title: Expression data of stimulated murine primary lung fibroblasts

first: Chang

last: Liu

address: 1 Xian Nong Tan Street, Xicheng District

institute: Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College

summary:
Pulmonary fibrosis (PF) is both an independent disease and a pathologic basis for fibroproliferative lung diseases. Understanding of underlying mechanisms of PF is critical for developing effective therapeutics. Fibroblasts activation and extracellular matrix deposition are critical in pathogenesis of PF. Stimulation of certain factors can induce profibrotic changes in fibroblasts. Evaluation of associated genes in treated fibroblasts is helpfu to analyze the profibrotic changes of this critical effector cell for PF.
We used microarrays to detail the global programme of gene expression following TGFβ and CCL1 stimulation of primary lung fibroblasts.

overall_design: Primary lung fibroblasts were isolated from murine lungs. We treated the cells with the classic profibrotic factor TGFβ as the positive control and CCL1 in triplicates.These stimulated samples as well as untreated fibroblasts were collected for RNA extraction and hybridization on Affymetrix microarrays.

first: Shan-shan

first: Xiao-xi

last: Lv


title: Lung epithelial signaling mediates early vaccine-induced CD4+ T cell activation and Mtb control

status: Public on Sep 14 2021

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

country: USA

institute: Washington University in St.Louis

type: Expression profiling by high throughput sequencing

summary: Tuberculosis (TB) is the leading cause of death due to a single infectious agent. The development of a TB vaccine that induces durable and effective immunity to Mycobacterium tuberculosis (Mtb) infection is urgently needed. Complete and early Mtb control can be induced in M. bovis Bacillus Calmette–Guérin (BCG) vaccinated hosts when the innate immune response is targeted to generate effective vaccine-induced immunity. In the present study, we show that the superior and early Mtb control that is mediated by innate activation of DCs is associated with mucosal localization of clonal activated vaccine-induced CD4+ T cells in the lung. Our studies also show that the lung epithelial cell signaling through the activation of nuclear factor kappa-light-chain-enhancer of activated B cells (NFKB pathway is critical for the mucosal localization of activated vaccine-induced CD4+ T cells for rapid Mtb control. Thus, our study provides novel insights into the immune mechanisms that can overcome TB vaccine bottlenecks and provide early rapid Mtb control.

overall_design: Lung cells were isolated from Mtb-infected unvaccinated mice (Unvac), Mtb-infected BCG vaccinated mice (Vac), and Mtb-infected BCG vaccinated mice that received Z-DC transfer (Vac+Z-DC) and subjected to single cell RNA sequencing (scRNA-Seq) to define immune cell populations driving enhanced vaccine-induced immunity.

first: Shibali

last: Das

first: Nancy

last: Marin-Agudelo

first: Ekaterina

last: Esaulova

first: Mushtaq

last: Ahmed

first: Amanda

last: Swain

first: Bruce

middle: A

last: Rosa

first: Makedonka

last: Mitreva

first: Javier

last: Rangel-Moreno

first: Deepak

last: Kaushal

middle: N

first: Shabaana

last: Khader


title: Activation of bivalent factor DLX5 cooperates with master regulator TP63 to promote squamous cell carcinoma [RNA-Seq]

city: Guangzhou

first: Yongsheng

last: Huang

address: 107 Yan Jiang West Road

country: China

institute: Sun Yat-Sen University

summary: To reconstruct systematically master regulator transcription factor (MRTF)-dependent transcription networks in squamous cell carcinomas (SCCs), a novel computational method (ELMER) was applied to 1,293 pan-SCC patient samples and identified 44 hyperactive SCC MRTFs. As the top candidate, DLX5 exhibits a notable bifurcate re-configuration of its bivalent promoter in cancer. Specifically, DLX5 maintains a bivalent state in normal tissues; it undergoes de novo DNA hypermethylation and transcriptional repression in multiple non-SCC cancers. In stark contrast, DLX5 promoter gains active histone marks and becomes transcriptionally activated in SCCs, which is mediated directly by SOX2. Functionally, DLX5 is essential for SCC viability, migration, anchorage-independent growth and xenograft proliferation. Mechanistically, DLX5 interacts and cooperates with TP63 to regulate ~2,000 enhancers and promoters, which converge on activating cancer-promoting pathways. Together, our data establish a novel and strong SCC-promoting factor, and elucidate a new epigenomic mechanism - bifurcate chromatin re-configuration - during cancer development.

overall_design: Retinal mRNA profiles of KYSE140 cells (before and after knockdown DLX5)  were generated by deep sequencing, in triplicate

first: Dong

last: Yin

first: De-Chen

last: Lin


title: Homoeologous Chromosome Exchange Explains the Creation of a QTL Affecting Soil‐Borne Pathogen Resistance in Tobacco

city: Raleigh

first: Ramsey

last: Lewis

state: NC

address: 101 Derieux PI

department: Crop and Soil Sciences Department

institute: North Carolina State University

summary:
Purpose: Investigate genes associated with Phn7.1, a major QTL influencing partial resistance to the soil-borne pathogen Phytophthora nicotianae in tobacco.
Methods: Resistant and susceptible tobacco near isogenic lines with and without Phn7.1 QTL were subjected to the inoculation with Phytophthora nicotianae suspension and suspension buffer without pathogen as control followed by sample collection at 42 hour past inoculation for RNA-seq analysis.
Results: Revealed gene expression profiles associated disease resistance and susceptiblilty.

overall_design: Tobacco Hicks near isogenic lines with and without Phn7.1 QTL were inoculated  with  Phytophthora nicotianae race 0 suspension and suspension buffer without pathogen as control. The root treated 42 hours post inoculation were used for RNA purificaton and RNAseq sequencing.

first: Rui

last: Shi


title: Activation of bivalent factor DLX5 cooperates with master regulator TP63 to promote squamous cell carcinoma [ChIP-Seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Genome binding/occupancy profiling of DLX5,TP63,H3K4me3 was performed in squamous carcinoma cell lines by ChIP sequencing.


title: Renal circadian rhythm dysregulation in lupus nephritis [array]

city: New York

first: Weijia

last: Zhang

state: NY

address: 1 Gustave L. Levy Pl

department: Renal

institute: Icahn School of Medicine at Mount Sinai

summary: This study examines the circadian gene expression of whole kidneys of young and nephritic NZB/W F1 mice

overall_design: Young mice were harvested at 12 weeks of age. Nephritic mice were harvested 2-3 weeks after nephritis onset (>300mg/dl proteinuria) but before the development of endstage renal failure (BUN >25). Kidneys were perfused with PBS and total RNA was isolated from perfused mouse kidneys using TRIzol reagent

first: Anne

last: Davidson

first: Zhengzi

last: Yi


title: Search for biomarkers of response to MitoQ in human breast cancer cell lines

status: Public on Sep 13 2021

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

country: Belgium

institute: Université catholique de Louvain

summary: For this projected we aimed to identifybiomarkers of response to a mitochondrial ROS inhibitor, MitoQ and its role in breast tumor metastasis. To do so, we performed an unbiased screening using RNAsequing. With this technique, we identified, in two human breast cancer metastatic cell lines (MDA-MB-231 and SKBR3), 13 commonly significant modulated genes that are involved in metabolic switches. Five of these genes were confirmed by RT-qPCR, and four were proved at protein level. In vivo experiments using an orthotopic model of the highly metastatic cell line MDA-MB-231 further demonstrated that modulation of some of the target genes can be observed in mice without tumor recurrence and without lung micrometastasis. Together, our results identified members of signaling pathways induced by mtROS in human metastatic breast cancer cells, and demonstrated that targeting mtROS in metastatic breast cancer can impair their invasive phenotype.

overall_design: Examination of gene expression modulations upon MitoQ treatment in 2 breast cancer cell lines

first: Tânia

last: Capelôa


title: Single cell transcriptional profile for hidradenitis suppurativa

city: Durham

middle: S

last: MacLeod

state: North Carolina

address: 40 Duke Medicine

department: Dermatology

institute: Duke University

summary: Hidradenitis suppurativa (HS) is a chronic inflammatory skin disease with a relapsing, remitting course. The disorder is characterized by painful abscesses and nodules in areas with high sweat gland and hair follicle density. The pathogenesis of HS is still incompletely understood. To provide insight into the cellular landscape of HS lesions, we utilized single-cell RNA sequencing (scRNA-seq) technology.

overall_design: We performed scRNA-seq in lesional skin from patients with HS and heathy donor.

first: Paula

last: Mariottoni

first: David

last: Brown

first: Tarannum

last: Jaleel

first: Vaibhav

last: Jain

first: Simon

last: Gregory


title: Renal circadian rhythm dysregulation in lupus nephritis [RNA-seq]

overall_design: Young mice were harvested at 12 weeks of age. Nephritic mice were harvested 2-3 weeks after nephritis onset (>300mg/dl proteinuria) but before the development of endstage renal failure (BUN >25). Remission was induced in nephritic mice with new onset proteinuria of less than 1 week duration measured twice 24 hrs apart using one dose of cyclophosphamide 50mg/kg and 6 doses of CTLA4Ig (200ug) and anti-CD40L (250ug) given over 2 weeks. Kidneys were harvested 8 weeks later from mice still in remission with proteinuria 30mg/dl. Kidneys were perfused with PBS and total RNA was isolated from perfused mouse kidneys using TRIzol reagent


title: Renal circadian rhythm dysregulation in lupus nephritis

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

overall_design: Refer to individual Series


title: Deficiency of the neurodevelopmental disorder-associated gene Cyfip2 alters retinal ganglion cell properties and visual acuity

status: Public on Sep 12 2021

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

summary: Intellectual disability (ID) is a neurodevelopmental disorder affecting approximately 0.5-3% of the population in the developed world. Individuals with ID exhibit deficits in intelligence and impaired adaptive behavior, frequently as well as visual impairments. Cytoplasmic FMR1-interacting protein 2 (CYFIP2) is an interacting partner of fragile X mental retardation protein, whose loss results in fragile X syndrome, the most common inherited cause of ID. Recently, CYFIP2 variants were found in patients with early-onset epileptic encephalopathy, developmental delay, and ID. Individuals with these CYFIP2 variants often exhibit visual impairments, however, the underlying mechanism is poorly understood. In the current study, we investigated the role of Cyfip2 in retinal and visual function by generating and analyzing mice in which Cyfip2 is depleted in the retina (Cyfip2 CKO mice). We found no major difference in the layer structure and cell composition between control and Cyfip2 CKO retinas, whereas a subset of genes associated with transporter and channel activity was differentially expressed in the Cyfip2 CKO retina. Multi-electrode array recordings showed more sustained and stronger response to positive flashes of ON ganglion cells in the Cyfip2 CKO retina, although we did not observe that Cyfip2 deficiency affects photoreceptor and ON bipolar cell functions by electroretinogram analysis. Furthermore, initial and late phase OKR analysis demonstrated that Cyfip2 deficiency impairs visual function at the organismal level. Together, our results shed light on the molecular mechanism underlying visual impairments observed in individuals with CYFIP2 variants and, more generally, in patients with neurodevelopmental disorders including ID.

overall_design: We performed RNA-sequencing analysis using the control and Cyfip2 CKO retina to assess transcriptional consequences of Cyfip2 deficiency in the retina.

first: Taro

last: Chaya

first: Takahisa

last: Furukawa


title: Activation of bivalent factor DLX5 cooperates with master regulator TP63 to promote squamous cell carcinoma

first: Yongsheng

last: Huang


title: Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution

city: Orsay

first: Olivier

last: Namy

address: Rue Gregor Mendel, bat 400

country: France

institute: CNRS, Université Paris-Sud

summary: The noncoding genome plays an important role in de novo gene birth and the emergence of genetic novelty. Nevertheless, how the properties of noncoding sequences could promote the birth of novel genes and shape the structural diversity and evolution of proteins remains unclear. Here, we investigated the potential of the noncoding genome of yeast to produce novel protein bricks that can give rise to novel genes or be integrated in pre-existing proteins, thus participating in protein structure evolution and diversity. Combining different bioinformatics approaches, we showed that intergenic ORFs of yeast encompass the large structural diversity of canonical proteins with the majority encoding peptides predicted as foldable. Then, we investigated the early stages of de novo gene birth with Ribosome Profiling and systematic reconstruction of yeast de novo gene ancestral sequences. We highlighted sequence and structural factors determining de novo gene birth and protein evolution. Finally, we showed a strong correlation between the fold potential of de novo genes and their ancestral ORFs reflecting the relationship between the noncoding genome and the protein structure universe.

overall_design: RiboSeq of two replicates of the same BY 4742 yeast  strain, to identify for alternative CDS in unanotated regions, such CDS are then called IGORFs if RiboSeq signal is detected.

first: Chris

last: Papadopoulos

first: Isabelle

last: Callebaut

first: Jean-Christophe

last: Gelly

last: Hatin

first: Maxime

last: Renard

last: Lespinet

last: Lopes


title: Expression data of Oral squamous cell carcinoma (OSCC) cell lines CAL27, SCC4 and SCC25 treated with oral commensals

status: Public on Sep 11 2021

city: Philadelphia

first: Nezar

last: Al-hebshi

state: Pennsylvania

address: 3223, North Broad Street, Mauice H. Kornberg School of Dentistry

department: Oral Health Sciences

institute: Temple University

summary: Oral bacterial species Streptococcus mitis, Neisseria flavescens, and Haemophilus parainfluenzae, and Porphyromonas gingivalis were each co-cultured with the OSCC cell lines CAL27, SCC4 and SCC25 individually. Total RNA was extracted from the cell lines, followed by gene expression profiling with microarray analysis.

overall_design: OSCC cell lines were allowed to attach for 24 h before the oral bacteria were added. After 24 h actively growing bacteria in their mid-log stage were added to OSCC cells, resulting in a total of 12 co-cultures (3 cell lines* 4 bacterial species).  All the co-cultures were performed in triplicates

first: Divyashri

last: Baraniya


title: Mutation of BrKAO2, encoding ent-kaurenoic acid oxidase, mediates leafy head formation by affecting GA biosynthesis in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

city: Shenyang

first: Shengnan

address: 120 Dongling Road Shenhe District Shenyang P.R. China

institute: Shenyang Agricultural University

summary: Leafy head is the main product of Chinese cabbage, and also is the primary character to determine its yield and quality. Cloning and characterizing key genes involved in leafy head formation is imperative for varietal improvement in Chinese cabbage. From an EMS mutagenesis population of a heading wild-type ‘FT’ of Chinese cabbage, we identified two allelic non-heading mutants, nhm3-1 and nhm3-2. Genetic analysis showed that the mutant character was controlled by a single recessive gene. MutMap and Kompetitive Allele Specific PCR genotyping results revealed that BraA05g012440.3C encoding an ent-kaurenoic acid oxidase 2 which functions in the GA biosynthetic pathway, was the causal gene for leafy-head formation, and we named it as BrKAO2. Two kinds of non-synonymous mutations in the second exon of BrKAO2 were responsible for the nhm3-1 and nhm3-2 mutant phenotype, respectively. BrKAO2 was expressed at all stages of leaf development, and there was no significant difference between the wild-type ‘FT’ and the mutants nhm3-1 and nhm3-2. The mutant phenotype was restored to the wild-type through the application of exogenous GA3. RNA-Seq was performed on the rosette leaves of wild-type ‘FT’, nhm3-1 and nhm3-1+GA3 plants, and a number of key genes involving in GA biosynthesis, signal transduction and leafy head development were identified. These findings indicated that BrKAO2 is responsible for leafy head formation of nhm3, and a new mechanism of the leafy head formation in Chinese cabbage was proposed.

overall_design: The RNA from the rosette leaves at the same position of wild-type ‘FT’, nhm3-1 and nhm3-1+GA3 in Chinese cabbage were sequenced by RNA-Seq, in triplicate.

first: Yue

last: Gao

first: Meihui

last: Xue

first: Junjie

last: Xu

first: Ruiqi

last: Liao

first: Shayu

last: Shang

first: Yonghui

last: Zhao

first: Chengyu

last: Li

first: Zhiyong

last: Liu

first: Hui

last: Feng


title: LncRNA SNHG17 contributes to proliferation, migration and poor prognosis of hepatocellular carcinoma

first: YUE

last: LUO

state: Guangdong

address: No.13 Shiliugang Road

department: Cancer Center

institute: Integrated hospital of traditional Chinese Medicine, Southern Medical University

summary: Long noncoding RNAs (lncRNAs) have been substantially reported to have critical roles in regulating tumorigenesis recent years. However, the expression pattern and biological function of SNHG17 in hepatocellular carcinoma (HCC) remain unclearly. Bioinformatics analysis and qRT-PCR were performed to detect the expression pattern of SNHG17 in HCC tissues, adjacent non-tumorous tissues and cell lines. The effect of SNHG17 on proliferation, migration and apoptosis of HCC were investigated by knockdown and overexpressing SNHG17 in HCC cell lines. RNA sequencing was utilized to explore the underlying mechanism. Utilizing publicly available TCGA-LIHC, GSE102079 HCC datasets and qRT-PCR, we found SNHG17 was significantly upregulated in HCC tissues and cell lines and was notably associated with larger tumor size, poorly differentiation, presence of vascular invasion and advanced TNM stage. Furthermore, gain- and loss-of-function studies demonstrated that SNHG17 promoted cell proliferation, migration and inhibited apoptosis of HCC. By employing RNA sequencing, we found knockdown of SNHG17 caused 1037 differentially expressed genes, highly enriched in several pathways, including metabolic, PI3K-Akt, cell adhesion, regulation of cell proliferation and apoptotic pathway, among them 92 were overlapped with SNHG17-related genes in TCGA-LIHC dataset. Furthermore, ERH, TBCA, TDO2 and PDK4 were successfully validated and found significantly dysregulated in HCC tissues. Moreover, HCC patients with higher SNHG17 expression had a relatively poor overall survival and disease-free survival and ERH, PDK4 also played markedly role in prognosis of HCC. Broadly, our findings illustrate that SNHG17 acts as a noncoding oncogene in HCC progression, suggesting its potential value as a novel target for HCC therapy.

overall_design: Total RNAs from Hep3B cells transfected with si-SNHG17-1 and si-NC were isolated by TRIzol reagent. Each group had three replicates.

last: Luo

first: Junhao

last: Lin

first: Jiakang

last: Zhang

first: Zhenghui

last: Song

first: Dayong

last: Zheng

first: Fengsheng

last: Chen

first: Xuefen

last: Zhuang

first: Aimin

first: Xinhui


title: Comparative transcriptomic analysis of the Drosophila melanogaster antennal olfactory subsystems.

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

summary: We identified genes whose expression is enriched in the D. melanogaster antennal olfactory subsystems that express Odorant receptors (Ors) or Ionotropic receptors (Irs) by microarray analysis of RNA extracted from antennae of wild-type (Oregon R P2) animals, ato mutants (which lack the Ir subsystem) and amos mutants (which lack the Or subsystem).

overall_design: Three biological replicates were analysed for each of the three genotypes: Oregon R P2, ato/Df(3R)p13 and amos. The mutant lines were back-crossed five times with Oregon R P2 prior to the experiment to isogenize the genetic background.

first: Michael

last: Saina

first: Richard

last: Benton


title: A bipartite element with allele-specific functions safeguards DNA methylation imprints at the Dlk1-Dio3 locus [4C-seq]

city: Braunschweig

first: Andreas

last: Kloetgen

state: NI

address: Inhoffenstr 7

department: Department for Computational Biology of Infection Research

country: Germany

institute: Helmholtz Centre for Infection Research

summary: Dysregulation of imprinted gene loci also referred to as loss of imprinting (LOI) can result in severe developmental defects and other diseases, but the molecular mechanisms that ensure imprint stability remain incompletely understood. Here, we dissect the functional components of the imprinting control region of the essential Dlk1-Dio3 locus (called IG-DMR) and the mechanism by which they ensure imprinting maintenance. Using pluripotent stem cells carrying an allele-specific reporter system, we demonstrate that the IG-DMR consists of two antagonistic regulatory elements: a paternally methylated CpG-island that prevents the activity of Tet dioxygenases and a maternally unmethylated regulatory element, which serves as a non-canonical enhancer and maintains expression of the maternal Gtl2 lncRNA by precluding de novo DNA methyltransferase function. Targeted genetic or epigenetic editing of these elements leads to LOI with either bi-paternal or bi-maternal expression patterns and respective allelic changes in DNA methylation and 3D chromatin topology of the entire Dlk1-Dio3 locus. Although the targeted repression of either IG-DMR or Gtl2 promoter is sufficient to cause LOI, the stability of LOI phenotype depends on the IG-DMR status, suggesting a functional hierarchy. These findings establish the IG-DMR as a novel type of bipartite control element and provide mechanistic insights into the control of Dlk1-Dio3 imprinting by allele-specific restriction of the active DNA (de)methylation machinery.

sample_organism:
Mus musculus
Mus musculus molossinus

platform_organism:
Mus musculus
Mus musculus molossinus

overall_design: Experiments were performed in duplicate to generate two technical replicates per sample. JF1/B6 iPSC’s (2 × 106) were crosslinked in 1% formaldehyde at room temperature for 10 min and quenched with 125 mM glycine for 5 min at room temperature. The cell pellets were washed twice in PBS and resuspended in 300 μl lysis buffer (10mM Tris-HCl (pH 8.0), 10mM NaCl, 0.2% Igepal CA630 (Sigma I8896), on ice for 20 min. Following centrifugation at 2,500g for 5 min at 4°C, the pellet was resuspended in in 50uL of 0.5% SDS and incubated for 10 min at 65°C. SDS was quenched with 145uL water and 25uL of 10% TritonX-100. 25ul of Cutsmart buffer was added with DpnII enzyme (10 μl; NEB, R0543M) and the samples were incubated overnight at 37 °C with 700rpm rotation. The samples were then diluted with 663μl Milli-Q water, 120 μl T4 ligation buffer (NEB B0202), 60ul ATP 10mM, 120 μl Triton X-100, 12ul BSA 10mg/ml and incubated with Ligase (5 μl, 400U/μl ; NEB M0202L) for 3h on a rotor at room temperature. The samples were then treated with proteinase K and reverse crosslinked overnight. Following RNAse treatment, phenol/chloroform extraction and DNA precipitation, the pellets were dissolved in 100 μl of 10 mM Tris pH 7.5 and digested overnight at 37°C by adding 20 μl Cutsmart buffer (NEB), 10ul μl NlaIII (NEB, R0125) and 70 μl Milli-Q water. Following enzyme inactivation, the samples were diluted in 2345 ul Milli-Q water, 300 ul 10×ligation buffer (NEB), 150ul ATP 10mM and incubated with, 5 μl T4 DNA ligase 2M U/ul (NEB, M0202M) overnight at 16°C. The DNA was purified by phenol/chloroform extraction, ethanol precipitation and Zymo columns (D4014). For allele-specific 4C-seq library preparation, primers were designed upstream of a SNP within IG-DMR. Due to lack of suitable restriction fragments on ΔMatTRE samples, non-allele specific libraries were prepared with the Gtl2 DMR as viewpoint. Library preparation was further performed by using a PCR strategy as previously described (Krijger et al. 2019). Briefly, 4x200 ng of 4C-template DNA was used to PCR amplify the libraries using the Roche Expand long template PCR system (Roche, 11681842001). Primers were removed using Ampure XP beads (Beckman Coulter, A63880). A second round of PCR was performed using the initial PCR library as a template, with overlapping primers to add the full adapters. The libraries were sequenced on a miSeq platform in SE150 mode.

first: Boaz

last: Aronson

first: Effie

last: Apostolou


title: Gene expression patterns in blood during human anaphylaxis, trauma, and sepsis

city: Subiaco

first: Anthony

last: Bosco

state: WA

address: 100 Roberts Road

country: Australia

institute: Telethon Kids Institute

summary:
Gene expression was profiled in peripheral blood samples collected from patients during anaphylaxis, trauma, or sepsis, and from healthy controls.
Patients were recruited from three Australian emergency departments (ED) between March 2011 and June 2013. Samples were collected at ED arrival (T0), 1 hour later (T1), and 3 hours post arrival (T2).

overall_design: The study design consisted of four disease phenotypes (anaphylaxis, sepsis, trauma, healthy controls) and up to 3 time points. Healthy controls were matched to patients within each study.

first: Erika

last: Bosio

first: Simon

last: Brown


title: The long noncoding RNA H19 regulates tumor plasticity in neuroendocrine prostate cancer

city: Tucson

first: Ritu

last: Pandey

state: Arizona

address: 1515 N Campbell Ave.,

department: Cellular and Molecular Medicine, Arizona Cancer Center

institute: University of Arizona

type: Methylation profiling by high throughput sequencing

summary: We report the effect of H19 knockdown on genome wide methylation by Enhanced Reduced Representation Bisulfite Sequencing (eRBBS) to detect quantitative base pair changes. Differential methylation genome wide analysis was done on NEPC derived organoid  expressing shH19 or a control vector.

overall_design: Three replicates of organoids each expressing shH19 and and  control vectors were utilized for ERBBS assay for differential methylation.

first: Neha

last: Singh

first: Andrew

last: Kraft


title: Infusion of human amniotic epithelial and mesenchymal stromal stem cells as a new therapeutic option for portal hypertension and cirrhosis

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

summary: Background and aims. Portal hypertension is the main consequence of cirrhosis, responsible for the complications defining clinical decompensation. The only cure for decompensated cirrhosis is liver transplantation, but it is a limited resource and opens the possibility of regenerative therapy. We investigated the potential of human amniotic membrane-derived mesenchymal stromal (hAMSCs) and epithelial (hAECs) stem cells for the treatment of portal hypertension and chronic liver disease. Methods. In vivo: hAMSCs and hAECs were isolated from human amniotic membranes. Cirrhotic rats with ascites (chronic CCl4 inhalation) received 4x10e6 hAMSCs, 4x10e6 hAECs, or vehicle (NaCl 0.9%) (intraperitoneal; n=10 per group). After 2-week we analyzed: a) portal pressure (PP) and liver microcirculatory function; b) liver sinusoidal endothelial (LSECs) and hepatic stellate (HSCs) cells phenotype; c) hepatic fibrosis, inflammation and hepatic function. In vitro: HSCs isolated from CCl4-cirrhotic rats were co-cultured with hAMSCs, hAECs or vehicle for 24h. RNA profile was analyzed by RNAseq. Results. Cirrhotic rats receiving hAMSCs or hAECs had significantly lower PP than vehicle-treated animals, together with improved liver microcirculatory function. This hemodynamic amelioration was associated with improvement in LSECs capillarization and HSCs de-activation, although hepatic collagen/fibrosis was not significantly reduced. Rats that received placenta derived stem cells had markedly reduced hepatic inflammation and oxidative stress. Finally, liver function tests significantly improved in rats receiving hAMSCs. In vitro experiments confirmed HSCs de-activation when co-cultured with stem cells. Conclusion. This pre-clinical study shows that infusion of human amniotic stem cells effectively decreases PP by ameliorating liver microcirculation, suggesting that it may represent a new treatment option for advanced cirrhosis with portal hypertension.

overall_design: RNA-seq applied to three HSC related groups (hAEC,hAMSC,Veh) (n=4)

first: A

last: Fernandez-Iglesias

first: J

middle: J

last: Gracia


title: chimeric eCLIP identifying the target genes of 5' tRNA-fMet1 half mediated by AGO2 in cystic fibrosis airway epithelial cells

city: Hanover

first: Zhongyou

last: Li

state: NH

address: 504 Remsen

institute: Geisel School of Medicine at Dartmouth

summary: 5’ tRNA-fMet1 half is delivered into cystic fibrosis airway epithelium cells by outer membrane vesicles and regulate gene expression. We used chimeric eCLIP to map transcriptome-wide interactions between 5’ tRNA-fMet1 half and target mRNAs mediated by AGO2.

overall_design: 5’ tRNA-fMet1 half or siRNA negative control (siNC) was transfected into cystic fibrosis airway epithelial cells from one donor to generate two samples. For each sample, an input and an immunoprecipitated sub-sample using an anti-AGO2 antibody were generated for cDNA library preparation. To deeply profile the target repertoire of 5’ tRNA-fMet1 mediated by AGO2, a 5’ tRNA-fMet1 half specific primer was used for targeted sequencing (targeted chimeric eCLIP).

first: Katja

last: Koeppen

first: Bruce

last: Stanton


title: RNA-dependent RNA polymerases in the black-legged tick produce Argonaute-dependent small RNAs and regulate genes

city: NARA

first: Katsutomo

last: Okamura

address: 8916-5 Takayama, Ikoma, NARA 630-0192 JAPAN

institute: Nara Institute of Science and Technology

type: Non-coding RNA profiling by high throughput sequencing

summary: Small regulatory RNAs (sRNAs) are involved in anti-viral defense and gene regulation. Although RNA-dependent RNA Polymerases (RdRPs) play essential roles in sRNA biogenesis in nematodes, plants and fungi, their involvement in other animals remains controversial. We identify abundant classes of ~22nt sRNAs that require specific combinations of RdRPs and sRNA effector proteins (Argonautes or AGOs) expressed in the tick ISE6 cell line. The RdRP-dependent sRNAs are mainly derived from sense and antisense strands of RNA polymerase III-transcribed genes and repetitive elements. Knockdown of AGO/RdRP causes miregulation of protein-coding genes.These results demonstrate that arachnid RdRPs are important sRNA biogenesis factors, and the discovery of novel pathways underscores the importance of characterizing sRNA biogenesis in various organisms to understand virus-vector interactions and exploit RNAi for pest control.

overall_design: For small RNA analysis, 9 small RNA libraries of ISE6 cells depleted of small RNA factors and 1 control sample were used. To study the chemical structures of 5’ and 3’ terminal nucleotides of tick sRNAs, oxidized sRNA library and 5'TriP enriched library were used. For total RNAseq analysis, three sets of knockdown experiments(knock down Ago-16, RdRP1 or RdRP3) were performed independently, with one set of control.

first: Canran

last: Feng

first: Kyosuke

last: Torimaru

first: Mandy

middle: Y

last: Lim

first: Kosuke

last: Tsuji

first: Li-Ling

last: Chak

first: Tetsuya

last: Tanaka

first: Junko

last: Iida


title: Transcriptional profiling of mouse liver of PPARgamma null mice

first: Federica

last: Gilardi

address: chemin de la Vulliette 4

department: University Center of Legal Medicine

institute: University of Lausanne

summary: We highlight sex dimorphism of NAFLD in a lipodystrophic mouse model obtained via total body deletion of PPARγ. The hepatic sex dimorphism is characterized by a more important hepatosteatosis in females compared to males, and is PPARγ- and sex-hormone-dependent. To characterize the molecular mechanisms underlying this phenotype microarray analysis of gene expression was performed in the liver of 7 and 20 week old mice, before and after the onset of the the hepatic sex-dimorphism.

overall_design: We examined 8 experimental groups: PpargΔ/Δ and control mice, male and females at 7 week and PpargΔ/Δ and control mice at 20 weeks. For each experimental group we analysed the transcriptional profile of 2/3 individual RNA from liver.

first: Mariano

last: Shiffrin

first: Carine

last: Winkler

first: Laure

last: Quignodon

first: Béatrice

last: Desvergne


title: ANTICANCER AGENT P-bi-TAT LINKS THE THYROID HORMONE RECEPTOR ON INTEGRIN αvβ3 TO CANCER CELL METABOLISM/ATP GENERATION.

city: Rensselaer

first: Sridar

middle: V

last: Chittur

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary: Microarray analysis was carried out on human GBM primary cells (GBM 10181360) and GBM cell line (U87)  exposed to P-bi-TAT (10-6 M tetrac equivalent) for 24 h and 48 h. P-bi-TAT significantly downregulated electron transport chain genes ATP5A1 (ATP synthase A1), ATP51, ATP5G2, COX6B1 (cytochrome c oxidase subunit 6B1), NDUFA8 (NADH dehydrogenase [ubiquinone] FA8), NDUFV2 and other NDUF genes, SLC25A6 (solute carrier group 2), UCP2 ([mitochondrial] uncoupling protein 2) and COX5A. The NDUF and ATP genes are also relevant to control of oxidative phosphorylation and transcription. Six additional NDUF genes linked to oxidative phosphorylation were affected. Conclusions. P-bi-TAT caused downregulation of expression of a panel of genes involved in electron transport, oxidative phosphorylation, and cytoplasmic ribosomal protein generation in GBM cells. A key component of the anticancer activity of P-bi-TAT relates to disordering of ATP generation mechanisms in tumor cells

overall_design: Studied the anticancer functions of P-bi-TAT in GBM cells in terms of modulation of transcription by the drug of genes essential to cancer cell mitochondrial function. Compared GBM primary cells (GBM 10181360) control with duplicate GBM 10181360 treated P-bi-TAT (30 µM) for 24 h and 48 h. Further duplicate GBM U87MG cells with GBM U87MG cells duplicates treated with P-bi-TAT (30 µM) for 24 h and 48 h.

first: Gennadi

last: Glinsky

first: Kavitha

last: Godugu

first: Thangirala

last: Sudha

first: Shaker

last: Mousa

first: Paul

last: Davis


title: Tumor DNA methylation in pediatric germ cell tumors

city: Minneapolis

first: Lauren

last: Mills

state: MN

address: 420 Delaware St SE

department: Department of Pediatrics

institute: University of Minnesota

type: Methylation profiling by genome tiling array

summary: Epigenomewide methylation profiling of tumor DNA from pediatric germ cell tumors by sex, tumor histology, tumor location and age at diagnosis. DNA methylation was measured using the Illumina Infinium HumanMethylation450 array

overall_design: Bisulfite converted DNA from 145 GCT tumor samples was hybridized to the Illumina HumanMethylation450 BeadChip array

first: Jenny

last: Poynter


title: Cocaine-related DNA methylation in neurons in the caudate nucleus alters the three dimensional structure of the IRXA gene cluster

city: Montreal

first: Gustavo

last: Turecki

state: Quebec

address: 6875 Boulevard LaSalle

department: Psychiatry

country: Canada

institute: McGill University

summary: This study investigates differences in DNA methylation that are associated with chronic cociane dependence in post-mortem dorsolateral caudate tissue samples from human brain.  The data were generated with reduced representation bisulfite sequencing (RRBS) and compared to data generated in caudate tissue from psychiatrically healthy controls.

overall_design: This study generated RRBS libraries from 28 males with a history of chronic cocaine dependence and cocaine toxicology at time of death, and 29 drug-naïve males.  Each sample was sequenced at least twice and raw reads were pooled for each individual. Raw data files represent pooled sequencing reads for each individual.


title: Thyrointegrin αvβ3 antagonist with potent Affinity in the treatment of Glioblastoma

summary: Microarray analysis was carried out on Glioblastoma GBM 10181360 and U87 cells treated with PBS for  24 h and 48 h .

overall_design: RNA isolation from the biological duplicates of GBM 10181360 and U87 cells treated with PBS

first: Nour

last: Darwish

first: Bruce

last: Hay


title: Transcriptomic heterogeneity of the prostate cancer

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

summary: The transcriptomic heterogeneity of the prostate cancer was tested by profiling histologically distinct but equally graded (Gleason score 4+5=9/10) cancer nodules from a surgically removed prostate cancer. We found that not only that the genes were differently regulated in the two nodules but also that expression fluctuations were differently controlled and the gene networks differently remodeled.

overall_design: Gene expressions were profiled in two equally graded (Gleason score 4+5=9/10) histologically distinct cancer nodules from a surgically removed prostate cancer

first: Sanda

last: A iacobas


title: Gene expression analysis of hiPSC-derived renal angiomyolipoma organoids

status: Public on Sep 10 2021

city: Boston

first: Dario

last: Lemos

address: 4 Blackfan Circle

institute: Brigham and Women's Hospital

summary: Angiomyolipomas (AMLs) are the most common renal manifestation in patients with Tuberous Sclerosis Complex. The recapitulation of AMLs experimentally has remained a challenge, precluding the study of tumor mechanisms. Here we used Next-Generation Sequencing to analyze the transcriptomes of renal organoids derived from TSC2-/-, TSC2+/- or TSC2+/+ human induced pluripotent stem cells (hiPSCs) derived from a patient diagnosed with Tuberous Sclerosis Complex. Organoids derived from TSC2-/- hiPSCs but not from isogenic TSC2+/- or TSC2+/+ hiPSCs shared a common transcriptional signature and a myomelanocytic cell phenotype with kidney AMLs.

overall_design: mRNA profiles of kidney organoids TSC2+/+, TSC2+/- or TSC2-/- hiPSCs

middle: R


title: A Single-Cell Atlas of Liver Metastases of Colorectal Cancer Reveals the Reprogramming of the Tumor Microenvironment in Response to Preoperative Chemotherapy

city: Guangzhou

first: liheng

last: che

address: Xin gang road

institute: Sun Yat sen university

summary: Metastasis is the primary cause of cancer-related mortality in colorectal cancer (CRC) patients. How to improve therapeutic options for patients with metastatic CRC (mCRC) is the core question for CRC treatment. However, the complexity and diversity of stromal context of the tumor microenvironment (TME) in liver metastases of CRC is not fully understood, and its influence on response to chemotherapy is unclear. Here we provide an in-depth analysis of transcriptional landscape of primary CRC, matched liver metastases and blood at single-cell resolution, and perform a systematic examination of transcriptional changes and phenotypic alteration of the TME in response to preoperative chemotherapy (PC). Based on 111,292 single-cell transcriptomes, our study reveals that TME of treatment-naïve tumors is characterized by higher abundance of less-activated B cells and higher heterogeneity of tumor-associated macrophages (TAMs). By contrast, in tumors treated with PC, we find activation of B cells, lower diversity of TAMs with immature and less activated phenotype, lower abundance of both dysfunctional T cells and ECM-remodeling cancer-associated fibroblasts (CAFs), and an accumulation of myofibroblasts. Our study provides a foundation for future investigation of the cellular mechanisms underlying liver metastasis of CRC and its response to PC, and opens up new possibilities for the development of therapeutic strategies for CRC.

overall_design:
Single-cell expression profiling of the liver metastases of CRC in treatment patients and untreated patients.
For data usage terms and conditions, please contact the principle investigator (Jianming Li, pathologylee@126.com).

first: Jianming

last: Li

first: Liheng

last: Che


title: FOXO3 regulates Smad3 and Smad7 through SPON1 circular RNA to inhibit idiopathic pulmonary fibrosis

city: Tianjin

first: Hailong

state: China

address: nankai

institute: Nankai

summary: Forkhead box protein O3 (FOXO3) has good inhibition ability toward fibroblast activation and extracellular matrix, especially for the treatment of idiopathic pulmonary fibrosis. How FOXO3 regulates pulmonary fibrosis remains unclear. In this study, we reported that FOXO3 had binding sequences with F-spondin 1 (SPON1) promoter, which can activate its transcription and selectively promote the expression of SPON1 circRNA (circSPON1) but not mRNA expression. We further demonstrated that circSPON1 was involved in the extracellular matrix deposition of HFL1. In the cytoplasm, circSPON1 directly interacted with TGF-β-induced Smad3 and inhibited the activation of fibroblasts by inhibiting nuclear translocation. Moreover, circSPON1 bound to miR-942-5p and miR-520f-3p that interfered with Smad7 mRNA and promoted Smad7 expression. This study revealed the mechanism of FOXO3 in the occurrence and development of pulmonary fibrosis. Potential therapeutic targets and new insights into the diagnosis and treatment of idiopathic pulmonary fibrosis based on circRNA were also provided.

overall_design: Transcriptional regulation of FOXO3 in HFL1 cells

first: Jinhe

first: Ruotong

last: Zhang


title: Difference in gene expression signatures of Ebf1-deficient pro-B cell lines with and without the ability to differentiate into T cell lineage

city: Isehara

first: Katsuto

last: Hozumi

state: Kanagawa

address: 143 Shimokasuya

department: Immunology

institute: Tokai University School of Medicine

summary: It was reported that Ebf1-deficient hematopoietic progenitor cells were expandable on OP9 stromal cells in the presence of SCF, Flt3L and IL7, and maintained with the potential for the differentiation into other hematopoietic lineages including T cells with Notch signaling. In contrast, we found that those on thymic stromal cells were similarly expanded but gradually lost their potential to T cell lineage. To know the molecular machinery to retain their potential, we compared their profiles of the transcripts by microarray analysis. Expression of three genes (Meis1, Hmga2 and Lmo2) from this signature was quantified in the same RNA samples by real-time PCR, confirming their difference in the stemness-related genes. It was revealed that Lmo2 is responsible for the maintenance of T-cell differentiation potential among them. Thereafter, the expression profiles were also compared between Ebf1-deficient pro-B cell lines without the potential and their enforced transfectants of Lmo2, showing the downstream targets of Lmo2 in early lymphoid progenitor cells.

overall_design: Whole genome microarray expression profiles of Ebf1-deficient pro-B cell lines with (E1112_1 & 2) and without (EBF_TI_1 & 2) the potential for T cell lineage were measured. Those were also detected from the pro-B cell line without the potential (EBF_NG_1 & 2) and its enforced tranfectant of Lmo2 (Lm2_1 & 2).

first: Ken-ichi

last: Hirano


title: Differentially expressed genes after transfection of siRNA in human cancer cell lines

city: Kagoshima

first: Kengo

last: Tanigawa

address: 8-35-1 Sakuragaoka

department: Pulmonary Medicine

institute: Kagoshima university

summary: To identify differentially expressed genes by siRNAs transfection in human cancer, lung squamous cell carcinoma cell lines were subjected to Agilent whole genome microarrays.

overall_design: Human lung squamous cell carcinoma cell lines (EBC-1 and SK-MES-1) were treated with siRNAs (siHELLS-3).

first: Naohiko

last: Seki


title: Role of 53BP1 in End Protection and DNA synthesis at DNA breaks [ChIP-seq]

city: Shanghai

first: Wei

last: Wu

state: Shanghai

address: 320 yueyang road

department: Center for Excellence in Molecular Cell Science

summary: Double-strand break (DSB) repair choice is greatly influenced by the initial processing of DNA ends. 53BP1 limits the formation of recombinogenic single strand DNA (ssDNA) in BRCA1-deficient cells leading to defects in homologous recombination (HR). However, the exact mechanisms by which 53BP1 inhibits DSB resection remain unclear. Previous studies have identified two potential pathways: protection against exonucleases presumably through the Shieldin (SHLD) complex binding to ssDNA, and localized DNA synthesis through the (CTC1-STN1-TEN1) CST and DNA polymerase alpha (Polα) to counteract resection. We present evidence here that 53BP1-mediated exonuclease protection plays a more significant role than CST/Polα synthesis in countering hyper-resection at DSBs in G1 phase. Using a combinatorial approach of END-seq, SAR-seq, and RPA ChIP-seq, we directly assessed the extent of resection, DNA synthesis, and ssDNA, respectively, at AsiSI-induced DSBs. We show that in the presence of 53BP1, Polα-dependent DNA synthesis reduces the fraction of resected DSBs and the resection lengths. However, in the absence of 53BP1, Polα activity is sustained on ssDNA yet does not substantially counter resection. In contrast, Exo1 nuclease activity is essential for hyperresection in the absence of 53BP1. Thus, 53BP1 inhibits resection mainly through end-protection rather than by promoting fill-in.

overall_design: We used a combinatorial approach of END-seq, SAR-seq, and RPA SSDS to characterize at nucleotide resolution the in vivo molecular events that regulate DSB resection.

first: Jacob

last: Paiano

first: Nicholas

last: Zolnerowich

first: Raphael

last: Pavani

first: Chen

last: Wang

first: Hongzhi

first: Li

last: Zheng

first: Binghui

last: Shen

first: Barry

last: Sleckman

first: Bo-Ruei

last: Chen

first: André

last: Nussenzweig


title: Chronic Exposure to Palmitic Acid Downregulates AKT in Beta-Cells through Activation of mTOR

city: Los Angeles

first: Bangyan

last: Stiles

state: CA

address: 1985 Zonal Ave.

department: PPSI

institute: University of Southern California

summary: High circulating lipids occurring in obese individuals and insulin resistant patients are considered a contributing factor to Type 2 Diabetes (T2D).  Exposure to high lipids is proposed to both protect and damage beta-cells under different circumstances.  By feeding mice high fat diet (HFD) for 2 weeks up to 14 months, we showed that HFD initially causes the beta-cells to expand in population whereas long-term exposure to HFD is associated with failure of beta-cells and the inability of animals to respond to glucose challenge.  To prevent the failure of beta-cells and the development of T2D, we explored the molecular mechanisms that underlie this biphasic response of beta-cells to lipid exposure. Using palmitic acid (PA) in cultured beta-cells and islets, we demonstrated that chronic exposure to lipids leads to reduced viability and inhibition of cell cycle progression concurrent with downregulation of a pro-growth/survival kinase AKT, independent of glucose.  To explore the mechanism further, we performed RNA-seq analysis in WT and AKT1-/- mice fed HFD for 4 months.  The data here is the results of this study.

overall_design: In this study, we fed 3 month old mice with high fat diet (60% kcal% FAT) for 4 months.  Islets were isolated and extracted for RNA.  RNA was sent to the equences.

first: Zhechu

last: Peng

first: Richa

last: Aggarwal

first: Ni

last: Zeng

middle: L


title: Engineered miniature CRISPR-Cas system for mammalian genome regulation and editing

city: Menlo Park

first: Stephen

last: Shang

state: California

address: 297 Jane Stanford Way

institute: Stanford University

summary: Compact and versatile CRISPR-Cas systems will enable genome engineering applications through high-efficiency delivery in a wide variety of contexts. Here we create an efficient miniature Cas system (CasMINI) engineered from the type V-F Cas12f (Cas14) system by guide RNA and protein engineering, which is less than half the size of currently used CRISPR systems (Cas9 or Cas12a). We demonstrate that CasMINI can drive high levels of gene activation (up to thousands-fold increases), while the natural Cas12f system fails to function in mammalian cells. We show that the CasMINI system has comparable activities to Cas12a for gene activation, is highly specific, and allows for robust base editing and gene editing. We expect that CasMINI can be broadly useful for cell engineering and gene therapy applications ex vivo and in vivo.

overall_design: mRNA profiles of dCasMINI-VPR and dCas12a-VPR activations. Samples were generated by deep sequencing, in replicate, using illumina NovaSeq 6000 platform.

first: Xiaoshu

last: Xu

first: Augustine

last: Chemparathy

first: Leiping

first: Hannah

last: Kempton

first: Muneaki

last: Nakamura

first: Lei

last: Qi


title: Comparative transcriptional analysis on cardiac ventricles between cryoinjury and moderate physical exercise in zebrafish

city: Giessen

first: Sven

last: Reischauer

state: Hessen

address: Auweg 129

department: Cardiology/Angiology

institute: Medical Clinic I - JLU

summary: We compared transcriptional changes between 1) Control vs. 96 hours post cardiac cryoinjury (hpci) and 2) Control vs. 96 hours post physical exercise.

overall_design: 1) Pool of 10X control vs. pool of 10X 96 hpci zebrafish ventricles. 2) Pool of 10X control vs. pool of 10X 4 days of physical exercise (in a beaker with magnetic stirrer) zebrafish ventricles. Fish were trained for eight hours a day with one hour rest in between, for 4 days in a row.

first: Srinivas

last: Allanki

first: Boris

last: Strilic

first: Lilly

last: Scheinberger

first: Yeszamin

last: Onderwater

first: Alora

last: Marks

first: Stefan

last: Günther

first: Khrievono

last: Kikhi

first: Didier

last: Stainier


title: Activin-A impedes the establishment of CD4+ T cell exhaustion and enhances anti-tumor immunity in the lung [RNA-seq]

city: Athens

first: Maria

last: Semitekolou

address: 4 Soranou Ephessiou St.

country: Greece

institute: Biomedical Reasearch Foundation Academy of Athens

summary:
Background:
Although tumor-infiltrating T cells represent a favorable prognostic marker for cancer patients, the majority of these cells are rendered with an exhausted phenotype. Hence, there is an unmet need to identify factors which can reverse this dysfunctional profile and restore their anti-tumorigenic potential. Activin-A is a pleiotropic cytokine, exerting a broad range of pro- or anti-inflammatory functions in different disease contexts, including allergic and autoimmune disorders and cancer. Given that activin-A exhibits a profound effect on CD4+ T cells in the airways and is elevated in lung cancer patients, we hypothesized that activin-A can effectively regulate anti-tumor immunity in lung cancer.
Methods:
To evaluate the effects of activin-A in the context of lung cancer, we utilized the OVA-expressing Lewis Lung Carcinoma mouse model as well as the B16F10 melanoma model of pulmonary metastases. The therapeutic potential of activin-A-treated lung tumor-infiltrating CD4+ T cells was evaluated in adoptive transfer experiments, using CD4-/--tumor bearing mice as recipients. In a reverse approach, we disrupted activin-A signaling on CD4+ T cells using an inducible model of CD4+ T cell-specific knockout of activin-A type I receptor. RNA-Sequencing analysis was performed to assess the transcriptional signature of these cells and the molecular mechanisms which mediate activin-A’s function. In a translational approach, we validated activin-A’s anti-tumorigenic properties using primary human tumor-infiltrating CD4+ T cells from lung cancer patients.
Results:
Administration of activin-A in lung tumor-bearing mice attenuated disease progression, an effect associated with heightened ratio of infiltrating effector to regulatory CD4+ T cells. Therapeutic transfer of lung tumor-infiltrating activin-A-treated CD4+ T cells, delayed tumor progression in CD4-/- recipients and enhanced T cell-mediated immunity. CD4+ T cells genetically unresponsive to activin-A, failed to elicit effective anti-tumor properties and displayed an exhausted molecular signature governed by the transcription factors Tox and Tox2. Of translational importance, treatment of activin-A on tumor-infiltrating CD4+ T cells from lung cancer patients augmented their immunostimulatory capacity towards autologous CD4+ and CD8+ T cells.
Conclusions:
In this study, we introduce activin-A as a novel immunomodulatory factor in the lung tumor microenvironment, which bestows exhausted CD4+ T cells with effector properties.

overall_design: In this study we induced the formation of lung tumors in WT and transgenic mice, which specifically lack the expression of ALK4 on CD4+ T cells (CD4/ALK4-KO). CD4+ T cells which infiltrated the lung tumors from both WT and CD4ALK4-KO mice were isolated and RNA was extracted. 4 samples in total were analyzed, consisting of 2 biological replicates from each mouse strain. Lung tumor-infiltrating CD4+ T cells from WT mice were used as control samples and the respective samples from CD4/ALK4-KO mice comprised the treated group.

first: Ioannis

last: Morianos


title: RNA-seq data of wild-type and Abcb11-deficient mice

first: Liping

last: Wang

address: No. 232, Outer Ring East Road, Guangzhou University Town, Panyu District

institute: Guangzhou University of Chinese Medicine

summary: RNA-seq analysis were applied to elucidate the transcriptional differences of wild-type and Abcb11-deficient mice. Comparison of female Abcb11-/- (Abcb11F) and female C57BL/6J mouse (WTF) livers identified 3,652 RNA species that were differentially expressed (1,809 genes upregulated and 1,843 genes downregulated; Padj < 0.05). Comparison of liver gene expression in Abcb11F versus non-tumor tissue of female Abcb11-/- mice (NTF) revealed 47 differentially expressed genes. Cross-comparison of the lists of differentially expressed genes in Abcb11F versus WTF and in Abcb11F versus NTF revealed 36 genes common to the two data sets.

overall_design: The RNA was extracted from the livers of 3 mice (12-month-old) per group. The RNA was extracted from the livers of 3 mice (12-month-old) per group. RNA quality was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Sequencing was performed on the Illumina HiSeq platform, and 125 bp/150 bp paired-end reads were generated. All reads that passed quality metrics were mapped using HISAT2 software. Differential expression analysis was performed using the DESeq2 R package (1.16.1). The P values were adjusted using the Benjamini and Hochberg method. An adjusted P-value (Padj) of 0.05 was set as the threshold for differentially expression.

first: L

first: Q

last: Luo

first: S

last: Zeng

first: Z

last: Liu


title: ENO1 suppresses cancer cell ferroptosis by degrading the mRNA of iron regulatory protein 1

city: Hefei

first: Tong

last: Zhang

address: huangshan road 443

institute: USTC

summary: ENO1 (α-Enolase 1) is a key glycolytic enzyme that catalyzes the dehydratation of 2-phosphoglycerate to phosphoenolpyruvate. It also belongs to a member of the RNA degradosome of Escherichia coli and facilitates RNA degradation, but it’s currently unknown whether ENO1 possesses similar function in eukaryotes. To test this possibility,we performed RNA-seq assays expressing NTC or ENO1 shRNA, respectively.

overall_design: We treated PLC cells expressing NTC or ENO1 shRNA, respectively. we next performed RNA extraction and sequenced on Illumina novaseq (Homo sapiens).

first: Shengqi

last: Shen

first: Ping

last: Gao

first: Huafeng


title: Single Cell RNA Sequencing of WT and Cdh5-cre Myct1 fl/fl Endothelium

city: Palo Alto

first: Christoph

last: Thaiss

address: 3181 Porter Dr.

department: Immunology and Pathology

institute: Arc Institute

summary: Edothelial cells were FACS sorted as CD31+CD45- population from PYMT-BO1 transplant tumor bearing WT and Cdh-cre Myct1 fl/fl mice on Day 14 post tumor transplantation

overall_design: Single-cell RNA-seq libraries were prepared using version 1 Chromium Single-cell 3′ Library, Gel Bead & Mutiplex Kit (10X Genomics). Sequencing was performed on Illumina NextSeq2500

first: Kyunghee

last: Choi

first: Ashraf

last: Ul Kabir

first: Madhav

last: Subramanian


title: Role of 53BP1 in End Protection and DNA synthesis at DNA breaks

first: Wei

last: Wu

institute: Center for Excellence in Molecular Cell Science

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

overall_design: Refer to individual Series


title: Residual homing of a α4β7-expressing β1+PI16+ regulatory T cell subset correlates with exposure-efficacy of vedolizumab

city: Erlangen

first: Mark

last: Dedden

state: Bayern

address: Schwabachanlage 12

department: Department of Medicine 1

institute: Universitätsklinikum Erlangen

summary: In vitro and in vivo data from our lab show that TReg cells exhibit a right-shifted vedolizumab binding profile compared with TEff cells. Consistently, in a certain concentration range, the residual adhesion, transmigration and homing of TReg cells was higher than that of TEff cells. To better understand why vedolizumab binding was different between TReg and TEff in a certain concentration range, we performed single cell RNA sequencing of Memory CD4 T cells expressing α4 and β7 integrin and compared cells binding to vedolizumab or not binding to vedolizumab (previously purified using FACS with fluorescently labelled vedolizumab).

overall_design: Examination of previously sorted CD4+ CD45RO+ alpha4+ beta7+ cells binding or not binding to vedolizumab at a certain concentration

first: Emily

last: Becker

first: Sebastian

last: Zundler

first: Philipp

last: Kirchner

first: Arif

middle: B

last: Ekici


title: Epigenetic effects of silver nanoparticles and ionic silver in Tetrahymena thermophila

city: Xiamen

first: Jun

last: Yang

address: 1799 Jimei Road, Xiamen, 361021 PR China

institute: Chinese Academy of Sciences

summary: The widespread use of silver nanoparticles (Ag NPs) has raised substantial health risks to environmental and human beings. Although various negative effects had been reported, little is known about the epigenetic toxicity induced by Ag+ and Ag NPs. This study characterized physiological and lncRNA profiles to explore the toxic effects and epigenetic mechanisms in Tetrahymena thermophila on exposure to Ag+ and three types of Ag NPs. We found that both of Ag+ and Ag NPs exhibited strong growth-inhibiting effects on T. thermophila. The toxicity was mainly caused by high levels of reactive oxygen species (ROS), which subsequently led to lipid peroxidation and mitochondrial dysfunction. As a defense mechanism against oxidative stress, the protist elicited an antioxidant response. Importantly, 1250 lncRNAs were differentially expressed under Ag+ or Ag NPs exposure relative to the non-exposure control, which were clustered into 15 expression modules in weighted gene co-expression network analysis. These gene modules exhibited toxicant-specific expression patterns, indicating that they play various regulatory roles, including cell growth inhibition, cell membrane cation channel activation, and oxidoreductase activity promotion. Taken together, this research illuminates how post-transcriptional mechanisms of a ciliated protozoa regulate responses to Ag+ and Ag NPs toxicities.

overall_design: We conducted lncRNA sequencing after the 24h-IC50 concentration of the Ag+ and three types of silver nanoparticles (Ag-Cit10, Ag-Cit80 and Ag-PVP80) were treatment on Tetrahymena thermophila for 24h, respectively. Each treatment conducted 3 replicates，and totally 15 samples were generated.

first: Yongbo

last: Pan

first: Senjie

last: Lin

first: Wenjing


title: A humanized Animal Model Predicts Clonal Evolution and Therapeutic Vulnerabilities in Myeloproliferative Neoplasms

status: Public on Sep 09 2021

city: St Louis

first: Grant

last: Challen

state: MO

address: 660 Euclid Avenue

department: Medicine

institute: Washington University School of Medicine

summary: We performed single cell RNA sequencing to ensure that the engrafted MF cells in NSGS mice retained the molecular properties of the patients cells. ScRNAseq profiles from peripheral blood mononuclear cells (PBMCs) from two independent cord blood and MF patient samples were compared to the engrafted hCD45+ cells from the bone marrow of NSGS mice at 12-weeks post-transplant.

overall_design: Human CD45+ cells were purified by FACS from CB- or MF-derived mononuclear cells as well as from NSGS xenografs. Purified cells were resuspended at 1,200 cells per uL in PBS + 0.04% BSA. cDNA synthesis, QC, and library sequencing are described in the manuscript in detail.

first: Hamza

last: Celik

first: Ethan

last: Krug

first: Christine

first: Wentao

last: Han

first: Hassan

last: Bjeije

first: Nancy

last: Issa

first: Won

middle: K

last: Koh

first: Maggie

last: Allen

first: Daniel

last: Fisher

first: Jared

last: Fowles

first: Tindao

last: Li

first: Matthew

middle: C

last: Stubbs

first: Holly

last: Koblish

first: Stephen

middle: T

last: Oh


title: Fatal cytokine release syndrome by an aberrant FLIP/STAT3 axis

city: Verona

first: Stefano

last: Ugel

address: Piazzale L.A. Scuro, 10

country: Italy

institute: University and Hospital Trust of Verona

summary: Inflammatory responses rapidly detect pathogen invasion and mount a regulated reaction. However, dysregulated anti-pathogen immune responses can provoke life-threatening inflammatory pathologies collectively known as cytokine release syndrome (CRS), exemplified by key clinical phenotypes unearthed during the SARS-Cov-2 pandemic. The underlying pathophysiology of CRS remains elusive. We found that FLIP, a protein that controls caspase-8 death pathways, was highly expressed in myeloid cells of COVID-19 lungs. FLIP controlled CRS by fueling a STAT3-dependent inflammatory program. Indeed, constitutive expression of a viral FLIP homologue in myeloid cells triggered a STAT3-linked, progressive and fatal inflammatory syndrome in mice, characterized by elevated cytokine output, lymphopenia, lung injury and multiple organ dysfunctions that mimicked human CRS. As STAT3-targeting approaches relieved inflammation, immune disorders, and organ failures in these mice, targeted intervention towards this pathway could suppress the lethal CRS inflammatory state.

overall_design: Characterization of the lung immune landscape of vFLIP and wild type (WT) mice using Chromium 10x single-cell RNA-seq (scRNA-seq) data.

first: Chiara

last: Musiu

first: Simone

last: Caligola

first: Alessandra

last: Fiore

first: Alessia

last: Lamolinara

first: Cristina

last: Frusteri

first: Francesco

middle: D

last: Del Pizzo

last: De Sanctis

first: Stefania

last: Canè

first: Annalisa

last: Adamo

first: Francesca

last: Hofer

first: Roza

middle: M

last: Barouni

first: Andrea

last: Grilli

first: Serena

last: Zilio

first: Paolo

last: Serafini

first: Evelina

last: Tacconelli

first: Katia

last: Donadello

first: Leonardo

last: Gottin

first: Enrico

last: Polati

first: Domenico

last: Girelli

first: Ildo

last: Polidoro

first: Piera

last: Iezzi

last: Angelucci

last: Capece

first: Ying

last: Chen

first: Zheng-Li

last: Shi

first: Peter

last: Murray

first: Marco

last: Chilosi

first: Ido

last: Amit

first: Silvio

last: Bicciato

first: Manuela

first: Vincenzo

last: Bronte


title: Effect of acute embryonic exposures to tris(4-chlorophenyl)methane and tris(4-chlorophenyl)methanol in the zebrafish

city: East Lansing

first: Karilyn

middle: E

last: Sant

state: MI

address: 1355 Bogue St., Life Science B440

department: Pharmacology & Toxicology

institute: Michigan State University

summary: Tris(4-chlorophenyl)methane (TCPM) and tris(4-chlorophenyl)methanol (TCPMOH) are two marine pollutants of emerging concern, found in marine mammals and coastal bird populations. Here, we assess the response to these compounds due to acute exposures in zebrafish embryos (from 96-100 hours post fertilization).

overall_design: We analyzed a total of 15 samples: Samples 1-5 were controls, exposed to 0.01% v/v dimethyl sulfoxide for 4 hours between 96-100 hours post fertilization. Samples 6-10 were exposed to 50 nM TCPM, and Samples 11-15 were exposed to 50 nM TCPMOH. Samples were collected from 3 experimental replicates, with randomized embryos acquired from 20 breeding pairs.

first: Julian

last: Navarrete


title: RNA-Sequencing analysis of liver tissue from healthy WT mice and Foxa3-Cre YAP1 knockout mice at 3-4 months of age

city: Pittsburgh

first: Satdarshan

last: Monga

state: PA

address: S-422 SBST, 200 Lothrop Street

department: Pathology

institute: University of Pittsburgh School of Medicine

summary: We developed a mouse model of bile duct paucity by deleting Yes-associated protein 1 (YAP1) in foregut endoderm progenitors, using the Foxa3 promoter to drive Cre expression. YAP1 KO mice are viable postnatally and survive long-term despite a complete failure of  intrahepatic bile duct development, resembling the liver phenotype of Alagille syndrome. We also observed no functional biliary regeneration over time. Adult YAP1 KO mice suffer from severe chronic cholestasis, but show minimal hepatocellular injury, suggesting that the hepatocytes have adapted to preserve liver function and reduce damage from the toxicity of bile acids and bilirubin. We used RNA-seq to analyze the gene expression patterns of whole liver tissue of adult YAP1 KO mice compared to WT, and found significant changes in metabolic activity, bile acid synthesis and transport that reflect hepatocyte reprogramming for survival.

overall_design: We analyzed 6 healthy liver tissue samples (3 male, 3 female) and 6 YAP1 KO liver tissue samples (3 male, 3 female).

first: Laura

last: Molina


title: Enhancer reactivation mediates adaptive resistance to FGFR inhibitors in triple-negative breast cancer [RNA_seq]

city: Boston

first: Xintao

last: Qiu

state: MA

address: 440 brookline ave

institute: Dana Faber Cancer Institute

summary: A subset of triple negative breast cancers (TNBC) are characterized by genetic alterations in fibroblast growth factor receptors (FGFR) including amplifications, activating mutations or gene fusions. However, despite this genetic evidence of FGFR-dependency, FGFR inhibitors have shown only limited clinical efficacy in TNBC, suggesting the presence of intrinsic or adaptive resistance mechanisms. Using genome-wide CRISPR screens, we found that resistance to FGFR inhibition is mediated by activation of the mTORC1 and YAP pathways. Prolonged FGFR inhibition increased expression of several amino acid transporters resulting in increased cellular level of certain amino acids and activation of the mTORC1 amino acid sensing pathway. Epigenomic analyses revealed that FGFR inhibition reorganized YAP/TEAD associated enhancers leading to the upregulation of YAP target genes including the amino acid transporters upstream of mTORC1. Remarkably, mTORC1 and FGFR inhibitors synergistically blocked the growth of TNBC cells in vitro and in patient-derived xenografts. These findings define a novel epigenetic feedback mechanism involving intracellular amino acid levels leading to targeted therapy resistance in TNBC, and offers a combinatorial drug treatment strategy to improve clinical outcomes for this aggressive breast cancer subtype.

overall_design: RNA-seq in CAL-120 cells treated with DMSO or infigratinib

first: Yihao

last: Li

first: Myles

last: Brown


title: Tracking bivalency through early mouse differentiation

city: Chicago

first: Rohan

middle: Nishant

last: Shah

state: IL

address: CLSC 856, 920 E. 58th Street

institute: University of Chicago

summary: Nucleosomes, composed of DNA and histone proteins, represent the fundamental repeating unit of the eukaryotic genome; posttranslational modifications of these histone proteins influence the activity of the associated genomic regions to regulate cell identity. Traditionally, trimethylation of histone H3K4 (H3K4me3) is associated with transcriptional initiation, whereas trimethylation of H3K27 (H3K27me3) is transcriptionally repressive. The apparent juxtaposition of these opposing marks, termed “bivalent domains”, was proposed to specifically demarcate of small set transcriptionally-poised lineage-commitment genes that resolve to one constituent modification through differentiation, thereby determining transcriptional status. Since then, many thousands of studies have canonized the bivalency model as a chromatin hallmark of development in many cell types. However, these conclusions are largely based on chromatin immunoprecipitations (ChIP) with significant methodological problems hampering their interpretation. Absent direct quantitative measurements, it has been difficult to evaluate the strength of the bivalency model. Here, we present reICeChIP, a calibrated sequential ChIP method to quantitatively measure H3K4me3/H3K27me3 bivalency genome-wide, addressing the limitations of prior measurements. With reICeChIP, we profile bivalency through the differentiation paradigm that first established this model: from naïve mouse embryonic stem cells (mESCs) into neuronal progenitor cells (NPCs). Our results cast doubt on every aspect of the bivalency model; in this context, we find that bivalency is widespread, does not resolve with differentiation, and is neither sensitive nor specific for identifying poised developmental genes or gene expression status more broadly. Our findings caution against interpreting bivalent domains as specific markers of developmentally poised genes.

overall_design: Internally calibrated chromatin immunoprecipitation (ICeChIP) of H3K4me3, H3K27me3, H3K9me3, and H3K4me3K27me3 bivalency in primed mouse embryonic stem cells and neuronal precursor cells with one replicate per cell type, as well as ChIP input corresponding to each cell type.

first: Adrian

last: Grzybowski

first: Jimmy

last: Elias

first: Zhonglei

first: Takamitsu

last: Hattori

first: Carolin

last: Lechner

middle: W

last: Lewis

first: Shohei

last: Koide

first: Beat

last: Fierz

first: Alexander

last: Ruthenburg


title: Developmental Analysis of compound leaf development in Arachis hypogaea

city: qingdao

first: RUIQI

last: SUN

address: No.72 Binhai Road,

institute: shandong university

summary: Transcriptomic profiles revealed that the common and unique different expression genes were identified in lateral leaflet and terminal leaflet, using petiole as a control.What's more, transcriptomic analysis was performed to compare the difference of a natural mutant with pentafoliate defects and wild type.

overall_design: Examination of 5 different tissues,which are 4 in wild type and 1 in mutant. Each of different tissue has three biological replicates

first: Ruiqi

last: Sun

first: Chuanen

last: Zhou

first: Shuangshuang

first: Zhenying

last: Peng


title: Role of Il-11 signaling in adult heart and fin regeneration in zebrafish

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: In adult mammals, tissue damage after myocardial infarction induces myofibroblast differentiation and the formation of a permanent, functionally inert scar.  However, the molecular mechanisms that govern myofibroblast differentiation and scarring remain poorly understood.  Some vertebrates like zebrafish display a remarkable regenerative potential with only limited and transient fibrosis after tissue damage, including in the heart.  Here, employing comparative expression profiling coupled with loss-of-function approaches, we identified the canonical Interleukin-11/Stat3 signaling axis as a core component of regeneration in zebrafish.  Notably, animals with loss of Interleukin-11 receptor (Il11ra) function reach adulthood without overt developmental defects, but exhibit strongly impaired cardiac regeneration with increased myofibroblast differentiation and the formation of a permanent collagenous scar, similar to what is observed in adult mammals.  Using zebrafish fate-mapping approaches, reporter lines and human primary cell culture methods, we provide evidence that Interleukin-11 signaling limits endothelial-to-myofibroblast transdifferentiation and maintains a pro-regenerative niche to promote cardiac regeneration. Altogether, our data reveal a vital role for endothelial Interleukin-11/Stat3 signaling in containing injury-induced cardiac fibrosis.

overall_design: 96 hours post cryoinjury cardiac ventricle samples from adult il11ra mutant vs. wild-type were analyzed in duplicates with each replicate derived by pooling 2 ventricles. 24 hours post amputation caudal fin samples from adult il11ra mutant vs. wild-type were analyzed in triplicates with each replicate derived from single fins.

first: Srinivas

last: Allanki

first: Sven

last: Reischauer

last: Guenther


title: Transcriptional Profiling of C. briggsae Temperate and Tropical representative strains after extreme cold

city: Novato

first: Rachel

last: Brem

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

summary: Different populations of the same species survive different environments through local adaptation. Temperature is one of the most important driving forces that could result in local adaptation. Here, we studied the influence of extreme low temperature on the survival of two genetically and geographically distinct populations of the free-living Caenorhabditis briggsae. We found that Caenorhabditis briggsae strains of temperate origin had a cold resistant phenotype, while those originating from a tropical climate had reduced survival after cold treatment. Using this phenotypic difference between geographically diverse populations as a model for how species adapt to their local environment, we then analyzed the transcriptional profiles of two Caenorhabditis briggsae strains of tropical and temperate origin to find genes that are involved in survival after extreme cold. In summary, the response to the extreme low temperature that clearly distinguishes the temperate and tropical Caenorhabditis briggsae strains could serve as an excellent example for studying local adaption of species that show genetic separation associated with their geographical distribution.

overall_design: mRNA profiles of C. briggsae AF16 and C. briggsae HK104 before and after cold (4C) treatment - two replicates; mRNA profile of AF16/HK104 hybrid before and after cold treatment - one replicate

first: Wenke

last: Wang

first: Anna

last: Flury


title: Enhancer reactivation mediates adaptive resistance to FGFR inhibitors in triple-negative breast cancer [scATAC_seq]

first: Xintao

last: Qiu

overall_design: scATAC-seq in breast cancer PDX tumors treated with control or infigratininb for 28 days

first: Yihao

last: Li

first: Myles

last: Brown


title: Enhancer reactivation mediates adaptive resistance to FGFR inhibitors in triple-negative breast cancer [PDX_RNA_seq]

overall_design: RNA-seq in breast cancer PDX tumors treated with control or infigratinib.


title: Transcriptome sequencing of human Duchenne muscular dystrophy and CRISPR-corrected myogenic cultures during secondary myogenic differentiation.

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

country: United Kingdom

institute: Queen Mary University of London

summary: We sought to investigate whether the reduced differentiation and fusion competence in DMD-R3381X cultures was due to aberrant myogenic gene expression. We performed transcriptome sequencing and analysis of DMD-R3381X and CORR-R3381X myogenic cultures during secondary differentiation at 0, 24 and 120 hours timepoints.

overall_design: RNA sequencing was performed on DMD-R3381X and CORR-R3381X myogenic cultures during secondary differentiation at 0, 24 and 120 hours timepoints. Three biological replicate per condition were performed.

first: Amaia

last: Paredes-Redondo

first: Jun

first: Yung-Yao

last: Lin


title: RNAseq analysis of treatment-resistant and sensitive breast cancer patient-derived organoids with paclitaxel treatments

city: Taipei City

first: Kelvin

middle: Kun-Chih

last: Tsai

address: 7F, 250 Wuxing St, Xinyi Dist

department: Graduate Institute of Clinical Medicine, College of Medicine

country: Taiwan

institute: Taipei Medical University

summary:
Huntsman Cancer Institute (HCI)-001 patient-derived organoids (PDOs) and HCI-002 PDOs obtained from Huntsman Cancer Institute, University of Utah (Nat Med. 2011 Oct 23;17(11):1514-20).
Purpose: The goals of this study is to identify molecular pathways and genes that are involved in the treatment responsiveness of breast cancer PDOs.
Methods: mRNA profiles of HCI-001 and HCI-002 PDOs were generated by Illumina NovaSeq 6000 platform for paired-end sequencing, 150-bp read length, for about 20 million raw reads per sample. RNA sequencing FASTQ files were processed with HISAT2 aligner in default mode with the Ensembl human transcriptome annotation (Build version GRCh38 and transcript annotation GRCh38.89). Differential gene expression analysis was performed using DESeq2 software. Enrichment analysis was performed using ClusterProfiler software.
Results: We mapped about 20 million sequence reads per sample to the human genome (build HG38) in the RNAs of HCI-001 and HCI-002 PDOs treated with paclitaxel or vehicle. We used a minimum expression cut-off of 1 FPKM in order to exclude low-levels genes and the RNA-seq data confirmed the difference expression of 67 known apoptosis-regulatory genes in treatment-sensitive PDOs (HCI-002) compare to treatment-resistant PDOs (HCI-001).
Conclusions: This study identified apoptosis-regulatory genes that are differentially induced or represeed in treatment-sensitive PDOs (HCI-002) or treatment-resistant PDOs (HCI-001).

overall_design: mRNA profiles of HCI-001 PDOs and HCI-002 PDOs treated with pacliaxel (20 uM) or vehicle for 48 hours

first: Valerie

last: Weaver


title: Consequences of postnatal Tshz3 deletion: implications for autism spectrum disorder

city: Marseille

first: Laurent

last: Fasano

address: Parc Scientifique de Luminy

institute: CNRS-AMU

summary: We recently identified heterozygous deletions of the gene TSHZ3, which encodes a Zn-finger transcription factor, in patients with a syndrome including autistic features and provided evidence in mice for a link between Tshz3 haploinsufficiency, defects in cortical projection neurons (CPNs) and autism spectrum disorder (ASD)-like abnormalities. To get more insight into when and where TSHZ3 is required for the proper development of the brain, we generated and characterized a novel mouse model of conditional Tshz3 deletion in projection neurons from postnatal day 2-3 onward. These mice exhibit altered cortical expression of genes encoding for synaptic components, electrophysiological and synaptic changes in layer 5 CPNs, impaired corticostriatal glutamate transmission and plasticity, as well as strong ASD-relevant behavioral deficits. These data, by revealing a crucial postnatal role of TSHZ3 in the development and function of the corticostriatal circuitry that might be determinant for ASD pathogenesis, offer a novel ASD model and further open the possibility for an early postnatal therapeutic window for the syndrome linked to TSHZ3 haploinsufficiency.

overall_design: Three independent replicates, each containing cortices from 3-4 mice (P34), were prepared for analysis.

first: Xavier

last: Caubit

first: Emeric

last: Dubois

first: Ahmed

last: Fatmi

first: Dany

last: Severac


title: Human Pumilio proteins directly bind the CCR4-NOT deadenylase complex to regulate the transcriptome

city: Galveston

first: Nathan

middle: David

last: Elrod

address: 1005 Strand Street

department: BMB

institute: University of Texas Medical Branch at Galveston

summary: Pumilio paralogs, PUM1 and PUM2, are sequence-specific RNA-binding proteins that are essential for vertebrate development and neurological functions. PUM1&2 function to negatively regulate gene expression by accelerating degradation of specific mRNAs. Here, we determined  the repression mechanism and impact of human PUM1&2 on the transcriptome. We identified subunits of the CCR4-NOT (CNOT) deadenylase complex required for stable interaction with PUM1&2 and to elicit CNOT-dependent repression. Isoform-level RNA sequencing revealed broad co-regulation of target mRNAs through the PUM-CNOT repression mechanism. Functional dissection of the domains of PUM1&2 identified a conserved N-terminal region that confers the predominant repressive activity via direct interaction with CNOT. In addition, we show that the DCP2 mRNA decapping enzyme has an important role in repression by PUM1&2 N-terminal regions. Our results support a molecular model of repression by human PUM1&2 via direct recruitment of CNOT deadenylation machinery in a decapping-dependent pathway.

overall_design: PAC-Seq examination of 18 samples (3 biological replicate sets of HCT116 cells: control knockdown; CNOT1 knockdown;  CNOTs 7 &8 knockdowns; PUMs 1 & 2 knockdowns; PUM1 knockdown; PUM2 knockdown: for 48 hours knockdown each)

first: Isioma

middle: I

last: Enwerem

first: Chung-Te

last: Chang

first: Ai

first: Ping

last: Ji

first: Jennifer

middle: A

last: Bohn

first: Yevgen

last: Levdansky

first: Eric

last: Wagner

first: Eugene

last: Valkov

first: Aaron

last: Goldstrohm


title: Mammalian circRNA Atlas

city: Jerusalem

first: Sebastian

last: Kadener

address: SIlberman Institute of Life Sciences, Edmund J. Safra Campus

country: Israel

institute: The Hebrew University of Jerusalem

summary: We developed a new pipeline for accurate circRNA detection. We build a new atlas for characterizing circRNA in human, monkey, mouse, rat and drosophila brain. Our approach allows full annotation of circRNAs with fewer false positives and negatives than any individual pipeline or combination of them. Moreover, our approach is more sensitive than any individual pipeline and allows more accurate quantification and larger number of differentially expressed circRNAs.

sample_organism:
Macaca mulatta
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: We obtained commercial purified RNA and performed rRNA depletion. Then we treated total RNA with RNAseR and prepared a library.

first: Avigayel

last: Rabin

first: Aaarti

last: Jajoo

first: Michela

last: Zaffagni


title: Enhancer reactivation mediates adaptive resistance to FGFR inhibitors in triple-negative breast cancer [CRISPR]

first: Xintao

last: Qiu

overall_design: genome-wide CRIPSR screen in human breast cancer cells

first: Yihao

last: Li

first: Myles

last: Brown


title: Enhancer reactivation mediates adaptive resistance to FGFR inhibitors in triple-negative breast cancer [ChIP_seq]

overall_design: ATAC-seq, H3K27ac ChIP-seq, YAP ChIP-seq and BRG1 ChIP-seq in CAL-120 cells treated with DMSO or infigratinib


title: Transcriptomic comparison of the vitamin A ester retinyl propionate and retinol in human keratinocytes

city: Mason

first: Joe

last: Sherrill

state: Ohio

address: 8700 Mason-Montgomery Rd

institute: Procter and Gamble

summary: Retinoids are potent skin care actives used to treat a number of common clinical and cosmetic skin conditions, including skin aging. Here, we compare the effects of retinyl proprionate and retinol on gene expression in immortalized human keratinocytes.

overall_design: Immortalized human keratinocytes (hTERT) were treated with 100nM retinyl proprionate or 100nM retinol for 24 hr and subjected to microarray profiling on the GeneTitan U219 array platform.

first: John

last: Oblong

first: Rui


title: Enhancer reactivation mediates adaptive resistance to FGFR inhibitors in triple-negative breast cancer

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

overall_design: Refer to individual Series


title: TRIM71 represses let-7 miRNA expression and activity via two independent molecular mechanisms

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Let-7 is a well-known pro-differentiation and tumor suppressor miRNA. TRIM71/LIN-41 was the first identified let-7 target, and it is a conserved stem cell-specific RNA-binding protein with an essential function in embryonic development and a proposed oncogenic role in several cancer types, such as hepatocellular carcinoma. Previous studies suggest a role for TRIM71 in miRNA regulation, since major changes have been observed in the miRNome of TRIM71-defiecient ESCs, and TRIM71 is able to interact with several proteins involved in the miRNA pathway.

overall_design: mRNA sequencing and analysis of Trim71 and Lin28a conditional (WT-WT), combinations ((WT-KO, KO-WT) and Trim71 and Lin28a KO mES cells (KO-KO)

first: Lucia

last: Torres Fernández

first: Sibylle

last: Mitschka

first: Thomas

last: Ulas

first: Julia

last: Windhausen

last: Schulze

first: Waldemar

last: Kolanus


title: The RNA helicase Ddx21 controls Vegfc-driven developmental lymphangiogenesis by balancing endothelial cell ribosome biogenesis and p53-p21 signalling [zebrafish]

city: Melbourne

first: Benjamin

last: Hogan

state: Victoria

address: 305 Grattan Street

department: Program in Organogenesis and Cancer

institute: Peter MacCallum Cancer Centre

summary: The development of a differentiated and functional vasculature requires coordinated control of cell fate specification, lineage differentiation and vascular network growth. Cellular proliferation is spatiotemporally regulated in developing vessel networks but how this is achieved and differentially controlled in specific lineages is unknown. Using a zebrafish forward genetic screen for mutants that form blood vessels but fail to form lymphatic vessels, we uncovered a mutant for the RNA helicase Ddx21. Ddx21 cell-autonomously regulates the early development of lymphatic endothelial cells. Ddx21 is essential for Vegfc-Vegfr3 driven endothelial cell proliferation. Ddx21 is an established regulator of ribosomal RNA transcription and in the absence of Ddx21, mutant lymphatic endothelial cells show reduced ribosome biogenesis. Ultimately, loss of Ddx21 leads to a p53-p21 dependent cell cycle arrest that blocks embryonic lymphangiogenesis. Thus, the RNA helicase Ddx21 coordinates the endothelial cell proliferative response to Vegfc-Vegfr3 signalling by balancing ribosome biogenesis and p53-p21 signalling. This mechanism may have therapeutic potential in diseases of excessive lymphangiogenesis such as in cancer metastasis or lymphatic malformation.

overall_design: LEC and VEC RNA profiles on sibling and ddx21 mutant cells obtained from zebrafish embryos

first: K

last: Koltowska


title: Single-cell RNA sequencing of niche cells from BMT and aGVHD-V mice

city: Tianjin

first: Quan

last: Gu

address: 288 Nanjing Road

institute: State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital

summary: We performed RNA-seq of MSCs  from BMT and aGVHD-V mice.

overall_design: Examination of gene expression profiles BMT and aGVHD-V sample

first: Yan

last: Lin

first: Hui

last: Cheng

first: Tao


title: Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes

city: Brisbane

first: Peter

last: Crisp

state: QLD

address: John Hines Building (62), The University of Queensland

department: School of Agriculture and Food Science

institute: The University of Queensland

summary: The genomic sequences of diverse varieties of many crop species continue to be produced at a frenetic pace. However, it remains challenging to develop complete annotations of functional genes and regulatory elements in these genomes. Here, we explore the potential to use DNA methylation profiles to develop more complete and refined annotations. Using leaf tissue in maize, we define ~100,000 unmethylated regions (UMRs) that account for 5.8% of the genome; 33,375 UMRs (1.3% of the genome) are found greater than 2 kilobase pairs from genes. UMRs are highly stable in multiple vegetative tissues and they capture the vast majority of accessible chromatin regions from leaf tissue. However, many UMRs are not accessible in leaf (leaf-iUMRs) and these represent a set of genomic regions with potential to become accessible in specific cell types or developmental stages. Leaf-iUMRs often occur near genes that are expressed in other tissues and are enriched for transcription factor (TF) binding sites of TFs that are also not expressed in leaf tissue. The leaf-iUMRs exhibit unique chromatin modification patterns and are enriched for chromatin interactions with nearby genes. The total UMRs space in four additional monocots ranges from 80-120 megabases, which is remarkably similar considering the range in genome size of 271 megabases to 4.8 gigabases. In summary, based on the profile from a single tissue, DNA methylation signatures pinpoint both accessible regions and regions poised to become accessible or expressed in other tissues. Thus, UMRs can provide powerful filters to distill large genomes down to the small fraction putative functional elements and facilitate the discovery of tens of thousands of novel candidate regulatory regions.

overall_design: WGBS for 6 maize B73 leaf samples.

first: Nathan

last: Springer


title: HD-ZIP IV transcription factor OCL4 and 21-nt phasiRNAs are dispensable for male fertility in maize anthers

city: St. Louis

first: Blake

middle: C.

last: Meyers

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary: The maize ocl4 mutants showed differing levels of male sterility, which seems correlating with the quantity of 21-nt phasiRNA remaining during pre-meiotic stage. In this case, sRNA and transcriptome was profiled and compared in this study, showed that OCL4 and 21-nt phasiRNAs are dispensable for male fertility in maize anthers.

overall_design: Examination of maize phasiRNAs in ocl4 mutants by high throughput sequencing for RNA-seq.

first: Pranjal

last: Yadava

first: Saleh

last: Tamim

first: Han

last: Zhang

first: Chong

last: Teng

first: Xue

last: Zhou

first: Virginia

last: Walbot


title: SPOP mutation reshapes chromatin landscape and transcriptional response to androgens [RNA-seq]

city: New York

first: Ivana

last: Grbesa

address: 413 E 69th St

department: Urology

institute: Weill Cornell Medicine

summary: To define the epigenomic response to AR activation, we employed the 3D organoid model of murine prostate tissue. Control and SPOP-mutant prostate organoids were stimulated with 10 nM dihydrotestosterone (DHT) or vehicle. Next, we performed the transcriptomic analysis (mRNA-seq) together with profiling of the accessibility landscape (ATAC-seq), transcription factor (AR, and FOXA1) binding and H3K4me2 modified nucleosomes.

overall_design: Genome-wide profiling of accessibility in Control (normal) and SPOP-mutant mouse prostate organoids.

first: Christopher

last: Barbieri


title: miR-21-dependent gene expression profile of B cells in imiquimod treated autoimmune-prone Sle1b mice

city: Hershey

first: Ziaur

last: Rahman

address: 500 University Drive

department: Microbilogy and Immunology

institute: Pennsylvania State University College of Medicine

summary: MicroRNAs (miRNAs) are involved in B cell responses that drive the loss of tolerance in systemic lupus erythematosus (SLE), though the role of many miRNAs remains uncharacterized. Here we studied the role of miR-21 in modulating the transcriptome and function of B cells in imiquimod treated autoimmune-prone Sle1b mice.

overall_design: B cells were sorted from IMQ treated autoimmune-prone Sle1b and Sle1b.miR-21KO mice.  Total RNA was isolated for RNAseq analysis.  N=4/group. 8 total samples.

first: Stephanie

last: Schell

first: Kristen

middle: N

last: Bricker

first: Adam

middle: J

last: Fike

first: Sathi

last: Chodisetti

first: Phillip

middle: P

last: Domeier

first: Nicholas

last: Choi

first: Melinda

last: Fasnacht

first: Steven

middle: F

last: Zeigler

middle: S


title: DET1-mediated COP1 regulation avoids HY5 activity over second-site targets to tune plant photomorphogenesis

city: Paris

first: Clara

last: Bourbousse

address: 9 quai Saint Bernard

department: UMR 7622 LBD

institute: Sorbonne Université

summary: DE-ETIOLATED1 (DET1) is a negative regulator of plant photomorphogenesis acting as a component of the C3D complex, which can further associate to CULLIN4 to form a CRL4C3D E3 ubiquitin ligase. CRL4C3D is thought to act together with CRL4COP1SPA ubiquitin ligase, to promote the ubiquitin-mediated degradation of the master regulatory transcription factor ELONGATED HYPOCOTYL5 (HY5), thereby controlling photomorphogenic gene regulatory networks. Yet, functional links between COP1 and DET1 have long remained elusive. Here, upon mass spectrometry identification of DET1 and COP1-associated proteins, we provide in vivo evidence that DET1 associates with COP1 to promote its destabilization, a process necessary to dampen HY5 protein abundance. By regulating HY5 over-accumulation, DET1 is critical to avoid its association to second-site loci, including many PIF3 target genes. Accordingly, excessive HY5 levels result in an increased HY5 repressive activity and are sufficient to trigger fusca-like phenotypes otherwise observed typically in COP1 and COP9 signalosome mutant seedlings. This study therefore identifies that DET1-mediated regulation of COP1 stability tunes down HY5 cistrome and avoids hyper-photomorphogenic responses that might compromise plant viability.

overall_design: 20 ChIP-seq libraries and 9 RNA-seq libraries were sequenced.

first: Léa

last: Wolff

first: Esther

last: Cañibano

first: Fredy

last: Barneche

first: Vicente

last: Rubio

first: Sandra

last: Fonseca


title: SPOP mutation reshapes chromatin landscape and transcriptional response to androgens [ATAC-seq]

first: Ivana

last: Grbesa

overall_design:
Genome-wide profiling of accessibility in Control (normal) and SPOP-mutant mouse prostate organoids.
Please note that each *bw file was generated from all replicates and is linked to the corresponding rep.1 sample records.


title: Expression data from Arabidopsis adult and juvenile plants under submergence and control conditions

city: Bologna

first: Federico

middle: Manuel

last: Giorgi

state: BO

address: Via Selmi 3

department: Department of Pharmacy and Biotechnology

institute: University of Bologna

summary:
Arabidopsis plants display superior tolerance to submergence at the juvenile stage. We characterized the transcriptomic response to submergence in juvenile and adult plants.
In this dataset, we include expression data from 2-week and 3-week old plants under dark air and dark submergence conditions.

overall_design: A total of 8 samples was analyzed. Two samples correspnding to 2-week old seedlings under dark aerobic conditions, two samples correspnding to 3-week old seedlings under dark aerobic conditions, two samples correspnding to 2-week old seedlings under dark submergence conditions and two samples correspnding to 3-week old seedlings under dark submergence conditions,

first: Liem

last: Bui

first: Beatrice

last: Giuntoli

first: Francesco

last: Licausi