanak-gu

department: biological sciences

country: South Korea

institute: Seoul National University

summary: Epigenetic regulation is important for establishing lineage-specific gene expression during early development. Although signaling pathways have been well-studied for regulation of trophectoderm reprogramming, epigenetic regulation of trophectodermal genes with histone modification dynamics have been poorly understood. Here, we identify that plant homeodomain finger protein 6 (PHF6) is a key epigenetic regulator for activation of trophectodermal genes using RNA-sequencing and ChIP assays. PHF6 acts as an E3 ubiquitin ligase for ubiquitination of H2BK120 (H2BK120ub) via its extended plant homeodomain 1 (PHD1), while the extended PHD2 of PHF6 recognizes acetylation of H2BK12 (H2BK12Ac). Intriguingly, the recognition of H2BK12Ac by PHF6 is important for exerting its E3 ubiquitin ligase activity for H2BK120ub. Together, our data provide evidence that PHF6 is crucial for epigenetic regulation of trophectodermal gene expression by linking H2BK12Ac to H2BK120ub modification.

overall_design: Gene expression profiling of WT and Phf6 KnockOut ZHBTc4 mouse embryonic cell lines untreated, treated with Doxycycline, or treated with Retinoic Acid.

first: Daechan

last: Park

first: S

last: Baek


title: Nuclear Role for Human Argonaute-1 as an Estrogen-dependent Transcription Coactivator

city: Ciudad Autónoma de Buenos Aires

first: Alberto

middle: R

last: Kornblihtt

address: Pabellón IFIBYNE, Ciudad Universitaria

country: Argentina

institute: CONICET_Universidad de Buenos Aires

summary: In mammals, argonaute (AGO) proteins have been characterized for their roles in small RNA-mediated post-transcriptional and also in transcriptional gene silencing. We report here a different role for AGO1 in estradiol-triggered transcriptional activation in human cells. We show that in MCF-7 mammary gland cells AGO1 associates to transcriptional enhancers of estrogen receptor alpha (ERα) and that this association is upregulated by treating the cells with estrogen (E2), displaying a positive correlation with the activation of these enhancers.

overall_design: Examination of AGO1 binding to chromatin in vehicle or estradiol treated MCF7 cells

first: Luciana

middle: I

last: Gómez Acuña

first: Ezequiel

last: Nazer

first: Santiago

last: Rodríguez-Seguí

first: Berta

last: Pozzi

first: Valeria

last: Buggiano

first: Luciano

last: Marasco

first: Eneritz

last: Agirre

first: Cody

last: He

first: Mariano

last: Alló


title: Next-Generation Sequencing Analysis of Wild Type and Rfx1-/- or Rfx2-/- or Rfx3-/- Mouse Ependymal Cells

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

institute: University of Geneva Medical School

summary: Purpose: This study was carried out to determine the consequences of inactivating either Rfx1, or Rfx2 or Rfx3 on gene expression during differentiation of mouse multiciliated ependymal cells.

overall_design: Methods: RNA was extracted from ex vivo differentiated mouse ependymal cells of E18.5 embryos from Rfx1-/- or Rfx2-/- or Rfx3-/- and control +/+ siblings.

first: Marie

last: Paschaki

last: Lemeille

first: Dominique

last: Baas

first: Laurette

last: Morlé

first: Jean

middle: L

last: Duteyrat

first: Emmanuèle

last: Barras

first: Fabien

last: Soulavie

first: Julie

last: Jerber

first: Joëlle

last: Thomas

first: Yong

last: Zhang

last: Holtzman

first: Walter

last: Reith

first: Bénédicte

last: Durand


title: Gene expression profile of clinical LUAD tumors and their paired non-cancerous adjacent tissues by RNA-seq analysis

city: Shanghai

first: Linhu

last: Zhai

address: 555 Zu Chong Zhi Road , Zhang Jiang Hi-Tech Park, Pudong, Shanghai

country: China

institute: Shanghai Institute of Materia Medica

summary:
Purpose: Transcriptomic analysis of clinical tissue samples is important in the precision medicine research. To explore the relationship between transcriptome and full proteome, 51 LUAD tumor tissues and 49 paired non-cancerous adjacent tissues were systematically analyzed by RNA sequencing.
Methods: RNASeq reads were adapter trimmed and data quality was assessed with the FastQC (version 0.11.7) software before any data filtering criteria may apply. Reads were mapped onto the human reference genome (GRCh38.p12 assembly) by using hisat2 software (v2.0.4). The mapped reads were assembled into transcripts or genes by using StringTie software (v1.3.4d) and the genome annotation file (hg38_ucsc.annotated.gtf). For quantification purpose, the relative abundance of transcript/gene was measured by a normalized metrics, FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
Results: In our study, RNA-seq analysis identified 16,188 genes with FPKM > 1, providing an opportunity to explore the relationship between the transcriptome and full proteome.
Conclusions: Our study provided an opportunity to explore the relationship between the transcriptome and full proteome of clinical LUAD tumors and their paired non-cancerous adjacent tissues.

overall_design: RNA-seq profiles of clinical LUAD tumor tissues (n = 51) and paired non-cancerous adjacent tissues (n = 49) generated by deep sequencing.

first: Jun-yu

last: Xu

first: Minjia

last: Tan


title: Role of Rnf40-dependent histone monoubiquitination in peripheral nervous system myelination [ChIP-Seq]

first: Michael

last: Wegner

summary: To address the role of monoubiquitination of histone H2B at lysine 120 (H2Bub1), we inactivated the responsible E3 ligase by deleting Rnf40 in developing Schwann cells. Rnf40 becomes important for proper Schwann cell development shortly before and during differentiation. Its absence in Schwann cells leads to a peripheral neuropathy. ChIP-Seq studies with H2Bub1-specific antibodies were performed on sciatic nerves from control mice and mice with a Schwann cell-specific deletion of Rnf40 to detect alterations in genomic H2Bub1 occupancy. These correlated with changes in the expression of genes associated with myelination and lipid metabolism.

overall_design: We determined the genome-wide H2Bub1 occupancy in sciatic nerves of 14-day old control mice (ctrl; carrying floxed Rnf40 alleles) and mice with a Schwann cell-specific Rnf40 deletion (cko; carrying Rnf40 alleles in combination with a Dhh::Cre transgene) using the Illumina HiSeq 2500 platform.

first: Franziska

last: Fröb

first: Elisabeth

last: Sock


title: Oral primo-colonizing bacteria modulate inflammation and gene expression in bronchial epithelial cells

status: Public on Jul 12 2020

city: Jout-en-Josas

first: Elliot

last: Mathieu

address: Domaine de Vilvert

department: MICALIS

country: France

institute: INRAE

summary: The microbiota of the mouth disperses into the lungs and both compartments share similar phyla. Considering the importance of the microbiota in the maturation of the immunity and physiology during the first days of life, we hypothesized that primo-colonizing bacteria of the oral cavity may induce immune responses in bronchial epithelial cells. Herein, we have isolated and characterized 57 strains of the buccal cavity of two human new-borns. These strains belong to Streptococcus, Staphylococcus, Enterococcus, Rothia and Pantoea genera; Streptococcus being the most represented. The strains were co-incubated with a bronchial epithelial cell line (BEAS-2B) and we established their impact on a panel of cytokines/chemokines and global changes in gene expression. The Staphylococcus strains, which appeared soon after birth, induced a high production of IL-8, suggesting they can trigger inflammation, whereas the Streptococcus strains were less associated with inflammation pathways. The genera Streptococcus, Enterococcus and Pantoea induced differential profiles of cytokine/chemokine/growth factor and set of genes associated with maturation of morphology. Altogether, our results demonstrate that the micro-organisms, primo-colonizing the oral cavity, impact immunity and morphology of the lung epithelial cells, with specific effects depending on the phylogeny of the strains.

overall_design: The overall design consisted of 7 samples of BEAS-2B cells treated with Streptococcus EMS321, Streptococcus EMS383, Streptococcus EMS3101, Enterococcus EME126, Enterococcus EME141, Enterococcus EME343 and Enterococcus EME394 versus unchallenged BEAS-2B cells. A minimum of four dye-swap hybridizations (4 biological replicates) were performed for each of the 7 samples analyzed. Unchallenged BEAS-2B cells were controls and challenged BEAS-2B cells with the bacterial strains were treated samples.

first: Chad

middle: W

last: MacPherson

first: Jocelyn

last: Belvis

first: Olivier

first: Véronique

last: Robert

first: Vinciane

last: Saint-Criq

first: Philippe

last: Langella

first: Thomas

last: Tompkins

first: Muriel


title: Role of Rnf40-dependent histone monoubiquitination in peripheral nervous system myelination

overall_design: Refer to individual Series


title: Short-Term Time-Restricted Feeding Alters Rhythmicity of Lipid and Amino Acid Metabolites in Overweight Men

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

summary: Time-restricted feeding improves metabolic health independently of dietary macronutrient composition or energy restriction. To understand the mechanisms underpinning the effects of time-restricted feeding, we investigated the metabolic and transcriptomic profile of skeletal muscle and serum samples from 11 overweight/obese men. In muscle, 4-10% of transcripts and 14% of metabolites were periodic, with the amplitude of the metabolites lower after time-restricted feeding. Core clock genes were unaltered by either intervention, while time-restricted feeding induced rhythmicity of genes related to lipid and amino acid transport. In serum, 49-65% of the metabolites had diurnal rhythms across both conditions, with the majority being lipids. Time-restricted feeding shifted the skeletal muscle metabolite profile from predominantly lipids to amino acids. Our results show time-restricted feeding differentially affects the amplitudes and rhythmicity of serum and skeletal muscle metabolites, and regulates the rhythmicity of genes controlling lipid and amino acid transport, without perturbing the core clock.

overall_design: The study employed two experimental dietary conditions and both required participants (11 overweight/obese men) to consume provided meals for five days consisting of ~32% of total energy intake (TEI) from carbohydrate, ~49% TEI from fat, and ~19% of TEI from protein. The timing of dietary intake differed between conditions, where energy was either consumed between a 15 h ‘unrestricted’ feeding (URF) window of 0700 to 2200 h or an 8 h ‘time-restricted’ feeding (TRF) window of 1000 to 1800 h. Participants were instructed to consume meals at standardized times throughout both experimental conditions (URF: meals consumed within ±30 min 0700, 1400 and 2100 h; TRF: meals at 1000, 1300 and 1700 h). Food was provided to be consumed on Day 0 (standardized diet) and for the first four days (Day 1-4) of each experimental condition. Instructions were provided on when to consume food (depending on condition). On the fifth day of each condition, participants arrived at ~0630 h and remained in the laboratory until ~0730 h the following day. Samples were obtained from vastus lateralis every 4 hours over 24 hours, to obtain a total of six skeletal muscle biopsies.

first: Leonidas

last: Lundell

first: Evelyn

middle: B

last: Parr

first: Brooke

last: Devlin

first: Ali

last: Altintas

first: Romain

last: Barrès

first: Juleen

last: Zierath

first: John

last: Hawley


title: Viral-mediated ubiquitination impacts interactions of host proteins with viral RNA and promotes viral RNA processing

status: Public on Jul 09 2020

city: Philadelphia

first: Matthew

middle: Darrell

last: Weitzman

state: PA

address: 4050 CTRB, 3501 Civic Center Blvd

department: Pathology & Laboratory Medicine

institute: Children's Hospital of Philadelphia

summary: Viruses promote infection by hijacking the host ubiquitin machinery to counteract or redirect cellular processes.  Adenovirus encodes two early proteins, E1B55K and E4orf6, that together co-opt a cellular ubiquitin ligase complex to overcome host defenses and promote virus production.  Adenovirus mutants lacking E1B55K or E4orf6 display defects in viral RNA processing and protein production, but previously identified substrates of the ligase do not explain these phenotypes.  Here we used a quantitative proteomics approach to identify substrates of E1B55K/E4orf6 that are ubiquitinated to facilitate RNA processing.  While cellular proteins known as substrates of E1B55K/E4orf6 are degraded by the proteasome, we uncovered RNA-binding proteins (RBPs) as high-confidence substrates which are not decreased in overall abundance.  We focused on two predominant RBPs, RALY and hnRNP-C, which we confirm are ubiquitinated without degradation.  Knockdown of RALY and hnRNP-C rescued levels of viral RNA splicing, protein, and progeny production during infection with E1B55K-deleted virus.  Furthermore, deletion of E1B55K resulted in increased interaction of hnRNP-C with viral RNA and attenuation of viral RNA processing.  These data suggest viral-mediated ubiquitination of RALY and hnRNP-C relieves a restriction on viral RNA processing, revealing an unexpected role for non-degradative ubiquitination in the manipulation of cellular processes during virus infection.

overall_design: Single-end eCLIP-Seq against hnRNP-C in uninfected HeLa cells, or 24 hours after wildtype Ad5 infection or delta-E1B55K (dl110) Ad5 infection

first: Christin

last: Herrmann

middle: D


title: Repression of the B cell identity factor Pax5 is not required for plasma cell development

city: Vienna

first: Moritz

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

summary: B cell and plasma cell fates are controlled by different transcriptional networks, as exemplified by the mutually exclusive expression and cross-antagonism of the B cell identity factor Pax5 and the plasma cell regulator Blimp1. It has been postulated that the repression of Pax5 by Blimp1 is essential for plasma cell development. Here, we challenged this hypothesis by analyzing the IghPax5/+ mouse, which expressed a Pax5 minigene from the immunoglobulin heavy-chain locus. Despite high Pax5 expression, plasma cells efficiently developed in young IghPax5/+ mice at steady state and upon immunization, while their number moderately declined in older mice. Although Pax5 significantly deregulated the plasma cell expression program, key plasma cell regulators were normally expressed in IghPax5/+ plasma cells. While IgM secretion by IghPax5/+ plasma cells was normal, IgG secretion was modestly decreased. Hence, Pax5 repression is not essential for robust plasma cell development and IgM secretion, although it is required for efficient IgG secretion and the accumulation of long-lived plasma cells.

overall_design:
11 RNA-Seq samples, 2 experiments:  experimental:51802,51803,51805 versus controls:51801,51804,51806  experimental:54807,54808,58411 versus controls:54806,58410
4 ChIP-Seq samples, 2 genomes (mouse with chicken spike in):  84330-3

first: Grace

last: Liu

first: Markus

last: Jaritz

first: Miriam

last: Woehner

first: Benedikt

last: Agerer

first: Andreas

last: Bergthaler

first: Stephen

middle: G

last: Malin

first: Meinrad

last: Busslinger


title: Transcript profiles in leaves of the salt-tolerant grapevine rootstock 1616C under salt and ER-stress

city: Ankara

last: ERGÜL

address: Gümüşdere  Yerleşkesi   Keçiören/ ANKARA

department: Biotechnology Institute

country: Turkey

institute: Ankara Üniversitesi  Biotechnology Institute & SİSBİOTEK

summary:
Grapevine rootstock 1616C shoots were sterilized and cultured on Murashige & Skoog (MS) medium containing 2% sucrose (w/v). Plantlets were grown in a growth chamber with a 16-h light/8-h dark cycle for 10 weeks at 25 °C.
Plantlets with 4–5 leaves were chosen for use in stress treatments. Experiments were conducted with treatment groups:
The control (C, without any chemical treatment), TM (treated with 5 μg mL-1 tunicamycin (TM)) and salt (treated with 400 mM NaCl).
Microarray analysis was performed and we investigated transcript profiles in leaves of the salt-tolerant grapevine rootstock 1616C under salt- and ER-stress at 6 and 24 hours

overall_design: 3 biological replication of each stress application and each control for 6 and 24 hour were performed and total 24 gene chip were used.

last: Ergül

first: Birsen

last: Aydemir

first: Canan

middle: Y

last: Özmen

first: Umut

last: Kibar

first: Filiz

last: Mutaf

first: Pelin

last: Büyük

first: Melike

last: Bakır


title: Genome-scale transcription–translation mapping reveals novel features of Zymomonas mobilis promoters and transcription units

city: Madison

first: Robert

last: Landick

state: WI

address: 1550 Linden Dr

institute: University of Wisconsin

summary: We collected sample-matched multiomics data including RNA-seq, transcription start site sequencing (TSS-seq), termination sequencing (term-seq), ribosome profiling, and label-free shotgun proteomic mass spectrometry across different growth conditions to improve annotation and assign functional sites in the Zymomonas mobilis subsp. mobilils ZM4 genome. Proteomics and ribosome profiling informed revisions of protein-coding genes, which included 44 start codon changes and 42 added proteins. We developed statistical methods for annotating transcript 5′ and 3′ ends enabling identification of 3940 TSSs and their corresponding promoters and 2091 transcription termination sites, which were distinguished from RNA processing sites by lack of an adjacent RNA 5′ end.

sample_organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

overall_design: 3 or 4 biological replicate samples of cells grown aerobically or anaerobically in rich media and anaerobically in minimal media. Samples were collected at growing phase and stationary phase time points.

first: Jessica

last: Vera

first: Indro

last: Ghosh

first: Yaoping

last: Zhang

first: Jose

last: Serate

first: Alex

last: Hebert

first: Josh

last: Coon


title: The Lyme disease bacterium, Borrelia burgdorferi, stimulates an inflammatory response in human choroid plexus epithelial cells

city: Grand Forks

first: Derick

last: Thompson

state: ND

address: 504 Hamline Street

department: Biomedical Sciences

institute: University of North Dakota

summary: We report the results of gene expression profiling via RNA-sequencing of primary human choroid plexus epithelial cells in vitro that were infected with Borrelia burgdorferi, the causative agent of Lyme disease. Epithelial cells were cultured with B. burgdorferi for 48 hours prior to RNA isolation. Following high-throughput sequencing via Illumina HiSeq 4000, a total of 258 differentially expressed genes were identified. Subsequent data analysis indicates an inflammatory and immune response generated by the epithelial cells following infection, marked by chemotactic cytokines and interferon stimulated genes. Several genes associated with tight and adherens junctions were found to be downregulated. These data represent the first study to investigate the impact of B. burgdorferi on choroid plexus epithelial cells, implicating the choroid plexus in the pathogenesis of neurological manifestations of Lyme disease.

overall_design: Primary human choroid plexus epithelial cells were infected with B. burgdorferi in vitro for 48 hours. RNA was isolated and sequenced via Illumina HiSeq 4000

first: Jordyn

last: Sorenson

first: Jacob

last: Greenmyer

first: Catherine

middle: A

last: Brissette

first: John

last: Watt


title: Accelerated knowledge discovery from omics data by optimal experimental design

city: Davis

first: Ilias

last: Tagkopoulos

state: California

address: 1 Shields Ave, Davis, CA 95616

institute: University of California, Davis

summary: How to design experiments that accelerate knowledge discovery on complex biological landscapes remains a tantalizing question. Here, we present OPEX, an optimal experimental design method to identify informative omics experiments for both experimental space exploration and model training. OPEX-guided exploration of  Escherichia coli's cross-behavior potential, when exposed to novel biocide and antibiotic combinations, led to accelerated knowledge discovery with predictive models that are more accurate while needing 44% fewer data to train. Selecting experiments favoring broader exploration followed by fine-tuning emerged as the optimal strategy. This led to the discovery of 29 cross-protection and 4 cross-vulnerability conditions, with further validation revealing the central role of chaperones, stress response proteins and transport pumps in cross-stress exposure. This work demonstrates how active learning can be used to automate omics data collection for training accurate predictive models, evidence-driven decision making and accelerated knowledge discovery in life sciences.

overall_design: We have 45 samples and each one has 3 biological replicates. The 45 samples include a control sample.

first: Xiaokang

last: Wang

first: Navneet

last: Rai

first: Beatriz

middle: M

last: Piovesan Pereira

first: Ameen

last: Eetemadi


title: LTi-like cells in the gut, mLN and spleen

city: Beijing

first: Wenyan

address: Tsinghua University

department: School of Medicine

institute: Institute for Immunology

summary: We plan to describe different characters of LTi-like cells from distinct tissues. Also, we further compare the LTi-like cells from both Id2fl/fl and RorccreId2fl/fl mLN and gut.

overall_design: 2 duplicates of mRNA profiles of 3 tissues

first: Yiping

last: Li

first: Xiaohuan

last: Guo


title: RNA-seq transcriptomic profiling in normal human thymocytes

city: Paris

first: Vahid

last: Asnafi

address: 149 rue de Sèvres

institute: APHP

summary: RNA-seq data to study the expression profiles in different stages of human T cell precursors

overall_design: RNA-Seq of 6 major human thymic subpopulations and 3 replicates of total thymus

first: Agata

last: Cieslak

first: Guillaume

last: Charbonnier

first: Yasmine

last: Kermezli

first: Melania

last: Tesio

first: Eve-Lyne

last: Mathieu

first: Mohamed

last: Belhocine

first: Aurore

last: Touzart

last: Hypolite

last: Andrieu

first: Joost

last: Martens

first: Eva

last: Janssen-Megens

first: Marta

last: Gut

first: Ivo

first: Nicolas

last: Boissel

first: Arnaud

last: Petit

first: Denis

last: Puthier

first: Elizabeth

last: Macintyre

first: Beatrice

last: Loriod

first: Aurélie

last: Bergon

first: Hendrik

last: Stunnenberg

first: Salvatore

last: Spicuglia


title: Analysis of exosomal circRNAs upon irradiation in pancreatic cancer cell repopulation

first: Ling

last: Tian

state: Shanghai

address: No. 650, New Songjiang Road

department: Institute of Translational Medicine

institute: Shanghai General Hospital

summary: Next generation sequencing (NGS) and bioinformatics were performed to analysis and annotate the expression profiles and functions of exosome-derived circRNAs in pancreatic cells during radiation. A total of 12572 circRNAs were identified, and 3580 circRNAs were annotated in literatures and circBase. There were 196 filtered differentially expressed circRNAs (182 for up-regulated and 14 for down-regulated, fold change > 2, p-value < 0.05). GO and KEGG analyses indicated that regulation of metabolic process and lysine degradation were the main biological processes and pathway enrichment. 4 circRNAs were chosen for qRT-PCR analysis to validate the sequencing. The hsa_circ_0002130-hsa-miR-4482-3p-NBN interaction network suggested potential miRNA sponges and target mRNAs. Our results provided potential functions of circRNAs to explore molecular mechanisms and therapeutic targets in pancreatic cancer cell upon irradiation.

overall_design: Examination of total RNA profiles of pancreatic cells-derived exosomes by NGS


title: Expression Profile Analysis of Rat Motoneurons During Myelination

city: Istanbul

first: Bilal

middle: Ersen

last: Kerman

state: Beykoz

address: Kavacik Mah. Ekinciler Cad. No:19

institute: Istanbul Medipol University

summary:
Disorders that disrupt myelin during development or in adulthood, such as multiple sclerosis and peripheral neuropathies, lead to severe pathologies, illustrating myelin’s crucial role in normal neural functioning. However, although our understanding of Schwann cell and oligodendrocyte biology is increasing, the signals that emanate from axons and regulate myelination remain largely unknown.
To identify the core components of the myelination process, we adopted a microarray analysis approach combined with laser capture microdissection of spinal motoneurons (MNs) during the myelinogenic phase of development.

overall_design: We isolated single MNs by LCM from the lumbar spinal cord of 1-day-old (during myelination) and 21-day-old (after completion of myelination) Wistar albino rats. 4 separate rat litters were used in the experiment, with animals from each litter divided into P1 and P21 experimental groups. This design resulted in four biological replicates for each age that were processed independently for microarray analysis using Affymetrix RAE230 2.0 genome arrays.

middle: E

first: Stéphane

last: Genoud

first: Burcu

middle: K

last: Vatandaslar

first: Ahmet

last: Denli

first: Shereen

last: Gosh

first: Xiangdong

last: Xu

first: Gene

last: Yeo

first: James

last: Aimone

first: Fred

last: Gage


title: Involvement of the DNA damage response kinase Rad53 and core histones in the transcriptional response to carbon source switch in budding yeast

city: Milan

first: Christopher

last: Bruhn

address: Via Adamello 16

country: Italy

institute: Fondazione Istituto FIRC di Oncologia Molecolare (IFOM)

summary: We applied RNA-Seq analysis to investigate the involvement of the DNA damage response kinase Rad53 and core histones in the transcriptional response to a carbon source switch from 2% glucose to 3% ethanol. Cells were cultured in synthetic complete medium with 2% glucose and switched to 3% ethanol. Samples were collleted in log phase in glucose, 1 hour after the switch (acute response) or 20 hours after the switch (adaptation). The data show that subtelomeric genes are repressed in sml1 rad53 mutants irrespective of the carbon source, in a histone-dependent manner. The data further show that Rad53 is not involved in the global carbon source switch response, but specifically in the expression of switch-inducible subtelomeric genes.

overall_design: The dataset includes 10 samples in experimental duplicates. sml1Δ = control (glucose, 1 hour ethanol, 20 hours ethanol), sml1Δrad53Δ = deletion of RAD53 (glucose, 1 hour ethanol, 20 hours ethanol), sml1Δhht2Δ = deletion of HHT2 which is one of two genes encoding histone H3 (glucose, 1 hour ethanol), sml1Δrad53Δhht2Δ = deletion of RAD53 and HHT2 (glucose, 1 hour ethanol). The control strain is sml1Δ because deletion of SML1 rescues the lethality of rad53Δ. The dataset allows the comparison of sml1Δrad53Δ vs. sml1Δ in glucose and at 1 hour and 20 hours after the carbon sourcce switch. It allows the contribution of HHT2 to transcriptional alterations in sml1Δrad53Δ in glucose and at 1 hour after the carbon source switch (sml1Δrad53Δhht2Δ vs. sml1Δrad53Δ).


title: Genome-wide CRISPRi screen for myriocin sensitivity

city: San Francisco

first: Manuel

last: Leonetti

address: 499 Illinois St 4th floor

institute: Chan Zuckerberg Biohub

summary: To delineate cellular pathways underlying cell growth in the absence of sphingolipid syntehsis, we performed a genome-wide CRISPRi screen to identify genetic modifiers of myriocin sensitivity in human K562 cells.

overall_design: Pooled CRISPR screening experiment. A library of constructs expressing sgRNAs were cloned and transduced as a pool in K562 cells. Cells were passaged in de-lipidated culture conditions and treated with 1 µM myriocin or DMSO. T0 ("time-zero", pre-treatment, 5-days post-infection) and myriocin/DMSO-treated endpoint samples (after 6 days of treatment) were harvested. Genomic DNA was processed and sequenced to obtain sgRNA counts in the cell population, and phenotypes were quantified by comparing representation at T0 and DMSO and myriocin-treated endpoints.

first: M

first: J

middle: S

last: Weissman


title: A transcriptomic analysis of diploid and triploid Atlantic salmon lenses with and without cataracts

status: Public on Jul 08 2020

city: Bodø

first: Pål

middle: A.

last: Olsvik

address: Universitetsalléen 11

department: Faculty of Biosciences and Aquaculture

country: Norway

institute: Nord University

summary:
To avoid negative environmental impacts of escapees and potential inter-breeding with wild populations, the Atlantic salmon farming industry has and continues to extensively test triploid fish that are sterile. However, they often show differences in performance, physiology, behavior and morphology compared to diploid fish, with increased prevalence of vertebral deformities and ocular cataracts as two of the most severe disorders.
Here, we investigated the mechanisms behind the higher prevalence of cataracts in triploid salmon, by comparing the transcriptional patterns in lenses of diploid and triploid Atlantic salmon, with and without cataracts. We assembled and characterized the Atlantic salmon lens transcriptome and used RNA-seq to search for the molecular basis for cataract development in triploid fish.
Transcriptional screening showed only modest differences in lens mRNA levels in diploid and triploid fish, with few uniquely expressed genes. In total, there were 165 differentially expressed genes (DEGs) between the cataractous diploid and triploid lens. Of these, most were expressed at lower levels in triploid fish. Differential expression was observed for genes encoding proteins with known function in the retina (phototransduction) and proteins associated with repair and compensation mechanisms.
The results suggest a higher susceptibility to oxidative stress in triploid lenses, and that mechanisms connected to the ability to handle damaged proteins are differentially affected in cataractous lenses from diploid and triploid salmon.

overall_design: The four treatment groups were diploid salmon without cataract (2N-), diplid salmon with cataract (2N+), triploid salmon without cataract (3N-) and triploid salmon with cataract (3N+). Sample number was n=6 for each group (2N-, 2N+, 3N-), except 3N+ which had n=8. A total of 26 lens samples were sequenced. For each sample, about 24 million 50 bp single-end reads were generated.

first: Roderick

middle: N

last: Finn

first: Sofie

middle: C

last: Remø

first: Per

last: Fjelldal

first: Francois

last: Chauvigné

first: Kevin

last: Glover

first: Tom

last: Hansen

first: Rune

last: Waagbø


title: Gene expression of SARS-CoV-2-infected Vero E6 cells

city: Bethesda

first: Eytan

last: Ruppin

address: 9000 Rockville Pike

institute: National Institutes of Health

summary: We conducted a high-throughput drug repositioning screen using the LOPAC®1280 and the ReFRAME drug libraries to identify existing drugs that harbor antiviral activity against SARS-CoV-2, in a Vero E6 cell-based assay. We additionally performed RNA sequencing on control and SARS-CoV-2 infected Vero E6 cells to study the biological changes after SARS-CoV-2 infection and to elucidate the potential mechanisms underlying the positive hits identified from our high-throughput screen. Vero E6 cells were either mock-infected or infected with SARS-CoV-2 USA-WA1/2020 (MOI = 0.3) with three replicates. Cells were harvested 24 hours after infection, and total RNA was extracted using the Qiagen® RNeasy® Plus Mini Kit. The quality of the extracted RNA was assessed with the Agilent® 2100 Bioanalyzer. Libraries were prepared from total RNA following ribosome RNA depletion using standard protocol according to Illumina®. Total RNA sequencing was then performed on the Illumina® NextSeq system; 150bp paired-end runs were performed and 100 million raw reads per sample were generated.

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: mRNA profiles of control (mock-infected) and 24h post-SARS-CoV-2-infection Vero E6 cells with three replicates.

first: Laura

last: Riva

first: Kuoyuan

last: Cheng

first: Sumit

last: Chanda


title: Serum metabolomics associating with circulating microRNA profiles reveal the role of miR-383-5p in rat hippocampus under simulated microgravity

city: Haidian District

first: Zhongquan

last: Dai

state: Beijing

address: No. 26 Beiqing Road

institute: Astronaut Research and training Center

summary:
Microgravity impacts various aspects of human health. Yet the mechanisms of spaceflight-induced health problems are not elucidated. Here we mapped the fusion systemic analysis of the serum metabolome and the circulating microRNAome in a hindlimb unloading rat model to simulate microgravity. The response of serum metabolites and microRNAs to simulated microgravity (SMG) was striking. Integrated pathway analysis of altered serum metabolites and target genes of the significantly altered circulating miRNAs with Integrated Molecular Pathway-Level Analysis (IMPaLA) software was mainly suggestive of modulation of neurofunctional signaling pathways. Particularly, we revealed significantly increased miR-383-5p and decreased aquaporin 4 (AQP4) - in the hippocampus. Utilizing Rrabies Virus Glycoprotein (RVG)-modified exosomes, delivery of miR-383-5p inhibited the expression of AQP4 not only in rat C6 glioma cells in vitro but also in the hippocampus in vivo. Using bioinformatics to map the crosstalk between the circulating metabolome and miRNAome could offer opportunities to understand complex biological systems under microgravity. Our present results suggested that the change of miR-383-5p level and its regulation of target gene AQP4 was one of the potential molecular mechanisms of microgravity induced cognitive impairment in the hippocampus.
MiRNA plays an important role during the adaptation to microgavity. In this study, effects of simulated microgravity on circulating microRNA profiles were performed to sreen different expression miRNA and gravity-sensitive miRNAs.

overall_design: To investigate the influence of simulated microgravity on the circulating miRNAome, the male SD rats were randomly assigned to the control group or the hindlimb unloading group to simulated microgravity for 28 days under 12hr light/ 12hr dark schedule.Total miRNA was extracted form Serum and used for miRNA microarrays analysis with 3 pooled control samples and 4 pooled Hindlimb suspension simulated mcirogravity samples (each pool was composed of 4 individual serum samples with the same volume)

first: Hongyu

last: Zhang

first: Jian

last: Chen

first: Feng

last: Wu

first: Chao

last: Yang

first: Hailong

last: Wang

first: Kai

last: Li

first: Yinghui


title: Multiexon deletion alleles of ATF6 linked to achromatopsia

city: La Jolla

first: R. Luke

last: Wiseman

address: 10550 North Torrey Pines Road

department: Molecular Medicine

institute: The Scripps Research Institute

summary: Achromatopsia (ACHM) is an autosomal recessive disease that results in severe visual loss. Symptoms of ACHM include impaired visual acuity, nystagmus, and photoaversion starting from infancy; furthermore, ACHM is associated with bilateral foveal hypoplasia and absent or severely reduced cone photoreceptor function on electroretinography. Here, we performed genetic sequencing in 3 patients from 2 families with ACHM, identifying and functionally characterizing 2 mutations in the activating transcription factor 6 (ATF6) gene. We identified a homozygous deletion covering exons 8–14 of the ATF6 gene from 2 siblings from the same family. In another patient from a different family, we identified a heterozygous deletion covering exons 2 and 3 of the ATF6 gene found in trans with a previously identified ATF6 c.970C>T (p.Arg324Cys) ACHM disease allele. Recombinant ATF6 proteins bearing these exon deletions showed markedly impaired transcriptional activity by qPCR and RNA-Seq analysis compared with WT-ATF6. Finally, RNAscope revealed that ATF6 and the related ATF6B transcripts were expressed in cones as well as in all retinal layers in normal human retina. Overall, our data identify loss-of-function ATF6 disease alleles that cause human foveal disease.

overall_design: Comparisons of the transcriptomes of transfected HEK293 cells overexpressing WT or mutant ATF6 alleles compared to non-transfected cells.

first: Wei-Chieh

middle: J

last: Chiang

first: Julia

last: Grandjean

first: Eun-Jin

last: Lee

first: Evan

middle: T

last: Powers

first: R

middle: L

first: Jonathan

middle: H

last: Lin


title: Next Generation Sequencing Facilitates Quantitative Analysis of the effects of PD-1 deficiency on sorted mouse pulmonary ILC2 Transcriptomes

city: Los Angeles

first: Georges Doumet

last: HELOU

address: 1450 Biggy St, NRT5505, Keck School of Medicine

department: Molecular Microbiology and Immunology

institute: University of Southern California

summary: Allergic asthma is a leading chronic disease associated with airway hyperreactivity (AHR). Type-2 innate lymphoid cells (ILC2s) are a potent source of T-helper 2 cytokines that promote AHR and lung inflammation. In this study, we evaluated the protective role of PD-1 on the development of AHR by focusing on its capacity to regulate ILC2 activation. We find that PD-1 is highly inducible in pulmonary ILC2s and shapes their transcriptional activity, activation and metabolism. Our findings provide new insights regarding the mechanisms of ILC2 regulation, which could be used in innovative approaches for the treatment of allergic asthma.

overall_design: mRNA profiles of sorted mouse pulmonary ILC2s from BALB/cByJ (WT) and PD-1 KO mice were generated by deep sequencing, in triplicate, using a NextSeq 500 (Illumina) system.

first: D

first: O

last: AKBARI


title: lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation [RIP-seq]

city: Boston

first: Alan

middle: C.

last: Mullen

state: MA

address: 55 Fruit St.

department: Department of Medicine

institute: Massachusetts General Hospital

overall_design: Analysis of BRD3 binding RNAs in human stem cells and definintive endoderm cells.

first: Kaveh

last: Daneshvar

first: Amin

last: Mahpour


title: Generation of Ionic Liquid Tolerant Pseudomonas putida KT2440 Strains via Adaptive Laboratory Evolution

city: San Diego

first: Bernhard

middle: O.

last: Palsson

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California, San Diego

summary: Transcriptome of the wildtype or evolved Pseudomonas putida KT2440

overall_design: Transcriptome was prepared from cell cultures of Pseudomonas putida KT2440 at the exponential phase

first: Hyungyu

last: Lim

first: Adam

last: Feist


title: Site-specific Wnt signalling explains regional differences in bone physiology – Evidence from a cross-species RNA-Seq study comparing osteocyte transcriptomes in the tibia and skull

city: Sheffield

first: Ning

address: Beech Hill Road

institute: University of Sheffield

summary: Local site-specific differences between bones in different regions of the skeleton account for their different properties and functions. To identify mechanisms behind these differences, we have performed a cross-species study comparing RNA transcriptomes of cranial and tibial osteocytes, from bones with very different primary functions and physiological responses, collected from the same individual mouse, rat and rhesus macaque. Bioinformatic analysis was performed to identify 32 genes changed in the same direction between sites and shared across all three species. Several well-established key genes in bone growth and remodelling were upregulated in the tibias of all three species (BMP7, DKK1, FGF1, FRZB, SOST). Many of them associate or crosstalk with the canonical Wnt signalling pathway. These results suggest Wnt signalling-related candidates for different control of regulatory mechanisms in bone homeostasis in the skull and tibia and indicate a different balance between genetically determined structure and feedback mechanisms to strains induced by mechanical loading at the different sites.

sample_organism:
Macaca mulatta
Mus musculus
Rattus norvegicus

overall_design: mRNA profile comparison of osteocytes in skull and long bone. It's a cross species study involving mouse, rat and rhesus macaques

first: Corinne

last: Niger

first: Gareth

middle: O

last: Richards

first: Tim

last: Skerry


title: An in vitro model of chronic wounding and its implication for age-related macular degeneration

city: Santa Barbara

first: Lindsay

last: Bailey-Steinitz

address: 6131 Biological Sci Bldg II

department: MCDB, NRI

institute: University of California, Santa Barbara

summary: Age-related macular degeneration (AMD) is a leading cause of blindness in the developed world. In this study we investigated changes in differentated human retinal pigmented epithelial (RPE) cells to acute compared to chronic wounding. There are many interesting phenotypic and transcriptomic changes that occur after chronic wounding compared to acute wounding conditions which may have implications for AMD.

overall_design: Examination of mRNA expression in acutely or chronicaly wounded human RPE cultures 5-hours, 24-hours and 8-days after final wound. Unwounded cultures served as controls.

first: Ying-Hsuan

last: Shih

first: Monte

last: Radeke

first: Pete

last: Coffey


title: Alteration in the transcriptome of lung resident fibroblast isolated from fibrotic lungs of TGFalpha mice upon genetic knockdown of  Aurora Kinase B

city: Cincinnati

first: Anil

middle: G

last: Jegga

state: OH

address: 240 Albert Sabin Way

department: Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

summary:
Pulmonary fibrosis (PF) is associated with many chronic lung diseases including Systemic sclerosis (SSc), Idiopathic Pulmonary Fibrosis (IPF) and Cystic Fibrosis (CF) which are characterized by the progressive accumulation of mesenchymal cells and formation of scar tissue. Pulmonary fibrosis is a dysregulated response to alveolar injury which causes  a progressive decline in lung function and refractory to current pharmacological therapies.  Airway and alveolar epithelial cells and mesenchymal cells contribute to pulmonary fibrosis but the cell-specific pathways and gene networks that are responsible for the pathophysiology are unknown. Our new findings have identified the abberent activation of Aurora Kinase B (AURKB) in lung resident fibroblast and myofibroblast in IPF lung biopsies and the mouse model of transforming growth factor-α (TGFα) and bleomycin induced fibrosis. In this study, we sought to determine the role of AURKB in transcriptome changes in lung resident fibroblast during pulmonary fibrosis. Our results showed that AURKB regulates the transcriptional changes that are required for the fibroblast activation processes such fibroproliferation, myofibroblast survival and extracellular matrix deposition during pulmonary fibrosis. Finally, this study demonstrates that AURKB is a critcal regulator of fibroblast activation in IPF and hence serve as a target for therapeutic intervention.

Grantee: Satish K Madala
Grantor: US Department of Defense funds
Grant ID: W81XWH-17-1-0666
Grant Title: Therapeutic Benefit of Hsp90 Inhibition in Pulmonary Fibrosis

overall_design: mRNA profiles of cultured fibrotic lung resident fibroblast isolated from TGFalpha mice on Dox for 10 days and treated with Control or AURKB-specific siRNA

first: Rajesh

last: Kasam

first: Sudhir

last: Ghandikota

first: Divyalakshmi

last: Soundararajan

first: Geereddy

middle: B

last: Reddy

first: Steven

last: Huang

first: Satish

last: Madala


title: Cardiolipin is required for membrane docking of mitochondrial ribosomes and protein synthesis

city: Perth

first: Stefan

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

country: Australia

institute: The Kids Research Institute Australia

summary: The mitochondrial inner membrane contains a unique phospholipid known as cardiolipin (CL), which stabilises the protein complexes embedded in the membrane and supports its overall structure. Recent evidence indicates that the mitochondrial ribosome may associate with the inner membrane to facilitate co-translational insertion of the hydrophobic oxidative phosphorylation (OXPHOS) proteins into the inner membrane. We generated three mutant knockout cell lines for the cardiolipin biosynthesis gene Crls1 to investigate the effects of cardiolipin loss on mitochondrial protein synthesis. Reduced CL levels caused altered mitochondrial morphology and transcriptome-wide changes that were accompanied by reduced uncoordinated mitochondrial translation rates and impaired respiratory supercomplex formation. Aberrant protein synthesis was caused by impaired formation and distribution of mitochondrial ribosomes. Reduction or loss of cardiolipin resulted in resulted in different mitochondrial and endoplasmic reticulum stress responses. We show that cardiolipin is required to stabilise the interaction of the mitochondrial ribosome with the membrane via its association with OXA1 during active translation. This interaction facilitates insertion of newly synthesised mitochondrial proteins into the inner membrane and stabilises the respiratory supercomplexes.

overall_design: Total RNA was isolated, in triplicate, from NIH-3T3 cells with Crls1WT, Crls1KO1, Crls1KO2, and Crls1KO3 genotypes and TruSeq libraries prepared, sequenced and analysed for differential expression.

first: Richard

last: Lee

first: Junjie

last: Gao

first: Anne-Marie

last: SHearwood

first: Judith

middle: A

last: Ermer

first: Vinzenz

last: Hofferek

first: James

last: Matthews

first: Minghao

last: Zheng

first: Gavin

last: Reid

first: Oliver

last: Rackham

first: Aleksandra

last: Filipovska


title: Fluvastatin-perturbed RNA expression in two t(4;14)-positive multiple myeloma cell lines

city: Toronto

first: Petr

last: Smirnov

state: ON

address: 27 King's College Cir

department: Medical Biophysics

institute: University of Toronto

summary: The goal of this study was to determine the gene expression changes following fluvastatin treatment in t(4;14)-positive multiple myeloma (MM) cell lines. To this end, two cell lines (KMS11 and NCI-H929) were treated with fluvastatin (2 micromolar) or ethanol as a solvent control for 24 hours. RNA was extracted and prepared for high-throughput sequencing in duplicate.

overall_design: Two cell lines, each treated with fluvastatin or ethanol as a solvent control (two replicates per treatment condition)

first: Joseph

last: Longo

first: Benjamin

last: Haibe-Kains

first: Trevor

last: Pugh

first: Linda

middle: Z

last: Penn


title: 22q11.2 deletion syndrome human cortical organoids

first: Aaron

last: Gordon

address: 695 Charles E. Young Drive South, Gonda 2306, Los Angeles, CA  90095-1761

department: Neurology

institute: UCLA

summary: We derived iPSC from individuals carrying a 22q11.2 deletion and controls and differentiated them into 3D cortical organoids.

overall_design:
Differentiation was performed across 14 control and 15 22q11.2 lines and sampled at 4 time points (days 25, 50, 75 and 100).
-------------------------------------------------
Authors state "Due to HIPPA compliance issues, submitters are unable to provide raw data" and "Due to  the way the data was collected we are unable at this time to submit it to dbGAP."

first: Se-Jin

last: Yoon

first: Themasap

last: Khan

first: Sergiu

middle: P

last: Pasca

first: Daniel

last: Geschwind


title: Epigenome analysis of NET samples

first: Paul

last: Meltzer

address: 9100 Rockville Pike

institute: NCI/NIH

summary:
Genome wide DNA methylation profiling of hereditary and sporadic NET using GPL21145
Bisulphite converted DNA from 96 samples were hybridised to the Illumina Infinium Epic Human Methylation Beadchip

overall_design: Methylation profiling of neuroendocrine tumors of varying clinical and molecular subtype

first: Electron

last: Kebebew

first: J

middle: K

last: Killian


title: DeepC: Predicting chromatin interactions using megabase scaled deep neural networks and transfer learning (NG Capture-C)

city: Oxford

first: Ron

last: Schwessinger

address: MRC WIMM, John Radcliffe Hospital, Headington

department: MRC Weatherall Institute if Molecular Medicine

institute: University of Oxford

summary: Understanding 3D genome structure requires high throughput, genome-wide approaches. However, assays for all vs. all chromatin interaction mapping are expensive and time consuming, which severely restricts their usage for large-scale mutagenesis screens or for mapping the impact of sequence variants. Computational models sophisticated enough to grasp the determinants of chromatin folding provide a unique window into the functional determinants of 3D genome structure as well as the effects of genome variation.  A chromatin interaction predictor should work at the base pair level but also incorporate large-scale genomic context to simultaneously capture the large scale and intricate structures of chromatin architecture. Similarly, to be a flexible and generalisable approach it should also be applicable to data it has not been explicitly trained on. To develop a model with these properties, we designed a deep neuronal network (deepC) that utilizes transfer learning to accurately predict chromatin interactions from DNA sequence at megabase scale. The model generalizes well to unseen chromosomes and works across cell types, Hi-C data resolutions and a range of sequencing depths. DeepC integrates DNA sequence context on an unprecedented scale, bridging the different levels of resolution from base pairs to TADs. We demonstrate how this model allows us to investigate sequence determinants of chromatin folding at genome-wide scale and to predict the importance of regulatory elements and the impact of sequence variations.

overall_design: To validate in silico predictions of chromatin interactions at high resolution and scale, we performed NG Capture-C (Davies 2016) from 220 viewpoints in two cell lines (K562 (WIMM transgenics facility) and GM12878 - LCLs (Coriell)), from which predicted chromatin interactions have been generated. These viewpoints comprise 81 CTCF sites and 139 intra domain viewpoints designed to avoid active element overlap. Library preparation and NG Capture-C was performed in biological triplicates with four unique adapters being used for each replicate to increase sequencing depth and minimize PCR duplicates. These were pooled for maximum resolution. Capture was performed with biotinylated oligonucleotides targeting sequences adjacent to DpnII sites at the viewpoints of interest.

first: Damien

last: Downes

first: Matthew

last: Gosden

first: Jim

middle: R

last: Hughes


title: lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation

first: Alan

last: Mullen

summary: Gene programs that control differentiation are regulated through the interplay between DNA, RNA, and protein. Cooperation among these fundamental cellular components can occur through highly structured interactions connecting domains formed by specific sequences of nucleotides, ribonucleotides, and/or amino acids and also through the assembly of biomolecular condensates. Here, we show that endoderm differentiation is regulated through the interaction of the long noncoding (lnc) RNA DIGITand the bromodomain and extra-terminal (BET) domain family protein BRD3. BRD3 forms phase-separated condensates that contain DIGIT, occupies enhancers of endoderm transcription factors, and is required for endoderm differentiation. Purified BRD3 binds to acetylated histone H3 lysine 18 (H3K18ac) in vitro and occupies regions of the genome enriched in H3K18ac during endoderm differentiation, including the key transcription factors that regulate endoderm differentiation. DIGIT is also enriched in regions of H3K18ac, and depletion of DIGIT results in decreased recruitment of BRD3 to these regions. Our findings support a model where cooperation between DIGIT and BRD3 at regions of H3K18ac regulates the transcription factors that drive endoderm differentiation and suggest a broader role for protein-lncRNA phase-separated condensates as regulators of transcription in development.

overall_design: BRD3 ChIP-seq was performed and analyzed to define the regions of the human genome occupied by BRD3 in human embryonic stem cells (hESCs) and after four days of endoderm differentiation.

first: Kaveh

last: Daneshvar

first: Chan

last: Zhou

first: Arcadia

last: Kratkiewicz

first: Sean

last: Moran


title: DeepC: Predicting chromatin interactions using megabase scaled deep neural networks and transfer learning (Tiled-C)

overall_design: To validate in silico predictions of chromatin interactions at high resolution comparable to Hi-C maps, we performed Tiled-C (Oudelaar and Beagrie et al.2019) over three regions in two cell lines (K562 (WIMM transgenics facility) and GM12878 - LCLs (Coriell)), from which predicted chromatin interactions have been generated. Tiled-C resolves the chromatin interactions over the selected regions at higher resolution and contrast then Hi-C currently can. Library preparation and NG Capture-C was performed in biological triplicates with four unique adapters being used for each replicate to increase sequencing depth and minimize PCR duplicates. These were pooled for maximum resolution. Tiled-C was performed with biotinylated double stranded oligonucleotides targeting sequences adjacent to DpnII sites at tiled restriction fragments over the regions of interest.


title: Global gene expression (transcriptome) analysis by mRNAseq on iPSC-derived MSCs

city: Hawthorn North

first: Kilian

last: Kelly

state: Victoria

address: PO Box 7165

institute: Cynata Therapeutics Limited

summary: Global gene expression (transcriptome) analysis was performed by messenger RNA sequencing (mRNAseq) on iPSC-derived MSCs produced in three separate lots to determine consistency in gene expression between lots.

overall_design:
Total RNA was extracted from iPSC-derived MSC samples, from which mRNA was then isolated, and analysed using the Illumina HiSeq 2500 platform. Normalised Transcripts Per Kilobase Million (TPM) counts for each sample were then calculated and plotted against one another, and the Pearson correlation was computed to determine the degree of consistency of gene expression and isoforms between samples.
contributor: The University of Wisconsin Bioinformatics Resource Center


title: KDM3A/Ets1 epigenetic axis contributes to PAX3/FOXO1-driven and independent disease-promoting gene expression in fusion-positive Rhabdomyosarcoma

status: Public on Jul 07 2020

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

summary: The goal of this study was to define functional and gene regulatory effects of KDM3A and Ets1, and their relationship to the PAX3/FOXO1 driver oncofusion, in fusion-positive Rhabdomyosarcoma.

overall_design: RNA-seq was used to define the effects of KDM3A and Ets1 shRNA-mediated depletion on gene expression in the patient-derived fusion-positive Rhabdomyosarcoma cell lines Rh41 and Rh30.

last: Jedlicka

first: Lays

middle: M

last: Sobral

first: Hannah

last: Hicks

first: Janet

last: Parrish

first: Tyler

middle: S

last: McCann

first: Joseph

last: Hsieh

first: James

last: Costello

first: Joshua

last: Black


title: Complementary networks of cortical somatostatin interneurons enforce layer specific control

city: Padova

first: Davide

last: Risso

address: Via C. Battisti, 241

institute: University of Padova

summary: The neocortex is functionally organized into layers. Layer four receives the densest bottom up sensory inputs, while layers 2/3 and 5 receive top down inputs that may convey predictive information. A subset of cortical somatostatin (SST) neurons, the Martinotti cells, gate top down input by inhibiting the apical dendrites of pyramidal cells in layers 2/3 and 5, but it is unknown whether an analogous inhibitory mechanism controls activity in layer 4. Using high precision circuit mapping, in vivo optogenetic perturbations, and single cell transcriptional profiling, we reveal complementary circuits in the mouse barrel cortex involving genetically distinct SST subtypes that specifically and reciprocally interconnect with excitatory cells in different layers: Martinotti cells connect with layers 2/3 and 5, whereas non-Martinotti cells connect with layer 4. By enforcing layer-specific inhibition, these parallel SST subnetworks could independently regulate the balance between bottom up and top down input.

overall_design: Six triple transgenic SST-TdT-X94 mice (age P97) were euthanized and their brains vibratome sectioned.  The somatosensory cortex was microdissected from the slices using a fine scalpel. We collected GFP+; tdTomato+ and cells into Sorting Solution (GFP+). We then collected a separate population of tdTomato+ irrespective of GFP fluorescence (tdT+) from the same batch of dissociated cells.  Separately, we performed the same procedure on two other batches of triple transgenic SST-TdT-X94 mice (age p45), but in these experiments we performed only the latter sort- collecting SST cells based on tdTomato fluorescence alone.

first: Alexander

last: Naka

first: David

last: Stafford


title: PQM-1 and Cobalt Chloride dependent gene expression changes in C. elegans

city: Freiburg

first: Thomas

last: Heimbucher

state: Baden Württemberg

address: Schaenzlestrasse 1

department: Biologie III

institute: Thomas Heimbucher

summary:
Worms were exposed to 5 mM CoCl2 at the early day 1 of adulthood stage for 6 hr and 20 hr. Untreated worms were used as controls. Worms were collected, RNA isolated and hybridized on 4x44K C. elegans arrays (Agilent) at 60C overnight, as previously described 1). Three biological replicates were used. Significant differentially-expressed gene sets were identified using one or two-class SAM 2).
1) Shaw, W. M., Luo, S., Landis, J., Ashraf, J. & Murphy, C. T. The C. elegans TGF-beta Dauer pathway regulates longevity via insulin signaling. Curr Biol 17, 1635-1645, doi:10.1016/j.cub.2007.08.058 (2007).
2) Tusher, V. G., Tibshirani, R. & Chu, G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 98, 5116-5121, doi:10.1073/pnas.091062498 (2001).

overall_design: All_pairs: Worms were exposed to 5 mM CoCl2 at the early day 1 of adulthood stage for 6 hours and 20 hours.


title: Dissecting the molecular programs governing interferon production by plasmacytoid dendritic cells during a viral infection in vivo

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

institute: CIML

summary: Plasmacytoid dendritic cells (pDC) are the major source of type I and type III interferons (IFN-I/III) during viral infections, in response to triggering of endosomal Toll Like Receptors (TLRs) 7 or 9 by viral single-stranded RNA or unmethylated CpG DNA, respectively. Interestingly, this function is restricted to a minor fraction of pDC (Zucchini et al. Int. Immunol. 2008). In this project, we aimed at identifying the molecular pathways involved in inducing IFN-I/III production in this minor faction of pDC during in vivo infection by the mouse cytomegalovirus (MCMV). To achive this goal, we infected with MCMV Ifnb1Eyfp mice, in which IFN-producing pDC can be detected by YFP expression (Scheu et al.  PNAS 2008). Thanks to this model, we were able to sort three distinct subsets of pDC: CD86-YFP- (not activated, non IFN-producing), CD86+YFP- (activated, non IFN-producing) and CD86+YFP+ (activated, IFN-producing) and to perform microarray analysis. This allowed us to select genes differentially expressed among these three subsets and to mine these data in order to identify  the related signaling pathways.

overall_design: Ifnb1Eyfp mice were infected or not with MCMV. Splenic pDC were isolated 36 hours after infection. The following pDC subsets were sorted: CD86-YFP-; CD86+YFP- and CD86+YFP+. The last subset was sorted exclusively from infected mice, while the other two were sorted from both uninfected and infected mice. We performed two independent sortings by pooling splenocytes of 4 (uninfected) or 10-12 (infected) Ifnb1Eyfp mice for each sorting. For each subset we sorted 10,000 cells.

first: Elena

last: Tomasello

first: Gilles

last: Bessou

first: Rabie

last: Chebi

first: Thien

first: Marc

last: Dalod


title: Nucleosomes protect DNA from irradiation-induced double strand breaks in living cells [BLISS human]

city: Milan

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

institute: OSR - San Raffaele Scientific Institute

summary: The number and position of breaks using BLISS-seq was measured in MCF-7 cells upon irradiation with 10 Gy and with or without the use of the antioxidant (N-acetylcysteine, NAC, 10mM).

overall_design: BLISS libraries are prepared from either NAC treated or untreated cells irradiated with 0, or 10 Gy of gamma-radiations. Each condition is represented with 2 or 3 biological replicates.

first: Francesca

last: Brambilla

first: Marco

middle: E

last: Bianchi

first: Alessandra

last: Agresti


title: Genome wide RNA-sequencing of sorted human pluripotent stem-cell derived endothelial cells with CLDN5-GFP reporter (GFP+ and GFP-)

city: Basel

first: Jitao David

last: Zhang

address: Grenzacherstrasse 124

department: Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel

institute: F. Hoffmann-La Roche

summary: CLDN5-GFP reporter has been engineered in hPSCs. These cells have been differentiated to Ecs. Differentaited Ecs were sorted into GFP+ and GFP- corresponding to CLDN5+ and CLDN5- to study gene expression of high-barrier resistance.

overall_design: ECs differentiated from engineered hPSC carrying the CLDN5-GFP reporter (2 separate clones) were  sorted with BD FACSAria III into GFP+ and GFP- populations (6 individual sorting procedures for each clone). RNA was isolated from all the samples and library generated that was sequenced using IIllumina Hiseq platform.

first: Filip

last: Roudnicky


title: An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease (RNA-seq with ERCC spike-in) [RNA-Seq]

city: Philadelphia

first: Yemin

last: Lan

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: We report the ERCC spike-in controlled RNA-seq in human hippocampus subject to normal aging and Alzheimer's disease.

overall_design: ERCC spike-in controlled RNA-seq in postmortal lateral temporal lobe of Alzheimer's disease affected brains (AD), control Old (Old) and control Young (Young).

first: Raffaella

last: Nativio

first: Berger

last: Shelley


title: Genome wide RNA-sequencing of human pluripotent stem-cell derived endothelial cells treated with TGF-beta receptor inhbitors with or without VEGFA stimulation

summary: Transcriptional response to TGF-beta receptor inhibtion with or without VEGFA stimulation

overall_design: ECs differentiated from engineered hPSC  were treated with DMSO or TGF beta receptor inhibitors (RepSox or SB431542) with or without VEGFA for 8h or 48h. Cells were lyzed after treatment, RNA was isolated and library generated that was sequenced on Illumina platform.


title: Cocaine-mediated circadian reprogramming in the striatum through a dopamine D2 receptor-PPARg circuit

status: Public on Jul 15 2020

city: irvine

first: Siwei

last: Chen

address: 66304 Verano Road South

department: Computer Science

institute: University of California, Irvine

summary: Cocaine-dependent genome-wide effects were analyzed, total RNAs were extracted from ventral striatum tissue punches and processed for RNA-seq analyses.

overall_design: Circadian expression of striatal genes after an acute cocaine challenge, WT and iMSN-D2RKO mice received an i.p. injection of either cocaine (Coc, 20 mg/kg) or saline (Sal) shortly after the beginning of the resting phase (zeitgeber time, ZT3). Animals from both groups were sacrificed every 4 hours (n=3/time point) and punches of ventral striatum collected at six time points over a full circadian cycle

first: Emiliana

last: Borrelli

first: Paolo

last: Sassone-Corsi


title: Effect of pre-exposure prophylaxis with tenofovir disoproxil fumarate and emtricitabine on gene expression

city: Seattle

first: Sean

last: Hughes

state: WA

address: 850 Republican St

institute: University of Washington

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

overall_design: Refer to individual Series


title: Effect of pre-exposure prophylaxis with tenofovir disoproxil fumarate and emtricitabine on gene expression in PBMC

summary: Pre-exposure prophylaxis (PrEP) with tenofovir disoproxil fumarate (TDF) and emtricitabine (FTC) effectively prevents infection with HIV-1. We sought to determine how use of these medications affects gene expression. We performed a small, prospective trial (https://clinicaltrials.gov/ct2/show/NCT02621242) of eight men initiating PrEP with TDF/FTC. We obtained blood before treatment initiation and after two months of daily use. We isolated RNA from cryopreserved peripheral blood mononuclear cells (PBMC). Gene expression was measured from all eight men at both time points.

overall_design: Gene expression was measured by Illumina HumanHT-12 v4 Expression BeadChips. Samples were paired with samples taken at baseline (pre-treatment) and after two months of daily oral use. PBMC were cryopreserved.  Samples were not replicated on the arrays.

first: Florian

last: Hladik

first: Claire

middle: N

last: Levy


title: Effect of pre-exposure prophylaxis with tenofovir disoproxil fumarate and emtricitabine on gene expression in the rectum

summary: Pre-exposure prophylaxis (PrEP) with tenofovir disoproxil fumarate (TDF) and emtricitabine (FTC) effectively prevents infection with HIV-1. We sought to determine how use of these medications affects gene expression. We performed a small, prospective trial (https://clinicaltrials.gov/ct2/show/NCT02621242) of eight men initiating PrEP with TDF/FTC. We obtained rectal biopsies before treatment initiation and after two months of daily use. We isolated RNA from rectal biopsies preserved with RNAlater. Gene expression was measured from all eight men at both time points.

overall_design: Gene expression was measured by Illumina HumanHT-12 v4 Expression BeadChips. Samples were paired with samples taken at baseline (pre-treatment) and after two months of daily oral use. Rectal biopsies were preserved with RNAlater at -80 degrees C. Samples were not replicated on the arrays.


title: Effect of pre-exposure prophylaxis with tenofovir disoproxil fumarate and emtricitabine on gene expression in the blood

summary: Pre-exposure prophylaxis (PrEP) with tenofovir disoproxil fumarate (TDF) and emtricitabine (FTC) effectively prevents infection with HIV-1. We sought to determine how use of these medications affects gene expression. We performed a small, prospective trial (https://clinicaltrials.gov/ct2/show/NCT02621242) of eight men initiating PrEP with TDF/FTC. We obtained blood before treatment initiation and after two months of daily use. We isolated RNA from whole blood (PAXgene tubes). Gene expression was measured from all eight men at both time points.

overall_design: Gene expression was measured by Illumina HumanHT-12 v4 Expression BeadChips. Samples were paired with samples taken at baseline (pre-treatment) and after two months of daily oral use. Whole blood samples were preserved at -80 degrees C in PAXgene tubes.  Samples were not replicated on the arrays.


title: Effect of pre-exposure prophylaxis with tenofovir disoproxil fumarate and emtricitabine on gene expression in the duodenum

summary: Pre-exposure prophylaxis (PrEP) with tenofovir disoproxil fumarate (TDF) and emtricitabine (FTC) effectively prevents infection with HIV-1. We sought to determine how use of these medications affects gene expression. We performed a small, prospective trial (https://clinicaltrials.gov/ct2/show/NCT02621242) of eight men initiating PrEP with TDF/FTC. We obtained duodenal biopsies before treatment initiation and after two months of daily use. We isolated RNA from duodenal biopsies preserved with RNAlater. Gene expression was measured from all eight men at both time points.

overall_design: Gene expression was measured by Illumina HumanHT-12 v4 Expression BeadChips. Samples were paired with samples taken at baseline (pre-treatment) and after two months of daily oral use. Duodenal biopsies were preserved with RNAlater at -80 degrees C. Samples were not replicated on the arrays.


title: Expression data from the HPB-ALL T-ALL cell line transduced with shETS1

city: Ann Arbor

first: Mark

middle: Yat-fung

last: Chiang

state: MI

address: 109 Zina Pitcher Place

department: Internal Medicine/Heme-onc

institute: University of Michigan

summary: To formally address the biological activity of ETS1 in vitro, we measured the transcriptional effect of ETS1 knock down by transducing HPB-ALL leukemia cell lines with a plKO - shETS1 and plko shLUC control. Samples were hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays. Log2 abundance estimates were obtained using gcrma package of Bioconductor, which is a version of the Robust Multi-Array Average (RMA) algorithm. We provide a supplementary file with gene annotation, which performs a two-sample T-test and computes an average fold-change.

overall_design: We performed microarray gene expression analysis of shETS1 vs. shRNA LUC, with 2 replicates per condition. Samples were assayed on 4 Affymetrix Human Genome U133 Plus 2.0 arrays.

first: Adolfo

last: Ferrando

first: Giusy

last: Della Gatta

first: Alberto

last: Ambesi

middle: Y

first: Rork

last: Kuick


title: A Phase 2 Randomized Sequence Open Label Expanded Safety and Acceptability Study of Oral Emtricitabine/Tenofovir Disoproxil Fumarate Tablet and Rectally-Applied Tenofovir Reduced-Glycerin 1% Gel

address: 850 Republican Street

department: Obstetrics and Gynecology

summary: Human immunodeficiency virus (HIV) disproportionately affects men who have sex with men (MSM) and transgender women (TGW). Safe and acceptable topical HIV prevention methods that target the rectum are needed. MTN-017 was a phase 2, 3-period, randomized sequence, open-label, expanded safety and acceptability crossover study comparing rectally applied reduced-glycerin (RG) 1% tenofovir (TFV) and oral emtricitabine/TFV disoproxil fumarate (FTC/TDF). In each 8-week study period participants were randomized to RG-TFV rectal gel daily, or RG-TFV rectal gel before and after receptive anal intercourse (RAI; or at least twice weekly in the event of no RAI), or daily oral FTC/TDF. MSM and TGW (n = 195) were enrolled from 8 sites in the United States, Thailand, Peru, and South Africa with mean age of 31.1 years (range 18-64). The clinical results were reported here https://www.ncbi.nlm.nih.gov/pubmed/27986684. For the gene expression study, rectal biopsies were obtained from a subset of participants (n = 36) in the United States (Pittsburgh) and Thailand (Bangkok). Biopsies were provided at baseline and after each study period.

overall_design: MTN-017 was a phase 2, multi-site, randomized, six-sequence, three-period, open-label crossover study. The two products were rectally applied reduced-glycerin (RG) 1% tenofovir (TFV) and oral emtricitabine/TFV disoproxil fumarate (FTC/TDF). The three treatments were RG-TFV gel daily, RG-TFV gel pericoitally, and oral TDF/FTC daily. Rectal biopsies were obtained at baseline and after each treatment period. There were 36 participants and each participant's baseline (pre-treatment) sample was used as a control. Samples were not replicated on the array.


title: Effect of antiretroviral prophylaxis on gene expression in peripheral blood mononuclear cells

summary:
It is important to understand how, if at all, antiretroviral prophylaxis with tenofovir disoproxil fumarate (TDF) alone or TDF in conjunction with emtricitabine (FTC) affects gene expression.  To ask this question, we used cryopreserved peripheral blood mononuclear cells (PBMC) from women enrolled in the Genital Mucosal Substudy (GMS) [1] of the Partners PrEP Study (NCT02621242) [2]. Partners PrEP was a randomized Phase III trial of oral TDF or TDF/FTC compared to placebo, which showed that either active drug was effective at protecting against HIV-1 infection. Samples were unpaired, with one sample per person, after 24-36 months of oral treatment with placebo, TDF, or TDF/FTC. Treatment adherence was based on plasma TDF concentrations.

Covariates included Nugent scores (for bacterial vaginosis), HSV-2 serology, age, and birth control method. Levels of natural and synthetic hormones (medroxyprogesterone acetate [MPA], estradiol [E2], ethinyl estradiol [EE2], levonorgestrel [LNG], etonogestrel [ENG], progesterone [P4], and norethisterone enanthate [NET-EN]) were measured in the serum.

1. Lund, J. M. et al. HIV-1-Neutralizing IgA Detected in Genital Secretions of Highly HIV-1-Exposed Seronegative Women on Oral Preexposure Prophylaxis. J. Virol. 90, 9855–9861 (2016).
2. Baeten, J. M. et al. Antiretroviral prophylaxis for HIV prevention in heterosexual men and women. N. Engl. J. Med. 367, 399–410 (2012).

overall_design: Gene expression was measured by Illumina HumanHT-12 v4 Expression BeadChips. Samples were unpaired, with one sample per person, after 24-36 months of oral treatment with placebo, TDF, or TDF/FTC. Samples from the drug arms were excluded if the TDF concentration was below the limit of detection. The final sample sizes were 20 placebo, 36 TDF, and 26 TDF/FTC. Samples were not replicated on the arrays.


title: Ets1 confers context-dependent activation of Notch signaling in T-cell leukemia [RNA-Seq]

summary: Notch activation is highly prevalent in several cancers, including more than 60% of cases of T-cell acute lymphoblastic leukemia (T-ALL). However, the use of pan-Notch inhibitors to treat cancers has been hampered by excessive toxicities, particularly affecting intestinal health. In order to combat Notch-driven oncogenic signals with less toxicity, one strategy is to target the transcriptional cofactors that promote tissue-specific Notch activation.  We previously showed that Zmiz1 is a direct Notch1 cofactor that selectively promotes T-cell development and leukemogenic functions of Notch1. Ets1 is an excellent candidate as a transcription factor (TF) that promotes Notch functions selectively in T-ALL since the scope of Ets1 expression is far more limited than Notch expression and since Ets1 co-occupies Notch-bound enhancers with  high frequency. Here, we used  comparative ChIP-Seq and gene expression methods to show that Ets1 withdrawal impaired Notch complex recruitment and H3K27 acetylation at co-bound enhancers and disabled shared oncogenic pathways. ChIP-Seq showed that Ets1 peaks overlapped with 73-76% of Zmiz1 peaks and 71-75% of Notch1 peaks. Ets1 knockdown reduced Notch1, Rbpj, and Zmiz1 occupancy at enhancers that regulate  genes that drive T-cell differentiation and/or T-ALL proliferation. RNA-Seq showed that Ets1 coregulated ~22% of Notch target genes with induction of Myc as a dominant and functional contribution. Our data support an emerging model in which transcription factors like Ets1 assist Notch in activating a subset of enhancers with important functions for T-cell leukemogenesis and development. Strategies that exploit the context dependence of Notch might combat the Notch pathway in cancer cells with less toxicity than pan-Notch inhibitors.

overall_design: RNA-Seq analysis of THP-6 cells, a human T-ALL cell line, that was transduced with shControl and two independent shEts1. Four biological replicates were performed for each shRNA.

first: Anna

last: McCarter

first: Rebecca

last: Tagett


title: Nucleosomes protect DNA from irradiation-induced double strand breaks in living cells (RNA-seq)

first: Jose

last: Garcia-Manteiga

summary: The depletion of HMGB1 reduces the deposition of histones on naked DNA (Celona et al, 2011). in primary MEFs and yeast. We verified that the downmodulation of HMGB1 decreases histone level also in a model of murine mesothelioma.  HMGB1 was KD in Murine Mesothelioma AB22 cells by the expression of a shRNA. Nucleosome positioning and occupancy were tested by ATAC-seq. Since a reduced amount of nucleosomes increase the cell sensitivity to gamma irradiatio, we tested the number and position of breaks using BLISS-seq.

overall_design: For the RNAseq experiment: total RNA was isolated from 3 biological replicates of shCTRL-AB22 cells and 3 biological replicates of shHMGB1-AB22 cells. for ATACseq experiment: 1 sample of shCTRL-AB22 cells is compared with 1 sample of shHMGB1-AB22 cells. for BLISS experiment: BLISS libraries are prepared from either shCTRL or shHMGB1-AB22 cells treated with 0, 3, 5 or 10 Gy of gamma-radiations. Each condition is represented with 2 biological replicates.

first: Francesca

last: Brambilla

first: Marco

last: Bianchi

first: Alessandra

last: Agresti


title: Nucleosomes protect DNA from irradiation-induced double strand breaks in living cells (BLISS)

type: Non-coding RNA profiling by high throughput sequencing


title: Nucleosomes protect DNA from irradiation-induced double strand breaks in living cells (ATAC-seq)


title: Nucleosomes protect DNA from irradiation-induced double strand breaks in living cells

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Epigenetic Suppression of Transgenic T-cell Receptor Expression via Gamma-Retroviral Vector Methylation in Adoptive Cell Transfer Therapy

status: Public on Jul 06 2020

city: Los Angeles

first: Theodore

middle: S.

last: Nowicki

state: CA

address: 2-159 Factor Building, 10833 Le Conte Avenue

department: Jonsson Comprehensive Cancer Center

institute: University of California Los Angeles

type: Methylation profiling by high throughput sequencing

summary: Transgenic T-cell receptor (TCR) adoptive cell therapies recognizing tumor antigens are associated with robust initial  response  rates,  but  frequent  disease  relapse.  This  usually  occurs  in  the setting  of  poor  long-term persistence of cells expressing the transgenic TCR, generated using murine stem cell virus (MSCV) -retroviral vectors.  Analysis  of  clinical transgenic adoptive  cell  therapy  products in  vivo revealed  that  despite  strong persistence  of  the  transgenic  TCR  DNA  sequence  over  time,  its  expression  was  profoundly  decreased  over time  at  the  RNA  and  protein  levels.  Patients  with  the  greatest  degrees  of  expression  suppression  displayed significant  increases  in  DNA  methylation  over time  within  the  MSCV  promoter  region,  as  well  as  progressive increases in DNA methylation within the entire MSCV vector over time. These increases in vector methylation occurred  independently of  its  integration  site  within  the  host  genomes.  These  results  have  significant implications for the design of future viral-vector gene engineered adoptive cell transfer therapies.

overall_design: 16 patients from our previous transgenic TCR ACT trials directed against MART-1 (n=4) and NY-ESO-1 (n=5) were selected for analysis. DNA library were prepared from PBMC samples at day 0 (infusion), day +30, and day +70. We then carried out target enrichment using RNA probes to capture the MSCV vector, followed by bisulfite conversion.

first: Colin

last: Farrell

last: Morselli

first: Liudmilla

last: Rubbi

first: Katie

last: Campbell

first: Mignonette

last: Macabali

first: Beata

last: Berent-Maoz

first: Begoña

last: Comin-Anduix

first: Matteo

last: Pellegrini

first: Antoni

last: Ribas


title: An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease

first: Yemin

last: Lan

state: PA

overall_design:
H3K27ac, H3K9ac, H3K122ac, H3K4me1 ChIP-seq and RNA-seq from Younger, Old and AD samples (lateral temporal lobe brains).

Refer to individual Series.