title: Pharmacological Basis for Use of a Novel Compound in Hyperuricemia: Anti-Hyperuricemic and Anti-Inflammatory Effects

last: Zhao

address: Xinzao Road

institute: Guangzhou Medical University

summary: RNA sequencing of kidney tissues was performed to explore the molecular basis of FxUD on alleviating inflammation.

overall_design: 9 transcriptomes including 3 controls, 3 models, and 3 treatments, respectively.


title: TLRL#30

status: Public on Dec 01 2021

city: Pamplona

first: Jose

last: Gonzalez

state: Navarra

address: C/PIO XII s/n

country: Spain

institute: FIMA

type: Expression profiling by high throughput sequencing

summary: RNAseq analysis of MC38-derived tumors treated in vivo for 24h with BO-112 (50μg) and/or DMXAA (100μg) intratumorally.

overall_design:
In vivo treated tumors were excised 24h after intratumoral injections with BO-112 and DMXAA and storaged in RNAlater at -20C until further processing. mRNA was isolated using Rneasy Mini Kit (Qiagen) following manufacture's instructions. RNAseq was performed by Macrogen using TruSeq Stranded mRNA library and NovaSeq 6000 sequencing system (Illumina)
Macrogen

first: Maite

last: Alvarez


title: Reduced representation bisulfite sequencing (RRBS) profiling of ER-Hoxa9-Lys-GFP cells over myeloid differentiation program

city: Philadelphia

first: Andres

last: Blanco

state: PA

address: 380 S. University Avenue, Hill Pavillion Room 414

department: Biomedical Sciences

country: USA

institute: University of Pennsylvania

type: Methylation profiling by high throughput sequencing

summary: Data reveal epigenome-wide trends associated with progression from the GMP-like state to the neutrophil-like state

overall_design: ER-Hoxa9 cells cultured with estradiol, 120 hours without estradiol, or with estradiol after pre-treatment with four different durations of estradiol withdrawal


title: Pevonedistat targets malignant cells in myeloproliferative neoplasms in vitro and in vivo via NFκB pathway inhibition

city: St. Louis

first: Tim

last: Kong

state: MO

address: CSRB 8838

institute: Washington University School of Medicine

summary: Targeted inhibitors of JAK2 (e.g. ruxolitinib) often provide symptomatic relief for myeloproliferative neoplasm (MPN) patients, but the malignant clone persists and remains susceptible to disease transformation. These observations suggest that targeting alternative dysregulated signaling pathways may provide therapeutic benefit. Previous studies identified NFκB pathway hyperactivation in myelofibrosis (MF) and secondary acute myeloid leukemia (sAML) that was insensitive to JAK2 inhibition. Here, we provide evidence that NFκB pathway inhibition via pevonedistat targets malignant cells in MPN patient samples as well as in syngeneic MPN and patient-derived xenograft mouse models that is non-redundant with ruxolitinib. Colony forming assays revealed preferential inhibition of MF colony growth compared to normal colony formation. In mass cytometry studies, pevonedistat blunted canonical TNF⍺ responses in MF and sAML patient CD34+ cells. Pevonedistat also inhibited hyperproduction of inflammatory cytokines more effectively than ruxolitinib. Upon pevonedistat treatment alone or in combination with ruxolitinib, MPN mouse models exhibited reduced disease burden and improved survival. These studies demonstrating efficacy of pevonedistat in MPN cells in vitro as well as in vivo provide a rationale for therapeutic inhibition of NFκB signaling for MF treatment. Based on these findings, a Phase I clinical trial combining pevonedistat with ruxolitinib has been initiated.

overall_design: mRNA profiling of HEL cells treated with ruxolitinib, pevonedistat, or combination.

first: Stephen

middle: T

last: Oh


title: Characterization of cardiomyocyte nuclei from the infarct border zone

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Mis-localized mitochondrial ribosomes guide ceramide-dependent mitophagy for inducing cell death via alterations of the bioenergetics and metabolism

city: Charleston

first: Natalia

last: Oleinik

state: SC

address: 87 Jonathan Lucas St

department: Biochemistry

institute: MUSC

summary: In this work, we set out experiments to determine the mechanisms that regulate mitochondrial trafficking of p17/PERMIT-CerS1 complex in response to Drp1 activation to induce mitophagy and cellular consequences of this process altering mitochondrial metabolism in cultured cells in situ and genetic mice models in vivo. The data revealed that mislocalized mitochondrial ribosomes on the outer membrane due to Drp1-mediated fission are recognized by p17/PERMIT for CerS1 localization leading to ceramide-dependent mitophagy in response to oxidative stress by the generation of nitric oxide species (NOS). This process then leads to mitochondrial dysfunction resulting in decreased malate/fumarate/aspartate exhaustion, which is restored and prevented by molecular and genetic ablation of p17/PERMIT, LC3, Drp1, and Parkin in cancer cells or patient-derived 2D-organoids or mice brains in response to SoSe or ceramide analog drug, LCL768.

overall_design: Human Head and neck cancer cells have been treated with SoSe or LCL657, total RNA was extracted and loaded on the NanoString  nCounter® Human  Metabolic Pathways Panel.

first: Besim

last: Ogretmen


title: Chromatin state barriers enforce an irreversible mammalian cell fate decision


title: Transcriptomic Landscape of Treatment - Naïve Non-Erosive Reflux Disease

city: Shanghai

first: Ye

address: 197 Ruijin Er Road

country: China

institute: Ruijin Hospital

summary: Non-Erosive Reflux Disease (NERD) is one of the most prominent and common forms of gastroesophageal reflux disease (GERD). We performed transcriptomic analysis (RNA sequencing) of esophageal biopsies from patients with NERD and healthy controls to increase understanding of complex cellular and molecular pathways in NERD.

overall_design: Patients with persistent symptoms suggestive of GERD (acid regurgitation and/or heart burn) and no previously antisecretory or prokinetic therapy were advised to undergo 24 h pH monitor and endoscopy in sequence. NERD was defined as abnormal 24 h pH parameters and normal endoscopic performance. Healthy voluntary controls were those with absence of GERD symptoms and normal endoscopic appearance. In each subject, specimen was taken at 5 cm above the squamo-columnar junction, from macroscopically intact mucosa, prior to any antisecretory and/or prokinetic therapy. In total, mucosal biopsies from patients with NERD (n=9)  and healthy controls (n=6) underwent RNA sequencing.

first: Duowu

last: Zou


title: AP-1 activation mediates postnatal cardiomyocyte maturation

first: Hongjie

last: Zhang

address: Siping Road

institute: Tongji University

summary: Mammalian cardiomyocytes rapidly mature after birth, with hallmarks such as cell-cycle exit, binucleation, and metabolic switch to oxidative phosphorylation of lipids. The causes and transcriptional programs regulating cardiomyocyte maturation are not fully understood yet. Thus, we performed single cell RNA-seq of neonatal and postnatal day 7 rat hearts to identify the key factors for this process and found AP-1 as a key factor to regulate cardiomyocyte maturation. To find the mechanism of AP-1 during cardiomyocyte maturation, we performed RNA-seq analysis of neonatal rat ventricular cardiomyocytes and found Ap-1 promote cardiomyocyte maturation by regulating cardiomyocyte metabolism.

overall_design: Single cell RNA-seq analysis of NRVCs postnatal day 1 and day 7; RNA-Seq analysis of knocking down Atf3 or Jun versus control (2 replicates per group).

first: Lijuan

last: Pei

first: Ke

last: Wei


title: Next generation sequencing of thymic dendritic cells after damage

city: Seattle

first: Kirsten

last: Cooper

state: WA

address: 1100 Fairview Ave. N, Rm S3-208

institute: Fred Hutchinson Cancer Research Center

summary: The thymus, which is the primary site of T cell development, is particularly sensitive to insult but also has a remarkable capacity for repair. However, the mechanisms orchestrating regeneration are poorly understood and delayed repair is common after cytoreductive therapies. Here, we demonstrate a trigger of thymic repair, centered on detecting the loss of dying thymocytes which are abundant during steady-state T cell development. Specifically, apoptotic thymocytes suppressed production of the regenerative factors IL-23 and BMP4 TAM receptor signalling and downstream activation of the Rho-GTPase Rac1, the intracellular pattern recognition receptor NOD2, and micro-RNA-29c. We found that the intracellular pattern recognition receptor NOD2, via induction of microRNA-29c, suppressed levels of the regenerative factors IL-23 and BMP4, in DCs and ECs, respectively. Transcriptome analysis in highly purified DCs after damage revealed highly similar inflammatory gene signatures and enrichment for NOD2 expression

overall_design: Thymi from 6-8wo mice were pooled and enzymatically digested. Freshly isolated and FACS purified thymic DCs (CD45+ MHC11+ CD11c+) were submitted for bulk RNA-seq. Library was generated using SMART-Seq v4 Ultra Low Input RNA Kit (Takara) and sequencing was run on Illumina HiSeq 2500. The sequence reads that passed  Illumina's base call quality threshold were aligned to mm10 using STAR v2.5.2a, and then analyzed using Subread featureCounts v1.6.0, edgeR, and limma.

first: Sinéad

last: Kinsella

first: Jarrod

last: Dudakov


title: Searching for the mechanism that mediates mefenoxam-acquired resistance in Phytophthora infestans and how it is regulated

city: Ithaca

first: Juliana

last: Gonzalez-Tobon

address: 236 Tower Rd

institute: Cornell University

type: Non-coding RNA profiling by high throughput sequencing

summary: Phytophthora infestans, the causal agent of late blight disease of potatoes, is mainly controlled by the use of fungicides. Isolates that are resistant to commonly used fungicides have been reported. Also, several studies show that originally mefenoxam-sensitive isolates acquire resistance to this fungicide when exposed to sub-lethal concentrations. This phenomenon, termed ‘mefenoxam-acquired resistance’, has been observed in different Phytophthora species and seems to be unique to mefenoxam. In this study, we aimed to elucidate the molecular mechanism mediating this type of resistance as well as a possible regulatory process behind it. A combination of computational analyses and experimental approaches was used to identify differentially expressed genes with a potential association to the phenomenon. These genes were classified into seven functional groups. Most of them seem to be associated with a pleiotropic drug resistance (PDR) phenotype, typically involved in the expulsion of diverse metabolites, drugs, or other substances out of the cell. Despite the importance of RNApolI for the constitutive resistance of P. infestans to mefenoxam, our results indicate no clear interaction between this protein and the acquisition of mefenoxam resistance. Several small non-coding RNAs (ncRNAs) were found to be differentially expressed and specifically related to genes mediating the PDR phenotype, thus suggesting a possible regulatory process. We propose a model of the molecular mechanisms acting within the cell when P. infestans acquires resistance to mefenoxam after exposed to sub-lethal concentrations of the fungicide. This study provides important insights into P. infestans’ cellular and regulatory functionalities.

overall_design: These data sets were generated via RNA-seq of small non-coding RNAs of Phytophthora infestans. Three strains used, two treatment conditions and three biological replicates each. For a total of 18 result files.

first: Richard

middle: R

last: Childers

first: Alejandra

last: Rodriguez

first: William

middle: E

last: Fry

first: Kevin

middle: L

last: Myers

first: Jeremy

last: Thompson

first: Silvia

last: Restrepo

first: Giovanna

last: Danies


title: RNA-seq of primary chondrocytes with ot without aberrant high shear stress treatment

first: Yu

last: Jin

state: State...

address: 639 Zhizaoju Road

institute: Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine

summary: In order to investigate the transcriptome changes underlying aberrant shear stress-induced cartilage pathogenesis, we subjected chondrocytes to Flexcell applinace and the constructed RNA libraries were sequenced on an Illumina HiSeq X Ten platform.

overall_design: Three biological replicates of primary chondrocytes subjected to high shear stress stimulation as well as not stimulated (control) were analyzed  (6 in total).

first: Zhenxia

last: Li

first: Yanran

last: Wu

first: Hairui

first: Zhen

last: Liu

first: Lu

first: Ningjuan

last: Ouyang

first: Ting

last: Zhou

first: Bing

last: Fang

first: Lunguo

last: Xia


title: Diagnostic accuracy of liquid biopsy in endometrial cancer

city: Gdańsk

first: Anna

last: Supernat

address: Dębinki 1

department: Division of Translational Oncology

country: Poland

institute: Medical University of Gdansk

summary:
INTRODUCTION. Liquid biopsies are a minimally invasive collection of a patient body fluid sample. In oncology, they offer several advantages compared to traditional tissue biopsies. However, potential of this method in endometrial cancer (EC) remains poorly explored. We studied the utility of tumor educated platelets (TEPs) and circulating tumor DNA (ctDNA) for preoperative EC diagnosis, including histology determination.
MATERIALS AND METHODS. TEPs from 297 subjects (53 EC patients, 40 patients with benign gynecologic conditions and 204 healthy women) were RNA-sequenced. DNA sequencing was performed in 519 primary tumor tissue samples and in16 plasma samples. Artificial intelligence was applied to sample classification.
RESULTS. Platelet-dedicated classifier yielded AUC of 93.1% in test set when discriminating between healthy subjects and cancer patients. However, the discrimination between endometrial cancer and benign gynecologic conditions was relatively low, with AUC of 60.7%. ctDNA-dedicated classifier discriminated primary tumor tissue samples with AUC of 91.4% and ctDNA blood samples with AUC of 87.5%.
CONCLUSIONS Liquid biopsies show potential in EC diagnosis. Both TEPs and ctDNA profiles coupled with artificial intelligence constitute a source of useful information. Further work, involving more cases, is warranted.

overall_design: RNA-seq of Tumor-educated platelets in ovarian carcinoma

first: Krzysztof

last: Pastuszak

first: Marta

last: Łukasiewicz

first: Robert

last: Różański

first: Sylwia

last: Łapińska-Szumczyk

first: Tomasz

last: Stokowy


title: Effect of the different isoforms of RPL22L1 protein on the transcriptome of human glioblastoma cells.

city: Boston

first: Ksenia

middle: S

last: Anufrieva

state: MA

address: 60 Fenwood Rd

institute: Brigham and Women's Hospital

summary: Glioblastoma multiforme (GBM) is characterized by an exceptionally high intratumoral heterogeneity. However, the molecular mechanisms underlying the origin of different GBM cell populations remain unclear. Here we found that the composition of ribosomes of GBM cells in the tumor core and edge differ due to alternative RNA splicing. The acidic pH in the core switches pre-mRNA splicing of the ribosomal gene RPL22L1 toward the RPL22L1b isoform. This allows cells to survive acidosis, increases stemness and correlates with worse patient outcome. Mechanistically, RPL22L1b promotes RNA splicing by binding to lncMALAT1 in the nucleus, resulting in its degradation. Contrarily, in the tumor edge region, RPL22L1a interacts with ribosomes in cytoplasm and upregulates translation of multiple mRNAs including TP53. We found that RPL22L1 isoform switch is regulated by SRSF4 and identified the compound, that inhibits this process and decreases tumor growth. These findings demonstrate how distinct GBM cell populations arise during tumor growth. Targeting this mechanism may decrease GBM heterogeneity and facilitate therapy.

overall_design: We created patient derived GBM neurospheres stably overexpressing different isofoms of RPL22L1 protein or an empty vector as a control. After RNA purification corresponding samples were sequenced using HiSeq 2500. The experiment was performed in two biological replicates.

first: Marat

last: Pavlyukov


title: Transcriptome of insulin signalling associated transcription factor targets

city: New Delhi

first: Neeraj

last: Kumar

state: Delhi

address: Ansari Nagar

country: India

institute: All India Institute of Medical Sciences, New Delhi

summary: We report the transcritional targets of transcription factor downstream of insulin signalling. We knocked down transcription factors under reduced insulin signalling in Caenorhabditis elegans and did transcriptom analysis. This study identified target genes interaction complexity in analogous genetic and experimental conditions. It aid in gaining insight into the new molecular mechanisms downstream of rIIS

overall_design: Whole worm RNA-Seq of control and reduced insulin signaling strains at L4/young adult stage.

first: Arnab

last: Mukhopadhyay


title: RNA-seq of lung fibroblasts in transgenic expressing hIGFBP5 (HOMO) and WT mice

first: Carol

last: Feghali-Bostwick

address: 96 Johnathan Lucas St Suite 816 MSC 637

department: Medicine - Rheumatology

institute: Medical University of South Carolina

summary: The main purpose of this project is to conduct expression profiling of primary lung fibroblasts from homozygous (HOMO) mice compared to wildtype (WT) mice to identify genes and pathways regulated by hIGFBP-5 in primary lung fibroblasts. The GO or KEGG enrichment analysis will be helpful for us to discover the DEG's function and the biological processes, pathways, molecular functions, and cellular components involved

overall_design: compare the expression profiling of lung fibroblasts in transgenic expressing hIGFBP5 (HOMO) and WT mice

first: Xinh-Xinh

last: Nguyen

first: Ludivine

last: Renaud


title: Transcriptional characterization of cardiomyocyte nuclei from the infarct border zone [RNA-Seq]

first: Vincent

last: Christoffels

summary: Expression analysis of cardiomyocytes from 8 week old mice with and without myocardial infarction

overall_design: RNA-seq on mouse cardiac tissue

first: Marie

last: Günthel

first: Karel

last: van Duijvenboden

middle: M


title: Per- and Polyfluoroalkyl Substance Exposure Combined with High-Fat Diet Supports Prostate Cancer Progression

city: Urbana

first: Zeynep

last: Madak Erdogan

state: IL

address: 1201 S Goodwin Ave

department: FSHN

institute: UIUC

summary: Per- and polyfluoroalkyl substances (PFAS) are synthetic chemicals utilized in various industrial settings, and include products such as flame retardants, artificial film-forming foams, cosmetics, non-stick cookware among others. Epidemiological studies suggest a link between increased blood PFAS levels and prostate cancer incidence, but the mechanism through which PFAS impact cancer development is unclear. To investigate the link between PFAS and prostate cancer, we evaluated the impact of metabolic alterations resulting from a high-fat diet combined with PFAS exposure on prostate tumor progression. Our studies are the first in the field to provide new and clinically relevant insights regarding novel metabolic and epigenetic states and support future development of effective preventative and therapeutic strategies for PFAS-induced prostate cancers. Our findings enhance understanding of how PFAS synergize with high-fat diets to contribute to prostate cancer development and establish an important basis to mitigate PFAS exposure.

overall_design: We evaluated in vivo prostate cancer xenograft models exposed to perfluorooctane sulfonate (PFOS), a type of PFAS compound, and different diets to study the effects of PFAS on prostate cancer progression and metabolic activity. Metabolomics and transcriptomics were used to understand the metabolic landscape shifts upon PFAS exposure. We evaluated metabolic changes in benign or tumor cells that lead to epigenomic reprogramming and altered signaling, which ultimately increase tumorigenic risk and tumor aggressiveness.

last: Madak-Erdogan

first: Ozan

middle: B

last: Imir

first: Qianying

last: Zuo

first: Yu-Jeh

last: Liu


title: Epigenetic characterization of cardiomyocyte nuclei from the infarct border zone [Cut & Run]

summary: H3K27 acetylation analysis of cardiomyocytes from 8 week old mice with and without myocardial infarction

overall_design: H3K27ac analysis using CUT&RUN-sequencing on mouse cardiac tissue


title: RNA-sequencing of cells derived from dermis and postmortem dura mater from the same subject

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Biochemistry and Biophysics

institute: UCSF

summary: Patient-derived cells hold great promise for precision medicine approaches in human health. Fibroblast cells have been a major source of human cells for reprogramming and differentiating into specific cell types for disease modeling. Such cells can be isolated at various stages during life (presymptomatic, symptomatic, and advanced disease) and thus can potentially be used to model different phases of disease progression. In certain circumstances, however, tissues are not collected during life and only postmortem tissues are the only available source of fibroblasts. Fibroblasts cultured from postmortem human dura mater of individuals with neurodegenerative diseases have been suggested as a primary source of cells for in vitro modeling of neurodegenerative diseases. Although fibroblast-like cells from human and mouse dura mater have been previously described, their utility for reprogramming and direct differentiation protocols requires further characterization. In this study, cells derived from dermal biopsies of living subjects were compared to cells derived from postmortem dura mater. In two instances, we have isolated and compared dermal and dural cell lines from the same subject. Notably, such striking differences were observed between cells of dermal and dural origin that their fibroblast nature was brought into question. Compared to dermal fibroblasts, postmortem dura mater-derived cells demonstrated different morphology, slower growth rates, and a higher rate of karyotype abnormality. Dura mater-derived cells also failed to express fibroblast protein markers. When dermal fibroblasts and dural-derived cells from the same subject were compared, they exhibited significant differences in gene expression profiles. Ultimately, dura mater-derived cells were found to originate from a mixed mural lineage consisting of smooth muscle cells and pericytes. Our study argues for rigorous karyotyping of all postmortem derived cell lines and highlights significant limitations of postmortem human dura mater-derived cells for modeling normal biology or disease-associated pathobiology.

overall_design: Examination of a dura mater-derived cell line compared to dermis fibroblasts from the same subject. Four technical replicates for each line.

first: Andrea

last: Argouarch

first: Kristle

last: Garcia


title: Derivation of porcine extra-embryonic endoderm cell lines reveals distinct signaling pathway and multipotency states

city: Hohhot

first: manling

last: zhang

address: university west road

institute: Inner Mongolia University

summary: We detected the gene expression differences between porcine extra-embryonic endoderm cells and naïve like and primed porcine ESCs. Gene expression of porcine extra-embryonic endoderm cells was distinct with porcine naïve like and primed embryonic stem cells. Pearson correlation analysis confirmed that porcine naïve like and primed ESCs have stronger correlation than the correlation between either pXEN cells and porcine naïve like ESCs or primed ESCs.  Porcine extra-embryonic endoderm cells have a distinct identity, clustering neither with porcine naïve like ESCs nor with primed ESCs. We confirmed that porcine extra-embryonic endoderm cells lack the expression of key pluripotency genes, such as Sox2, Pou5f1 and Klf4, but they expressed other pluripotency genes, such as Sall4, Lin28a and Klf5. Furthermore, porcine extra-embryonic endoderm cells robustly express Gata4, Gata6 and Sox17 as well as genes encoding ExEn-associated cell surface proteins or basement membrane components Pdgfra, Col4a2, Lama1, Lamb1, Sparc, Ihh, Hnf4a and Dab2, which is in contrast to porcine naïve like ESCs that express these genes at a low level or lack expression altogether

overall_design: mRNA profiles of 3 porcine extra-embryonic endoderm cell lines, 2 naïve like embryonic stem cell lines and 2 primed embryonic stem cell lines in porcine.

first: Manling

last: Zhang

first: Yong

last: Jin

first: Xihe

last: Li

first: Rongfeng


title: Comparison between HPV+ / p16+ versus the HPV-/p16-  from HNSCC patients

city: Mexico City

first: Patricia

middle: Piña

last: Sánchez

state: CDMX

address: Cuauhtémoc Avenue

department: Medical Research Unit in Oncological Diseases

country: Mexico

institute: IMSS

summary:
Head and neck squamous cell carcinomas are heterogeneous neoplasms that show clinical and biological differences in association with the human papillomavirus (HPV). To provide adequate therapeutic strategies, biological and clinical characterization is essential to stratify patients based on prognostic and predictive factors. Reports on HNSCC are scarce in Mexico, thus in the present study, we analyze 414 cases of HNSCC, including those of the oropharynx (OPSCC), larynx (LASCC), and oral cavity (OCSCC). We determined the presence of HPV and p16 expression. Global expression profiles were analyzed with Affymetrix HTA 2.0 microarray in 25 selected cases HPV+/p16+ versus HPV-/p16-.
In our study we analyze 25 samples derived from HNSCC patients. 18 samples were HPV-/p16- and 7 HPV+/p16+. We compared the HPV-/p16- versus the HPV+/p16+ and identified differentially expressed RNAs with a fold change greater than 1.5 or less than -1.5. These data were used to obtain 98 genes that are differentially expressed in absence of HPV. The present study offers information regarding clinical and molecular characteristics of HNSCC, both associated and unassociated with HPV, in Mexican patients.

overall_design: 25 total samples were analyzed. The samples were collected from Unidad Médica de Alta Especialidad de Oncología del Centro Médico Nacional Siglo XXI, of the Instituto Mexicano del Seguro Social (Mexican Social Security Institute). We compared HPV+/p16+ and HPV-/p16- of patients with HNSCC . A fold change greater than 1.5 or less than -1.5 and a p-value ≤ 0.05 were used to compare gene expression.

first: Galo

middle: A

last: Méndez Matías

first: Cindy

middle: K

last: Velázquez-Velázquez

first: Rosario

last: Castro-Oropeza

last: Piña Sanchez


title: Effect of the different isoforms of RPL22L1 protein on the transcriptome of human glioblastoma cells and their interactome

first: Ksenia

last: Anufrieva

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

overall_design: Refer to individual Series


title: Terahertz Exposure Enhances Neuronal Synaptic Transmission and Oligodendrocyte Differentiation in vitro

city: xi'an

first: yang

last: caixia

address: No. 169, Changle West Road, Xi 'an

institute: fourth military medical university

summary: Terahertz (THz) frequency occupies a large portion of the electromagnetic spectrum that is between the infrared and microwave region. Recent advances in THz application have stimulated interests regarding the biological effects associated with this frequency range. In current study, we report that irradiation with a single-frequency THz laser on primary mice cortical neuron cultures and oligodendrocyte cultures results in dose dependent irradiation specific changes in cellular function and gene expression. In neuron cultures, THz irradiation increases excitatory synaptic transmission and neuronal firing activities. Microarray assay reveals neuronal gene expression dynamics after THz exposure, which are highly consistent with morphology and electrophysiology results. Besides, certain schedule of THz irradiation inhibits the proliferation of oligodendrocyte precursor cells (OPCs) and promotes OPC differentiation. Notably, the myelination process in neuron-oligodendrocyte cocultures is enhanced after THz exposure. In summary, our observations suggest that THz irradiation in certain frequency can modulate the functions of neuron and oligodendrocyte, with different sensitivity to THz between neuronal cell types. These results may provide important understanding of the mechanisms that govern THz interactions with nervous systems and suggest THz wave as a new strategy for neuromodulation.

overall_design: THz irradiation was delivered to the cultures in long duration: cultures were irradiated for 3 hr, one time a day. Neurons were irradiated from 5 day in vivo (5 DIV) to 9 DIV and collected at 12 DIV for microarray.

first: Xianghui

last: Zhao

first: Ming

first: Yuming

first: Haiying

first: Keke

last: Ren

first: Qian

last: Xue

first: Haifeng

first: Wenting

last: Wang

first: Shengxi

last: Wu


title: Interactome of different isoforms of RPL22L1 protein in human glioblastoma cells

overall_design: We performed precipitation of RNA that interacts with different isoforms of RPL22L1 protein in glioblastoma cells. Ribosomal RNA was depleted and obtained samples were sequenced using HiSeq 2500 (RIPseq experiment).

first: Marat

last: Pavlyukov


title: Deciphering the conserved dynamic transcriptional signature and regulatory software governing neuronal fate commitment

city: Catania

first: Sebastiano

last: Cavallaro

address: Via Paolo Gaifami, 18

country: Italy

institute: IRIB-CNR

summary: The transcriptional program underlying neuronal apoptosis and survival has to date been partially characterized. However, the complete spectrum of genes/proteins as well as the ‘regulatory software’ controlling neuronal fate decisions remain almost entirely unknown. Here, for the first time, we characterized the earliest molecular events following the induction of neuronal apoptosis and its rescue by three potent anti-apoptotic growth factors (GFs), in order to identify key genes and upstream regulators primarily responsible for driving execution of these processes. A core set of 175 survival-related genes (SRGs) with opposite transcriptional signatures between apoptosis and GF-mediated survival was identified. Promoter motif analysis of SRGs revealed a repertoire of intrinsic upstream regulators that may drive the apoptotic/survival switch, with Hoxd9 predicted to be the master regulator. Finally, the clinical implication of SRGs in the pathogenesis of neurological and neuropsychiatric diseases, here emerged, suggested their potential utility as targets for treating these severe disorders.

overall_design: Time-course transcriptional analysis of serum-deprived cerebellar granule neurons (CGNs) after 0.5h, 1h and 3h switch from 25 mM (K25) to 5 mM KCl (K5), in the presence or absence of a maximal effective dose of SP (200 nM), Pacap (100 nM) or Igf1 (3.26 pM). Four biological replicates (derived from the same litter) for each experimental condition (K25, K5, K5+SP, K5+Pacap, K5+Igf1) were analyzed.

first: Giovanna

last: Morello

first: Valentina

last: La Cognata

first: Maria

last: Guarnaccia

first: Antonio

middle: G

last: Spampinato

first: Giulia

last: Gentile

first: Ambra

last: Villari


title: Insights into ROS-dependent signalling underlying transcriptomic plant responses to the herbicide 2,4-D

city: Campanillas

first: Rocio

last: Bautista

state: Malaga

address: C/ Severo Ochoa, 34. Parque Tecnologico

department: Edificio de Bioinnovacion

institute: Universidad de Malaga

summary: The synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D) functions as an agronomic weed control herbicide. High concentrations of 2,4-D induce plant growth defects, particularly leaf epinasty and stem curvature. Although the 2,4-D phenotype is associated with ROS production, little is known about ROS-dependent signalling. In this study, by using T-DNA Arabidopsis mutants to silence peroxisomal acyl CoA oxidase 1 (acx1-2), we identified ACX1 as one of the main sources of ROS production and as partly the cause of the epinasty phenotype following the application of 2,4-D. Transcriptomic analyses of WT plants after treatment with 2,4-D revealed a ROS-related peroxisomal footprint in early plant responses, while other organelles, such as mitochondria and chloroplasts, are involved in later responses. Interestingly, a group of ACX1-dependent transcripts in plant responses to 2,4-D, previously associated with epinasty, is related to auxin biosynthesis, metabolism and signalling. We found that protein AUXIN SIGNALING F-BOX 3 (AFB3), a component of SCF (ASK-cullin-F-box) E3 ubiquitin ligase complexes, which functions as an auxin receptor and mediates Aux/IAA proteasomal degradation, acts downstream of ACX1 and is involved in the epinasty phenotype induced by 2,4-D. We also found that protein degradation associated with ubiquitin E3-RING and E3-SCF-FBOX in ACX1-dependent signalling in plant responses to 2,4-D is significantly regulated over longer treatment periods.

overall_design:
Col-0 was the background used for all the Arabidopsis seeds in the study: WT and the transgenic lines acx1-2 (kindly donated by Dr. J. León; SALK_041464). Seeds were sown in moistened soil and grown in 16 h light and 8 h dark photoperiod cycles at 22 and 20 ºC, respectively, under 120 µE and at 60 % relative humidity. The effect of 2,4-dichlorophenoxyacetic acid (2,4-D) on Arabidopsis plants was analysed by spraying 23 mM 2,4-D solution (1% dimethyl sulfoxide acid, DMSO and 1% EtOH), and plant leaves were collected after 1 and 72 h post treatment (hpt). Control plants were sprayed with 1% DMSO and 1% EtOH. Treatment times, 2,4-D concentrations and treatment techniques used in this study had been previously optimised. 2,4-D- and DMSO/EtOH (control)-sprayed leaves of similar sizes and developmental stages were sampled at 1 and 72 h. For microarray analysis, three independent biological replicates, each composed of leaves pooled from at least 5 different plants, were used per experimental condition.
Time course

first: María

middle: C

last: Romero-Puertas

first: M

last: Peláez-Vico

first: Diana

last: Pazmiño

last: Rodríguez-Serrano

first: Rocío

first: Aurelio

last: Gómez-Cadenas

last: Gonzalo Claros

first: José

last: León

first: Luisa

last: Sandalio


title: ChIP-seq profiling of H3K4me3, H3K27ac, H3K27me3, V5-HOXA9-AM, and V5-ER-HOXA9-AM cells before and after inducing irreversible commitment to myeloid differentiation

city: Philadelphia

first: Andres

last: Blanco

address: 380 S. University Avenue, Hill Pavillion Room 414

institute: University of Pennsylvania

summary: Data reveal epigenome-wide trends in histone modifications and Hoxa9 binding sites associated with irreversible commitment from the GMP-like state to the neutrophil-like state

overall_design: ER-Hoxa9 cells cultured with estradiol, 120 hours without estradiol, or with estradiol after pre-treatment with four different durations of estradiol withdrawal


title: RNA seq NVP-BEZ235 treatment of U87MG cells

city: Edinburg

first: Megan

middle: Erin

last: Keniry

state: TX

address: 1201 W. University Dr.

department: Biology

institute: UTRGV

summary: Glioblastoma (GBM) is the most lethal primary brain cancer that lacks effective molecular targeted therapies. PI3K/AKT/mTOR signaling pathway is activated in 90% of all Glioblastoma Multiforme (GBM) tumors. To gain insight into the impact of the PI3K Pathway on GBM metabolism, we treated U87MG GBM cells with 50nM NVP-BEZ235 (PI3K and mTOR a dual inhibitor) for four days and identified differentially expressed genes with RNA-seq analysis.

overall_design: U87MG cells were treated with 50nM NVP-BEZ235 for 4 days and analyzed by RNA seq


title: ATAC-seq profiling of ER-Hoxa9-Lys-GFP cells before and after inducing irreversible commitment to myeloid differentiation

summary: Data reveal epigenome-wide trends associated with irreversible commitment from the GMP-like state to the neutrophil-like state


title: MicroRNA array expression during  normal urinary bladder wound healing

first: Clara Ibel

last: Chamorro Jimenez

address: Center for Molecular Medicine (CMM) Karolinska University Hospital L8:02 Sweden

department: Department of Women's and Children's Health

country: Sweden

institute: Karolinska Institute

summary: Urinary bladder wound healing is today pooorly chracterized.  MicroRNAs are small non-coding RNA molecules with regulatory functions. In this study we aimed at identifying microRNAs expressed during bladder wound healing.   We performed Affymetrix microRNA profiling of the rodent urinary bladder during healing of a surgically created wound.

overall_design: Rat urinary bladder were collected at 0 hours ( control non wounded animals), 2 days and 8  days  post insicional wound and sutures, 4 animals per time point were incliuded. The Affymetrix microRNA GeneChip Array plates (Affymetrix, Thermo Fisher) were used in this study according to the manufacturer’s instructions at the core facility for Bioinformatics and Expression Analysis (BEA, Karolinska Institutet, Stockholm, Sweden)

first: Clara

middle: I

last: Chamorro

first: Jesper

last: Eisfeldt

first: Oliver

last: Willacy

first: Nikolai

last: Juul

first: Magdalena

last: Fossum


title: The effects of MuRF1 knockout, sex, and a high fat diet consumption on gastrocnemius muscle transcriptomics.

city: Iowa City

first: Michael

last: Chimenti

state: IA

address: 431 Newton Road

department: Iowa Institute of Human Genetics

institute: University of Iowa

summary: MuRF1 is an E3 ubiquitin ligase known to play a role in skeletal muscle atrophy.  Our objectives in this study were to gain further insight into the roles MuRF1 plays in skeletal muscle and to determine if this is influenced by sex and/or consumption of a high fat diet.  To address these objectives we used RNA sequencing to analyze the transcriptome of gastrocnemius muscle from 30 week old, MuRF1 knockout (-/-) and wild type, male and female mice fed a chow or high fat diet (HFD).

overall_design: 31 samples were analyzed consisting of 3-4 replicates per group

first: Jennifer

last: Norman

first: Andrea

last: Marshall

first: Luis

last: deSousa

first: John

last: Rutledge

first: Sue

last: Bodine


title: Epigenetic Regulation of Nuclear Lamina-Associated Heterochromatin by HAT1 and the Acetylation of Newly Synthesized Histones [ChIP-seq]

city: Columbus

first: Mark

last: Parthun

state: OH

address: 1060 Carmack Rd.

department: Biological Chemistry and Pharmacology

institute: The Ohio State University

summary: We report that HAT1 regulates chromatin accessibility of large chromosomal domains that correspond to regions of high H3K9 methylation density.

overall_design: Examination of H3 K9me2 and H3 K9me3 histone marks in mouse immortalized mouse embryonic fibroblasts.

last: Parhtun


title: RNA-seq on Kelly neuroblastoma cells transfected with the following miRNA: non-targeting scrambled control, miR-99b-5p, miR-380-3p, miR-485-3p, miR-100-3p, miR-1915-3p, miR-1283

city: Darlinghurst

first: Niantao

last: Deng

state: NSW

address: 384 Victoria Street

department: Cancer Theme

country: Australia

institute: Garvan Institute of Medical Research

summary: The aim of this experiment was to determine the genes regulated by several miRNA identified through high-throughput screening to have chemosensitising activity in neuroblastoma cells.

overall_design: Kelly cells were transfected with miRNAs and harvested 48 hr later for gene expression analysis by RNA-seq

first: Holly

last: Holliday

first: Eoin

last: Dodson

first: Alexander

last: Swarbrick


title: Antioxidants in culture and vitrification media alters mouse liver and placenta gene expression

city: Melbourne

first: Thi

middle: Thanh Mai

last: Truong

state: VIC

address: Gate 12 Royal Parade, Parkville

department: BioSciences

institute: The University of Melbourne

summary: A multitude of factors encompassing assisted reproductive technologies present compounding stresses and cause synergistic damage to cell function and embryo development in vitro. We have previously reported that antioxidant supplementation of culture and vitrification media ameliorate some of the detrimental effects of in vitro culture and cryopreservation. The aim of this study was to identify the molecular mechanisms by which antioxidants improve embryo and fetal development by comparing mRNA profiles of E14.5 post-implantation fetal (liver) and placental tissue following supplementation of either in vitro culture or vitrificiation media with or without antioxidants. In vitro samples are compared with tissues derived from in vivo derived fetuses and placentae.

overall_design: Post-implantation mouse liver and placenta (E14.5) mRNA profiles following in vitro culture or vitrification in the presence or absence of antioxidants, or from in vivo derived embryos.

first: Alexandra

last: Harvey

first: David

last: Gardner


title: RNA-seq profiling of ER-Hoxa9-Lys-GFP cells before and after inducing irreversible commitment to myeloid differentiation

first: Andres

last: Blanco

state: PA

summary: Data reveal transcriptome-wide gene expression trends associated with irreversible commitment from the GMP-like state to the neutrophil-like state


title: BET inhibitor UM-002 reduces GBM proliferation and invasion

city: Washington, DC

first: Nagi

last: Ayad

state: District Of Columbia

address: 3970 Reservoir Rd NW

department: Department of Oncology

institute: Georgetown University

summary: Bromodomain and extraterminal domain (BET) proteins have emerged as therapeutic targets in multiple cancers, including the most common primary adult brain tumor glioblastoma (GBM). Although several bet inhibitors have entered clinical trials, few are brain penetrant. We have generated UM-002, a novel brain penetrant BET inhibitor that reduces GBM cell proliferation in vitro and in a human cerebral brain organoid model. Since UM-002 is more potent than other BET inhibitors, it could potentially be developed for GBM treatment. Furthermore, UM-002 treatment reduces the expression of cell-cycle related genes in vivo, and reduces the expression of invasion related genes within the non-proliferative cells present in tumors as measured by single cell RNAsequencing. These studies suggest that BET inhibition alters the transcriptional landscape of GBM tumors, which has implications for designing combination therapies. Importantly, they also provide an integrated dataset that combines in vitro and ex vivo studies with in vivo single-cell RNA-sequencing to characterize a novel BET inhibitor in GBM.

overall_design: Single-cell analysis of PDX GBM22 orthotopic xenografts treated with either the novel BET inhibitor UM-002 (5mg/kg/d) or DMSO

first: Robert

last: Suter

first: Anna

last: Jermakowicz

first: Matthew

middle: J

last: Rybin


title: Silencing of ER and integrative stress responses in mistranslating mouse liver

city: Zürich

first: Peter

last: Leary

address: Winterthurerstrasse 190

department: Functional Genomics Center Zürich

country: Switzerland

institute: ETH Zürich

summary: We here studied proteostatic networks in liver with increased levels of ribosomal misreading, using mice expressing the Rps2-A226Y ribosomal ambiguity (ram) mutation. Surprisingly, we found that Rps2-A226Y mice lack activation of the eIF2 kinase/ATF4 pathway, the main component of the integrated stress response (ISR). In addition, we find a general downregulation of ER stress responses, possibly by the action of Sirtuin-1, as indicated by reduced mRNAs for lipogenic pathways and acute phase proteins. Downregulation of ER stress responses came along with activation of alternate proteostatic pathways including the proteasome and the formation of stress granules.

overall_design: mRNA expression profiles of liver from Rps2-A226Y mutant mice, expressed under a cre-lox system, and wild type (WT) ubiquitous Cre recombinase expressing mice at 15 months of age.

first: Dimitri

last: Shcherbakov

first: Erik

last: Böttger


title: Protein arginine methyltransferase 5 regulates AKT activation via methylation to promote metastasis

city: Shanghai

first: Xiao-Ou

last: Zhang

state: Shanghai

address: 1239 Siping Road

institute: Tongji University

summary: We used the differential gene expression profiling in neuroblastoma cells after PRMT5 inhibition to decipher the mechanisms PRMT5 regulates neuroblastoma.

overall_design: CHLA-20 and NGP cells were treated with PRMT5 inhibitor and characterized the gene expression with RNA-seq.

first: Lei

last: Huang

first: Qiong

last: Wu


title: Stable reference genes selected from RNAseq data do not offer any significant advantage over conventional reference genes for normalizing qPCR assays

city: London

first: Jacqueline

last: Mitchell

address: 5 Cutcombe Road

department: Department of Basic & Clinical Neuroscience

country: United Kingdom

institute: King's College London

summary: Using robust reference genes which are stably expressed across the samples to normalized qPCR data in a study is crucial. The choice of such reference genes are made based on different approaches. Additionally, a growing body of literature suggests the use of RNA-seq as a prerequisite for choosing optimal reference genes. In this study, we raised two major questions. Firstly, is RNA-seq necessary to find stably expressing genes that could be used as reference genes to normalize qPCR data? In order to address this question we have devised a previously described statistical pipeline of ours to best select the reference genes. Interestingly, we found that RNA-seq is not necessarily needed to find optimal reference genes. Addressing this question raised the second question, is this pipeline is effective for cross-sectional studies and longitudinal studies and in different models of various species. We report that our statistical pipeline that combines two different approaches works robustly in both of the setups we have tried.

overall_design: Comparison of two approaches (stably expressed genes from RNA-seq or conventional genes) to find the optimal reference genes for qPCR analyses.

first: Nirmal

last: Sampathkumar

first: Venkat

last: Sundaram

first: Prakroothi

last: Danthi

first: Rasha

last: Barakat

first: Shiden

last: Solomon

first: Mrityunjoy

last: Mondal

first: Ivo

last: Carre

first: Tatiana

last: Jalkh

first: Aïda

last: Padilla-Ferrer

first: Julien

last: Grenier

first: Charbel

last: Massaad


title: ATAC-seq profiling of ER-Hoxa9-Lys-GFP cells over myeloid differentiation program

first: Andres

last: Blanco

department: Biomedical Sciences

summary: Data reveal epigenome-wide trends associated with progression from the GMP-like state to the neutrophil-like state

overall_design: ER-Hoxa9 cells cultured with estradiol (E2) or at 9 timepoints after withdrawal of E2


title: Plasmodium falciparum HRP2-mediated brain cortical organoid damage is Toll-Like Receptor dependent and is attenuated via Neuregulin-1/ErbB4 signaling

city: Atlanta

first: Adriana

last: Harbuzariu

state: Georgia

address: 720 Westiview Dr SW, HG Room 354

department: MBI

institute: Morehouse School of Medicine

summary:
Human cerebral malaria (HCM) is a severe complication of Plasmodium falciparum infection associated with high mortality rates predominantly in children that live in sub-Saharan Africa. Histine rich protein 2 (HRP2) is a diagnostic and prognostic marker that can be detected in peripheral blood, cerebrospinal fluid and cord blood. Recent studies confirm that HRP2 crossess the compromised blood brain barrier (BBB) during HCM and infiltrate brain parenchyma. Treatments with HRP2 in murine experimental cerebral malaria (ECM) model recapitulate these effects. We tested the hypothesis that treatment of induced pluripotent stem cells (iPSC)-derived brain cortical organoids with HRP2 will recapitulate the brain effects. We assessed the effects of HRP2 treatment on ultrastructure, expression of markers of viability and inflammation neurons, astrocytes and microglia in organoids. We tested the neuroprotective effects of Neuregulin 1 (NRG1) against the HRP2 treatment.
In the study presented here, we assessed the inflammatory genes induced by HRP2 using the Immunology Panel on the nCounter system (NanoString) and results were analyzed using nSolver softaware.

overall_design: We treated 50 days old cortical organoids (n=3) for 26 hours with 4.2 μg/ml HRP2 with or without 100 ng/ml NRG1, while untreated (n=3) organoids were used as control.

first: Annette

last: Nti

first: Keri

last: Oxendine Harp

first: Juan

last: Carlos Cespedes

first: Adel

last: Dris

first: Jonathan

last: Stiles


title: Epigenetic Regulation of Nuclear Lamina-Associated Heterochromatin by HAT1 and the Acetylation of Newly Synthesized Histones [pMEF_RNA_Seq]

first: Mark

last: Parthun

summary: We report that HAT1 regulates chromatin accessibility of large chromosomal domains.  We also report that changes in chromatin accessibility are not strictly correlated to changes in transcription.

overall_design: Measuring transcription in HAT1 WT and KO pMEFs by RNA-Seq.

last: Parhtun


title: Torque Teno Mini Virus as a cause of childhood acute promyelocytic leukemia lacking PML/RARA fusion

city: Bologna

first: Valentina

last: Indio

state: Bologna

address: via Giuseppe Massarenti,11

institute: University of Bologna

summary: We describe a case of a child affected by a relapsed PML/RARA-negative acute promyelocytic leukemia (APL) rescued by a combination of all-trans retinoic acid (ATRA) and arsenic trioxide (ATO) and subsequent HSCT. We provide evidence of the presence of a chimeric viral transcript generated through genomic integration of a Torque Teno Mini Virus sequence into RARA intron 2, the recurrent breakpoint of all chimeric RARA fusions found in APL. This generates an in-frame TTMV/RARA chimeric fusion that is highly expressed at disease diagnosis and relapse and fully cleared at remission achievement.

overall_design: Whole transcriptome sequencing of acute promyelocytic leukemia lacking PML/RARA fusion

first: Annalisa

last: Astolfi


title: Chip-seq For Meis2 on embryonic (E16) and adult DRG

city: LYON

first: MARMIGERE

last: FREDERIC

address: 32/34 Av. Tony Garnier

department: Institut de génomique fonctionelle de Lyon

country: France

institute: CNRS

summary: The goal was to identify DNA binding sites for the transcription factor Meis2 in native embryonic day 16 (E16) and adult sensory neurons from dorsal root ganglion (DRGs).

overall_design:
4 samples were analysed: sample 1 from embryonic (E16) DRG; sample 2 non-precipitated from embryonic (E16) DRG;  sample 3 from adult DRG; sample 4 non-precipitated from adult DRG

***Please note that the raw data files are not provided for this record as they have been lost****

first: Frederic

last: Marmigere

first: Fabrice

last: Bouilloux


title: Epigenetic Regulation of Nuclear Lamina-Associated Heterochromatin by HAT1 and the Acetylation of Newly Synthesized Histones [pMEF_ATAC_Seq]

summary: We report that HAT1 regulates chromatin accessibility of large chromosomal domains.

overall_design: Measuring chromatin accessibility in HAT1 WT and KO pMEFs by ATAC-Seq


title: Epigenetic Regulation of Nuclear Lamina-Associated Heterochromatin by HAT1 and the Acetylation of Newly Synthesized Histones [imMEF_ATAC_Seq]

overall_design: Measuring chromatin accessibility in HAT1 WT and KO imMEFs by ATAC-Seq


title: Epigenetic Regulation of Nuclear Lamina-Associated Heterochromatin by HAT1 and the Acetylation of Newly Synthesized Histones

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

overall_design: Refer to individual Series


title: Vaping but not past smoking is significantly associated with dysregulation of genes in blood leukocytes: targeting of mitochondrial and immune response genes

city: Los Angeles

first: Ahmad

last: Besaratinia

address: 1450 Biggy Street, NRT building, First Floor, Office No: 1509A, M/C 9603

department: Preventive Medicine

institute: University of Southern California

summary: Background: Adult vapers are likely to co-use electronic cigarettes (e-cigs) and combustible cigarettes or have a prior history of smoking. Teasing out the health consequences of vaping in adults, while accounting for the confounding effects of smoking, remains a research priority. Methods: We have segregated the biological effects of vaping from smoking by constructing the whole transcriptome in leukocytes of healthy adult vapers (with and without a history of smoking) and exclusive smokers in comparison to control nonsmokers non-vapers (n = 37, 22, 23, respectively). Results: Age- and sex-adjusted limmaVoom analysis of RNA-seq data showed significant dysregulation of key genes and molecular pathways in both vapers and smokers as compared to controls. The extent of transcriptomic effects, as reflected by the number of differentially expressed genes, was more pronounced in smokers than vapers (683 vs. 92). Computational modeling, combining primary and sensitivity analyses, revealed that e-cig use, but not past smoking, is significantly associated with gene dysregulation in vapers. Comparative analysis of the gene networks and canonical pathways impacted in vapers and smokers showed strikingly similar biological outcomes in the two groups, although the number of affected genes was several-fold higher in smokers than vapers. Of significance is the preferential targeting of mitochondrial genes in both vapers and smokers, consistent with impaired functional networks, which are known to drive mitochondrial DNA-related disorders. Equally remarkable is the dysregulation of immune response genes in both vapers and smokers, modulated by upstream cytokines, including members of the interleukin and interferon family, that play a crucial role in inflammation. Conclusions: The concurrent targeting of mitochondrial- and immune response genes in vapers and smokers suggests a consequential role for vaping and smoking in inflammation. Our findings accord with the growing evidence on the central role of mitochondria as signaling organelles that govern fundamentals of immunity and inflammatory response. In view of the widespread use of e-cigs among youth and young adults, these novel findings have significant implications for tobacco regulatory science and public health.

overall_design: (N=82 total); Experimental 1: Vapers (N=37); Experminemtal 2: Smokers (N=22); Controls | Nonsmokers non-vapers (N=23). No replicate sample is included.

first: Stella

last: Tommasi

first: Niccolo

last: Pabustan

first: Meng

last: Li

first: Yibu

last: Chen

first: Kimberly

middle: D

last: Siegmund


title: Transcriptional and chromatin-based partitioning mechanisms uncouple protein scaling from cell size

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

institute: STANFORD UNIVERSITY

summary: Biosynthesis scales with cell size such that protein concentrations generally remain constant as cells grow. As an exception, synthesis of the cell-cycle inhibitor Whi5 ‘sub-scales’ with cell size so that its concentration is lower in larger cells to promote cell-cycle entry. Here, we find that a transcriptional control uncouples Whi5 synthesis from cell size and, screening for similar genes, identify histones as the major class of sub-scaling transcripts besides WHI5. Histone synthesis is thereby matched to genome content rather than cell size. Such sub-scaling proteins are challenged by asymmetric cell division because proteins are typically partitioned in proportion to new-born cell volume. To avoid this fate, Whi5 uses chromatin-binding to partition similar protein amounts to each new-born cell regardless of cell size. Finally, disrupting both Whi5 synthesis and chromatin-based partitioning compromises G1 size control. Thus, specific transcriptional and partitioning mechanisms determine protein sub-scaling to control cell size.

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: ChIP-seq and RNA-seq libraries associated with the project

first: Matthew

middle: P

last: Swaffer

first: Devon

last: Chandler-Brown

first: Jacob

last: Kim

first: Maurice

last: Langhinrichs

first: William

last: Greenleaf

first: Anshul

last: Kundaje

first: Kurt

last: Schmoller

first: Jan

last: Skotheim


title: Localized phosphorylation of RNA Polymerase II by G1 cyclin-Cdk promotes cell cycle entry

summary: The cell cycle is thought to be initiated by cyclin-dependent kinases (Cdk) inactivating transcriptional inhibitors of cell cycle gene-expression. In budding yeast, the G1 cyclin Cln3-Cdk1 complex is thought to directly phosphorylate Whi5, thereby releasing the transcription factor SBF and committing cells to division. Here, we report that Cln3-Cdk1 does not phosphorylate Whi5, but instead phosphorylates the RNA Polymerase II subunit Rpb1’s C-terminal domain (CTD) on S5 of its heptapeptide repeats. Cln3-Cdk1 binds SBF-regulated promoters(8) and Cln3’s function can be performed by the canonical S5 kinase Ccl1-Kin28 when synthetically recruited to SBF. Thus, Cln3-Cdk1 triggers cell division by phosphorylating Rpb1 at SBF-regulated promoters to promote transcription. Our findings blur the distinction between cell cycle and transcriptional Cdks to highlight the ancient relationship between these processes.

overall_design: ChIP-seq

first: Mardo

last: Kõivomägi

first: Jonathan

last: Turner


title: Expression data from SW620/sh control and SW620/shMACC1

city: Berlin

first: Dennis

last: Kobelt

address: Robert-Rössle-Str. 10

country: Germany

institute: ECRC/Charite Berlin

summary:
MACC1 is a decisive driver of metastasis. In this data set the expression changes of shRNA mediated knock down is analyzed.
We used microarrays to detail the global programme of gene expression changing upon MACC1 knock down.

overall_design: Cells were collected from in vitro cell of three different passages (as indicated in the sample characteristics field). Between the passages there was one week of cultivation.

first: Ulrike

last: Stein


title: Transcriptional signatures in iPSC-derived neurons are reproducible across labs when differentiation protocols are closely matched

city: Bethesda

first: Xylena

last: Reed

state: MD

address: 35 Convent Dr. bldg 35 Rm1A1015

department: National Institute on Aging

institute: NIH

summary: Reproducibility of expression patterns in iPSC-derived cells from different labs is an important first step in ensuring replication of biochemical or functional assays that are performed in different labs. Here we show that reproducible gene expression patterns from iPSCs and iPSC-derived neurons matured and collected at two separate laboratory locations can be achieved by closely matching protocols and reagents. While there are significant differences in gene expression between iPSCs and differentiated neurons, as well as between different donor lines of the same cell type, transcriptional changes that vary with laboratory sites are relatively small. These results suggest that making great efforts to match protocols, reagents and technical methods between labs may improve the reproducibility of iPSC-derived cell models.

overall_design: We used two different iPSC donor lines at two laboratory sites. 33i N=3, CS25i N=2. Cells were partially differentiated in forebrain neurons at one site then half were shipped to the second lab. Partially differentiated cells were thawed and matured in both labs starting on the same day. We collected RNA from iPSC and iPSC derived neurons from each line at each site. Differential expression analysis was done to identify sources of variance.

first: Melanie

last: Cobb

first: Gaia

last: Skibinski

first: Dorien

last: Roosen

first: Alice

last: Kaganovich

first: Jinhui

last: Ding

first: Steve

last: Finkbeiner

first: Mark

middle: R

last: Cookson


title: Loss of mutual protection between osteoclasts and chondrocytes in damaged joints: effects on osteoclast-mediated cartilage degradation via matrix metalloproteinases

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

institute: University of Oxford

summary: Osteoclasts are multinucleated, bone-resorbing cells. However, they also digest cartilage during skeletal maintenance, development and in degradative conditions including osteoarthritis, rheumatoid arthritis and primary bone sarcoma. This study explores the mechanisms behind the osteoclast–cartilage interaction. Human osteoclasts differentiated on acellular human cartilage expressed osteoclast marker genes (e.g. CTSK, MMP9) and proteins (TRAP, VNR), visibly damaged the cartilage surface and released glycosaminoglycan in a contact-dependent manner. Direct co-culture with chondrocytes during differentiation increased large osteoclast formation (p < 0.0001) except when co-cultured on dentine, when osteoclast formation was inhibited (p = 0.0002). Osteoclasts cultured on dentine inhibited basal cartilage degradation (p = 0.012). RNA-seq identified MMP8 overexpression in osteoclasts differentiated on cartilage versus dentine (8.89-fold, p = 0.0133), while MMP9 was the most highly expressed MMP. Both MMP8 and MMP9 were produced by osteoclasts in osteosarcoma tissue. This study suggests that bone-resident osteoclasts and chondrocytes exert mutually protective effects on their ‘native’ tissue. However, when osteoclasts contact non-native cartilage they cause degradation via MMPs. Understanding the role of osteoclasts in cartilage maintenance and degradation might identify new therapeutic approaches for pathologies characterized by cartilage degeneration.

overall_design: Osteoclasts were cultured for 10 days on plastic (no substrate), on elephant ivory (dentine) and human cartilage from OA patients (frozen to kill chondrocytes).

first: Helen

last: Knowles


title: RNA-Sequencing of STING competent and STING-KO cells after transfection with dacA (Listeria monocytogenes)

first: Alexander

middle: T

last: Bell

state: Maryland

address: 37 Convent Drive

department: National Cancer Institute

institute: National Institutes of Health

summary: HEK-Blue™ ISG Cells and HEK-Blue™ ISG-KO-STING Cells (Invivogen) were transfected with dacA (Listeria monocytogenes) for 12 and 24 hours. Through this approach, we described the STING-dependent and STING-independent transcriptional response to dacA. Our analysis reveals a STING-dependent enrichment of interferon stimulated genes beginning 12 hours post-transfection, and a STING-independent enrichment of genes associated with protein translation and oxidative phosphorylation.

overall_design: Transcriptional responses to dacA transfection in STING-WT and STING-KO cells.

first: Steven

last: Shema

first: Madeline

last: Wong

first: John

last: Schiller


title: microRNA sequencing analysis in obstructive sleep apnea and its adverse consequences

city: Hsinchu

first: Tingwen

last: Chen

address: No. 75, Boat Street, East District

country: Taiwan

institute: National Yang Ming Chiao Tung University

summary: Illumina MiSeq next generation sequencing chip was used to identify differentially expressed miRs by comparing peripheral blood mononuclear cell samples between OSA patients and healthy non-snorers.

overall_design: prospective comparison of whole genome microRNA profiles in PBMC samples between 16 OSA patients and 6 matched healthy non-snorers, Samples from two or four participants of the same group were pooled together.

first: Yung-Che

first: Ting-Wen


title: Generation of Allogeneic Hematopoietic Stem Cell-Engineered Invariant Natural Killer T cells for Off-the-Shelf Immunotherapy [VDJ-seq]

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

summary: While T cell-based immunotherapies have shown promising clinical responses, current cancer treatments are restricted to autologous cellular products due to the risk of graft-versus-host disease (GvHD) by allogeneic cell transfer. Invariant natural killer T (iNKT) cells are ideal cell carriers for developing off-the-shelf allogeneic cellular therapy because they are powerful immune cells targeting a broad range of cancers without causing GvHD. However, current immunotherapies using iNKT cells are impeded by their extremely low number in cancer patients. In this study, we aimed to overcome this limitation by generating a large number of iNKT cells through TCR engineering of human hematopoietic stem cells (HSCs) and differentiation of HSCs to iNKT cells in an in vitro cultured system. Additionally, Chimeric antigen receptor (CAR) engineering and the CRISPR-Cas9 gene editing tool were utilized to enhance the tumor killing efficacy of iNKT cells and eliminate HLA molecules on their surface, making the cellular product suitable for cancer therapy and allogeneic adoptive transfer. Our results demonstrated successful generation of the promising off-the-shelf B cell maturation antigen (BCMA)-CAR engineered iNKT cells for treating multiple myeloma, and the same strategy will be applied to multiple cellular products for treating other cancers.

overall_design: Examination of T cell receptor V(D)J recombination in different subtypes.

first: Yanruide

last: Li

first: Matteo

last: Pellegrini

first: Lili

last: Yang


title: Genome-wide liver transcriptomic profiles from chow-fed, high fat diet (HFD) fed, and HFD + AC261066 (Retinoic Acid Receptor Beta-2 Selective Agonist) fed mice

city: New York

first: Xiaohan

last: Tang

address: 1300 York Ave.

institute: Weill Cornell Medicine

summary: Using a high fat diet (HFD) mouse model of nonalcoholic fatty liver disease (NAFLD) with 60% of the energy derived from fat, we determined the effects of AC261066, a RARbeta2 selective agonist, on the liver transcriptome. We analyzed disease signature pathways using our genome-wide RNA-seq data from AC260166 treated livers and show that AC261066 limits the mRNA increases of NAFLD driver genes PKLR, FASN, THRSP, and CHCHD6. Moreover, AC261066’s effects on the hepatic stellate cell (HSC) secretome signature and changes in other transcripts that contribute to fibrosis suggest that AC261066 suppresses the initiation of liver fibrosis, which characterizes NASH. Our RNA-seq data also indicate an anti-inflammatory effect of AC261066. In conclusion, based on our genome-wide analysis of the transcriptome of NAFLD, we suggest that AC261066 has potential therapeutic relevance for the prevention/treatment of NAFLD and NASH.

overall_design: Examination of genome-wide transcript levels in mouse liver samples.

first: Xiao-Han

first: Lorraine

last: Gudas


title: ZKSCAN3 knockout HCT116 colorectal cancer cell line

city: Seoul

first: Yong Jun

last: Kim

address: 26 Kyungheedaero

department: Department of Pathology

country: South Korea

institute: Kyung Hee University

summary: ZKSCAN3 is an oncogenic transcription factor in a set of human malignant tumors including colon, prostate, bladder, and cervical cancers. We investigated that ZKSCAN3 acts as a downstream effector of oncogenic Wnt/beta-catenin signaling pathway. Deletion or knockdown of ZKSCAN3 increased MAD2L2 expression, resulting in delaying the cell cycle progression by increasing the time laps between prometaphase and telophase. Our study demonstrates that ZKSCAN3 mediates oncogenic Wnt/beta-catenin signals and induces chromosomal instability by suppressing MAD2L2 at the early stage of colon cancer development.

overall_design: ZKSCAN3 KO HCT116 colorectal cancer cell line was generated using CRISPR/Cas9 gene editing technique. Biological triplicates of RNA seqeuncing was performed.

first: Sun

last: Lee

first: Jae-Hoon

last: Park


title: circRNA-sequencing analysis of plasma exosomes in hepatocellular carcinoma

city: Ji Nan

first: Xiangyu

last: Zhai

state: China

address: Department of general surgery, Qilu hospital of Shandong University，Wenhuaxi Road

institute: Qilu hospital of Shandong University

summary: Hepatocellular carcinoma (HCC) is currently the third leading cause of death worldwide and the most common type of primary liver cancer, finding noninvasive biomarkers for HCC diagnostic and prognostic are very urging. Previous genomic studies mainly focus on finding miRNA biomarkers for HCC. In this study, we focus on finding circRNA fragments suitable for serving as hcc biomarkers with plasma exosomal RNA-seq..

overall_design: RNA-seq of plasma exosomal RNA collected from HCC patients, healthy donors, each with 6 replicates

first: Bin

last: Jin


title: mRNA vaccine efficacy in a severe COVID-19 model: attenuated activation of pulmonary immune cells after the challenge

city: Manhattan

first: Aliza

last: Rubenstein

state: NY

address: 1 Gustave L. Levy Pl

institute: Icahn School of Medicine at Mount Sinai

summary: mRNA-1273, an mRNA-based vaccine for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is efficacious in mouse and non-human primate models of mild COVID-19. Hamsters exhibit more severe clinical disease from SARS-CoV-2, making it an important model to evaluate vaccine efficacy. Here we show that mock-vaccine treated hamsters infected with SARS-CoV-2 show weight loss and pulmonary infection with pathological changes and increased activated interstitial macrophages and other immune cell types. Prime-boost administration of mRNA-1273 elicited dose-independent robust binding and neutralizing antibodies, ameliorated weight loss and suppressed virus replication in the upper and lower airways. Vaccination largely prevented pulmonary pathological changes, antiviral immune cell activation and changes in cell type composition although increases in some immune cell types and activation of regulatory pathways were found and coincided with an anamnestic antibody response. The results characterize unexpected pulmonary cellular responses to SARS-CoV-2 in vaccinated animals that were shared but greatly attenuated, when compared to mock-vaccinated animals. The efficacy of mRNA-1273 is demonstrated as a two-dose vaccination schedule in a model of severe COVID-19.

overall_design: Single cell RNA sequencing was conducted on fourteen samples of the Syrian golden hamster lung tissue. Samples were from naïve, mock-vaccinated + SARS-CoV-2 infected, and mRNA-1273 vaccinated + SARS-CoV-2 infected hamsters.

first: Michelle

last: Meyer

first: Yuan

last: Wang

first: Darin

last: Edwards

first: Gregory

last: Smith

first: Palaniappan

last: Ramanathan

first: Chad

middle: E

last: Mire

first: Colette

last: Pietzsch

first: Xi

first: Yongchao

last: Ge

first: Wan

middle: S

last: Cheng

first: Carole

last: Henry

first: Angela

last: Woods

first: Ling

middle: Z

first: Guillaume

last: Stewart-Jones

first: Kevin

middle: W

last: Bock

first: Mahnaz

last: Minai

first: Bianca

last: Nagata

first: Sivakumar

last: Periasamy

first: Pei

middle: Y

last: Shi

first: Barney

last: Graham

first: Ian

middle: N

last: Moore

first: Irene

last: Ramos

first: Olga

last: Troyanskaya

first: Elena

last: Zaslavsky

first: Andrea

last: Carfi

first: Stuart

last: Sealfon

first: Alexander

last: Bukreyev


title: LSD1 inhibitors trigger myeloid differentiation by targeting the LSD1-GSE1 interaction on chromatin

city: Milan

first: Fabio

last: Bedin

address: Via Olgettina 60

institute: SR-TIGET


title: LSD1 inhibitors trigger myeloid differentiation by targeting the LSD1-GSE1 interaction on chromatin [RNA-seq]

summary: The histone de-methylase LSD1 is over-expressed in different haematological tumours, like AML, where it sustains carcinogenesis by promoting the clonogenic potential of leukemic stem cells.  Emerging as a promising epigenetic target for the treatment of these tumour types, various LSD1 inhibitors have been developed in the last years, despite their mechanism of action in cancer cells is often not fully clarified. In this study, we characterized a novel mode of action of the inhibitors MC2580 and DDP-38003 and demonstrated that they trigger myeloid differentiation of AML by down-regulating GSE1 protein, a LSD1 interactor on chromatin. By studying the phenotypic effects of GSE1 depletion in NB4 cells, we observed a strong decrease of cell proliferation in vitro, and of tumour growth in vivo. Comparing the transcriptomic changes induced by GSE1 knock-down with those elicited by LSD1 pharmacological inhibition, we found a common set of genes up-regulated and linked with immune response and cytokine-mediated signalling. Mechanistically, we found that several promoters of these genes are bound by both LSD1 and GSE1 at basal state and that GSE1 binding is strongly reduced upon LSD1 inhibition, as a consequence of its reduced expression. By describing for the first time that LSD1-GSE1 interaction on chromatin enforces the silencing of genes linked to myeloid differentiation and by highlighting that this interaction can be overcome by LSD1 inhibitors, our study offers a new perspective on the use of these compounds to trigger differentiation in leukaemia through GSE1 modulation.

overall_design: Effect of the transcriptomic changes after GSE1 knock-down (KD) and LSD1 pharmacological inhibition by RNA-seq in NB4 cells.

first: Nicosia

last: Luciano

first: Ceccaci

last: Elena

first: Bedin

last: Fabio

first: Bonaldi

last: Tiziana


title: Genome-wide maps of chromatin state in AIMP1 overexpression (OE) and wildtype (WT) cells in multiple myeloma

city: Nanjing

first: Rong

middle: Fang

last: Wei

state: Jiangsu

address: 138 Xianlin Road

institute: Nanjing Unveristy of Chinese Medicine

summary: We found Acetyl-H3 was upregulated when AIMP1 overexpressed. Then, we used CHIP-seq to find binding-DNA with acetyl-H3 protein.

overall_design: Immunoprecipitation using acetyl H3 antibody. Purify DNA and map reads to reference geneome. And High throughout sequence analysis were performed.

first: Rongfang


title: Transcriptome analaysis of Bcl11b-deficient aortas

city: Boston

first: Francesa

last: Seta

state: MA

address: 650 Albany St Evans Biomed Research Ctr

department: Medicine

institute: Boston University

summary: B-cell leukemia 11b (BCL11B) is a transcription factor known as an essential regulator of T lymphocytes and neuronal development during embryogenesis. A genome-wide association study (GWAS) showed that a gene desert region downstream of BCL11B, known to function as a BCL11B enhancer, harbors single nucleotide polymorphisms (SNPs) associated with increased arterial stiffness. However, a role for BCL11B in the adult cardiovascular system is unknown. Based on these human findings, we sought to examine the relation between BCL11B and arterial function. Here we report that BCL11B is expressed in the vascular smooth muscle (VSM) where it regulates vascular stiffness. RNA sequencing of aortas from WT and Bcl11b null mice (BSMKO) identified the cyclic guanosine monophosphate (cGMP)-protein kinase G (PKG) as the most significant differentially regulated signaling pathway in BSMKO compared to WT mice. BSMKO aortas showed decreased levels of PKG1, increased levels of Ca++-calmodulin-dependent serine/threonine phosphatase calcineurin (PP2B) and their common phosphorylation target, vasodilator-stimulated phosphoprotein (pVASPS239), a regulator of cytoskeletal actin rearrangements. Decreased pVASPS239 in BSMKO aortas was associated with increased actin polymerization (F/G actin ratio). Functionally, aortic force, stress, wall tension and stiffness, measured ex vivo in organ baths, were increased in BSMKO aortas, and BSMKO mice had increased pulse wave velocity, the in vivo index of arterial stiffness. Despite having no effect on blood pressure or microalbuminuria, increased arterial stiffness in BSMKO mice was associated with increased incidence of cerebral microbleeds compared to age-matched WT littermates. In conclusion, we have identified VSM BCL11B as a crucial regulator of aortic smooth muscle function and a potential therapeutic target for vascular stiffness.

overall_design: Examination of changes in transcriptome of whole aortas from WT and vascular smooth muscle-specific Bcl11b KO mice

first: Eric

last: Helm

first: Dorina

last: Avram

first: Francesca


title: Molecular characterization of NICOTINAMIDASE 3 gene in perspective of drought tolerance mechanism in Arabidopsis

city: Yokohama-Shi, Tsurumi Ku

first: Khurram

last: Bashir

state: Kanagawa

address: 1-7-22 Suehiro-cho

department: Center for Sustainable Resource Science

country: Japan

institute: RIKEN

summary: Gene expression profiles of roots and shoots of WT and NIC3 OX plants under control and 5 days rought-stressed conditions were analyzed using the custom microarray (GPL19830).

overall_design: Seeds of Arabidopsis thaliana (Col-0 ecotype) were grown on MS medium at 22°C under 16-h-light/8-h-dark for 10 days. Plantlets were then transferred to ceramics granular soil (size 2.5L, Sakatanotane, Japan) and grown for 5 days at 22°C. The drought treatment was then commenced by removing excess water from the trays and ceasing any subsequent watering. Roots and shoots were harvested separately  under control conditions and at  5 days after the onset of drought treatment.

first: Zarnab

last: Ahmad

first: Akihiro

last: Matsui

first: Maho

last: Tanaka

first: Motoaki

last: Seki


title: Expression profiling of death-related genes in ZIKV-infected SH-SY5Y cells

city: Recife

first: Leila

last: Mendonça Vieira

state: Pernambuco

address: Av Prof. Moraes Rego, 1235 - Cidade Universitaria

department: LAVITE

country: Brazil

institute: FIOCRUZ

summary:
Analysis of death triggering pathways activated by experimental Zika virus infection in SH-SY5Y cells by expression profiling of 42 genes related to survival, anti-apoptotic and proapoptotic responses, and death receptors pathway, and 06 endogenous control genes.
Commercially available neuroblastoma SH-SY5Y cells were grown in vitro, experimentally infected with Zika virus (MOI 0.5), and MOCK- and ZIKV-infected cells were harvested at 1 and 2 days post-infection. We used TaqMan ™ Array Human Apoptosis via Death Receptors (Thermo Fisher Scientific, MA, USA) to quantitate gene expression during ZIKV infection in SH-SY5Y cells.

overall_design: qPCR gene expression profiling. Two replicate samples of each timepoint post-infection (1 and 2 days post-infection) were infected separately as indicated in the summary. We used two replicate samples of mock-infected cells as control samples. Equal amounts of cDNA of each timepoint was added to each real time PCR reaction.

last: Mendonca-Vieira


title: Alveolar organoid model

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

summary: Rationale: Alveolar epithelial type 2 (AT2) cells are stem/progenitor cells in the adult lung and their maintenance and regulation is achieved through their interaction with mesenchymal cells which constitute their niches. However, the precise identity of the niche cells is still elusive.  Objectives: To characterize the niche cells capable of supporting the self-renewal of AT2 stem cells in the murine model.  Methods: The alveolar organoid model was used to test the efficiency of different subpopulations of mesenchymal cells isolated by FACS from well-established (PdgfraGFP, Axin2LacZ, Fgf10LacZ) reporter mice to support the self-renewal of mature AT2 cells. The reporter-positive cells where pre-sorted based on Cd45neg Cd31neg Epcamneg Sca1pos. Additional selection was achieved using LipidTOX staining for cells containing high level of neutral lipids. Organoid size and colony formation efficiency after 2 weeks in culture were quantified. RNAscope combined with immunofluorescence on adult lungs. qPCR, gene array were used to characterize the niche cells.  Measurements and main results: A subset of Sca1+; Fgf10-expressing cells positive for LipidTox staining  in the distal mesenchyme is efficient in the self-renewal and differentiation of AT2 stem cells. Co-staining of adult lung by using ISH and IF staining for Fgf10 and Sftpc respectively, indicate that 28% of Fgf10+ cells are located to close to AT2 cells. These cells do not overlap with Fgf7-expressing cells. Gene array comparing MANC (Cd45Neg Cd31Neg EpcamNeg Sca1Pos Axin2LacZ/FDGPos) with Fgf10Pos Lipofibroblasts (Cd45Neg Cd31Neg EpcamNeg Sca1Pos  Fgf10LacZ/FDGPos) support that these two cell subsets are different and express differential markers that can be further used for the respective characterization of these cells.  Conclusions: We have demonstrated for the first time that Fgf10Pos LIF cells play important role to support AT2 stem cells in terms of self-renewal and differentiation toward the AT1 cell type. These cells appear different from the previously characterized MANC and display a similar activity in eliciting AT2 self-renewal.

overall_design: 4 groups, each with 2 biological replicates

first: Sara

last: Taghizadeh

first: Saverio

last: Bellusci


title: CPEB4 regulate mRNA involved in adipogenesis and macrophage recruitment in white adipose tissue.

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

summary: Study of the potential CPEB4 mRNA targets in 3T3-L1 adipocytes. Here we show how CPEB4 is critical for the adipocye maturation during adipogenesis as well as contibute to the macrophage recruitment that takes place during adipose tissue expansion

overall_design: 3 samples for experiment, including Input, IP CPEB4 and IP IgG as control. 4 replicates included in the study. Results obtained from an interaction analisis

first: Núria

last: Pell

first: Mercedes

last: Fernandez

first: Raul

last: Mendez


title: Retrieving high-resolution chromatin interactions and decoding enhancer regulatory potential in silico

city: Göttingen

first: Argyris

last: Papantonis

address: Robert-Koch-Straße 40

department: Institut für Pathologie

institute: Universitätsmedizin Göttingen

summary: The advent of the chromosome conformation capture (3C) and related technologies has profoundly renewed our understaning of three-dimensional chromatin folding in mammalian nuclei. Alongside these experimental approaches, numerous computational tools for handling, normalizing, visualizing, and ultimately detecting interactions in 3C-type datasets are being developed. Here, we present Bloom, a comprehensive method for the analysis of 3C-type data matrices on the basis of Dirichlet process mixture models that addresses two important open issues. First, it retrieves occult interaction patterns from sparse data, like those derived from single-cell or “native” Hi-C experiments; thus, bloomed sparse data can now be used to study interaction landscapes at high-resolution. Second, it detects enhancer-promoter interactions with high sensitivity and inherently assigns an interaction frequency score (IFS) to each contact. Using enhancer perturbation data of different throughput, we show that IFS accurately quantifies the regulatory influence of each enhancer on its target promoter. As a result, Bloom allows decoding of complex regulatory landscapes by generating functionally-relevant enhancer atlases solely on the basis of 3C-type data.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: HiC experiments on 5x106 mESC and 106 CM cells.

first: Eduardo

last: Gusmao

first: Athanasia

last: Mizi

first: Lilija

last: Brant

first: Papantonis

last: Argyris


title: Small cell lung cancer

city: Shanghai

first: Cao

last: Jy

address: Yueyang Road

institute: CAS

type: Genome variation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Mutation in H82 P0,P1,P2,P3,P4 tumors

summary: Detect the mutation in tumors with etoposide plus cisplatin treatment

overall_design: H82 P0,P1,P2,P3,P4 tumors

first: Chenchen

last: Guo

first: Hongbin

last: Ji


title: RNA-sequencing: HNSCC tissue and adjacent normal tissue

first: Guoxin

last: Ren

address: 639 Zhi-zao-ju Road, Shanghai, China

institute: Shanghai ninth hospital

summary: RNA sequencing for 8 samples

overall_design: Examing 2 conditions, each with 4 replicates

first: guoxin

last: ren

first: houyu

last: ju


title: MeRIP sequencing in HUVEC cell lines

city: Chongqing

first: Huang

last: Wu

address: 10 Changjiang Access Road

department: Department of Blood Transfusion

institute: Daping Hospital, Army Medical University

summary: We have used MeRIP-seq to explore m6A modification  profiles in  HUVEC cell lines.

overall_design: Examination of m6A modification in HUVEC cell lines.

first: Qin

last: Bai


title: Changes in CIDEA expression associate with adipocytes size and functionality in adolescent obese girls

city: New Haven

first: Elena

last: Tarabra

state: Connecticut

address: 330 cedar street

department: Endocrinology/Pediatrics

country: USA

institute: Yale University - School of Medicine

summary: About 20% of youth are obese with higher risk for cardiovascular disease and type 2 diabetes (T2D). We have recently reported that in obese adolescents altered pattern of fat distribution is associated with insulin resistance and T2D. In particular, the high ratio of visceral AT depot (VAT) to abdominal subcutaneous AT depot (SAT) (high VAT/(VAT+SAT)) was associated with a metabolically unhealthy phenotype with high risk for insulin resistance and T2D. CIDEA (Cell death inducing DNA fragmentation factor-alpha-like A) is a member of CIDE family and it is not only involved in the promotion of cell death and DNA fragmentation but it also plays critical roles in the lipid droplets formation and growth. Here we demonstrated in abdominal SAT from adolescent obese girls with high VAT/(VAT+SAT) a significant reduction of CIDEA expression associated with an increase in fasting insulin, serum FFA and consequent insulin resistance. We also demonstrated a direct correlation between CIDEA expression and fraction of large cells and an inverse correlation with small adipocytes number and pre-adipocytes proliferation. After gaining weight, we observed an increase in adipocytes cell diameter but a decrease in CIDEA expression, and the transcriptomic analysis showed a gene profile linked to adipocyte dysfunction. Together, these data suggested that in subjects with high VAT/(VAT+SAT) decreased CIDEA expression is associated with an increase in adipocyte cell sizing and consecutive insulin resistance.

overall_design: Human Abdominal Subcutaneous Adipose tissue (SAT) mRNA profiles of 18 obese subjects and SAT mRNA profile of 4 subjects returned after gaining weight (sequencing using Illumina Hi-Seq4000).

first: Jessica

last: Nouws

first: Alla

last: Vash-Margita

first: Marc

last: Hellerstein

first: Veronika

last: Shabanova

first: Sarah

last: McCollum

first: Bridget

last: Pierpont

first: Dejian

last: Zhao

first: Gerald

last: Shulman

first: Sonia

last: Caprio


title: LSD1 inhibitors trigger myeloid differentiation by targeting the LSD1-GSE1 interaction on chromatin [ChIP-seq]

first: Fabio

last: Bedin

overall_design: ChIP-seq profiling of a V5-tagged isoform of GSE1 transduced in NB4 cells and treated for 24h with the LSD1 inhibitor MC2580 and DMSO as control.

first: Nicosia

last: Luciano

first: Ceccaci

last: Elena

first: Bedin

last: Fabio

first: Bonaldi

last: Tiziana


title: Gene expression in H82R cells

first: Cao

last: Jy

country: China

summary: H82R cells was derived from H82 P4 tumors and was resistant to etoposide plus cisplatin

overall_design: H82R cells

first: Chenchen

last: Guo

first: Hongbin

last: Ji


title: Microbial regulation of hexokinase 2 links mitochondrial metabolism and cell death in colitis

city: Kiel

first: Neha

last: Mishra

address: Rosalind-Franklin-Str. 12

institute: Institute of Clinical Molecular Biology

summary: Hexokinases (HK) catalyze the first step of glycolysis and thereby limit its pace. HK2 is highly expressed in the gut epithelium, plays a role in immune responses and is upregulated in inflammation and ulcerative colitis 1-3. Here, we examined the microbial regulation of HK2 and its impact on intestinal inflammation by generating mice lacking HK2 specifically in intestinal epithelial cells (Hk2∆IEC). Hk2∆IEC mice were less susceptible to acute intestinal inflammation upon challenge with dextran sodium sulfate (DSS). Analyzing the epithelial transcriptome from Hk2∆IEC mice during acute colitis revealed downregulation of cell death signaling and mitochondrial dysfunction dependent on loss of HK2. Using intestinal organoids derived from Hk2∆IEC mice and Caco-2 cells lacking HK2, we identified peptidyl-prolyl cis-trans isomerase (PPIF) as a key target of HK2-mediated regulation of mitochondrial permeability and repression of cell-death during intestinal inflammation. The microbiota strongly regulated HK2 expression and activity. The microbially-derived short-chain fatty acid (SCFA) butyrate repressed HK2 expression and oral supplementation protected wildtype but not Hk2∆IEC mice from DSS colitis. Our findings define a novel mechanism how butyrate may act as a protective factor for intestinal barrier homeostasis and suggest targeted HK2 inhibition as a promising therapeutic avenue in intestinal inflammation.

overall_design: RNA-seq of colon tissue of WT and Hk2∆IEC mice at days 0, 3 and 7 during DSS colitis

first: Felix

last: Sommer

first: Jacob

last: Hamm

first: Finn

last: Hinrichsen

first: Philip

last: Rosenstiel


title: RNA-sequencing of skeletal stem cells (SSC) and mesenchymal stem cells (MSC) from hindlimb unloaded and reloaded mice

city: Jupiter

first: Donald

middle: G.

last: Phinney

state: Florida

address: 130 Scripps Way Bldg A215

department: Molecular Medicine

institute: The Scripps Research Institute

summary: Disuse osteoporosis (DO) occurs in response to mechanical unloading of the skeleton and results in structural changes that compromise bone strength leading to increased fracture risk. Although skeletal stem cells (SSCs) are the main source of osteoblasts and adipocytes in adult bone marrow, whether DO impacts SSC function has not been established. Here, three-month-old male C57BL/6 mice were subjected to a hindlimb unloading (HU) model of disuse osteoporosis for 8 or 14 weeks by tail suspension. Control mice (ambulatory or AMB) were allowed normal use of their hindlimbs. An additional cohort underwent an 8-week recovery period after 8-weeks of unloading. Bone marrow-derived, LepR+ skeletal stem cells (SSCs) were isolated by FACS (n=3 or 4) and pooled prior to RNA isolation. Where indicated, cultured, immuno-depleted, bone marrow-derived mesenchymal stem cells (MSCs) were also collected (n=3) and pooled prior to RNA isolation.  Generated libraries were subjected to NGS RNA-seq analysis on the Illumina NextSeq 500. These data delineate unique physiological adaptations to prolonged unloading, demonstrate that DO results in increased leptin expression and sympathetic signaling within the BM niche.

overall_design: RNA-seq analysis of RNA derived from hindlimb unloaded and reloaded mouse FACS-isolated for LepR+ SSCs or cultured and immuno-depleted MSCs.

middle: G

first: Cori

last: Booker

first: Christopher

middle: L

last: Haga


title: Roles of LOX and LOXL1 on the transcriptome of hepatic stellate cells

city: Beijing

first: Wei

last: Chen

state: Beijing

address: No. 95 Yong’an road, Xicheng District

department: Beijing Friendship Hospital

institute: Capital Medical University

summary: Our previous studies have found that LOX and LOXL1 were highly upregulated in advanced liver fibrosis; herein, we aimed to investigate the roles of LOX and LOXL1 in hepatic stellate cells.

overall_design: LOX or LOXL1 siRNA (25nM) was transfected into TGFβ1-treated (10ng/ml) LX-2 cells (n=3 for each group) for 48 hours. Total RNA was isolated using Trizol reagent (Invitrogen, USA). Agilent 2100 Bioanalyzer (Agilent Technologies, USA) was used to evaluate the RNA quality. One μg RNA was used to generate cDNA library. We performed RNA-seq by BGISEQ-500.

first: Hong

last: You


title: Nicotinamide promotes human pluripotent stem cells differentiation into cardiomyocytes [1]

city: Macau

first: Ren

last: Zhili

address: Avenida da Universidade

institute: University of Macau

summary: Nicotinamide, the amide form of vitamin B3, is essential to maintain the human fetal development. It benefits the ectoderm and endoderm development, but its influence in mesoderm differentiation is elusive. In this study, we reported that nicotinamide regulated the gene expression of cardiovascular system, and it induced functional cardiomyocytes which was independent of canonical WNT signaling. Through a kinase screening, we found that nicotinamide inhibited the activity of P38δ to promote cardiomyocyte differentiation. Furthermore, we compared the gene expression of cardiomyocytes induced by WNT inhibitor IWP-2, nicotinamide or P38 inhibitor SB202190. The results showed that the cardiomyocytes induced by nicotinamide had similar gene expression profile compared with P38 inhibitor, which indicated nicotinamide promoted cardiac differentiation via the inhibition of P38.

overall_design: Total RNA obtained from human embryonic stem cell (hESC) culture in E8 medium for 3 days(E8 72 hrs), E8 medium with nicotinamide 10 mM treatment for 3 days (Nam 72 hrs).

first: Guokai


title: Concurrent Disruption of Ras-Erk and NF-κB Pathways Induces Circadian Deregulation and Hepatocarcinogenesis

city: La Jolla

first: Kaisa

last: Hanley

address: 9500 Gilman Drive MC 0864

institute: University of California San Diego

summary: Mice with hepatocyte-specific deletion of both Shp2 and IkkB were generated, which disrupted basal levels of Ras-ERK and NF-kB signaling. These mice exhibited accelerated liver tumor formation compared to either single knockout alone.  RNA-Seq analysis of whole liver and isolated hepatocytes from all genotypes were performed to identify tumor-promoting factors in the DKO model. Along with inflammatory and

overall_design: 24 samples were analyzed from whole liver samples or isolated hepatocytes from 2-month old male mice with knockout of Shp2 and/or IkkB; 3 biological replicates per genotype; WT C57/BL6 mice used as controls

first: Gaowei

last: Wang

first: Yan

last: Liang

first: Gen-Sheng

last: Feng


title: Intratumoral heterogeneity of DNA methylation in an ovarian metastasis from lobular breast cancer

city: Hannover

first: Helge

last: Stark

address: Carl-Neuberg-Straße 1

department: Institute of Pathology

institute: Medical School Hannover

type: Methylation profiling by genome tiling array

summary: In lobular breast cancer, metachronous distant metastasis may become evident many years after primary tumor diagnosis and often affect the ovary. Little is known about tumor dormancy and intratumoral heterogeneity of DNA methylation in metastasis from lobular breast cancer.  In this exploratory analysis, DNA methylation patterns were studied in six spacially separated regions of an ovarian metastasis from lobular breast cancer.

first: Matthias

last: Christgen

first: Hans

last: Kreipe


title: ARID1A modules estrogen receptor signaling in endometrial cancer

city: Wuhan

first: Hanyang

last: Hu

state: Please Select

address: School of Basic Medical Sciences, Wuhan University

institute: Wuhan University

summary: To investigate the role of ARID1A in estrogen receptor positive endometrial cancers, we performed RNAseq in control and ARID1A-knockdown Ishikawa cells treated with DMSO,E2 and E2+Fulvestrant for 8 hours.

overall_design: RNAseq of the ARID1A knockdown and control Ishikawa cells with treatment of DMSO,E2 and E2+Fulvestrant for 8 hours

first: Lulu

last: Ji


title: Temporal Analyses of Cardiac Chromatin Accessibility, DNA Methylation and Epigenomic Structure Reveal Locus-Specific Regulation [RNA-seq]

city: Los Angeles

first: Tom

last: Vondriska

state: CA

address: 650 Charles E Young Dr, BH553

institute: UCLA

summary: Heart failure can be induced or ameliorated by regulation of chromatin modifying enzymes. Because so many chromatin factors regulate gene expression, we used ATAC-seq to report the status of a given locus at any time—the sum total of all epigenetic modifiers—in a mouse model of pressure overload hypertrophy. Early compensation of pressure overload at 3 days was associated with widespread changes in chromatin accessibility and DNA methylation, the majority of which persisted to the decompensated phase (3 weeks), revealing the temporal nature of epigenomic compensation to pathologic stimuli. A cardiac-specific CTCF depletion model was used to examine how this protein maintains basal cardiac chromatin function and revealed that loss of CTCF causes widespread changes in accessibility and methylation that are distinct from those in pressure overload. Less than half of the gene expression changes occurring at either time point after pressure overload were explained by the actions of DNA methylation alone and accessibility was likewise an imperfect predictor of transcription. Distal enhancers were paired with genes based on chromatin structural data and the regulatory actions of these elements examined in the context of DNA methylation and accessibility: enhancer actions require specific combinations of transcription factors and histone modifications at different stages of disease and to execute a specific transcriptional event (methylation and accessibility alone were insufficient to predict the behavior). In summary, these studies characterize the logic employed at different coding, regulatory, and noncoding regions to regulate chromatin accessibility and transcription, providing a resource of epigenomic data at distinct temporal stages of heart failure.

overall_design: Diferences in chromatin accessibility, DNA methylation and gene expression at early (3 days) and late (3 weeks) stage of cardiac disease, and during cardiac-specific CTCF depletion. TAC (transverse aortic constriction) samples represent mice with diseased hearts.

first: Douglas

last: Chapski

first: Thomas

middle: M

first: Manuel

last: Rosa-Garrido